/* ingenwin.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * =========================================================================== * * File Name: ingenwin.c * * Author: Fasika Aklilu * * Version Creation Date: 8/10/01 * * $Revision: 6.8 $ * * File Description: handles windowing for ingenue * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include typedef struct ingsaveinfo{ TexT text; } IngSaveInfo, PNTR IngSaveInfoPtr; typedef struct selectdata { VieweR vwr; Boolean returnFALSE; Uint2 entityID; Uint2 itemID; Uint2 itemtype; Uint2 segID; } IngSelectData, PNTR IngSelectPtr; /******************************************************************************* Error messages and Global Variables *******************************************************************************/ static char szErrMsg1[]="Attempt to open the Genome Viewer without a BioSeq object."; static char szErrMsg2[]="Genome Viewer was unable to build its internal data structures."; static char szErrMsg3[]="Genome Viewer was unable to start its GUI."; static char szErrMsg4[]="Genome Viewer was unable to find BioSeq(eID,iID)."; static char szErrMsg5[]="Genome Viewer was unable to create a Raw representation of a single segmented BioSeq(eID,iID)."; static CharPtr IngfeatDefLabels[FEATDEF_MAX]={"Alignments", "Genes", "Organism", "Coding Regions", "Proteins", "preRNA", "mRNA", "tRNA", "rRNA", "snRNA", "scRNA", "otherRNA","Publications", "Sequence Tracking", "Imported", "Allele", "Attenuator", "C region", "CAAT signal", "Imported CDS", "Conflict", "D loop", "D segment", "Enhancer", "Exon", "GC signal", "iDNA", "Intron", "J segment", "LTR", "Mature Peptide", "Misc Binding Site", "Misc Difference", "Misc Feature", "Misc Recomb", "Misc RNA", "Misc Signal", "Misc Structure", "Modified Base", "Mutation", "N Region", "Old Sequence", "PolyA Signal", "PolyA Site","Precursor RNA", "Primary Transcript", "Primer Binding Site","Promotor", "Protein Binding Site", "RBS", "Repeat Region", "Repeat Unit", "Replication Origin", "S region", "Satellite", "Signal Peptide", "Source", "Stem Loop", "STS", "TATA Signal", "Terminator", "Transit Peptide", "Unsure", "V Region", "V Segment", "Variation", "Virion", "3' Clip", "3' UTR", "5' Clip", "5' UTR", "10 Signal", "35 Signal", "Site Reference" , "Region", "Comment", "Bond", "Site", "Retriction Site", "User Defined" , "Transcription Initiation", "Custom Numbering","Protein 2-D Structure", "Non Std Residue", "Heterogens", "Bio Source" , "Preprotein", "Mature Peptide aa","Signal Peptide aa", "Transit Peptide aa"}; /* extern */ extern Uint1 featDefTrack2[]; /* static */ static Uint2 fDefLookup[FEATDEF_MAX];/* maps featDefTrack to featDefFilter */ static Uint2 WinCounter=0; /* keep track of open windows */ static IngMsgInfo msg; /* contains info for highlighting segments */ static Uint1Ptr seq; /* buffer for GC content */ /******************************************************************************* Static Function Declarations *******************************************************************************/ static Boolean Ing_SelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata); static Boolean Ing_DeSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata); static Boolean Ing_DeSelectGenericPrim (SegmenT seg, PrimitivE prim, Uint2 segID,Uint2 primID, Uint2 primCt, VoidPtr userdata); static void Ing_ZoomerClickProc(VieweR v, SegmenT s, PoinT pt); static void Ing_ResizeMainWindow(IngGenomeViewerPtr igvp,WindoW w, Boolean first); static void Ing_Ruler1ClickProc(VieweR v, SegmenT s, PoinT pt); static void Ing_Ruler1DragProc(VieweR v, SegmenT s, PoinT pt); static void Ing_Ruler1ReleaseProc(VieweR v, SegmenT s, PoinT pt); static void Ing_UpdateZoomerVals(IngGenomeViewerPtr igvp, Int4 scaleX); static void Ing_MoveCursor(IngGenomeViewerPtr igvp, Int4 from, Int4 to, Boolean bFirst); static void Ing_FeatViewerClickProc(VieweR v, SegmenT s, PoinT pt); static void Ing_FeatViewerPanProc(VieweR v, SegmenT s); static void Ing_SequenceClickProc(VieweR v, SegmenT s, PoinT pt); static Boolean Ing_PopulateZoomer(IngGenomeViewerPtr igvp); static Int4 Ing_GetBPMaxScale(IngGenomeViewerPtr igvp); static Int4 Ing_GetTPMaxScale(IngGenomeViewerPtr igvp, Int2 vwidth); static SeqFeatPtr Ing_CreateNewFeature(Uint2 entityID, Uint2 itemID, BioseqPtr product, Uint1 seqfeattype, Uint1 featdeftype, CharPtr label, SeqLocPtr slp_feat, CharPtr color); static void Ing_ResetTitle(IngGenomeViewerPtr igvp, Boolean clear); static Int2 LIBCALLBACK Ing_OM_MsgFunc (OMMsgStructPtr ommsp); /******************************************************************************* Function : Ing_PopulateDetailedPage() Purpose : Bottom (Detailed) viewer drawing function *******************************************************************************/ extern void Ing_PopulateDetailedPage(Pointer data) { Int4 scaleX=0; Int4 top; Int4 bottom; IngGenomeViewerPtr igvp=NULL; BioseqPtr bsp=NULL; Uint4 nRows; IngExploreSegs gpn; Int2 nSegments; Char scale_buf[35]={""}; SelStructPtr ssp=NULL; IngSelectData sel; Boolean bSelected = FALSE; IngReportPtr Report = NULL; igvp=(IngGenomeViewerPtr)data; if (!igvp) return; WatchCursor(); ssp=ObjMgrGetSelected(); Reset(igvp->vBottom); igvp->pictBottom=DeletePicture(igvp->pictBottom); Reset(igvp->vRuler2); igvp->pictRuler2=DeletePicture(igvp->pictRuler2); Update(); igvp->pictBottom=CreatePicture(); igvp->pictRuler2=CreatePicture(); scaleX=igvp->scaleX; if (igvp->bsp) bsp=igvp->bsp; else{ bsp=GetBioseqGivenIDs (igvp->entityID, igvp->itemID, OBJ_BIOSEQ); igvp->bsp=bsp; } if (bsp==NULL){ ErrPostEx(SEV_ERROR, 0, 0, szErrMsg4); ArrowCursor(); return; } /*check the sequence length; could be undef.*/ if (bsp->length==(Int4)-1){ ErrPostEx(SEV_ERROR, 0, 0, szErrMsg5); ArrowCursor(); return; } gpn.seg = igvp->pictRuler2; gpn.viewer = igvp->vRuler2; gpn.idx = 1; gpn.GrData = &igvp->GrData; gpn.left = igvp->from; gpn.right = igvp->to; gpn.scaleX = scaleX; gpn.seqbuf = igvp->seqbuf; gpn.bShowGC = igvp->bShowGC; gpn.bLabels = igvp->bLabels; gpn.bTop = FALSE; gpn.bRegister = TRUE; gpn.procID = igvp->procID; gpn.userKey = igvp->userKey; gpn.messagefunc = Ing_OM_MsgFunc; gpn.data = (Pointer)igvp; nSegments = SeqMgrExploreSegments(bsp, (Pointer)&gpn, Ing_ExploreSegments); /*this bioseq doesn't have any segments*/ if (nSegments==0){ igvp->idx = 2; top = igvp->GrData.SegBoxHeight; bottom = top-igvp->GrData.SegBoxHeight; Ing_AddGCRect(igvp->pictRuler2, igvp->bsp->id, igvp->entityID, igvp->itemID, OBJ_BIOSEQ, igvp->seqbuf, 0, top, igvp->SeqLength, bottom, scaleX, Seq_strand_plus, TRUE, TRUE, igvp->idx, igvp->bShowGC); igvp->bSegmented = FALSE; } else{ igvp->bSegmented = TRUE; } Ing_AddRuler(igvp->pictRuler2, 2*igvp->GrData.SegBoxHeight, igvp->from, igvp->to, scaleX, 1, TRUE); AttachPicture(igvp->vRuler2, igvp->pictRuler2, (igvp->xposition<=0?INT4_MIN:igvp->xposition), INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vRuler2, Ing_SequenceClickProc, NULL, NULL, NULL); nRows = Ing_PopDetailedPage(bsp, igvp->pictBottom, gpn.left, gpn.right, igvp->GrData.pClr, scaleX, 0, igvp->bLabels, igvp->isExons, &igvp->talign); nRows+=2; igvp->last_feat_position_bottom = nRows*(-20); /* add white characters to align picture with ruler */ AddAttribute(igvp->pictBottom, COLOR_ATT, WHITE_COLOR, 0, 0, 0, 0); sprintf(scale_buf, "%d", igvp->from); AddLabel(igvp->pictBottom, 0, igvp->last_feat_position_bottom, scale_buf, SMALL_TEXT, 0, LOWER_CENTER, 0); AddLine(igvp->pictBottom, 0, igvp->last_feat_position_bottom, (igvp->to - igvp->from), igvp->last_feat_position_bottom, 0, 0); AttachPicture (igvp->vBottom,igvp->pictBottom, (igvp->xposition<=0?INT4_MIN:igvp->xposition), INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vBottom,Ing_FeatViewerClickProc,NULL,NULL, Ing_FeatViewerPanProc); while (ssp){ /* reselect objects in windows */ sel.entityID = ssp->entityID; sel.itemID = ssp->itemID; sel.itemtype = ssp->itemtype; if (igvp->bOverviewSelected){ sel.vwr = igvp->vTop; sel.returnFALSE = FALSE; ExploreSegment (igvp->pictTop, (Pointer) &sel, Ing_SelectPrim); } sel.vwr = igvp->vRuler2; sel.returnFALSE = TRUE; ExploreSegment (igvp->pictRuler2, (Pointer) &sel, Ing_SelectPrim); sel.vwr = igvp->vBottom; sel.returnFALSE = TRUE; ExploreSegment (igvp->pictBottom, (Pointer) &sel, Ing_SelectPrim); ssp = ssp->next; } if (igvp->hReport){ Report = (IngReportPtr)GetObjectExtra(igvp->hReport); if(Report) Ing_PopulateReport(Report, igvp); } Ing_ResetTitle(igvp, FALSE); ArrowCursor(); } /******************************************************************************* Function : Ing_PopulateOverviewPage() Purpose : Top (Overview) viewer drawing functions *******************************************************************************/ extern void Ing_PopulateOverviewPage(Pointer data, Boolean UpdateRuler) { Int4 maxScaleX; IngGenomeViewerPtr igvp; BioseqPtr bsp = NULL; Uint4 nLines; Char scale_buf[35] = {""}; igvp = (IngGenomeViewerPtr)data; if (!igvp) return; WatchCursor(); Reset(igvp->vTop); igvp->pictTop = DeletePicture(igvp->pictTop); if(UpdateRuler){ Reset(igvp->vRuler1); igvp->pictRuler1 = DeletePicture(igvp->pictRuler1); } Update(); igvp->pictTop = CreatePicture(); if (UpdateRuler) igvp->pictRuler1 = CreatePicture(); maxScaleX = igvp->maxScaleX; if (igvp->bsp) bsp = igvp->bsp; else{ bsp = GetBioseqGivenIDs (igvp->entityID, igvp->itemID, OBJ_BIOSEQ); igvp->bsp = bsp; } if (bsp==NULL){ ErrPostEx(SEV_ERROR, 0, 0, szErrMsg4); ArrowCursor(); return; } /*check the sequence length; could be undef.*/ if (bsp->length==(Int4)-1){ ErrPostEx(SEV_ERROR, 0, 0, szErrMsg5); ArrowCursor(); return; } if (UpdateRuler) Ing_PopOverviewRuler(igvp->vRuler1, igvp->pictRuler1, bsp, igvp->GrData, igvp->from, igvp->to, igvp->seqbuf, igvp->maxScaleX); nLines=Ing_PopOverviewPage(bsp, igvp->pictTop, igvp->from, igvp->to, igvp->GrData.pClr, maxScaleX, &igvp->talign); igvp->last_feat_position_top=nLines*(-20); /* add scale value in white to vTop to align picture to ruler */ AddAttribute(igvp->pictTop, COLOR_ATT, WHITE_COLOR, 0, 0, 0, 0); sprintf(scale_buf, "%d", igvp->from); AddLabel(igvp->pictTop, 0, igvp->last_feat_position_top, scale_buf, SMALL_TEXT, 0, LOWER_CENTER, 0); AddAttribute(igvp->pictTop, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); AttachPicture (igvp->vRuler1,igvp->pictRuler1, INT4_MIN, INT4_MAX, UPPER_LEFT, MAX(1, maxScaleX) , 1, NULL); SetViewerProcs(igvp->vRuler1,Ing_Ruler1ClickProc,Ing_Ruler1DragProc,Ing_Ruler1ReleaseProc, NULL); AttachPicture (igvp->vTop, igvp->pictTop, INT4_MIN, INT4_MAX, UPPER_LEFT, MAX(1,maxScaleX) , 1, NULL); SetViewerProcs(igvp->vTop, NULL ,NULL,NULL, NULL); ArrowCursor(); } /******************************************************************************* Function : Ing_GetNamesZoomedVal() Purpose : get from, to and scale data for bottom (Detailed) viewer *******************************************************************************/ static void Ing_GetNamesZoomedVal(VieweR vMain,Int4Ptr from, Int4Ptr to, Int4Ptr scaleX,Int4 MaxLength) { Int4 scale_X; BoxInfo port; ViewerBox(vMain,NULL,&port,NULL,&scale_X,NULL); if (from) *from=port.left; if (to) { *to=port.right; if (port.right>MaxLength){ (*to)=MaxLength; if (port.left<0)(*to)+=ABS(port.left); } } if (scaleX) *scaleX=scale_X; } /******************************************************************************* Function : Ing_ExpandRegion(), Ing_DoRange(), Ing_GotoProc(), Ing_ShowALLProc() Purpose : functions to show a limited range of the loaded sequence *******************************************************************************/ static void Ing_ExpandRegion(IngGenomeViewerPtr igvp, Int4 start, Int4 end) { RecT rc; Int4 scaleX; Int4 from, to; Int4 index; PrimitivE prim; igvp->SeqLength=ABS(end-start); igvp->from=start; igvp->to=end; if (igvp->slp) SeqLocFree(igvp->slp); igvp->slp=SeqLocIntNew(start, end, Seq_strand_plus, (SeqIdPtr)igvp->bsp->id); /* update Zoomer values, and select center bar */ GetPosition(igvp->vTop, &rc); igvp->maxScaleX=Ing_GetTPMaxScale(igvp, rc.right-rc.left); scaleX=Ing_GetBPMaxScale(igvp); ExploreSegment (igvp->pictZoom, (Pointer)igvp->vZoom, Ing_DeSelectGenericPrim); Ing_UpdateZoomerVals(igvp, scaleX); index=8; igvp->scaleX=igvp->scale_array[index-1]; prim=GetPrimitive(igvp->pictZoom,(Uint2)index); HighlightPrimitive (igvp->vZoom, igvp->pictZoom, prim, FRAME_PRIMITIVE); /* re populate pictures */ Ing_PopulateOverviewPage((Pointer)igvp, TRUE); Ing_PopulateDetailedPage((Pointer)igvp); Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to,NULL,igvp->SeqLength); igvp->xposition=from; Ing_MoveCursor(igvp ,from,to,TRUE); } static void Ing_DoRange(ButtoN b) { IngGenomeViewerPtr igvp; IngRangePtr rnp; Int4 start=0, end=0; WindoW w; BioseqPtr bsp; PrimitivE prim; w=ParentWindow(b); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); rnp=(IngRangePtr)GetObjectExtra(b); if ((!igvp) || (!rnp)) return; bsp=igvp->bsp; start=MAX(0, Ing_GetValue(rnp->left)); end=MIN(Ing_GetValue(rnp->right), igvp->bsp->length-1); if (start>=end){ if (start==end) return; Message (MSG_OK, "_from_ is greater than _to_"); return; } Ing_ExpandRegion(igvp, start, end); } static void Ing_GotoProc(ButtoN b) { Ing_DoRange(b); } static void Ing_ShowALLProc(ButtoN b) { IngGenomeViewerPtr igvp=NULL; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(b)); Ing_ExpandRegion(igvp, 0, igvp->bsp->length-1); } /*************************************************** Function : Ing_UpdateGCGraph(), Ing_ShowGCContent(); Ing_ShowComplexity() Purpose : Show or update display of GC rich regions on sequence; Show low complexity regions ***************************************************/ static void Ing_UpdateGCGraph(IngGenomeViewerPtr igvp) { IngExploreSegs gpn; Int4 top; Int4 bottom; Int4 scaleX; Reset(igvp->vRuler2); igvp->pictRuler2=DeletePicture(igvp->pictRuler2); Update(); igvp->pictRuler2=CreatePicture(); scaleX=igvp->scaleX; if (igvp->bSegmented){ gpn.idx=1; gpn.seg=igvp->pictRuler2; gpn.viewer=igvp->vRuler2; gpn.GrData=&igvp->GrData; gpn.seqbuf=igvp->seqbuf; gpn.bsp=igvp->bsp; gpn.scaleX=igvp->scaleX; gpn.bShowGC = igvp->bShowGC; gpn.bRegister = TRUE; gpn.procID = igvp->procID; gpn.userKey = igvp->userKey; if (igvp->slp){ gpn.left=GetOffsetInBioseq(igvp->slp, igvp->bsp, SEQLOC_LEFT_END); gpn.right=GetOffsetInBioseq(igvp->slp, igvp->bsp, SEQLOC_RIGHT_END); } else{ gpn.left=igvp->from; gpn.right=igvp->to; } SeqMgrExploreSegments(igvp->bsp, (Pointer)&gpn, Ing_ExploreSegments); } else{ igvp->idx = 2; top=(2*igvp->GrData.SegBoxHeight); bottom=top-igvp->GrData.SegBoxHeight; Ing_AddGCRect(igvp->pictRuler2, igvp->bsp->id, igvp->entityID, igvp->itemID, OBJ_BIOSEQ, igvp->seqbuf, 0, top, igvp->SeqLength, bottom, scaleX, Seq_strand_plus, TRUE, TRUE, igvp->idx, igvp->bShowGC); } Ing_AddRuler(igvp->pictRuler2, 2*igvp->GrData.SegBoxHeight, igvp->from, igvp->to, scaleX, 1, TRUE); AttachPicture(igvp->vRuler2, igvp->pictRuler2, (igvp->xposition<=0?INT4_MIN:igvp->xposition), INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vRuler2, Ing_SequenceClickProc, NULL, NULL, NULL); } extern Uint1Ptr Ing_FillSeqBuffer(BioseqPtr bsp, SeqLocPtr slp, Int4 from, Int4 to) { Uint1Ptr buffer; Int2 ctr; SeqPortPtr spp; Uint1Ptr temp_seq; Int4 buf_len, i; Uint1Ptr seq = NULL; buffer=(Uint1Ptr) MemNew (sizeof(Uint1)*101); MemSet((Pointer)buffer, '\0', sizeof(Char)*101); temp_seq=NULL; seq = (Uint1Ptr) MemNew (sizeof(Uint1)*(to-from+1)); if (slp) { spp = SeqPortNewByLoc(slp, Seq_code_ncbi4na); } else { spp = SeqPortNew (bsp, from, to, 0, Seq_code_ncbi4na); } if (spp == NULL) { ErrPostEx (SEV_ERROR, 0, 0, "%s", "GV- Failed on SeqPortNew"); return NULL; } temp_seq = seq; do { ctr = SeqPortRead(spp, buffer, 100); if (ctr > 0) { i = 0; buf_len = ctr; while (buf_len > 0) { *temp_seq = (Uint1)buffer[i]; temp_seq++; i++; buf_len--; } } } while (ctr != SEQPORT_EOF * -1); SeqPortFree(spp); if (buffer) MemFree(buffer); return seq; } static void Ing_GenericCancelButton(ButtoN b) { WindoW w; w=ParentWindow(b); Remove(w); } /***************************************************** Function: Ing_PopulateCpG(); Ing_ResizeCpGWindow(); Ing_CreateCpGReport(); Ing_CloseCpGWindow() Purpose: Print CpG island report ****************************************************/ typedef struct ing_motifinfo { VieweR v; SegmenT seg; CharPtr name; Pointer motif; } IngMInfo, PNTR IngMInfoPtr; static void Ing_PopulateCpG(IngMInfoPtr minfo) { ACT_CGInfoPtr temp = NULL; FloatHi confidence; Char str[500] = {""}; RecT rc; Int4 row = 0; Int4 winsize; Int2 slen, swidth; Int2 cxChar, nchars; SegmenT seg; VieweR v; v = minfo->v; Reset(v); DeletePicture(minfo->seg); Update(); minfo->seg = CreatePicture(); seg = minfo->seg; GetPosition(v, &rc); winsize = (rc.right-rc.left) - 3*stdCharWidth; SetSmallFont(); sprintf(str, " -- CpG islands -- "); slen = StringLen(str); swidth = StringWidth(str); cxChar=(Int2)ceil((float)swidth/slen); nchars=(Int2)ceil((float)winsize/cxChar); row += Ing_PrintText(str, seg, row, winsize, RED_COLOR, 0); temp = (ACT_CGInfoPtr)minfo->motif; while (temp != NULL){ confidence = (FloatHi)(temp->length/(FloatHi)(temp->c * temp->g)); sprintf(str, "CpG: %d to %d Conf: %f", temp->from + 1, temp->to + 1, confidence); row += Ing_PrintText(str, seg, row, winsize, BLACK_COLOR, 0); temp = temp->next; } AttachPicture (v, seg, INT4_MIN, INT4_MAX, UPPER_RIGHT, 1 , 1, NULL); } static void Ing_CloseCpGWindow(WindoW w) { IngMInfoPtr minfo = NULL; ACT_CGInfoPtr cpg, tmp; minfo = GetObjectExtra(w); if (!minfo){ Remove(w); return; } cpg = (ACT_CGInfoPtr)minfo->motif; while (cpg){ tmp = cpg->next; MemFree(cpg); cpg = tmp; } Remove(w); return; } static void Ing_ResizeCpGWindow(WindoW w) { RecT rcW, rcR, rcVsb, rcHsb; Int2 height,width,gap,vsbWidth; Int2 hsbWidth,in; BaR vsb; BaR hsb; IngMInfoPtr minfo = NULL; VieweR v; minfo = (IngMInfoPtr) GetObjectExtra(w); if (!minfo) return; v = minfo->v; ObjectRect(w, &rcW); width= rcW.right-rcW.left; height= rcW.bottom-rcW.top; SafeHide(v); Update(); vsb = GetSlateVScrollBar ((SlatE) v); hsb = GetSlateHScrollBar ((SlatE) v); GetPosition(v, &rcR); GetPosition(vsb, &rcVsb); GetPosition(vsb, &rcHsb); vsbWidth=rcVsb.right-rcVsb.left; hsbWidth=rcHsb.right-rcHsb.left; gap=10; in=2; rcR.right=rcR.left+width-in-vsbWidth; rcR.bottom=rcR.top+height-in-gap-hsbWidth; SetPosition(v, &rcR); Ing_PopulateCpG(minfo); SafeShow(v); Update(); } static WindoW Ing_CreateCpGReport(ACT_CGInfoPtr cpg) { WindoW w; VieweR v; SegmenT pict; IngMInfoPtr minfo = NULL; Int2 left_margin; left_margin=5*stdCharWidth; w = DocumentWindow(left_margin, -65 ,550, 250, "CpG Report", Ing_CloseCpGWindow, Ing_ResizeCpGWindow); v = CreateViewer(w, 500 ,200, TRUE, TRUE); pict = CreatePicture(); minfo = (IngMInfoPtr)MemNew(sizeof(IngMInfo)); minfo->motif = (Pointer) cpg; minfo->v = v; minfo->seg = pict; Ing_PopulateCpG(minfo); SetObjectExtra(w, (Pointer)minfo, StdCleanupExtraProc); Show(w); return w; } /***************************************************** Function: Ing_PopulateMotif(); Ing_ResizeMotifWindow(); Ing_CreateMotifReport(); Ing_CloseMotifWindow() Purpose: Print Motif report ****************************************************/ static void Ing_PopulateMotif(IngMInfoPtr minfo) { MotifInfoPtr temp = NULL; CharPtr name = NULL; FloatHi confidence; Char str[500] = {""}; RecT rc; Int4 row = 0; Int4 winsize; Int4 slen, swidth; Int2 cxChar, nchars; VieweR v; SegmenT seg; v = minfo->v; Reset(v); DeletePicture(minfo->seg); Update(); minfo->seg = CreatePicture(); seg = minfo->seg; GetPosition(v, &rc); winsize = (rc.right-rc.left) - 3*stdCharWidth; SetSmallFont(); name = minfo->name; sprintf(str, " -- %s -- ", name); slen = StringLen(str); swidth = StringWidth(str); cxChar = stdCharWidth; nchars= (Int2)ceil((float)winsize/cxChar); row += Ing_PrintText(str, seg, row, winsize, RED_COLOR, 0); temp = (MotifInfoPtr)minfo->motif; while (temp != NULL){ sprintf(str, "%s: %d to %d Strand: %s Score: %f", name, temp->start + 1, temp->stop + 1, (temp->strand==Seq_strand_minus)?"minus":"plus", temp->score); row += Ing_PrintText(str, seg, row, winsize, BLACK_COLOR, 0); temp = temp->next; } AttachPicture (v, seg, INT4_MIN, INT4_MAX, UPPER_RIGHT, 1 , 1, NULL); } static void Ing_CloseMotifWindow(WindoW w) { IngMInfoPtr minfo = NULL; MotifInfoPtr motif, tmp; minfo = GetObjectExtra(w); if (!minfo){ Remove(w); return; } MemFree(minfo->name); motif = (MotifInfoPtr)minfo->motif; while (motif){ tmp = motif->next; MemFree(motif); motif = tmp; } Remove(w); return; } static void Ing_ResizeMotifWindow(WindoW w) { RecT rcW, rcR, rcVsb, rcHsb; Int2 height,width,gap,vsbWidth; Int2 hsbWidth,in; BaR vsb; BaR hsb; VieweR v; CharPtr name = NULL; IngMInfoPtr minfo = NULL; minfo = (IngMInfoPtr) GetObjectExtra(w); if (!minfo) return; v = minfo->v; ObjectRect(w, &rcW); width= rcW.right-rcW.left; height= rcW.bottom-rcW.top; SafeHide(v); Update(); vsb = GetSlateVScrollBar ((SlatE) v); hsb = GetSlateHScrollBar ((SlatE) v); GetPosition(v, &rcR); GetPosition(vsb, &rcVsb); GetPosition(vsb, &rcHsb); vsbWidth=rcVsb.right-rcVsb.left; hsbWidth=rcHsb.right-rcHsb.left; gap=10; in=2; rcR.right=rcR.left+width-in-vsbWidth; rcR.bottom=rcR.top+height-in-gap-hsbWidth; SetPosition(v, &rcR); Ing_PopulateMotif(minfo); SafeShow(v); Update(); } static WindoW Ing_CreateMotifReport(MotifInfoPtr motif, CharPtr name) { WindoW w; VieweR v; SegmenT pict; IngMInfoPtr minfo; Int2 left_margin; left_margin=5*stdCharWidth; w = DocumentWindow(left_margin, -65 ,550, 250, "Motif Report", Ing_CloseMotifWindow, Ing_ResizeMotifWindow); v = CreateViewer(w, 500 ,200, TRUE, TRUE); pict = CreatePicture(); minfo = (IngMInfoPtr)MemNew(sizeof(IngMInfo)); minfo->name = name; minfo->motif = (Pointer)motif; minfo->v = v; minfo->seg = pict; Ing_PopulateMotif(minfo); SetObjectExtra(w, (Pointer)minfo, StdCleanupExtraProc); Show(w); return w; } /*************************************************** Function : Ing_CpGProc(); Ing_PolyAProc(); Ing_RepeatProc(); Ing_SignalPeptideProc(); Ing_KozakProc(); Ing_UserMotifProc() Purpose : Find motif functions ***************************************************/ static void Ing_CpGProc(IteM i) { IngGenomeViewerPtr igvp=NULL; WindoW w=NULL; WindoW ReportW; SeqLocPtr slp = NULL; ACT_CGInfoPtr cpg = NULL, temp = NULL; MsgAnswer ans; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Searching for CpG islands ...."); cpg = ACT_FindCpG (igvp->bsp); if (cpg == NULL){ Message (MSG_OK, "No CpG islands found"); goto end; } ReportW = Ing_CreateCpGReport(cpg); ans = Message (MSG_YN, "Annotate CpG islands?"); if (ans == ANS_YES) { IngfeatDefTrack[FEATDEF_misc_feature]=2; temp = cpg; while (temp != NULL){ slp = SeqLocIntNew(temp->from, temp->to, Seq_strand_plus, igvp->bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_misc_feature, "CpG island", slp, NULL); temp = temp->next; } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); } end: ArrowCursor(); Ing_ProgressEnd(igvp); if (ans == ANS_NO) Select(ReportW); } static void Ing_PolyAProc(IteM i) { IngGenomeViewerPtr igvp=NULL; WindoW w=NULL; WindoW ReportW; SeqLocPtr slp = NULL; MotifInfoPtr polya = NULL; MotifInfoPtr temp; MsgAnswer ans; CharPtr name; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Searching for Poly A sites ...."); polya = MOT_FindPolyA(igvp->bsp); if (polya == NULL){ Message (MSG_OK, "No Poly A sites found"); goto end; } name = StringSave("Poly A site"); ReportW = Ing_CreateMotifReport(polya, name); ans = Message (MSG_YN, "Annotate Poly A sites?"); if (ans == ANS_YES) { IngfeatDefTrack[FEATDEF_misc_feature]=2; temp = polya; while (temp != NULL){ slp = SeqLocIntNew(temp->start, temp->stop, temp->strand, igvp->bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_polyA_signal, "Poly A site", slp, NULL); temp = temp->next; } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); } end: ArrowCursor(); Ing_ProgressEnd(igvp); if (ans == ANS_NO) Select(ReportW); } static void Ing_RepeatsProc(IteM i) { IngGenomeViewerPtr igvp=NULL; WindoW w=NULL; WindoW ReportW; SeqLocPtr slp = NULL; MotifInfoPtr repeats = NULL; MotifInfoPtr temp; MsgAnswer ans; CharPtr name; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Searching for Repeats ...."); repeats = MOT_FindRepeats(igvp->bsp); if (repeats == NULL){ Message (MSG_OK, "No Repeats found"); goto end; } name = StringSave("Repeats"); ReportW = Ing_CreateMotifReport(repeats, name); ans = Message (MSG_YN, "Annotate Repeats?"); if (ans == ANS_YES) { IngfeatDefTrack[FEATDEF_misc_feature]=2; temp = repeats; while (temp != NULL){ slp = SeqLocIntNew(temp->start, temp->stop, temp->strand, igvp->bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_repeat_region, "Repeat", slp, NULL); temp = temp->next; } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); } end: ArrowCursor(); Ing_ProgressEnd(igvp); if (ans == ANS_NO) Select(ReportW); } static void Ing_KozakProc(IteM i) { IngGenomeViewerPtr igvp=NULL; WindoW w=NULL; WindoW ReportW; SeqLocPtr slp = NULL; MotifInfoPtr kozaks = NULL; MotifInfoPtr temp; MsgAnswer ans; CharPtr name; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Searching for Kozak motifs ...."); kozaks = MOT_FindKozak(igvp->bsp); if (kozaks == NULL){ Message (MSG_OK, "No Kozak motifs found"); goto end; } name = StringSave("Kozak"); ReportW = Ing_CreateMotifReport(kozaks, name); ans = Message (MSG_YN, "Annotate Kozak?"); if (ans == ANS_YES) { IngfeatDefTrack[FEATDEF_misc_feature]=2; temp = kozaks; while (temp != NULL){ slp = SeqLocIntNew(temp->start, temp->stop, temp->strand, igvp->bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_misc_feature, "Kozak", slp, NULL); temp = temp->next; } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); } end: ArrowCursor(); Ing_ProgressEnd(igvp); if (ans == ANS_NO) Select(ReportW); } static void Ing_SignalPeptideProc(IteM i) { IngGenomeViewerPtr igvp=NULL; WindoW w=NULL; WindoW ReportW; SeqLocPtr slp = NULL; MotifInfoPtr signal = NULL; MotifInfoPtr temp; MsgAnswer ans; CharPtr name; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Searching for signal peptide ...."); signal = MOT_FindSignalPeptide(igvp->bsp); if (signal == NULL){ Message (MSG_OK, "No Signal Peptide motif found"); goto end; } name = StringSave("Signal Peptide"); ReportW = Ing_CreateMotifReport(signal, name); ans = Message (MSG_YN, "Annotate Signal Peptide?"); if (ans == ANS_YES) { IngfeatDefTrack[FEATDEF_misc_feature]=2; temp = signal; while (temp != NULL){ slp = SeqLocIntNew(temp->start, temp->stop, temp->strand, igvp->bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_sig_peptide, "Signal Peptide", slp, NULL); temp = temp->next; } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); } end: ArrowCursor(); Ing_ProgressEnd(igvp); if (ans == ANS_NO) Select(ReportW); } static void Ing_FindMotif(ButtoN b) { IngGenomeViewerPtr igvp=NULL; WindoW w=NULL; WindoW ReportW; SeqLocPtr slp = NULL; BioseqPtr bsp = NULL; MotifInfoPtr user = NULL; MotifInfoPtr temp; IngSaveInfoPtr userinfo; Char motif[100] = {""}, str[50]= {""}; MsgAnswer ans; CharPtr name; userinfo = (IngSaveInfoPtr)GetObjectExtra(b); if (!userinfo) return; w=ParentWindow(b); Hide(w); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Searching for your motif ...."); bsp = igvp->bsp; GetTitle(userinfo->text, motif, sizeof(motif)); if (!StringHasNoText(motif)) user = MOT_MotifSearch(motif, bsp, ISA_aa(bsp->mol)); else { ErrPostEx(SEV_WARNING, 0, 0, "%s", "Enter a motif string"); goto end; } if (user == NULL){ Message (MSG_OK, "Your motif - %s - was not found", motif); goto end; } sprintf(str, "%s", motif); name = StringSave(str); ReportW = Ing_CreateMotifReport(user, name); ans = Message (MSG_YN, "Annotate Motifs?"); if (ans == ANS_YES) { IngfeatDefTrack[FEATDEF_misc_feature]=2; temp = user; while (temp != NULL){ slp = SeqLocIntNew(temp->start, temp->stop, temp->strand, bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_misc_feature, "user motif", slp, NULL); temp = temp->next; } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); } Remove(w); ArrowCursor(); Ing_ProgressEnd(igvp); if (ans == ANS_NO) Select(ReportW); return; end: Show(w); ArrowCursor(); Ing_ProgressEnd(igvp); } static void Ing_UserMotifProc(IteM i) { IngGenomeViewerPtr igvp = NULL; IngSaveInfoPtr userinfo = NULL; GrouP g, g1, g2; WindoW w; ButtoN b; igvp = (IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); if (!igvp) return; userinfo = (IngSaveInfoPtr)MemNew(sizeof(IngSaveInfo)); w = FixedWindow(-50, -33, -10, -10,"Find User Defined Motif", StdCloseWindowProc); g = HiddenGroup(w, -2, -2, NULL); g1 = HiddenGroup(g, 2, 1, NULL); StaticPrompt(g1, "MOTIF string : ", 0, 0, systemFont, 'l'); userinfo->text = DialogText(g1, "", 20, NULL); g2= HiddenGroup(g, 2, 1, NULL); b = DefaultButton(g2, "Find", Ing_FindMotif); SetObjectExtra(b, (Pointer)userinfo, StdCleanupExtraProc); PushButton(g2, "Cancel", Ing_GenericCancelButton); SetObjectExtra(w, (Pointer)igvp, NULL); Select(w); Show(w); return; } static void Ing_ShowGCContent(IteM i) { IngGenomeViewerPtr igvp; WindoW w; Int4 scaleX; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Computing GC content...."); if (igvp->bShowGC){ igvp->bShowGC = FALSE; SetTitle(igvp->d_Win->GC, "Show GC content"); } else { igvp->bShowGC = TRUE; SetTitle(igvp->d_Win->GC, "Hide GC content"); } if (igvp->seqbuf==NULL){ igvp->seqbuf = Ing_FillSeqBuffer(igvp->bsp, igvp->slp, igvp->from, igvp->to); seq = igvp->seqbuf; } if (igvp->seqbuf){ Ing_GetNamesZoomedVal(igvp->vBottom, NULL, NULL,&scaleX,igvp->SeqLength); Ing_UpdateGCGraph(igvp); } ArrowCursor(); Ing_ProgressEnd(igvp); return; } static void Ing_ShowComplexity(IteM i) { IngGenomeViewerPtr igvp = NULL; WindoW w = NULL; SeqLocPtr slp_feat = NULL; SeqLocPtr slp_dust = NULL; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Running Dust...."); if (igvp->bDustExists==TRUE){ /* already drawn */ if (!IngfeatDefFilter[FEATDEF_REGION]){ IngfeatDefTrack[FEATDEF_REGION]=2; IngfeatDefFilter[FEATDEF_REGION]=TRUE; ObjMgrSendMsg(OM_MSG_UPDATE, igvp->entityID, 0, 0); } goto end; } slp_dust = BioseqDust (igvp->bsp, 0, igvp->bsp->length-1, 20, 16, 5, 1); if (slp_dust == NULL){ ErrPostEx (SEV_WARNING, 0, 0, "%s", "Ingenue found no low complexity regions in this sequence"); goto end; } IngfeatDefTrack[FEATDEF_REGION]=2; igvp->bDustExists = TRUE; while ((Boolean)(slp_feat=SeqLocFindNext(slp_dust,slp_feat))){ Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_REGION, "low complexity", slp_feat, NULL); } ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); end: ArrowCursor(); Ing_ProgressEnd(igvp); return; } /*************************************************** Function : Ing_CreateNewFeature(); Ing_MakeSlpList(); Ing_MakeLocListFromSAP() Purpose : Create and annotate a new feature; make SeqLocPtr list of start and stops to pass into Ing_CreateNewFeature() ***************************************************/ static SeqFeatPtr Ing_CreateNewFeature(Uint2 entityID, Uint2 itemID, BioseqPtr product, Uint1 seqfeattype, Uint1 featdeftype, CharPtr label, SeqLocPtr slp_feat, CharPtr color) { SeqFeatPtr sfp=NULL; OMProcControl ompc; ObjMgrPtr omp=NULL; ObjMgrProcPtr ompp=NULL; CharPtr loc=NULL; GeneRefPtr grp=NULL; CdRegionPtr cdr=NULL; ImpFeatPtr ifp=NULL; RnaRefPtr rrp=NULL; Uint1 rnatype=0; BioseqPtr bsp = NULL; sfp=SeqFeatNew(); if (!sfp) return NULL; sfp->idx.subtype = featdeftype; sfp->data.choice = seqfeattype; if (StringCmp(label, "low complexity")!= 0){ sfp->location = (SeqLocPtr)SeqLocPackage(slp_feat); } else { sfp->location = slp_feat; } SetSeqFeatProduct(sfp, product); loc = SeqLocPrint (sfp->location); if (loc == NULL) { loc = StringSave ("?"); } omp=ObjMgrReadLock(); if (seqfeattype==SEQFEAT_GENE){ grp = GeneRefNew (); sfp->data.value.ptrvalue = (Pointer) grp; ompp=ObjMgrProcFind(omp, 0, "Edit Gene", 0); bsp = (BioseqPtr)GetPointerForIDs(entityID, itemID, OBJ_BIOSEQ); sfp->location = SeqLocMerge(bsp, sfp->location, NULL, TRUE, FALSE, FALSE); } else if (seqfeattype==SEQFEAT_CDREGION){ cdr=CdRegionNew(); sfp->data.value.ptrvalue = (Pointer) cdr; ompp=ObjMgrProcFind(omp, 0, "Edit CdRgn", 0); } else if (seqfeattype==SEQFEAT_RNA){ /* sep = SeqMgrGetSeqEntryForData(product); */ /* if (sep != NULL){ */ /* vnp = SeqEntryGetSeqDescr(sep, Seq_descr_name, NULL); */ rrp = RnaRefNew(); rrp->type = 2; sfp->data.value.ptrvalue = (Pointer) rrp; ompp=ObjMgrProcFind(omp, 0, "Edit RNA", 0); } else if (seqfeattype==SEQFEAT_REGION){ ompp=ObjMgrProcFind(omp, 0, "Edit RgnFeat", 0); } else if (seqfeattype==SEQFEAT_IMP){ ifp=ImpFeatNew(); ifp->key = StringSave("misc_feature"); sfp->data.value.ptrvalue=(Pointer)ifp; sfp->qual = GBQualNew(); sfp->qual->qual = StringSave("standard_name"); sfp->qual->val = StringSave(label); ompp=ObjMgrProcFind(omp, 0, "Edit Unclassified ImpFeat", 0); } if (StringHasNoText(label)) label = (CharPtr) FeatDefTypeLabel (sfp); if (label == NULL) { label = "?"; } /* sfp->comment=StringSave(label); */ /* tab-delimited files */ if (color!=NULL) sfp->title=StringSave(color); else if (label) sfp->title=StringSave(label); MemSet ((Pointer) &ompc, 0, sizeof (OMProcControl)); ompc.input_entityID = entityID; ompc.input_itemID = itemID; ompc.input_itemtype = OBJ_BIOSEQ; ompc.output_itemtype = OBJ_SEQFEAT; ompc.output_data = (Pointer)sfp; ompc.proc=ompp; ObjMgrUnlock(); if (! AttachDataForProc (&ompc, FALSE)) { Message (MSG_ERROR, "Create Feature failed"); } return sfp; } typedef struct ing_ivalinfo { Int4 start1; Int4 stop1; Int4 start2; Int4 stop2; struct ing_ivalinfo PNTR next; } IngIvalInfo, PNTR IngIvalInfoPtr; static IngIvalInfoPtr Ing_IvalInfoFree ( IngIvalInfoPtr ival ) { IngIvalInfoPtr next; while (ival != NULL) { next = ival->next; MemFree (ival); ival = next; } return NULL; } static IngIvalInfoPtr Ing_GetAlignmentIntervals (SeqAlignPtr sap, Int4 from_row, Int4 to_row, Int4 from, Int4 to, Uint1 strand) { AlnMsg2Ptr amp1; AlnMsg2Ptr amp2; IngIvalInfoPtr ival; IngIvalInfoPtr ival_head; IngIvalInfoPtr ival_prev; SeqIdPtr master = NULL; Int4 tmp; Int4 from_aln, to_aln; Int4 start, stop; if (sap == NULL || sap->saip == NULL) return NULL; strand = AlnMgr2GetNthStrand(sap, 2); if (!(from == 0 && to == -1)){ from_aln = AlnMgr2MapBioseqToSeqAlign(sap, from, from_row); to_aln = AlnMgr2MapBioseqToSeqAlign(sap, to, from_row); if (from_aln == -2 || to_aln == -2) return NULL; if (from_aln > to_aln) { tmp = from_aln; from_aln = to_aln; to_aln = tmp; } } else{ from_aln= from; to_aln = to; } amp1 = AlnMsgNew2(); amp1->from_aln = from_aln; amp1->to_aln = to_aln; amp1->row_num = from_row; amp2 = AlnMsgNew2(); amp2->from_aln = from_aln; amp2->to_aln = to_aln; amp2->row_num = to_row; ival_head = ival_prev = NULL; while (AlnMgr2GetNextAlnBit(sap, amp1) && AlnMgr2GetNextAlnBit(sap, amp2)) { if (amp1->type == AM_SEQ && amp2->type == AM_SEQ) { ival = (IngIvalInfoPtr)MemNew(sizeof(IngIvalInfo)); ival->start1 = amp1->from_row; ival->stop1 = amp1->to_row; ival->start2 = amp2->from_row; ival->stop2 = amp2->to_row; if (Seq_strand_minus == strand){ if (ival_head == NULL) ival_head = ival; else { ival->next = ival_head; ival_head = ival; } } else { if (ival_head == NULL) ival_head = ival_prev = ival; else { ival_prev->next = ival; ival_prev = ival; } } } } AlnMsgFree2(amp1); AlnMsgFree2(amp2); return ival_head; } static IngIvalInfoPtr Ing_OldGetAlignmentIntervals (SeqAlignPtr sap, Int4 from_row, Int4 to_row, Int4 from, Int4 to, Uint1 strand) { AlnMsg2Ptr amp1; AlnMsg2Ptr amp2; IngIvalInfoPtr ival; IngIvalInfoPtr ival_head; IngIvalInfoPtr ival_prev; SeqIdPtr master = NULL; Int4 tmp; Int4 from_aln, to_aln; Int4 start, stop; if (sap == NULL || sap->saip == NULL) return NULL; if (!(from == 0 && to == -1)){ from_aln = AlnMgr2MapBioseqToSeqAlign(sap, from, from_row); to_aln = AlnMgr2MapBioseqToSeqAlign(sap, to, from_row); if (from_aln == -2 || to_aln == -2) return NULL; if (from_aln > to_aln) { tmp = from_aln; from_aln = to_aln; to_aln = tmp; } } else{ from_aln= from; to_aln = to; } amp1 = AlnMsgNew2(); amp1->from_aln = from_aln; amp1->to_aln = to_aln; amp1->row_num = from_row; amp2 = AlnMsgNew2(); amp2->from_aln = from_aln; amp2->to_aln = to_aln; amp2->row_num = to_row; ival_head = ival_prev = NULL; while (AlnMgr2GetNextAlnBit(sap, amp1) && AlnMgr2GetNextAlnBit(sap, amp2)) { if (amp1->type == AM_SEQ && amp2->type == AM_SEQ) { ival = (IngIvalInfoPtr)MemNew(sizeof(IngIvalInfo)); ival->start1 = amp1->from_row; ival->stop1 = amp1->to_row; ival->start2 = amp2->from_row; ival->stop2 = amp2->to_row; if (ival_head == NULL) ival_head = ival_prev = ival; else { ival_prev->next = ival; ival_prev = ival; } } } AlnMsgFree2(amp1); AlnMsgFree2(amp2); return ival_head; } static IngIvalInfoPtr MergeAdjacentIntervals ( IngIvalInfoPtr list ) { IngIvalInfoPtr curr, last, next; if (list != NULL) { curr = list->next; last = list; while (curr != NULL) { next = curr->next; if (curr->start2 == last->stop2 + 1) { last->stop2 = MAX (curr->stop2, last->stop2); MemFree (curr); last->next = next; } else { last = curr; } curr = next; } } return list; } static SeqLocPtr Ing_MakeLocListFromSAP(SeqAlignPtr salp, Boolean gap_split) { SeqLocPtr head = NULL; IngIvalInfoPtr ival; IngIvalInfoPtr ival_head; SeqIntPtr sinp; SeqLocPtr slp; SeqPntPtr spp; Uint1 strand; SeqIdPtr sip = NULL; Int4 from_row, to_row; sip = AlnMgr2GetNthSeqIdPtr(salp, 2); strand=AlnMgr2GetNthStrand(salp, 2); from_row = 2; to_row = 1; ival_head = (IngIvalInfoPtr)Ing_GetAlignmentIntervals (salp, from_row, to_row, 0, -1, strand); if (!ival_head) return NULL; ival_head = MergeAdjacentIntervals (ival_head); if (ival_head != NULL) { if (gap_split) { for (ival = ival_head; ival != NULL; ival = ival->next) { slp = SeqLocIntNew(ival->start1, ival->stop1, strand, sip); SeqLocAdd (&head, slp, TRUE, FALSE); } } else { for (ival = ival_head; ival->next != NULL; ival = ival->next) continue; slp = SeqLocIntNew(ival_head->start1, ival->stop1, strand, sip); SeqLocAdd (&head, slp, TRUE, FALSE); } } Ing_IvalInfoFree (ival_head); return head; } static SeqLocPtr Ing_OldMakeLocListFromSAP(SeqAlignPtr sap) { SeqLocPtr slp_head = NULL; SeqLocPtr slp1 = NULL, slp2 = NULL; SeqLocPtr slp = NULL; AlnMsg2Ptr amp1 = NULL; AlnMsg2Ptr amp2 = NULL; SeqIdPtr sip = NULL; Uint1 strand = 0; Boolean more = FALSE; Boolean bLastmasterwasgap = FALSE; Int4 i = 0, j = 0; Int4 numivals = 0; Int4Ptr ivals = NULL; sip=AlnMgr2GetNthSeqIdPtr(sap, 1); strand=AlnMgr2GetNthStrand(sap, 2); numivals= AlnMgr2GetNumSegs(sap); ivals = (Int4Ptr)MemNew(sizeof(Int4)*2*numivals); amp1 = AlnMsgNew2(); amp2 = AlnMsgNew2(); amp1->from_aln = 0; amp1->to_aln = -1; amp1->row_num = 1; amp2->from_aln = 0; amp2->to_aln = -1; amp2->row_num = 2; while ((Boolean)(more = AlnMgr2GetNextAlnBit(sap, amp2))){ AlnMgr2GetNextAlnBit(sap, amp1); if (amp2->type == AM_SEQ){ if (amp1->type == AM_GAP){ bLastmasterwasgap = TRUE; } else { if (Seq_strand_minus == strand){ if (!bLastmasterwasgap){ i += 2; ivals[i-2] = amp1->from_row; } else bLastmasterwasgap = FALSE; ivals[i-1] = amp1->to_row; } else { slp=SeqLocIntNew(amp1->from_row, amp1->to_row, strand, sip); if (slp_head==NULL){ slp_head=slp; } else { SeqLocAdd(&slp_head, slp, TRUE, FALSE); } } } } } AlnMsgFree2(amp1); AlnMsgFree2(amp2); /* repack if on minus strand */ if (Seq_strand_minus == strand){ for(j = i - 1; j >= 0; j -= 2){ slp=SeqLocIntNew(ivals[j-1], ivals[j], strand, sip); if (slp_head==NULL){ slp_head=slp; } else { SeqLocAdd(&slp_head, slp, TRUE, FALSE); } } } MemFree(ivals); return slp_head; } static SeqLocPtr Ing_MakeSlpList(ValNodePtr vnp_list, Int4 numivals, Int4Ptr ivals, Uint1 strand, SeqIdPtr sip) { SeqLocPtr slp_head=NULL; SeqLocPtr slp=NULL; Int4 i; ValNodePtr vnp=NULL; if (vnp_list){ vnp=vnp_list; while (vnp !=NULL){ slp=(SeqLocPtr)vnp->data.ptrvalue; if (slp_head==NULL){ slp_head=slp; } else { SeqLocAdd(&slp_head, slp, TRUE, FALSE); } vnp=vnp->next; } ValNodeFree(vnp_list); } else { if (!(strand == Seq_strand_minus)){ for(i=0; i<(2*numivals); i+=2){ slp=SeqLocIntNew(ivals[i], ivals[i+1], strand, sip); if (slp_head==NULL){ slp_head=slp; } else { SeqLocAdd(&slp_head, slp, TRUE, FALSE); } } } else { for(i=(2*numivals)-1; i>=0; i-=2){ slp=SeqLocIntNew(ivals[i-1], ivals[i], strand, sip); if (slp_head==NULL){ slp_head=slp; } else { SeqLocAdd(&slp_head, slp, TRUE, FALSE); } } } } return slp_head; } /******************************************************************************* Function : Ing_RunORFinder(), Ing_DotMatrixProc() Purpose : Calls to toolkit applications *******************************************************************************/ static void Ing_RunORFinder(IteM i) { WindoW w; IngGenomeViewerPtr igvp=NULL; ValNodePtr orflist=NULL; ValNodePtr vnp=NULL; SeqLocPtr slp=NULL; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp==NULL) return; WatchCursor(); Ing_ProgressNew(igvp, "Running ORF finder...."); if (igvp->bOrfExists==TRUE){ if (!IngfeatDefFilter[FEATDEF_misc_feature]){ IngfeatDefTrack[FEATDEF_misc_feature]=2; IngfeatDefFilter[FEATDEF_misc_feature]=TRUE; ObjMgrSendMsg(OM_MSG_UPDATE, igvp->entityID, 0, 0); } goto end; } orflist = (ValNodePtr)GetOrfList(igvp->bsp, 200); if (orflist==NULL){ ErrPostEx (SEV_WARNING, 0, 0, "%s", "Ingenue found no open reading frames in this sequence"); goto end; } IngfeatDefTrack[FEATDEF_misc_feature]=2; igvp->bOrfExists = TRUE; orflist = (ValNodePtr)ClearNonMetOrfs (orflist); vnp=orflist; while (vnp){ slp=(SeqLocPtr)vnp->data.ptrvalue; Ing_CreateNewFeature(igvp->entityID, igvp->itemID,NULL, SEQFEAT_IMP, FEATDEF_misc_feature, "orf", slp, NULL); vnp=vnp->next; } ValNodeFree(orflist); ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); end: ArrowCursor(); Ing_ProgressEnd(igvp); return; } static void Ing_DotMatrixProc(IteM i) { SeqAlignPtr sap=NULL; SelStructPtr ssp; IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); ssp = ObjMgrGetSelected(); if (ssp == NULL){ Ing_GetFileForDotMatrix(i); ArrowCursor(); return; } if (ssp->itemtype != OBJ_SEQALIGN) { ErrPostEx(SEV_ERROR, 0, 0, "MUST select seqalign"); ArrowCursor(); return; } if (ssp) { sap = (SeqAlignPtr)GetPointerForIDs(ssp->entityID, ssp->itemID, OBJ_SEQALIGN); if (sap == NULL) { ErrPostEx(SEV_ERROR, 0, 0, "Error in copying seqalign"); ArrowCursor(); return; } Ing_CreateDotMatrixForm(igvp, sap, NULL, NULL); } ArrowCursor(); return; } /******************************************************************************* Function(s) : Ing_SelectPrim(), Ing_DeSelectPrim(), Ing_DeSelectGenericPrim() Purpose : ExploreSegment() select/deselect callbacks *******************************************************************************/ static Boolean Ing_SelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Uint2 entityID=0; Uint2 itemID=0; Uint2 itemtype=0; IngSelectPtr selp=NULL; if (!prim) return TRUE; selp = (IngSelectPtr) userdata; GetPrimitiveIDs(prim, &entityID, &itemID, &itemtype, 0); if (entityID == selp->entityID && itemID == selp->itemID && itemtype == selp->itemtype){ if (primID){ HighlightPrimitive(selp->vwr, seg, prim, FRAME_PRIMITIVE); if (selp->returnFALSE) return FALSE; } else { HighlightSegment (selp->vwr, seg, FRAME_SEGMENT); if (selp->returnFALSE) return FALSE; } } return TRUE; } static Boolean Ing_DeSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Uint2 entityID=0; Uint2 itemID=0; Uint2 itemtype=0; IngSelectPtr selp=NULL; if (!prim) return TRUE; selp = (IngSelectPtr) userdata; GetPrimitiveIDs(prim, &entityID, &itemID, &itemtype, NULL); if (entityID == selp->entityID && itemID == selp->itemID && itemtype == selp->itemtype){ if (primID){ HighlightPrimitive (selp->vwr, seg, prim, PLAIN_PRIMITIVE); if (selp->returnFALSE) return FALSE; } else { HighlightSegment(selp->vwr, seg, PLAIN_SEGMENT); if (selp->returnFALSE) return FALSE; } } return TRUE; } static Boolean Ing_DeSelectAll(SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Int1 highlight=0; IngSelectPtr selp=NULL; if (!prim) return TRUE; selp = (IngSelectPtr) userdata; if (primID){ GetPrimDrawAttribute (prim, NULL, NULL, NULL, NULL, NULL, &highlight); if (highlight == FRAME_PRIMITIVE) HighlightPrimitive (selp->vwr, seg, prim, PLAIN_PRIMITIVE); } else { highlight = SegmentStyle(seg); if (highlight == FRAME_SEGMENT) HighlightSegment (selp->vwr, seg, PLAIN_SEGMENT); } return TRUE; } static Boolean Ing_DeSelectGenericPrim (SegmenT seg, PrimitivE prim, Uint2 segID,Uint2 primID, Uint2 primCt, VoidPtr userdata) { Int1 highlight; VieweR v; v = (VieweR)userdata; GetPrimDrawAttribute (prim, NULL, NULL, NULL, NULL, NULL, &highlight); if (highlight != PLAIN_PRIMITIVE) HighlightPrimitive (v, seg, prim, PLAIN_PRIMITIVE); return TRUE; } /*********************************************************************** Function: Ing_InitAlignArrays() Purpose : Initialize alignment tracking arrays *************************************************************/ extern void Ing_InitAlignArrays(IngTrackAlignsPtr tap, Boolean bFirst) { if (!bFirst){ if (tap->hidelist) ValNodeFree(tap->hidelist); if (tap->showlist) ValNodeFree(tap->showlist); if (tap->namelist) MemFree(tap->namelist); if (tap->hnamelist) MemFree(tap->hnamelist); } tap->hidelist = NULL; tap->showlist = NULL; tap->namelist = NULL; tap->hnamelist = NULL; tap->showindex =0; tap->hideindex = 0; tap->update = TRUE; } /******************************************************************************* Function(s) : Ing_InitMainDataPtr(), Ing_MainDataNew(), Ing_MainDataFree() Purpose : to create, initialize, or free the main data structure *******************************************************************************/ static void Ing_InitMainDataPtr(IngGenomeViewerPtr igvp) { igvp->hMain=NULL; igvp->hReport=NULL; igvp->slp=NULL; igvp->bsp=NULL; igvp->bspIsLocked=FALSE; igvp->filetype=0; igvp->seqbuf=NULL; igvp->vRuler1=NULL; igvp->vTop=NULL; igvp->vRuler2=NULL; igvp->vTop=NULL; igvp->bOverviewSelected=FALSE; igvp->bDustExists=FALSE; igvp->bOrfExists=FALSE; igvp->bShowGC = FALSE; igvp->TopHeight = 200; igvp->last_feat_position_top=0; igvp->last_feat_position_bottom = 0; igvp->xposition=0; igvp->ZoomedVal=1; igvp->scaleX=1; igvp->maxScaleX=1; igvp->bMaxScale=FALSE; igvp->defline=NULL; /* feature descriptors */ igvp->defline2 = NULL; igvp->data = NULL; igvp->bLabels=TRUE; /* show-hide labels on features */ igvp->isExons = FALSE; /* option to display spidey output */ /* init progress window vars */ igvp->progress_string=NULL; igvp->progress_timer=0; igvp->progress_running=FALSE; /* init align tracking arrays */ Ing_InitAlignArrays(&igvp->talign, TRUE); } extern IngGenomeViewerPtr Ing_MainDataNew(void) { IngGenomeViewerPtr igvp=NULL; igvp=(IngGenomeViewerPtr)MemNew(sizeof(IngGenomeViewer)); if (!igvp) return NULL; Ing_InitMainDataPtr(igvp); return igvp; } static IngGenomeViewerPtr Ing_MainDataFree(IngGenomeViewerPtr igvp) { if (igvp->vZoom) igvp->vZoom=DeleteViewer(igvp->vZoom); if (igvp->vTop) igvp->vTop=DeleteViewer(igvp->vTop); if (igvp->vBottom) igvp->vBottom=DeleteViewer(igvp->vBottom); if (igvp->vRuler1) igvp->vRuler1=DeleteViewer(igvp->vRuler1); if (igvp->vRuler2) igvp->vRuler2=DeleteViewer(igvp->vRuler2); if (igvp->scale_array)MemFree(igvp->scale_array); if (igvp->slp) SeqLocFree(igvp->slp); if (igvp->seqbuf) MemFree(igvp->seqbuf); if (igvp->GrData.pClr) Ing_FreeColorTable(igvp->GrData.pClr); if (igvp->defline) MemFree(igvp->defline); if (igvp->defline2) MemFree(igvp->defline2); if (igvp->entity_list) MemFree(igvp->entity_list); Ing_InitAlignArrays(&igvp->talign, FALSE); return igvp; } /******************************************************************************* Function(s) : Ing_AllButPartsCount() Purpose : counter the number of bioseqs given a seqentry *******************************************************************************/ static Int4 Ing_AllButPartsCount (SeqEntryPtr sep, Pointer mydata, SeqEntryFunc mycallback, Int4 index, Int2 indent) { BioseqSetPtr bssp; if (sep == NULL) return index; if (IS_Bioseq (sep)) { if (mycallback != NULL) (*mycallback) (sep, mydata, index, indent); return index + 1; } if (Bioseq_set_class (sep) != 4) { if (mycallback != NULL) (*mycallback) (sep, mydata, index, indent); index++; } bssp = (BioseqSetPtr) sep->data.ptrvalue; sep = bssp->seq_set; indent++; while (sep != NULL) { index = Ing_AllButPartsCount (sep, mydata, mycallback, index, indent); sep = sep->next; } return index; } /******************************************************************************* Function(s) : Ing_ResetTitle(); Ing_GetFastaTitle(); Ing_GetScoreAndEvalue() Purpose : set title for highlighted object; get full length fasta description *******************************************************************************/ static void Ing_ResetTitle(IngGenomeViewerPtr igvp, Boolean clear) { RecT rc; Int2 width, stringwd; Int2 nchars, nrows; Int2 nlines; Int2 len; CharPtr c=NULL, end=NULL, str=NULL; Int4 i; SetTitle(igvp->featInfo[0], ""); SetTitle(igvp->featInfo[1], ""); SetTitle(igvp->featInfo[2], ""); SetTitle(igvp->featInfo[3], ""); if (!igvp->defline) return; if (clear && igvp->defline){ MemFree(igvp->defline); igvp->defline=NULL; if (igvp->defline2){ MemFree(igvp->defline2); igvp->defline2 = NULL; } return; } GetPosition(igvp->deflineg, &rc); nchars=MIN(130, (rc.right-rc.left)/igvp->GrData.cxChar); len=StringLen(igvp->defline); nlines = (Int2)ceil((float)len/nchars); for (i=0; i<3; i++){ if ((i+1)>nlines){ SetTitle(igvp->featInfo[i], ""); } else { str=StringSave(igvp->defline); c=str+(i*nchars); len=StringLen(c); nchars=MIN(len, nchars); end=c+nchars; *end='\0'; SetTitle(igvp->featInfo[i], c); MemFree(str); } } SetTitle(igvp->featInfo[i], igvp->defline2); } static CharPtr Ing_GetFastaTitle (BioseqPtr bsp, CharPtr pretext, CharPtr posttext) { CharPtr title = NULL; CharPtr prep, postp, predum = "", postdum = ""; Char idbuf[L_ID], defbuf[L_DEF]; Int4 prelen = 0, postlen = 0; SeqIdPtr sip; if (bsp != NULL) { if ((sip = bsp->id) != NULL) { if (pretext != NULL) { prelen = StrLen (pretext); prep = pretext; } else { prep = predum; } if (posttext != NULL) { postlen = StrLen (posttext); postp = posttext; } else { postp = postdum; } if ((title = (CharPtr) MemNew (sizeof (Char) * (L_T+prelen+postlen))) != NULL) { switch (sip->choice) { case SEQID_LOCAL: idbuf[0] = '\0'; if (sip->data.ptrvalue != NULL) StrNCpy (idbuf, ((ObjectIdPtr) sip->data.ptrvalue)->str, L_ID-1); idbuf[L_ID-1] = '\0'; break; default: FastaId (bsp, idbuf, L_ID); break; } FastaDefLine (bsp, defbuf, L_DEF, NULL, NULL, 0); sprintf (title, "%s%s %s%s", prep, idbuf, defbuf, postp); } } } return title; } extern void Ing_GetScoreAndEvalue(SeqAlignPtr sap, CharPtr PNTR eval_buff, CharPtr PNTR bit_score_buff) { Int4 score, number; FloatHi bit_score, evalue; Char buff1[10]={""}, buff2[10]={""}; GetScoreAndEvalue(sap, &score, &bit_score, &evalue, &number); if (evalue < 1.0e-180) sprintf (buff1, "0.0"); else if (evalue < 1.0e-99) sprintf (buff1, "%2.0le", evalue); else if (evalue < 0.0009) sprintf (buff1, "%3.1le", evalue); else if (evalue < 1.0) sprintf (buff1, "%4.3lf", evalue); else sprintf (buff1, "%5.1lf", evalue); *eval_buff = StringSave(buff1); if (bit_score > 9999) sprintf(buff2, "%4.3le", bit_score); else if (bit_score > 99.9) sprintf(buff2, "%4.1lf", bit_score); else sprintf(buff2, "%4.2lf", bit_score); *bit_score_buff = StringSave(buff2); } /******************************************************************************* Function : Ing_MsgFlush() Purpose : kill the viewer in response to a OM_MSG_FLUSH message Return value : OM_MSG_RET_OK if success *******************************************************************************/ static Int2 Ing_MsgFlush(IngGenomeViewerPtr igvp,OMMsgStructPtr ommsp) { if (igvp->entityID==ommsp->entityID && ((igvp->itemID==ommsp->itemID && ommsp->itemtype==OBJ_BIOSEQ) || (ommsp->itemID == 0 && ommsp->itemtype==0))){ if (igvp->bspIsLocked) BioseqUnlock(igvp->bsp); ObjMgrFreeByEntityID(igvp->entityID); Ing_MainDataFree(igvp); Remove(igvp->hMain); #ifdef ING_STANDALONE WinCounter--; if (!WinCounter) Ing_StartupWindow(); #endif } return(OM_MSG_RET_OK); } /******************************************************************************* Function : Ing_OM_MsgFunc() Purpose : message callback for the viewer *******************************************************************************/ static Int2 LIBCALLBACK Ing_OM_MsgFunc (OMMsgStructPtr ommsp) { OMUserDataPtr omudp; IngGenomeViewerPtr igvp=NULL; IngSelectData sel; SeqMgrFeatContext sfc; Int4 start=0, stop=0; Int4 s1=0, s2=0, n=1; Int4 score=0, number=0; AlnMsg2Ptr amp; Boolean refresh=FALSE; Char buf[255]={""}; CharPtr str1=NULL; Char str2[300]={""}; CharPtr loc=NULL; BioseqPtr bsp=NULL, bsp_sap=NULL; SeqAlignPtr salp=NULL; SeqIdPtr sip=NULL; SeqEntryPtr sep=NULL; Uint2 entityID=0; Uint2 itemID=0; Uint2 itemtype=0; Uint2 segID=0; Int2 highlight; IngReportPtr Report=NULL; CharPtr eval_buff, bit_score_buff; omudp = (OMUserDataPtr)(ommsp->omuserdata); igvp = (IngGenomeViewerPtr)omudp->userdata.ptrvalue; /* if (igvp->procID != omudp->procid) return OM_MSG_RET_OK; */ bsp=GetBioseqGivenIDs (igvp->entityID, igvp->itemID, OBJ_BIOSEQ); if (!bsp) return (OM_MSG_RET_OK); if (!igvp) return(OM_MSG_RET_OK); if (igvp->hReport) Report=(IngReportPtr)GetObjectExtra(igvp->hReport); switch (ommsp->message) { case OM_MSG_DEL: break; case OM_MSG_CREATE: break; case OM_MSG_UPDATE: if (ObjMgrGetDirtyFlag (ommsp->entityID)) refresh=TRUE; break; case OM_MSG_SELECT: entityID=ommsp->entityID; itemID=ommsp->itemID; itemtype=ommsp->itemtype; MemSet((Pointer)buf, '\0', sizeof(buf)); sel.entityID=entityID; sel.itemID=itemID; sel.itemtype=itemtype; sel.segID=msg.segID; if (itemtype == OBJ_BIOSEQ || itemtype == OBJ_SEQID){ sel.vwr = igvp->vRuler2; sel.returnFALSE= TRUE; ExploreSegment(igvp->pictRuler2, (Pointer) &sel, Ing_SelectPrim); } else { /* highlight object in overview if picture is not compressed */ if (igvp->maxScaleXvTop; sel.returnFALSE=FALSE; ExploreSegment (igvp->pictTop, (Pointer) &sel, Ing_SelectPrim); igvp->bOverviewSelected=TRUE; } /* highlight object in feature window */ sel.vwr=igvp->vBottom; sel.returnFALSE=TRUE; ExploreSegment (igvp->pictBottom, (Pointer) &sel, Ing_SelectPrim); } /* get defline label */ if (msg.labelmsg==0) { Ing_ResetTitle(igvp, TRUE); } else if (msg.labelmsg == 2) { if (itemtype == OBJ_BIOSEQ || itemtype == OBJ_SEQID){ if (itemtype == OBJ_BIOSEQ){ bsp = (BioseqPtr)GetPointerForIDs(ommsp->entityID, ommsp->itemID, OBJ_BIOSEQ); } else { sip =(SeqIdPtr)GetPointerForIDs(ommsp->entityID, ommsp->itemID, OBJ_SEQID); bsp = BioseqLockById(sip); } if (bsp) { str1=Ing_GetFastaTitle(bsp, NULL, NULL); if (igvp->defline) MemFree(igvp->defline); igvp->defline = StringSave(str1); if (igvp->defline2) MemFree(igvp->defline2); igvp->defline2 = NULL; } else { if (igvp->defline) MemFree(igvp->defline); igvp->defline=StringSave("Sequence: Unknown"); if (igvp->defline2){ MemFree(igvp->defline2); igvp->defline2 = NULL; } } Ing_ResetTitle(igvp, FALSE); } else if (itemtype==OBJ_SEQFEAT) { SeqMgrGetDesiredFeature(entityID, bsp, itemID, 0, NULL, &sfc); if (&sfc) { FeatDefLabel(sfc.sfp, buf, sizeof(buf)-1, OM_LABEL_BOTH); sprintf(str2, "%.150s", buf); if (igvp->defline) MemFree(igvp->defline); igvp->defline=StringSave(str2); loc=SeqLocPrint(sfc.sfp->location); if (loc) sprintf(str2, "%.150s", loc); else sprintf(str2, "len: %d - %d", sfc.left, sfc.right); if (igvp->defline2) MemFree(igvp->defline2); igvp->defline2 = StringSave(str2); } else{ if (igvp->defline) MemFree(igvp->defline); igvp->defline=StringSave("Feature: Unknown"); if (igvp->defline2){ MemFree(igvp->defline2); igvp->defline2 = NULL; } } Ing_ResetTitle(igvp, FALSE); } else if (itemtype==OBJ_SEQALIGN){ salp=(SeqAlignPtr)GetPointerForIDs(ommsp->entityID, ommsp->itemID, OBJ_SEQALIGN); sip=AlnMgr2GetNthSeqIdPtr(salp, 2); AlnMgr2GetNthSeqRangeInSA(salp, 1, &start, &stop); MemSet((Pointer)str2, '\0', sizeof(str2)); bsp_sap=BioseqLockById(sip); if (bsp_sap){ str1=Ing_GetFastaTitle(bsp_sap, "SeqAlign: ", NULL); loc=SeqLocPrint(salp->bounds); if (salp->score){ MemSet((Pointer)buf, '\0', sizeof(buf)); Ing_GetScoreAndEvalue(salp, &eval_buff, &bit_score_buff); if (loc) sprintf(buf, " %.150s Score = %s Expect = %s", loc, bit_score_buff, eval_buff); else sprintf(buf, "len: %d - %d Score = %s Expect = %s", start + 1, stop + 1, bit_score_buff, eval_buff); MemFree(eval_buff); MemFree(bit_score_buff); } else { if (loc) sprintf(buf, " %.150s", loc); else sprintf(buf, "len: %d - %d", start + 1, stop + 1); } BioseqUnlock(bsp_sap); if (igvp->defline) MemFree(igvp->defline); igvp->defline=StringSave(str1); if (igvp->defline2) MemFree(igvp->defline2); igvp->defline2 = StringSave(buf); Ing_ResetTitle(igvp, FALSE); } else { if (salp){ sprintf(str2, "%s", "SeqAlign: "); if (sip){ MemSet((Pointer)buf, '\0', sizeof(buf)); SeqIdWrite(sip, buf, PRINTID_FASTA_LONG, 41); StringCat(str2, buf); AlnMgr2IndexSeqAlign(salp); loc=SeqLocPrint(salp->bounds); if (salp->score){ MemSet((Pointer)buf, '\0', sizeof(buf)); Ing_GetScoreAndEvalue(salp, &eval_buff, &bit_score_buff); if (loc) sprintf(buf, " %.150s Score = %s Expect = %s", loc, bit_score_buff, eval_buff); else sprintf(buf, "len: %d - %d Score = %s Expect = %s", start + 1, stop + 1, bit_score_buff, eval_buff); MemFree(eval_buff); MemFree(bit_score_buff); } else { if (loc) sprintf(buf, " %.150s", loc); else sprintf(buf, "len: %d - %d", start + 1, stop + 1); } } else { StringCat(str2, "Unknown"); } } if (igvp->defline) MemFree(igvp->defline); igvp->defline=StringSave(str2); if (igvp->defline2) MemFree(igvp->defline2); igvp->defline2 = StringSave(buf); Ing_ResetTitle(igvp, FALSE); } } } /* highlight spidey report */ if (itemtype==OBJ_SEQALIGN && Report!=NULL && msg.segID){ Ing_HighlightReportWindow(Report, FRAME_SEGMENT, msg.segID, (igvp->isExons?TRUE:FALSE)); Report->isPrevSelected=TRUE; Report->last_segID=msg.segID; } break; case OM_MSG_DESELECT: sel.entityID=ommsp->entityID; sel.itemID=ommsp->itemID; sel.itemtype=ommsp->itemtype; if (sel.itemtype == OBJ_BIOSEQ || sel.itemtype == OBJ_SEQID){ sel.returnFALSE=FALSE; sel.vwr=igvp->vRuler2; ExploreSegment (igvp->pictRuler2, (Pointer) &sel, Ing_DeSelectAll); } else { sel.segID = msg.segID; sel.returnFALSE=FALSE; sel.vwr=igvp->vBottom; ExploreSegment (igvp->pictBottom, (Pointer) &sel, Ing_DeSelectAll); } if (igvp->bOverviewSelected){ sel.vwr=igvp->vTop; ExploreSegment (igvp->pictTop, (Pointer) &sel, Ing_DeSelectAll); igvp->bOverviewSelected = FALSE; } if (Report!=NULL){ Ing_HighlightReportWindow(Report, PLAIN_SEGMENT, 0, (igvp->isExons?TRUE:FALSE)); Report->isPrevSelected=FALSE; Report->last_segID=0; } break; case OM_MSG_CACHED: break; case OM_MSG_UNCACHED: break; case OM_MSG_TO_CLIPBOARD: break; case OM_MSG_SETCOLOR: break; case OM_MSG_FLUSH: Ing_MsgFlush(igvp,ommsp); break; default: break; } /* data has been altered --> refresh all viewers */ if (refresh){ Ing_InitAlignArrays(&igvp->talign, FALSE); SeqMgrIndexFeatures (igvp->entityID, NULL); Ing_PopulateOverviewPage((Pointer)igvp, FALSE); Ing_PopulateDetailedPage((Pointer)igvp); Ing_ResetTitle(igvp, TRUE); } return OM_MSG_RET_OK; } /******************************************************************************* Function : Ing_MoveCursor(), Ing_DoMoveCursor() Purpose : draw grey cursor on Ruler1 *******************************************************************************/ static void Ing_DoMoveCursor(VieweR v, SegmenT pict, Int2 SegBoxTop, Int2 SegBoxBottom, Int4 from, Int4 to,Int4 MaxLength, Boolean bFirst, Uint1Ptr grayClr) { Int2 Half; WindoW temport; PrimitivE prim=NULL; enumPrimAddOrder oldOrder; Int4 scaleX,scaleY; Int4 primwidth; PntInfo worldPt; PoinT viewerPt; RecT rc,rc2, rcV; BoxInfo boxCursor; BoxInfo boxSeg; temport=SavePort(ParentWindow(v)); /*the cursor always has the index 1*/ prim=GetPrimitive(pict, 1); if (prim && !bFirst){/*the first time this function is called (when the viewer is loaded, the cursor prim doesn't exist yet*/ ViewerBox(v,NULL,NULL,&rc,&scaleX,&scaleY); PrimitiveBox(prim,scaleX,scaleY,&boxCursor); if (prim){ DeletePrim(pict, prim); worldPt.x=boxCursor.left; worldPt.y=boxCursor.top; Nlm_MapWorldToViewer(v,worldPt,&viewerPt); rc2.left=viewerPt.x; rc2.top=viewerPt.y; worldPt.x=boxCursor.right; worldPt.y=boxCursor.bottom; Nlm_MapWorldToViewer(v,worldPt,&viewerPt); rc2.right=viewerPt.x; rc2.bottom=viewerPt.y; Select(v); InvalRect(&rc2); RestorePort(temport); Update(); } } /*the cursor must be displayed before everything else*/ oldOrder=ChangeAddPrimOrder(ADD_TO_HEAD); GetPosition(v, &rcV); /*the cursor always has an index=1*/ AddAttribute(pict, COLOR_ATT|STYLE_ATT, (grayClr?grayClr:YELLOW_COLOR), SOLID_LINE, 0, 0, 0); AddRectangle(pict,MAX(1,from),SegBoxTop, to,SegBoxBottom, NO_ARROW,TRUE,1); ChangeAddPrimOrder(oldOrder); ViewerBox(v,NULL,NULL,&rc,NULL,NULL); worldPt.x=from; worldPt.y=0; Nlm_MapWorldToViewer(v,worldPt,&viewerPt); rc.left=viewerPt.x; worldPt.x=to; worldPt.y=0; Nlm_MapWorldToViewer(v,worldPt,&viewerPt); rc.right=viewerPt.x+1; temport=SavePort(ParentWindow(v)); Select(v); InvalRect(&rc); RestorePort(temport); Update(); } static void Ing_MoveCursor(IngGenomeViewerPtr igvp, Int4 from, Int4 to, Boolean bFirst) { Int2 SegBoxTop; Int2 SegBoxBottom; Uint1 grayClr1[3]; Uint1 grayClr2[3]; RecT rc; grayClr1[0]=230; grayClr1[1]=230; grayClr1[2]=230; grayClr2[0]=248; grayClr2[1]=248; grayClr2[2]=248; GetPosition(igvp->vRuler1, &rc); SegBoxTop=9*igvp->GrData.SegBoxHeight; SegBoxBottom = -200; Ing_DoMoveCursor(igvp->vRuler1,igvp->pictRuler1, SegBoxTop, SegBoxBottom,from,to,igvp->SeqLength, bFirst, grayClr1); /* if (igvp->last_feat_position_top != 0){ SegBoxTop = 40; SegBoxBottom = igvp->last_feat_position_top - 20; Ing_DoMoveCursor(igvp->vTop, igvp->pictTop, SegBoxTop, SegBoxBottom, from, to, igvp->SeqLength, bFirst, grayClr2); } */ } static Boolean Ing_BuildStartupPage(IngGenomeViewerPtr igvp) { SegmenT segRuler,segLines, pictControl; BioseqPtr bsp; Int4 nSegments; IngExploreSegs gpn; if (igvp==NULL) return(FALSE); Ing_PopulateOverviewPage((Pointer)igvp, TRUE); Ing_PopulateDetailedPage((Pointer)igvp); return(TRUE); } /***************************************************************************** Function: Ing_UpdateZoomerVals(), Ing_PopulateZoomer(), Ing_ZoomProc(), Ing_ZoomerClickProc() Purpose: zoom functions *****************************************************************************/ static void Ing_UpdateZoomerVals(IngGenomeViewerPtr igvp, Int4 scaleX) { Int4 index, z, sFactor; z=15; sFactor=MAX(1, scaleX/z); for (index=z; index>1; index--) { igvp->scale_array[index-1] = MAX(1, scaleX); scaleX -=sFactor; } igvp->scale_array[index-1] = MAX(1, igvp->scale_array[index]/2); igvp->scaleX=igvp->scale_array[igvp->scale_index]; } static Boolean Ing_PopulateZoomer(IngGenomeViewerPtr igvp) { Int4 index, x1, x2; Int4 y1, y2; Int4 width; Int4 z, sFactor; PrimitivE prim; Uint1 zoomClr[3]; Int4 scaleX; zoomClr[0]=0; zoomClr[1]=0; zoomClr[2]=0; scaleX=Ing_GetBPMaxScale(igvp); z = 15; igvp->scale_array=(Int4Ptr)MemNew(sizeof(Int4)*z); sFactor = MAX(1, scaleX/z); width = z; x1 = 4; x2 = 2*(x1+width); y1 = 0; y2 = -1; AddAttribute(igvp->pictZoom, COLOR_ATT, BLUE_COLOR, 0, 0, 0, 0); AddLabel (igvp->pictZoom, (x1+x2)/2 , y1, "OUT", SMALL_TEXT, 0, UPPER_CENTER, 0); AddAttribute(igvp->pictZoom, COLOR_ATT, zoomClr, 0, 0, 0, 0); for (index=z; index>2; index--) { prim=AddRectangle(igvp->pictZoom, x1, y1, x2, y2, 0, TRUE,(Uint2) index); x1+=1; x2-=1; y1-=4; y2-=4; igvp->scale_array[index-1] = MAX(1, scaleX); if (index==8){ HighlightPrimitive (igvp->vZoom, igvp->pictZoom, prim, FRAME_PRIMITIVE); igvp->scaleX=MAX(1, scaleX); igvp->scale_index=index-1; } scaleX -=sFactor; if (index==z) igvp->zoomFbar=prim; } AddRectangle(igvp->pictZoom, x1, y1, x2, y2, 0, TRUE,(Uint2)index); igvp->scale_array[index] = MAX(1, scaleX); AddAttribute(igvp->pictZoom, COLOR_ATT, RED_COLOR, 0, 0, 0, 0); AddRectangle(igvp->pictZoom, x1+1, y1-4, x2-1, y2-4, 0, TRUE,(Uint2) index-1); igvp->scale_array[index-1] = MAX(1, igvp->scale_array[index]/2); /* AddAttribute(igvp->pictZoom, COLOR_ATT, MAGENTA_COLOR, 0, 0, 0, 0); */ /* AddLabel (igvp->pictZoom, (x1+x2)/2 , y2-2*igvp->GrData.cyChar , "-", MEDIUM_TEXT, 0, UPPER_CENTER, 0); */ AttachPicture (igvp->vZoom,igvp->pictZoom, INT4_MIN, INT4_MAX, UPPER_RIGHT, 1 , 1, NULL); SetViewerProcs(igvp->vZoom,Ing_ZoomerClickProc,NULL,NULL, NULL); return TRUE; } static void Ing_ZoomProc(IngGenomeViewerPtr igvp) { Int4 from, to; Ing_PopulateDetailedPage((Pointer)igvp); Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to,NULL,igvp->SeqLength); igvp->xposition=from; Ing_MoveCursor(igvp, from, to, FALSE); } static void Ing_ZoomerClickProc(VieweR v, SegmenT s, PoinT pt) { PrimitivE prim; Uint2 primCT, primID=0, segID; Int4 scaleX; IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(v)); if (!igvp) return; if (FindSegPrim(v, pt, NULL, NULL, &prim)) { FindSegment(v, pt, &segID, &primID, &primCT); if (primID==0) return; ExploreSegment (s, (Pointer)v, Ing_DeSelectGenericPrim); HighlightPrimitive (v, s, prim, FRAME_PRIMITIVE); scaleX = MAX(1, igvp->scale_array[((int)primID)-1]); if (primID==15) igvp->bMaxScale=TRUE; else igvp->bMaxScale=FALSE; igvp->scale_index=primID-1; igvp->scaleX=scaleX; Ing_ZoomProc(igvp); } } /***************************************************************************** Function: Ing_FeatViewerClickProc(), Ing_FeatViewerPanProc(), Ing_SequenceClickProc(), Ing_Ruler1ClickProc(), Ing_Ruler1DragProc(), Ing_Ruler1ReleaseProc() Purpose: click and scroll main window functions *****************************************************************************/ static void Ing_FeatViewerClickProc(VieweR v, SegmenT s, PoinT pt) { PrimitivE prim=NULL; Uint2 entityID=0,itemID=0,itemtype=0; Uint2 primID=0; Uint2 segID=0; Int1 highlight=0; IngGenomeViewerPtr igvp=NULL; SeqLocPtr slp=NULL; Int4 start, stop; Int4 i; Char str1[100], str2[50]; Uint2 strand; Int2 handled; SegmenT subSeg=NULL; IngSelectData sel; SelStructPtr ssp=NULL; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(v)); if (!igvp) return; /* if click was on a primitive */ if (subSeg=FindSegPrim(v, pt, NULL, NULL, &prim)){ GetPrimitiveIDs(prim, &entityID, &itemID, &itemtype, &primID); if (entityID && itemID && itemtype){ if (!primID){ highlight=SegmentStyle(subSeg); segID=SegmentID(subSeg); msg.segID=segID; } else { GetPrimDrawAttribute (prim, NULL, NULL, NULL, NULL, NULL, &highlight); msg.segID=primID; } msg.labelmsg=2; if (highlight == PLAIN_PRIMITIVE){ if (shftKey){ ObjMgrAlsoSelect(entityID, itemID, itemtype, 0, NULL); } else ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } else if (!dblClick){ ObjMgrDeSelect(entityID, itemID, itemtype, 0, NULL); } if (dblClick) { WatchCursor (); handled=GatherProcLaunch (OMPROC_EDIT, FALSE, entityID, itemID, itemtype, 0, 0, itemtype, 0); ArrowCursor(); if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) { ErrPostEx(SEV_ERROR, 0, 0,"Unable to launch editor on feature." ); } } } else { Ing_ResetTitle(igvp, TRUE); ssp=ObjMgrGetSelected(); if (ssp) ObjMgrDeSelectAll(); } } else { Ing_ResetTitle(igvp, TRUE); ssp=ObjMgrGetSelected(); if (ssp) ObjMgrDeSelectAll(); } } static void Ing_FeatViewerPanProc(VieweR v, SegmenT s) { IngGenomeViewerPtr igvp; WindoW hParent; Int4 from,to, scaleX; PntInfo worldPt; PoinT viewerPt; hParent=ParentWindow(v); if (!hParent) return; igvp=(IngGenomeViewerPtr)GetObjectExtra(hParent); if (!igvp) return; /*move the cursor*/ Ing_GetNamesZoomedVal(igvp->vBottom,&from,&to,&scaleX,igvp->SeqLength); if (igvp->xposition != from){ worldPt.x=from; worldPt.y=0; Nlm_MapWorldToViewer(igvp->vBottom,worldPt,&viewerPt); igvp->xposition=from; AttachPicture(igvp->vRuler2, igvp->pictRuler2, from, INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vRuler2, Ing_SequenceClickProc, NULL, NULL, NULL); Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to,&scaleX,igvp->SeqLength); Ing_MoveCursor(igvp, from, to, FALSE); igvp->xposition=from; } } static void Ing_SequenceClickProc(VieweR v, SegmenT s, PoinT pt) { IngGenomeViewerPtr igvp=NULL; Uint2 entityID=0; Uint2 itemID=0; Uint2 itemtype=0; Uint2 primID=0; PrimitivE prim; SelStructPtr ssp=NULL; igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(v)); ssp=ObjMgrGetSelected(); if (FindSegPrim(v, pt, NULL, NULL, &prim)) { GetPrimitiveIDs(prim, &entityID, &itemID, &itemtype, &primID); if (entityID && itemID && itemtype){ msg.labelmsg=2; ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); return; } } Ing_ResetTitle(igvp, TRUE); } PoinT startPt; PoinT stopPt; static void Ing_Ruler1ClickProc(VieweR v, SegmenT s, PoinT pt) { RecT rc; Int4 from, to; IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(v)); Ing_GetNamesZoomedVal(igvp->vRuler1,&from,&to, NULL,igvp->SeqLength); if (pt.xto) pt.x=to; startPt=pt; stopPt=pt; } static void Ing_Ruler1DragProc(VieweR v, SegmenT s, PoinT pt) { IngGenomeViewerPtr igvp; Int4 offset, LscaleX,scaleX, from, to, diff; PntInfo worldPt; PoinT viewerPt; RecT cursor, rc, rcDetail; WindoW temport; igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(v)); if (igvp->bMaxScale) return; Ing_GetNamesZoomedVal(igvp->vRuler1,&from,&to, &LscaleX,igvp->SeqLength); if (pt.xto) pt.x=to; stopPt=pt; Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to, &scaleX,igvp->SeqLength); worldPt.x=(from+to)/2; worldPt.y=0; Nlm_MapWorldToViewer(v,worldPt,&viewerPt); offset = (stopPt.x -viewerPt.x)*LscaleX; diff=to-from; from+=offset; to=from+diff; igvp->xposition=from; Ing_MoveCursor(igvp,from,to, FALSE); AttachPicture(igvp->vRuler2, igvp->pictRuler2, from, INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vRuler2,Ing_SequenceClickProc,NULL,NULL, NULL); AttachPicture(igvp->vBottom, igvp->pictBottom, from, INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vBottom,Ing_FeatViewerClickProc,NULL,NULL, Ing_FeatViewerPanProc); } static void Ing_Ruler1ReleaseProc(VieweR v, SegmenT s, PoinT pt) { IngGenomeViewerPtr igvp; Int4 offset, LscaleX,scaleX, from, to, diff; PntInfo worldPt; PoinT viewerPt; RecT cursor, rc, rcDetail; BaR hsb; WindoW temport; igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(v)); if (igvp->bMaxScale) return; GetPosition(v, &rc); if (pt.xrc.right) pt.x=rc.right; stopPt=pt; Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to, &scaleX,igvp->SeqLength); igvp->xposition=from; Ing_GetNamesZoomedVal(igvp->vRuler1,NULL, NULL, &LscaleX,igvp->SeqLength); worldPt.x=(from+to)/2; worldPt.y=0; Nlm_MapWorldToViewer(v,worldPt,&viewerPt); offset = (stopPt.x -viewerPt.x)*LscaleX; diff=to-from; from+=offset; to=from+diff; igvp->xposition=from; Ing_MoveCursor(igvp,from,to, FALSE); AttachPicture(igvp->vRuler2, igvp->pictRuler2, from, INT4_MAX, UPPER_LEFT, MAX(1, scaleX), 1, NULL); SetViewerProcs(igvp->vRuler2,Ing_SequenceClickProc,NULL,NULL, NULL); AttachPicture(igvp->vBottom, igvp->pictBottom, from, INT4_MAX, UPPER_LEFT, MAX(1,scaleX) , 1, NULL); SetViewerProcs(igvp->vBottom,Ing_FeatViewerClickProc,NULL,NULL, Ing_FeatViewerPanProc); } /***************************************************************************** Function: Ing_ReadIn2ndBsp(), Ing_ReadSpideyInfo(), Ing_ReadDotMatrixInfo(), Ing_ReadInBlastAsn(), Ing_FGetLine(), Ing_ParseSeqIdFile(), Ing_ReadInFeatureTable() Purpose: read in sequence, seqannot or seqid-list files *****************************************************************************/ static void Ing_ReadIn2ndBsp (IngGenomeViewerPtr igvp, CharPtr path, CharPtr GI_list) { BioseqPtr bsp_1=NULL; bsp_1=(BioseqPtr)GetBioseqGivenIDs(igvp->entityID, igvp->itemID, OBJ_BIOSEQ); if (!bsp_1) return; Ing_CreateBlast2SeqsForm(igvp, bsp_1, path, GI_list); } static void Ing_ReadSpideyInfo(IngGenomeViewerPtr igvp, CharPtr path, CharPtr GI_list) { BioseqPtr bsp_1=NULL; bsp_1=(BioseqPtr)GetBioseqGivenIDs(igvp->entityID, igvp->itemID, OBJ_BIOSEQ); if (!bsp_1) return; Ing_CreateSpideyForm(igvp, bsp_1, path, GI_list); } static void Ing_ReadDotMatrixInfo(IngGenomeViewerPtr igvp, CharPtr path, CharPtr GI_list) { BioseqPtr bsp_1=NULL; bsp_1=(BioseqPtr)GetBioseqGivenIDs(igvp->entityID, igvp->itemID, OBJ_BIOSEQ); if (!bsp_1) return; Ing_CreateDotMatrixForm(igvp, NULL, path, GI_list); } static void Ing_ReadInBlastAsn (IngGenomeViewerPtr igvp, FILE * ifp) { Pointer dataptr; Uint2 datatype, entityID, itemID; BioseqPtr bsp; SeqAlignPtr n_sap=NULL; SeqAlignPtr salp=NULL; SeqIdPtr sip=NULL; SeqAnnotPtr sanp=NULL; Int4 start, i; Int4 stop; Char str[10]; IngReportPtr Report=NULL; if (ifp == NULL) return; dataptr = ReadAsnFastaOrFlatFile (ifp, &datatype, NULL, FALSE, TRUE, TRUE, TRUE); if (!dataptr) goto end; if (datatype==OBJ_SEQANNOT){ sanp = (SeqAnnotPtr)(dataptr); sanp->name=StringSave("Blast file"); bsp=(BioseqPtr)GetBioseqGivenIDs(igvp->entityID, igvp->itemID, OBJ_BIOSEQ); Ing_AttachSeqAnnotToSeqEntry(igvp->entityID, sanp, bsp); ObjMgrSetDirtyFlag(igvp->entityID, TRUE); ObjMgrSendMsg(OM_MSG_UPDATE, igvp->entityID, 0, 0); } else{ Message (MSG_OK, "File is not a seqannot"); } end: ArrowCursor(); return; } static CharPtr Ing_FGetLine (FILE *fp) { ValNodePtr charp=NULL, vnp; CharPtr buffer = NULL; Char c; Int4 j, len=0; c = (Char)fgetc(fp); while (c!=255 && c!=NULLB && c!=EOF && c!='\0' && c!='\n') { if (c!='\t' && c!='\015') { ValNodeAddInt (&charp, 1, (Int4)c); len++; } c = (Char)fgetc(fp); if (c==EOF) { return NULL; } } if (charp) { buffer = (CharPtr)MemNew((size_t)((len+5)*sizeof(Char))); for (j=0, vnp=charp; vnp!=NULL; vnp=vnp->next, j++) buffer[j] = (Char) vnp->data.intvalue; buffer[j]='\0'; ValNodeFree (charp); } else if (c=='\0' || c=='\n') { buffer = (CharPtr)MemNew((size_t)(sizeof(Char))); buffer[0]='\0'; } return buffer; } extern CharPtr Ing_ParseSeqIdFile(FILE * fp) { CharPtr line=NULL; CharPtr GI_list=NULL; CharPtr ptr=NULL; BioseqPtr bsp=NULL; Boolean found = FALSE; line = Ing_FGetLine(fp); if (line==NULL) return NULL; while (line != NULL && !found) /* find first non-empty line */ { if (!StringHasNoText(line)) { if (StringLen(line) > 0) found = TRUE; } else { MemFree(line); line = Ing_FGetLine(fp); if (line==NULL) return NULL; } } if (!StringHasNoText(line)) { line = TrimSpacesAroundString(line); ptr = strtok(line, "\t"); GI_list=StringSave(ptr); GI_list=Ing_StringCat(GI_list, " "); MemFree(line); line = Ing_FGetLine(fp); } while(line != NULL){ if (!StringHasNoText(line)) { line = TrimSpacesAroundString(line); ptr = strtok(line, "\t"); GI_list=Ing_StringCat(GI_list, ptr); GI_list=Ing_StringCat(GI_list, " "); MemFree(line); line = Ing_FGetLine(fp); } else { MemFree(line); line = Ing_FGetLine(fp); } } return GI_list; } static void Ing_ReadInFeatureTable (IngGenomeViewerPtr igvp, FILE * ifp) { Pointer dataptr; Uint2 datatype, entityID; BioseqPtr bsp; Uint2 itemID; SeqFeatPtr sfp; SeqAnnotPtr sanp; Int4 start, i; Int4 stop; IngReportPtr Report=NULL; if (ifp == NULL) return; WatchCursor(); dataptr = ReadAsnFastaOrFlatFile (ifp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE); if (!dataptr) return; if (datatype==OBJ_SEQANNOT){ sanp = (SeqAnnotPtr)(dataptr); bsp=(BioseqPtr)GetBioseqGivenIDs(igvp->entityID, igvp->itemID, OBJ_BIOSEQ); entityID =Ing_AttachSeqAnnotToSeqEntry(igvp->entityID, (SeqAnnotPtr) dataptr, bsp); ObjMgrSetDirtyFlag(igvp->entityID, TRUE); ObjMgrSendMsg(OM_MSG_UPDATE, igvp->entityID, 0, 0); } else { Message (MSG_OK, "File is not a seqannot"); } ArrowCursor (); return; } /***************************************************************************** Function: Ing_StringCat() Purpose: concatinates checking that sufficient memory is allocated *****************************************************************************/ extern CharPtr Ing_StringCat(CharPtr a, CharPtr b) { CharPtr temp=NULL; Int4 strlen=0; strlen=StringLen(a); strlen+=StringLen(b); temp=(CharPtr)MemNew(sizeof(Char)*(strlen+1)); StringCat(temp, a); StringCat(temp, b); MemFree(a); return temp; } /***************************************************************************** Function: Ing_AssembleGenscanInfo(), Ing_ReadInGenscan() Purpose: parse genscan output from file *****************************************************************************/ static void Ing_AssembleGenscanInfo(IngGenomeViewerPtr igvp, IngInfoPtr lip) { Int4 i = 0; IngInfoPtr lip_tmp; Int4 n; Int4Ptr ivals=NULL; Uint1 strand; CharPtr tmp; SeqLocPtr slp_list=NULL; SeqLocPtr slp=NULL; if (lip == NULL) return; lip_tmp = lip; while (lip_tmp != NULL) { i++; lip_tmp = lip_tmp->next; } n = 0; ivals = (Int4Ptr)MemNew(2*i*sizeof(Int4)); lip_tmp = lip; while (lip_tmp != NULL) { if ((tmp = StringStr(lip_tmp->fields[1], "PlyA")) != NULL) { } else if ((tmp = StringStr(lip_tmp->fields[1], "Prom")) != NULL) { } else { if ((tmp = StringStr(lip_tmp->fields[2], "+"))!= NULL) strand = Seq_strand_plus; else strand = Seq_strand_minus; ivals[n] = atoi(lip_tmp->fields[3]); ivals[n+1] = atoi(lip_tmp->fields[4]); n+=2; } lip_tmp = lip_tmp->next; } slp_list=Ing_MakeSlpList(NULL, n/2, ivals, strand, igvp->bsp->id); Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, SEQFEAT_IMP, FEATDEF_misc_feature, "genscan predicted gene", slp_list, NULL); MemFree(ivals); } static void Ing_ReadInGenscan(FILE *ifp, IngGenomeViewerPtr igvp) { Boolean found=FALSE, first_pass=FALSE; Int4 i; Int4 len; CharPtr letter=NULL, str=NULL; CharPtr line=NULL; IngInfoPtr lip=NULL; IngInfoPtr lip_head=NULL; IngInfoPtr lip_prev=NULL; CharPtr ptr=NULL; Int4 prevlen; Int4 seq; CharPtr tmp; WatchCursor(); line = NULL; line = Ing_FGetLine(ifp); if (line==NULL) goto end; found = FALSE; while (line != NULL && !found) /* find first non-empty line */ { if (!StringHasNoText(line)) { if (StringLen(line) > 0) found = TRUE; } else { MemFree(line); line = Ing_FGetLine(ifp); if (line==NULL) goto end; } } found = FALSE; while (!found/* && line != NULL */) { tmp = StringStr(line, "----"); if (tmp != NULL) found = TRUE; MemFree(line); line = Ing_FGetLine(ifp); if (line==NULL) goto end; } if (line==NULL) goto end; lip_prev = lip_head = NULL; while ((tmp = StringStr(line, "Predicted")) == NULL) { if (StringHasNoText(line)) { if (lip_head != NULL){ Ing_AssembleGenscanInfo(igvp, lip_head); } lip_prev = lip_head = NULL; } else { line = TrimSpacesAroundString(line); ptr = strtok(line, " "); lip = (IngInfoPtr)MemNew(sizeof(IngInfo)); for (i=0; i<5; i++) { lip->fields[i] = StringSave(ptr); ptr = strtok(NULL, " "); } if (lip_head != NULL) { lip_prev->next = lip; lip_prev = lip; } else lip_head = lip_prev = lip; MemFree(line); } line = Ing_FGetLine(ifp); if (line==NULL) goto end; } end: ObjMgrSetDirtyFlag(igvp->entityID, TRUE); ObjMgrSendMsg(OM_MSG_UPDATE, igvp->entityID, 0, 0); ArrowCursor(); return; } /***************************************************************************** Function: Ing_ReadALine(), Ing_GetSeqFeatType(), Ing_GetFeatDefType(), Ing_GetStrand() Purpose: parse genscan output from file *****************************************************************************/ static CharPtr Ing_ReadALine (CharPtr str, size_t size, FILE *fp) { Char ch; CharPtr ptr; CharPtr rsult; if (str == NULL || size < 1 || fp == NULL) return NULL; *str = '\0'; rsult = fgets (str, size, fp); if (rsult != NULL) { ptr = str; ch = *ptr; while (ch != '\0' && ch != '\n' && ch != '\r') { ptr++; ch = *ptr; } *ptr = '\0'; } return rsult; } static Uint1 Ing_GetFeatDefType(CharPtr str) { if (StringCmp(str, "Gene") == 0 || StringCmp(str, "gene")==0) return FEATDEF_GENE; else if (StringCmp(str, "CDS")==0) return FEATDEF_CDS; else if (StringCmp(str, "mRNA") == 0) return FEATDEF_mRNA; else if (StringCmp(str, "STS") == 0) return FEATDEF_STS; else if (StringCmp(str, "variation")==0) return FEATDEF_variation; else return FEATDEF_misc_feature; } static Uint1 Ing_GetSeqFeatType(CharPtr str) { if (StringCmp(str, "Gene") == 0 || StringCmp(str, "gene")==0) return SEQFEAT_GENE; else if (StringCmp(str, "CDS")==0) return SEQFEAT_CDREGION; else if (StringCmp(str, "mRNA") == 0) return SEQFEAT_RNA; else if (StringCmp(str, "STS") == 0) return SEQFEAT_REGION; else if (StringCmp(str, "variation")==0) return SEQFEAT_REGION; else return SEQFEAT_IMP; } static Uint1 Ing_GetStrand(CharPtr str) { if (str == NULL) return Seq_strand_unknown; if (StringCmp(str, "plus") == 0) return Seq_strand_plus; else if (StringCmp(str, "minus") == 0) return Seq_strand_minus; else if (StringCmp(str, "both")==0) return Seq_strand_both; else return Seq_strand_unknown; } /***************************************************************************** Function: Ing_FreeLip(), Ing_AssembleTabDelimited(), Ing_ReadInTabDelimited(), is_in_range() Purpose: functions to parse tab delimited file Tab Delimited format: 1) Top of the file must contain '>Tab Delimited'. 2) Columns.. 1=start, 2=stop, 3=feature name, 4=uniqueID, 5=unit number(if it is part of a set), 6=color(choices are [red, black, cyan, green, magenta, purple, gray, yellow and blue]), 7=score, 8=strand. *****************************************************************************/ static IngInfoPtr Ing_FreeLip(IngInfoPtr lip, Boolean delete_last) { IngInfoPtr lip_tmp; Int4 i; lip_tmp=lip; /* lip=lip->next; */ if (!delete_last){ while (lip->next !=NULL){ /* don't delete the last node */ for (i=0; i<4; i++) { if (lip_tmp->fields[i]) MemFree(lip_tmp->fields[i]); } MemFree(lip_tmp); lip_tmp=lip; lip=lip->next; } } else{ while (lip !=NULL){ /* don't delete the last node */ for (i=0; i<4; i++) { if (lip_tmp->fields[i]) MemFree(lip_tmp->fields[i]); } MemFree(lip_tmp); lip_tmp=lip; lip=lip->next; } } return NULL; } static void Ing_AssembleTabDelimited(IngGenomeViewerPtr igvp, IngInfoPtr lip, CharPtr id_ptr, Uint1 seqfeattype, Uint1 featdeftype, Int4 left, Int4 right) { Int4 numivals =0; IngInfoPtr lip_tmp; Int4 n, right_col, left_col; CharPtr tmp=NULL; Uint1 strand; CharPtr color = NULL; Int4 score; CharPtr UID=NULL; Int4Ptr ivals=NULL; CharPtr label=NULL; SeqLocPtr slp_list=NULL; if (igvp==NULL || lip == NULL) return; lip_tmp = lip; while (lip_tmp != NULL) { numivals++; lip_tmp = lip_tmp->next; } lip_tmp = lip; strand=Ing_GetStrand(lip_tmp->fields[7]); if (lip_tmp->fields[6]) score=atoi(lip_tmp->fields[6]); else score=1; if (lip_tmp->fields[5]) color = lip_tmp->fields[5]; if (lip->fields[3]){ UID = (Char*) MemNew(sizeof(Char)*20); sprintf(UID, "%s",lip->fields[3]); } else UID=NULL; n = 0; if (numivals>1){ ivals = (Int4Ptr)MemNew(2*numivals*sizeof(Int4)); while (lip_tmp != NULL) { left_col=atoi(lip_tmp->fields[0]); right_col=atoi(lip_tmp->fields[1]); if ((!(left_colright && right_col>right))){ /* if (strand==Seq_strand_minus){ */ /* ivals[n] = right_col; */ /* ivals[n+1] = left_col; */ /* } */ /* else{ */ ivals[n] = left_col; ivals[n+1] = right_col; /* } */ } n+=2; lip_tmp = lip_tmp->next; } slp_list=Ing_MakeSlpList(NULL, n/2, ivals, strand, igvp->bsp->id); } else /* just one piece */ { left =MAX(left, atoi(lip->fields[0])) ; right = MIN(right, atoi(lip->fields[1])); slp_list = SeqLocIntNew(left, right, strand, igvp->bsp->id); } if (lip->fields[2]){ label = (Char*) MemNew(sizeof(Char)*100); sprintf(label, "(user) %s, %s",lip->fields[2], UID); } else { label= (Char*) MemNew(sizeof(Char)*100); sprintf(label, "(user) Undefined"); } Ing_CreateNewFeature(igvp->entityID, igvp->itemID, NULL, seqfeattype, featdeftype, label, slp_list, color); MemFree(ivals); MemFree(label); MemFree(UID); } static Boolean is_in_range(IngInfoPtr lip, Int4 left, Int4 right) { IngInfoPtr lip_tmp; Uint1 strand; Int4 right_end, left_end; if (left==0 && right==0) return TRUE; lip_tmp=lip; strand=Ing_GetStrand(lip_tmp->fields[7]); if (strand==Seq_strand_minus){ right_end=(atoi(lip_tmp->fields[0])); } else{ left_end=(atoi(lip_tmp->fields[0])); } while (lip_tmp->next != NULL) { lip_tmp = lip_tmp->next; } if (strand==Seq_strand_minus){ left_end=(atoi(lip_tmp->fields[1])); } else{ right_end=(atoi(lip_tmp->fields[1])); } if ((!(left_endright && right_end>right))){ return TRUE; } else return FALSE; } static void Ing_ReadInTabDelimited(IngGenomeViewerPtr igvp, BioseqPtr bsp, FILE *ifp) { Boolean found=FALSE; Boolean SAVE=FALSE; Boolean first_pass=TRUE; Boolean was_saved=FALSE; Int4 i; Int4 len; CharPtr letter=NULL; Char line[1000]; IngInfoPtr lip=NULL; IngInfoPtr lip_tmp=NULL; IngInfoPtr lip_new=NULL; IngInfoPtr lip_head=NULL; IngInfoPtr lip_prev=NULL; CharPtr ptr=NULL, id_ptr=NULL; Int4 prevlen, left=0, right=0; Int4 seq; Uint1 type; CharPtr tmp=NULL, str=NULL, label_str=NULL; WatchCursor(); if (bsp==NULL) goto end; MemSet((Pointer)line, '\0',sizeof(line)); str=Ing_ReadALine(line, sizeof(line),ifp); found = FALSE; if (igvp->slp){ left=GetOffsetInBioseq(igvp->slp, bsp, SEQLOC_LEFT_END); right=GetOffsetInBioseq(igvp->slp, bsp, SEQLOC_RIGHT_END); } else{ left=0; right=igvp->SeqLength; } while (str!= NULL && !found) /* find first non-empty line */ { if (!StringHasNoText(line)) { if (StringNCmp(line, ">Tab Delimited", 14) == 0) { id_ptr = strtok(line+9, " "); found = TRUE; str = Ing_ReadALine(line, sizeof(line),ifp); } else { ErrPostEx(SEV_ERROR, 0, 0, "feature file must begin with \'>Tab Delimited\'"); goto end; } } else { MemFree(line); str = Ing_ReadALine(line, sizeof(line), ifp); } } if (!found) goto end; lip_prev = lip_head = NULL; i=1; while (str != NULL) { if (SAVE) { if (is_in_range(lip, left, right)){ if (lip_new != NULL){ Ing_AssembleTabDelimited(igvp, lip_new, id_ptr, Ing_GetSeqFeatType(lip_new->fields[2]), Ing_GetFeatDefType(lip_new->fields[2]), left, right); lip_new=Ing_FreeLip(lip_new, TRUE); lip_prev=lip_head=lip; } } SAVE=FALSE; was_saved=TRUE; } else{ ptr = strtok(line, "\t"); lip = (IngInfoPtr)MemNew(sizeof(IngInfo)); for (i=0; ifields[i] = str; ptr = strtok(NULL, "\t"); } if (lip->fields[4] == NULL || (StringCmp(lip->fields[4], "1")==0)){ if (!first_pass){ SAVE=TRUE; label_str=str; if (lip_head) lip_new=lip_head; else lip_new=lip; } } if (first_pass) first_pass=FALSE; if (!SAVE && lip_head!=NULL) { lip_prev->next = lip; lip_prev = lip; } else { if (!lip_head) lip_head = lip_prev = lip; } MemSet((Pointer)line, '\0', sizeof(line)); str = Ing_ReadALine(line, sizeof(line), ifp); } } /* save the last 2 lines */ if (SAVE) { if (lip_new->fields[0] != NULL){ Ing_AssembleTabDelimited(igvp, lip_new, id_ptr, Ing_GetSeqFeatType(lip_new->fields[2]), Ing_GetFeatDefType(lip_new->fields[2]), left, right); lip_new=Ing_FreeLip(lip_new, TRUE); } was_saved=TRUE; } if (lip_head->fields[0] && (!was_saved)){ Ing_AssembleTabDelimited(igvp, lip_head, id_ptr, Ing_GetSeqFeatType(lip_head->fields[2]), Ing_GetFeatDefType(lip_head->fields[2]),left, right); lip_head=Ing_FreeLip(lip_head, TRUE); } else if (lip->fields[0]) { Ing_AssembleTabDelimited(igvp, lip, id_ptr, Ing_GetSeqFeatType(lip->fields[2]), Ing_GetFeatDefType(lip->fields[2]), left, right); lip=Ing_FreeLip(lip, TRUE); } ObjMgrSetDirtyFlag(igvp->entityID, TRUE); ObjMgrSendMsg(OM_MSG_UPDATE, igvp->entityID, 0, 0); end: ArrowCursor(); return; } /***************************************************************************** Function: SqnGetBioseqGivenSeqLoc(), GetBioseqReferencedbyAnnot(), Ing_AttachSeqAnnotToSeqEntry() Purpose: attach a new feature (packaged in a seqannot) to a bioseq *****************************************************************************/ static BioseqPtr SqnGetBioseqGivenSeqLoc (SeqLocPtr slp, Uint2 entityID) { BioseqPtr bsp=NULL; SeqEntryPtr sep=NULL; SeqIdPtr sip=NULL; SeqLocPtr tmp=NULL; if (slp == NULL) return NULL; bsp = NULL; sip = SeqLocId (slp); if (sip != NULL) { bsp = BioseqFind (sip); } else { tmp = SeqLocFindNext (slp, NULL); if (tmp != NULL) { sip = SeqLocId (tmp); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); bsp = GetBioseqGivenSeqLoc (slp, entityID); } } } } return bsp; } static BioseqPtr GetBioseqReferencedByAnnot (SeqAnnotPtr sap, Uint2 entityID) { SeqAlignPtr align; BioseqPtr bsp; DenseDiagPtr ddp; DenseSegPtr dsp; SeqFeatPtr feat; SeqGraphPtr graph; SeqIdPtr sip; SeqLocPtr slp; StdSegPtr ssp; SeqLocPtr tloc; if (sap == NULL) return NULL; switch (sap->type) { case 1 : feat = (SeqFeatPtr) sap->data; while (feat != NULL) { slp = feat->location; if (slp != NULL) { bsp = SqnGetBioseqGivenSeqLoc (slp, entityID); if (bsp != NULL) return bsp; } feat = feat->next; } break; case 2 : align = (SeqAlignPtr) sap->data; while (align != NULL) { if (align->segtype == 1) { ddp = (DenseDiagPtr) align->segs; if (ddp != NULL) { for (sip = ddp->id; sip != NULL; sip = sip->next) { bsp = BioseqFind (sip); if (bsp != NULL) return bsp; } } } else if (align->segtype == 2) { dsp = (DenseSegPtr) align->segs; if (dsp != NULL) { for (sip = dsp->ids; sip != NULL; sip = sip->next) { bsp = BioseqFind (sip); if (bsp != NULL) return bsp; } } } else if (align->segtype == 3) { ssp = (StdSegPtr) align->segs; if (ssp != NULL && ssp->loc != NULL) { for (tloc = ssp->loc; tloc != NULL; tloc = tloc->next) { bsp = BioseqFind (SeqLocId (tloc)); if (bsp != NULL) return bsp; } } } align = align->next; } break; case 3 : graph = (SeqGraphPtr) sap->data; while (graph != NULL) { slp = graph->loc; if (slp != NULL) { bsp = SqnGetBioseqGivenSeqLoc (slp, entityID); if (bsp != NULL) return bsp; } graph = graph->next; } break; default : break; } return NULL; } extern Uint2 Ing_AttachSeqAnnotToSeqEntry (Uint2 entityID, SeqAnnotPtr sap, BioseqPtr bsp) { Int2 genCode; SeqEntryPtr oldscope; OMProcControl ompc; SeqEntryPtr sep; SeqFeatPtr sfp = NULL; if (sap == NULL) return entityID; if (bsp==NULL) bsp =GetBioseqReferencedByAnnot (sap, entityID); if (bsp == NULL) return entityID; if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; sep = GetBestTopParentForData (entityID, bsp); genCode = SeqEntryToGeneticCode (sep, NULL, NULL, 0); SetEmptyGeneticCodes (sap, genCode); } MemSet ((Pointer) &ompc, 0, sizeof (OMProcControl)); ompc.input_entityID = entityID; ompc.input_itemID = GetItemIDGivenPointer (entityID, OBJ_BIOSEQ, (Pointer) bsp); ompc.input_itemtype = OBJ_BIOSEQ; ompc.output_itemtype = OBJ_SEQANNOT; ompc.output_data = (Pointer) sap; if (! AttachDataForProc (&ompc, FALSE)) { Message (MSG_ERROR, "Ing_AttachSeqAnnotToSeqEntry failed"); } else if (sfp != NULL) { PromoteXrefs (sfp, bsp, entityID); } return entityID; } /******************************************************************************* Function : Ing_RunIngenue() Purpose : starts up a new window *******************************************************************************/ static void Ing_RunIngenue(IngGenomeViewerPtr igvp, BioseqPtr bsp, Uint2 entityID) { ObjMgrPtr omp=NULL; OMProcControl ompc; ObjMgrProcPtr ompp=NULL; Int2 ret; WinCounter++; omp=ObjMgrReadLock(); ompp=ObjMgrProcFind(omp, 0, "Ing_StandAlone", 0); ompc.input_itemtype = OBJ_BIOSEQ; ompc.input_data=(Pointer)bsp; ompc.input_choice=(Pointer)igvp; ompc.input_entityID=entityID; ompc.proc = ompp; ObjMgrUnlock(); if (ompp != NULL) { ret = (*(ompp->func))((Pointer)&ompc); switch(ret) { case OM_MSG_RET_ERROR: ErrShow(); break; default: break; } } } /***************************************************************************** Function: Ing_FileOpenSpecial(), Ing_FileOpenMain() Purpose: additional data (Special) file, or as the main (Main)sequence data to be viewed *****************************************************************************/ static Boolean Ing_FileOpenSpecial(IngGenomeViewerPtr igvp, CharPtr path, CharPtr GI_list) { IngReportPtr Report=NULL; FILE* fp=NULL; BioseqPtr bsp=NULL; RecT rcLines, rcControl, rcFeats; Boolean DoUpdate=TRUE; Int4 scaleX; WindoW temport, w; Char strErr[50]={""}; if (!igvp) return FALSE; if (path != NULL || GI_list !=NULL){ if (!StringHasNoText(path)){ if (!(fp = FileOpen(path, "r"))) { sprintf(strErr, "Ingenue can't find file %s", path); Message (MSG_OK, strErr); return FALSE; } /* if file of seqid list, get GI_list */ if (igvp->filetype > 119){ GI_list=Ing_ParseSeqIdFile(fp); path = NULL; FileClose(fp); fp=NULL; if (!GI_list) return FALSE; if (igvp->filetype == Ing_SEQIDLISTFORBLAST) igvp->filetype=ALIGN_BLAST2SEQ; if (igvp->filetype == Ing_SEQIDLISTFORSPIDEY) igvp->filetype = Ing_SPIDEY; } } if (igvp->filetype==ALIGN_BLAST2SEQ) Ing_ReadIn2ndBsp(igvp, path, GI_list); else { if (igvp->filetype==Ing_GENSCAN){ Ing_ReadInGenscan(fp, igvp); } else if (igvp->filetype==Ing_SPIDEY){ Ing_ReadSpideyInfo(igvp, path, GI_list); DoUpdate=FALSE; } else if (igvp->filetype==ALIGN_FILE) { Ing_ReadInBlastAsn(igvp,fp); DoUpdate=FALSE; } else if (igvp->filetype==Ing_FEAT_TABLE) { Ing_ReadInFeatureTable(igvp, fp); igvp->talign.update = TRUE; } else if (igvp->filetype==Ing_TBDL){ Ing_ReadInTabDelimited(igvp, igvp->bsp, fp); igvp->talign.update = TRUE; } else if (igvp->filetype == Ing_DOTMATRIX) { Ing_ReadDotMatrixInfo(igvp, path, GI_list); DoUpdate = FALSE; } else if (FALSE){/* seqid file*/ GI_list=Ing_ParseSeqIdFile(fp); if (!GI_list) return FALSE; bsp=(BioseqPtr)GetBioseqGivenIDs(igvp->entityID, igvp->itemID, OBJ_BIOSEQ); if (!bsp) return FALSE; if (igvp->filetype==Ing_SEQIDLISTFORSPIDEY) Ing_CreateSpideyForm(igvp, bsp, NULL, GI_list); if (igvp->filetype==Ing_SEQIDLISTFORBLAST) Ing_CreateBlast2SeqsForm(igvp, bsp, NULL, GI_list); DoUpdate=FALSE; } if (fp) FileClose(fp); if (DoUpdate){ Ing_PopulateOverviewPage((Pointer)igvp, FALSE); Ing_PopulateDetailedPage((Pointer)igvp); } } } else{ return FALSE; } return TRUE; } static Boolean Ing_FileOpenMain(CharPtr path, IngGenomeViewerPtr igvp) { FILE * fp; Uint2 datatype, entityID; SeqEntryPtr sep_orig=NULL, sep=NULL; BioseqPtr bsp=NULL; Pointer dataptr=NULL; Char strErr[50]={""}; WatchCursor(); Ing_ProgressNew(igvp, "Reading File....."); if (path != NULL) { if (!(fp = FileOpen(path, "r"))) { ArrowCursor(); Ing_ProgressEnd(igvp); sprintf(strErr, "Ingenue can't find your file %s", path); Message (MSG_OK, strErr); return FALSE; } if ((dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, TRUE, TRUE, FALSE, FALSE)) != NULL) { if (datatype==OBJ_SEQENTRY || datatype==OBJ_BIOSEQ){ sep= GetTopSeqEntryForEntityID(entityID); igvp->entity_list=(IngEntityPtr)MemNew(sizeof(IngEntity)); igvp->entity_list->entityID=entityID; igvp->entity_list->itemID=1; igvp->entity_list->bspcount=Ing_AllButPartsCount(sep, NULL, NULL, 0,0); igvp->entity_list->Sips=SAM_ExtractSips(sep); bsp=BioseqFindInSeqEntry((SeqId *)igvp->entity_list->Sips->data.ptrvalue, sep);/* get bsp of first SeqId */ } else { Message (MSG_OK, "File is not a bioseq or seqentry"); ArrowCursor(); Ing_ProgressEnd(igvp); return FALSE; } FileClose(fp); if (!bsp) { ArrowCursor(); Ing_ProgressEnd(igvp); return FALSE; } igvp->cur_sip=(SeqId *)igvp->entity_list->Sips->data.ptrvalue; igvp->cur_target=1; FileClose(fp); Ing_ProgressEnd(igvp); Ing_RunIngenue(igvp, bsp, entityID); } else { Ing_ProgressEnd(igvp); FileClose(fp); } } else{ ArrowCursor(); Ing_ProgressEnd(igvp); return FALSE; } ArrowCursor(); return TRUE; } static Int4 Ing_GetTPMaxScale(IngGenomeViewerPtr igvp, Int2 vwidth) { Int4 SeqLabel, scale; SeqLabel=(igvp->SeqLength)/6; scale = MAX(1, (igvp->SeqLength +SeqLabel )/(vwidth*igvp->ZoomedVal)); return scale; } static Int4 Ing_GetBPMaxScale(IngGenomeViewerPtr igvp) { RecT rc; Int2 vwidth; GetPosition(igvp->vBottom, &rc); vwidth = rc.right-rc.left; if (!igvp->maxScaleX) igvp->maxScaleX=Ing_GetTPMaxScale(igvp, vwidth); return MIN(Ing_MaxScale, igvp->maxScaleX); } /******************************************************************************* Function : Ing_ResizeMainWindow(), Ing_ResizeWin() Purpose : resize window functions *******************************************************************************/ static void Ing_ResizeMainWindow(IngGenomeViewerPtr igvp, WindoW w, Boolean bfirst) { Int4 diff, Zoom, scaleX; RecT rcDlg; RecT rcVsb,rcHsb, rcZoom, rcInfo; RecT rcTop; RecT rcRuler1; RecT rcBottom; RecT rcRuler2; RecT rcGoto; RecT rcPrompt; Int2 height,width,gap,vsbWidth; Int2 in, hsbHeight; Int2 GotoHeight; Int2 RulerHeight, InfoHeight; Int2 PromptHeight; Int2 TopHeight; Int2 ZoomWidth; Int4 i; Int4 line_height; BaR vsb,hsb; /*main window size*/ ObjectRect(w,&rcDlg); width= rcDlg.right-rcDlg.left; height= rcDlg.bottom-rcDlg.top; SafeHide(igvp->vRuler1); SafeHide(igvp->vTop); SafeHide(igvp->vRuler2); SafeHide(igvp->vBottom); SafeHide(igvp->vZoom); SafeHide(igvp->deflineg); SafeHide(igvp->progress_prompt); /* reset static prompt */ Update(); vsb = GetSlateVScrollBar ((SlatE) igvp->vBottom); hsb = GetSlateHScrollBar ((SlatE) igvp->vBottom); GetPosition(igvp->vTop, &rcTop); GetPosition(igvp->vRuler1, &rcRuler1); GetPosition(igvp->vBottom, &rcBottom); GetPosition(igvp->vRuler2, &rcRuler2); GetPosition(igvp->vZoom, &rcZoom); GetPosition(igvp->deflineg, &rcInfo); GetPosition(igvp->progress_prompt, &rcPrompt); GetPosition(hsb,&rcHsb); GetPosition(igvp->d_Win->Goto, &rcGoto); GetPosition(vsb,&rcVsb); gap=10; in=2; hsbHeight=rcHsb.bottom-rcHsb.top; vsbWidth=rcVsb.right-rcVsb.left; RulerHeight=(RULERDEFHEIGHT*igvp->GrData.cyChar); TopHeight=igvp->TopHeight; InfoHeight=rcInfo.bottom-rcInfo.top; GotoHeight=rcGoto.bottom-rcGoto.top; PromptHeight = rcPrompt.bottom-rcPrompt.top; ZoomWidth = rcZoom.right - rcZoom.left; line_height = LineHeight(); rcRuler1.bottom=rcRuler1.top+RulerHeight + 20; rcRuler1.right=width-in-2*vsbWidth; rcTop.right= rcRuler1.right+vsbWidth; rcTop.top=rcRuler1.bottom; rcTop.bottom=rcTop.top+TopHeight; rcRuler2.top=rcTop.bottom+2*gap; rcRuler2.right=rcRuler1.right; rcRuler2.bottom=rcRuler2.top+RulerHeight + 20; rcBottom.top=rcRuler2.bottom; rcBottom.right=rcRuler1.right+vsbWidth; rcBottom.bottom=height-hsbHeight-2*gap-PromptHeight; rcPrompt.top = rcBottom.bottom + hsbHeight + gap; rcPrompt.bottom= rcPrompt.top + igvp->GrData.cyChar; rcZoom.right = MAX(rcRuler1.right, rcGoto.right+gap+ZoomWidth); rcZoom.left = rcZoom.right - ZoomWidth; rcGoto.bottom = rcGoto.top + GotoHeight; rcInfo.top = rcGoto.bottom + in; rcInfo.bottom = rcInfo.top + line_height; rcInfo.right = rcZoom.left - gap; SetPosition(igvp->vRuler1, &rcRuler1); SetPosition(igvp->vTop, &rcTop); SetPosition(igvp->vZoom, &rcZoom); SetPosition(igvp->deflineg, &rcInfo); SetPosition(igvp->vRuler2, &rcRuler2); SetPosition(igvp->vBottom, &rcBottom); SetPosition(igvp->progress_prompt, &rcPrompt); for (i = 0; i < 4; i++){ SetPosition(igvp->featInfo[i], &rcInfo); rcInfo.top += line_height; rcInfo.bottom += line_height; } /*rescale the Picture/Viewer windows*/ diff = rcTop.right-rcTop.left; scaleX=Ing_GetTPMaxScale(igvp, diff); igvp->maxScaleX=scaleX; if (!bfirst){ scaleX=Ing_GetBPMaxScale(igvp); Ing_UpdateZoomerVals(igvp, scaleX); } if (bfirst){ SafeShow(igvp->vRuler1); SafeShow(igvp->vTop); SafeShow(igvp->vZoom); SafeShow(igvp->vRuler2); SafeShow(igvp->vBottom); SafeShow(igvp->deflineg); SafeShow(igvp->progress_prompt); Update(); } } static void Ing_ResizeWin(WindoW w) { IngGenomeViewerPtr igvp; Int4 from,to; igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (!igvp) return; Ing_ResizeMainWindow(igvp,w, FALSE); Ing_PopulateOverviewPage((Pointer) igvp, TRUE); Ing_PopulateDetailedPage((Pointer)igvp); /* attach zoomer picture */ AttachPicture (igvp->vZoom,igvp->pictZoom, INT4_MIN, INT4_MAX, UPPER_RIGHT, 1 , 1, NULL); SetViewerProcs(igvp->vZoom,Ing_ZoomerClickProc,NULL,NULL, NULL); Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to,NULL,igvp->SeqLength); Ing_MoveCursor(igvp,from,to, TRUE); igvp->xposition=from; SafeShow(igvp->vRuler1); SafeShow(igvp->vTop); SafeShow(igvp->vZoom); SafeShow(igvp->vRuler2); SafeShow(igvp->vBottom); SafeShow(igvp->deflineg); SafeShow(igvp->progress_prompt); Update(); } /*********************************************************** Function(s): .. Purpose: Open procs *************************************************************/ static void Ing_OpenAcceptProc(ButtoN b) { FILE * fp; IngGenomeViewerPtr igvp; Char path [PATH_MAX]={""}, GI_list[PATH_MAX]={""}; IngFileOpenDataPtr dfodp=NULL; WindoW w; w=ParentWindow(b); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (!igvp) return; dfodp=(IngFileOpenDataPtr)GetObjectExtra(b); if (!dfodp) return; GetTitle(dfodp->PathName, path, sizeof(path)); if (StringHasNoText (path)) { GetTitle(dfodp->GI, GI_list, sizeof(GI_list)); if (StringHasNoText (GI_list)) { Message (MSG_OK, "Enter file name, GI or Accession number"); Select (w); Show (w); Select (dfodp->PathName); return; } } Hide(ParentWindow(b)); /* if -- new sequence */ if (igvp->filetype <= 1){ if (Ing_FileOpenMain(path, igvp)){ Remove(ParentWindow(b)); ProcessEvents(); } else{ SetTitle(dfodp->PathName, ""); Disable(dfodp->OK); Show(ParentWindow(b)); } } else{ if (Ing_FileOpenSpecial(igvp, path, GI_list)){ Remove(ParentWindow(b)); } else{ SetTitle(dfodp->PathName, ""); Disable(dfodp->OK); Show(ParentWindow(b)); } } end: if (dfodp->hStart){ Remove(dfodp->hStart); dfodp->hStart=NULL; } /* else complain */ } static void Ing_OpenTextProc(TexT t) { Char szFName[PATH_MAX]={""}; WindoW hOpenDlg; IngFileOpenDataPtr igodp; igodp = (IngFileOpenDataPtr) GetObjectExtra (t); if (igodp==NULL) return; GetTitle(t, szFName, sizeof(szFName)-1); if (StringLen(szFName) == 0){ Enable(igodp->g_GI); Disable(igodp->OK); } else{ Enable(igodp->OK); Disable(igodp->g_GI); } } static void Ing_OpenCancelProc(ButtoN b) { IngFileOpenDataPtr dfodp=NULL; dfodp=(IngFileOpenDataPtr)GetObjectExtra(b); if (dfodp && dfodp->hStart){ Select(dfodp->hStart); Show(dfodp->hStart); } Remove(ParentWindow(b)); } static void Ing_OpenBrowseProc(ButtoN b) { IngFileOpenDataPtr igodp=NULL; Char path[PATH_MAX]={""}; igodp = (IngFileOpenDataPtr) GetObjectExtra (b); if (igodp==NULL) return; if (GetInputFileName (path, sizeof(path), NULL, NULL)){ SetTitle(igodp->PathName, path); Ing_OpenTextProc(igodp->PathName); } return; } static void Ing_NetOpen_access(TexT t) { Char szAccess[50]={""}; WindoW hOpenDlg; IngFileOpenDataPtr dfodp=NULL; hOpenDlg=(WindoW)ParentWindow(t); if (!hOpenDlg) return; dfodp = (IngFileOpenDataPtr) GetObjectExtra (t); if (dfodp==NULL) return; GetTitle(t, szAccess, sizeof(szAccess)); if (StringLen(szAccess) == 0){ Enable(dfodp->g_File); Disable(dfodp->OK); } else { Enable(dfodp->OK); Disable(dfodp->g_File); } return; } static void Ing_InputFileType(PopuP pops) { IngGenomeViewerPtr igvp=NULL; Int2 value; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(pops)); if (!igvp) return; value=GetValue(pops); if (igvp->filetype==ALIGN_BLAST){ if (value == 2) igvp->filetype = Ing_SEQIDLISTFORBLAST; } else if (igvp->filetype==Ing_SPIDEY){ if (value == 2) igvp->filetype = Ing_SEQIDLISTFORSPIDEY; } } extern void Ing_OpenFromFileORNetwork(IngGenomeViewerPtr igvp) { WindoW hOpenDlg=NULL; GrouP g, c, g_top; IngFileOpenDataPtr dfodp=NULL; ButtoN b,b1,b2; TexT t1; if (igvp==NULL) return; dfodp=(IngFileOpenDataPtr)MemNew(sizeof(IngFileOpenData)); hOpenDlg = MovableModalWindow(-30, -20, -10, -10, "Ingenue - Get Sequence", NULL); g_top = HiddenGroup (hOpenDlg, -1, 4, NULL); g = NormalGroup(g_top, -3, 1, "File name:", systemFont, NULL); dfodp->g_File=g; SetGroupMargins(g, 10, 10); SetGroupSpacing(g, 10, 20); dfodp->pops = PopupList (g, TRUE, Ing_InputFileType); PopupItem (dfodp->pops, "Asn or Fasta file"); PopupItem (dfodp->pops, "list of SeqIds"); SetValue(dfodp->pops, 1); dfodp->PathName = DialogText(g,"",15,Ing_OpenTextProc); SetObjectExtra(dfodp->PathName, (Pointer)dfodp, StdCleanupExtraProc); b = PushButton(g, " browse...", Ing_OpenBrowseProc); SetObjectExtra (b, (Pointer) dfodp, NULL); /* dfodp->OK = DefaultButton(g, "Accept", Ing_OpenAcceptProc); */ StaticPrompt (g_top, "OR", 0, LineHeight(), systemFont, 'c'); g = NormalGroup (g_top, -1, 1, "GI or Accession", systemFont,NULL); dfodp->g_GI=g; SetGroupMargins(g, 10, 10); SetGroupSpacing(g, 10, 20); dfodp->GI=DialogText (g, "", 15, Ing_NetOpen_access); SetObjectExtra(dfodp->GI, (Pointer)dfodp, NULL); /*retrieve - cancel*/ g = HiddenGroup (g_top, -2, -1, NULL); dfodp->OK=DefaultButton (g, "Accept", Ing_OpenAcceptProc); Disable(dfodp->OK); b2 = PushButton(g, "Cancel", Ing_OpenCancelProc); SetObjectExtra (dfodp->OK, (Pointer) dfodp, NULL); SetObjectExtra (hOpenDlg, (Pointer)igvp, NULL); Select(hOpenDlg); Show(hOpenDlg); } extern void Ing_FileOpenProc(IngGenomeViewerPtr igvp, WindoW hStart) { IngFileOpenDataPtr dfodp=NULL; WindoW hOpenDlg; GrouP g,g4; ButtoN b,b1,b2; TexT t1; if (igvp==NULL) return; dfodp=(IngFileOpenDataPtr)MemNew(sizeof(IngFileOpenData)); hOpenDlg = MovableModalWindow(-30, -20, -10, -10, "Ingenue - Open a local file", NULL); g = NormalGroup(hOpenDlg, -2, 2, "File name:", systemFont, NULL); SetGroupMargins(g, 10, 10); SetGroupSpacing(g, 10, 20); t1 = DialogText(g,"",25,Ing_OpenTextProc); SetObjectExtra(t1, (Pointer)dfodp, StdCleanupExtraProc); b = PushButton(g, " browse...", Ing_OpenBrowseProc); SetObjectExtra (b, (Pointer) dfodp, NULL); dfodp->pops=NULL; b1 = DefaultButton(g, "OK", Ing_OpenAcceptProc); Enable(b1); b2 = PushButton(g, "Cancel", Ing_OpenCancelProc); SetObjectExtra (b1, (Pointer) dfodp, NULL); SetObjectExtra (b2, (Pointer) dfodp, NULL); Disable(b1); dfodp->OK = b1; dfodp->PathName=t1; dfodp->hStart=hStart; SetObjectExtra (hOpenDlg, (Pointer) igvp, NULL); Select(hOpenDlg); Show(hOpenDlg); } static void Ing_OpenGenscan(IteM i) { IngGenomeViewerPtr igvp; WindoW w; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); igvp->filetype=Ing_GENSCAN; Ing_FileOpenProc(igvp, NULL); } static void Ing_OpenBlast(IteM i) { IngGenomeViewerPtr igvp; WindoW w; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); igvp->filetype=ALIGN_FILE; Ing_FileOpenProc(igvp, NULL); } static void Ing_OpenFeatTable(IteM i) { IngGenomeViewerPtr igvp; WindoW w; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); igvp->filetype=Ing_FEAT_TABLE; Ing_FileOpenProc(igvp, NULL); } static void Ing_OpenTabDel(IteM i) { IngGenomeViewerPtr igvp; WindoW w; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); igvp->filetype=Ing_TBDL; Ing_FileOpenProc(igvp, NULL); } /******************************************************************************* Function : Ing_EditFeature(), Ing_DeleteFeature(), Ing_MarkSeqAnnot() Purpose : Edit or delete features *******************************************************************************/ static void Ing_EditFeature(IteM i) { SelStructPtr ssp=NULL; IngGenomeViewerPtr igvp=NULL; Int2 handled; SeqEntryPtr sep; ssp=ObjMgrGetSelected(); if (!ssp) { ErrPostEx(SEV_ERROR, 0, 0,"need to select a feature" ); return; } igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); WatchCursor (); handled=GatherProcLaunch (OMPROC_EDIT, FALSE, ssp->entityID, ssp->itemID, ssp->itemtype, 0, 0, ssp->itemtype, 0); ArrowCursor(); if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) { ErrPostEx(SEV_ERROR, 0, 0,"unable to launch editor on feature" ); } } typedef struct ing_markdata { SeqAlignPtr parent; Boolean bSpidey; Int4 idx; } IngMarkData, PNTR IngMarkPtr; static void is_parent_spidey(SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp=NULL; BioseqSetPtr bssp=NULL; SeqAnnotPtr sanp=NULL; SeqAlignPtr salp=NULL; SeqAlignPtr parent=NULL; IngMarkPtr markp = NULL; Boolean bSpidey = FALSE; markp=(IngMarkPtr)mydata; parent = markp->parent; if (IS_Bioseq(sep)) { bsp = (BioseqPtr)sep->data.ptrvalue; sanp = bsp->annot; } else if (IS_Bioseq_set(sep)) { bssp = (BioseqSetPtr)sep->data.ptrvalue; sanp = bssp->annot; } else return; while (sanp != NULL) { if (sanp->type == 2) {/*seqalign*/ if (StringCmp(sanp->name, "Spidey") == 0){ bSpidey = TRUE; } salp=(SeqAlignPtr)sanp->data; if (salp==parent){ if (bSpidey){ markp->bSpidey = TRUE; } return; } } sanp=sanp->next; } } static void Ing_MarkSeqAnnot(SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp=NULL; BioseqSetPtr bssp=NULL; SeqAnnotPtr sanp=NULL; SeqAlignPtr salp=NULL; SeqAlignPtr parent=NULL; IngMarkPtr markp = NULL; Boolean bSpidey = FALSE; Boolean bNoParent = FALSE; Int4 idx = 0; markp=(IngMarkPtr)mydata; parent = markp->parent; if (IS_Bioseq(sep)) { bsp = (BioseqPtr)sep->data.ptrvalue; sanp = bsp->annot; } else if (IS_Bioseq_set(sep)) { bssp = (BioseqSetPtr)sep->data.ptrvalue; sanp = bssp->annot; } else return; while (sanp != NULL) { if (sanp->type == 2) {/*seqalign*/ if (StringCmp(sanp->name, "Spidey") == 0){ bSpidey = TRUE; idx++; } salp=(SeqAlignPtr)sanp->data; if (salp==parent){ sanp->idx.deleteme=1; if (bSpidey){ markp->bSpidey = TRUE; markp->idx = idx; } return; } } sanp=sanp->next; } } static void Ing_DeleteFeature(IteM i) { SelStructPtr ssp=NULL; SeqFeatPtr sfp=NULL; SeqAlignPtr child=NULL, parent=NULL; SeqAlignPtr salp_head=NULL; SeqAlignPtr salp_prev=NULL; SeqAlignPtr salp=NULL; Boolean Only_sap=FALSE; SeqEntryPtr sep=NULL; Boolean found=FALSE; IngGenomeViewerPtr igvp=NULL; Uint2 entityID = 0; IngMarkData marked; ssp=ObjMgrGetSelected(); if (!ssp) return; else entityID = ssp->entityID; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); if(!igvp) return; while (ssp){ if (ssp->entityID!=0 && ssp->itemID!=0){ if (ssp->itemtype==OBJ_SEQALIGN){ child=(SeqAlignPtr)GetPointerForIDs(ssp->entityID, ssp->itemID, OBJ_SEQALIGN); if (!child) goto next; parent=AlnMgr2GetParent(child); salp=(SeqAlignPtr)parent->segs; while (salp && !found) { if (salp == child) found = TRUE; else { if (salp_head) salp_prev = salp; else salp_head = salp_prev = salp; salp = salp->next; } } if (!found) goto next; if (salp_head != NULL) { salp_prev->next = salp->next; salp->next = NULL; SeqAlignFree(salp); } else { if (salp->next==NULL) Only_sap=TRUE; else { salp_head = salp->next; salp->next = NULL; SeqAlignFree(salp); } } if (!Only_sap){ parent->segs = (Pointer)salp_head; if (parent->saip != NULL) AMAlignIndex2Free2(parent); parent->saip=NULL; AlnMgr2IndexLite(parent); marked.parent = parent; marked.idx = 0; marked.bSpidey = FALSE; sep = GetTopSeqEntryForEntityID(igvp->entityID); SeqEntryExplore(sep,(Pointer)&marked, is_parent_spidey); if (marked.bSpidey){ Disable(igvp->d_Win->mrnaorexons); } } else{ marked.parent = parent; marked.idx = 0; marked.bSpidey = FALSE; sep = GetTopSeqEntryForEntityID(igvp->entityID); SeqEntryExplore(sep,(Pointer)&marked, Ing_MarkSeqAnnot); DeleteMarkedObjects(igvp->entityID, OBJ_SEQENTRY, (Pointer)sep); if (marked.bSpidey){ Ing_DeleteSpidey(igvp, marked.idx); } } } else if (ssp->itemtype==OBJ_SEQFEAT){ sfp=(SeqFeatPtr)GetPointerForIDs(ssp->entityID, ssp->itemID, OBJ_SEQFEAT); sfp->idx.deleteme=TRUE; DeleteMarkedObjects(ssp->entityID, OBJ_SEQFEAT, (Pointer)sfp); } } next: ssp = ssp->next; } if (entityID){ ObjMgrSetDirtyFlag (entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0); ObjMgrDeSelectAll(); } return; } /*********************************************************** Function : Ing_ReplaceAllMismatched() Purpose : Replace mismatched residues in genomic sequence ***********************************************************/ typedef struct ing_repmismatched{ SeqAlignPtr sap; TexT start; TexT stop; ButtoN all; ButtoN gaps; ButtoN inserts; GrouP region; } IngRepMismatched, PNTR IngRepMismatchedPtr; static void Ing_ReplaceCancelProc(ButtoN b) { Remove(ParentWindow(b)); } static void Ing_ReplaceMismatchedProc(ButtoN b) { IngGenomeViewerPtr igvp = NULL; IngRepMismatchedPtr rmp = NULL; WindoW w; Int4 start, stop; Char str[20]={""}; w = ParentWindow(b); igvp = (IngGenomeViewerPtr)GetObjectExtra(w); rmp = (IngRepMismatchedPtr)GetObjectExtra(b); Hide(w); if (igvp == NULL || rmp == NULL){ Show(w); return; } if (!GetStatus(rmp->all)){ GetTitle(rmp->start, str, sizeof(str)); start = atoi(str); GetTitle(rmp->stop, str, sizeof(str)); stop = atoi(str); } Ing_ReplaceAllMismatchedInLocation(igvp, rmp->sap, start, stop, GetStatus(rmp->all), GetStatus(rmp->gaps), GetStatus(rmp->inserts)); Remove(w); } static void Ing_ReplaceAllProc(ButtoN b) { IngRepMismatchedPtr rmp; rmp = (IngRepMismatchedPtr)GetObjectExtra(b); if(GetStatus(rmp->all)) Disable(rmp->region); else Enable(rmp->region); } static void Ing_CreateMismatchedDialog(IngGenomeViewerPtr igvp, SeqAlignPtr salp) { IngRepMismatchedPtr rmp = NULL; WindoW w; Int4 start, stop; GrouP g, g1, g2, g3, main; ButtoN b; Char buf[20]={""}; AlnMgr2GetNthSeqRangeInSA(salp, 1, &start, &stop); rmp = (IngRepMismatchedPtr)MemNew(sizeof(IngRepMismatched)); w = MovableModalWindow(-50, -33 ,-10, -10, "Spidey", NULL); SetObjectExtra(w, (Pointer) igvp, NULL); rmp->sap = salp; main = HiddenGroup(w, 1, 3, NULL); rmp->all = CheckBox(main, "Replace All Mismatches in Alignment", Ing_ReplaceAllProc); SetObjectExtra(rmp->all, (Pointer)rmp, NULL); SetStatus(rmp->all, TRUE); g1 = NormalGroup(main, 1, 1, "- OR Select Range - ", NULL, NULL); rmp->region = g1; g = HiddenGroup(g1, 5, 1, NULL); StaticPrompt(g, "Genomic coordinates: ", 0, 0, programFont, 'l'); StaticPrompt(g, "from", 0, 0, programFont, 'l'); sprintf(buf, "%d", start + 1); rmp->start = DialogText(g, buf, 5, NULL); StaticPrompt(g, " to", 0, 0, programFont, 'l'); sprintf(buf, "%d", stop + 1); rmp->stop = DialogText(g, buf, 5, NULL); Disable(rmp->region); rmp->gaps = CheckBox(main, "Fill in gaps on genomic", NULL); SetStatus(rmp->gaps, TRUE); rmp->inserts = CheckBox(main, "Delete inserts on genomic", NULL); SetStatus(rmp->inserts, TRUE); g2 = HiddenGroup(main, 2, 1, NULL); b = DefaultButton(g2, "Accept", Ing_ReplaceMismatchedProc); PushButton(g2, "Cancel", Ing_ReplaceCancelProc); SetObjectExtra(b, (Pointer)rmp, NULL/* StdCleanupExtraProc */); Select(w); Show(w); } static void Ing_ReplaceAllMismatched(IteM i) { IngGenomeViewerPtr igvp = NULL; SelStructPtr ssp; SeqAlignPtr salp = NULL; igvp = (IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); ssp = ObjMgrGetSelected(); while (ssp){ salp=(SeqAlignPtr)GetPointerForIDs(ssp->entityID, ssp->itemID, ssp->itemtype); if (salp){ Ing_CreateMismatchedDialog(igvp, salp); } ssp = ssp->next; } } /******************************************************************************* Function : Ing_AnnotateAlignmentCancel(), Ing_AnnotateAlignmentAccept(), Ing_AnnotateAlignmentForm() Purpose : change an alignment into a feature *******************************************************************************/ #define _success_ 1 #define _already_exists_ 2 #define _failed_to_map_ 3 typedef struct ing_progfeat { BioseqPtr bsp_mrna; Int4 mRNA_left; Int4 genomic_left; Char name[300]; CharPtr orig_loc; CharPtr new_loc; CharPtr str_prot; CharPtr str_new; Uint1 type; Boolean found; Boolean prot_ok; Uint1 status; Uint1 strand; struct ing_progfeat PNTR next; } IngProgFeat, PNTR IngProgFeatPtr; typedef struct ing_annotalign { BioseqPtr bsp_mrna; SeqFeatPtr sfp_mrna; Boolean holes; ButtoN propc; WindoW w; VieweR viewer; SegmenT seg; Int4 rowNum; SeqAlignPtr child; GrouP feat_type; GrouP gap_split; LisT feat_list; Int4 nList; IngProgFeatPtr pfp; struct ing_annotalign PNTR next; } IngAnnotAlign, PNTR IngAnnotAlignPtr; Boolean mRNAFilter[FEATDEF_MAX]; Boolean mRNATrack[FEATDEF_MAX]; Uint2 mRNALookup[FEATDEF_MAX]; static Boolean LIBCALLBACK Ing_CheckGenFeats(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) { Char str[500]={""}; IngProgFeatPtr pfp = NULL; pfp = (IngProgFeatPtr)sfc->userdata; FeatDefLabel(sfp, str, sizeof (str) - 1, OM_LABEL_BOTH); if (StringCmp(pfp->name, str) == 0 && pfp->type == sfc->featdeftype){ pfp->found = TRUE; return (FALSE); } return (TRUE); } static void Ing_PropagateClickProc(VieweR v, SegmenT s, PoinT pt) { IngGenomeViewerPtr igvp=NULL; SelStructPtr ssp=NULL; PrimitivE prim; Uint2 entityID=0; Uint2 itemID=0; Uint2 itemtype=0; Uint2 primID=0; /* igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(v)); if (!igvp) return; ssp=ObjMgrGetSelected(); if (ssp){ ObjMgrDeSelect(ssp->entityID, ssp->itemID, ssp->itemtype, 0, NULL); } if (FindSegPrim(v, pt, NULL, NULL, &prim)) { GetPrimitiveIDs(prim, &entityID, &itemID, &itemtype, &primID); if (entityID && itemID && itemtype){ msg.labelmsg=2; ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); return; } } Ing_ResetTitle(igvp, TRUE); */ } static void Ing_DrawScale(SegmenT seg, Int2 margin, Int4 res, Int4 pos, Int4 ybase, Int2 chw, Int2 Fh) { Int4 x, y; Char str[15] = {""}; Uint1 blue[3]; blue[0] = 0; blue[1] = 125; blue[2] = 245; x = margin + (pos * chw) + chw/2; y = ybase + Fh; sprintf(str,"%d", res); AddAttribute(seg, COLOR_ATT, blue, 0,0,0,0); AddLabel(seg, x, y, str, SMALL_TEXT, 0, UPPER_CENTER, 0); AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); AddLabel(seg, x, y - 2, ".", SMALL_TEXT, 0, UPPER_CENTER, 0); } static void Ing_HighlightMismatch(SegmenT seg, Int2 margin, Int4 pos, Int4 ybase, Int2 chw, Int2 Fh) { Int4 x1, x2, y1, y2; Uint1 yellow[3]; yellow[0] = 224; yellow[1] = 224; yellow[2] = 0; x1 = margin + (pos * chw); x2 = x1 + chw; y1 = ybase + Fh; y2 = ybase - Fh; AddAttribute(seg, COLOR_ATT, yellow, 0,0,0,0); AddRectangle (seg, x1, y1, x2, y2, 0, TRUE, 0); AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); } #define BLOCK_SIZE 10 static void Ing_PrintCompProteins (IngAnnotAlignPtr aap, IngProgFeatPtr pfp) { Int4 len_orig, len_new, len_min, width_orig; Int4 n; Int4 i, j, k, row, add; Int4 start, exit; Int2 winsize, cxChar, nchars_row; Int2 last_pos = 0; Int2 margin, Fh, strw_new = 0, strw_orig = 0; Uint1 clr[3], cl2[3]; CharPtr str_orig, str_new; CharPtr buf_orig, buf_new; CharPtr orig, new; Char str1[200] = {""}, str2[10] = {""}; RecT rc; SegmenT seg; str_orig = pfp->str_prot; str_new = pfp->str_new; if (str_orig == NULL || str_new == NULL) return; /* should add a message here */ margin = StringWidth("Genomic - "); clr[0] = 210; clr[1] = 154; clr[2] = 14; cl2[0] = 224; cl2[1] = 95; cl2[2] = 39; seg = aap->seg; GetPosition(aap->viewer, &rc); winsize = (rc.right - rc.left) - (margin + 3*stdCharWidth); row = aap->rowNum; n = 1; start = 1; len_orig = StringLen(str_orig); len_new = StringLen(str_new); len_min = MIN(len_orig, len_new); width_orig = StringWidth(str_orig); cxChar = (Int2)ceil((float)width_orig/len_orig); nchars_row=(Int2)((float)winsize/cxChar) - 10; nchars_row -= nchars_row % 10; if (nchars_row <= 0) return; Fh = FontHeight(); buf_orig = (CharPtr)MemNew(sizeof(Char)*(nchars_row + 1)); buf_new = (CharPtr)MemNew(sizeof(Char)*(nchars_row + 1)); sprintf(str1, "Translated Protein Lengths - Genomic: %d, mRNA: %d", len_new, len_orig); row += Ing_PrintText(str1, seg, row, winsize + margin, cl2, 0); row++; orig = str_orig; new = str_new; for (i = 0; i < len_min; i += nchars_row){ AddAttribute(seg, COLOR_ATT, clr, 0,0,0,0); AddLabel(seg, 0, row * (-15), "Genomic - " , SMALL_TEXT, 0, UPPER_RIGHT, 0); AddLabel(seg, 0, (row + 1) * (-15), "mRNA - " , SMALL_TEXT, 0, UPPER_RIGHT, 0); for (j = 0; (j < nchars_row) && (n < len_min + start); j++){ if (*orig != *new){ Ing_HighlightMismatch(seg, margin, j, row * (-15), cxChar, Fh); } if (!(Boolean)((j)% BLOCK_SIZE)){ Ing_DrawScale(seg, margin, n, j, row * (-15), cxChar, Fh); } buf_new[j] = *new; buf_orig[j] = *orig; new++; orig++; n++; } buf_orig[j] = '\0'; buf_new[j] = '\0'; AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); AddLabel(seg, margin, row * (-15), buf_new , SMALL_TEXT, 0, UPPER_RIGHT, 0); AddLabel(seg, margin, (row + 1) * (-15), buf_orig , SMALL_TEXT, 0, UPPER_RIGHT, 0); strw_new = StringWidth(buf_new); strw_orig = StringWidth(buf_orig); row += 4; } last_pos = j; if (n < len_new + start){ if (last_pos < nchars_row) row -= 4; exit = len_new - len_min + last_pos; for (i = last_pos; i <= exit; i += nchars_row){ AddAttribute(seg, COLOR_ATT, clr, 0,0,0,0); AddLabel(seg, 0, row * (-15), "Genomic - " , SMALL_TEXT, 0, UPPER_RIGHT, 0); for (k = last_pos, j = 0; (k < nchars_row) && (n < len_new + start); j++, k++){ if (!(Boolean)(k % BLOCK_SIZE)){ Ing_DrawScale(seg, margin, n, k, row * (-15), cxChar, Fh); } buf_new[j] = *new; new++; n++; } buf_new[j] = '\0'; AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); AddLabel(seg, margin + strw_new, row * (-15), buf_new , SMALL_TEXT, 0, UPPER_RIGHT, 0); row +=4; strw_new = last_pos = 1; } } else if (n < len_orig + start){ if (last_pos < nchars_row) row -= 4; exit = len_orig - len_min + last_pos; for (i = 0; i <= exit; i += nchars_row){ AddAttribute(seg, COLOR_ATT, clr, 0,0,0,0); AddLabel(seg, 0, (row + 1) * (-15), "mRNA - " , SMALL_TEXT, 0, UPPER_RIGHT, 0); for (k = last_pos, j = 0; (k < nchars_row) && (n < len_orig + start); k++, j++){ if (!(Boolean)(k % BLOCK_SIZE)){ Ing_DrawScale(seg, margin, n, k, row * (-15), cxChar, Fh); } buf_orig[j] = *orig; orig++; n++; } buf_orig[j] = '\0'; AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); AddLabel(seg, margin + strw_orig, (row + 1) * (-15), buf_orig , SMALL_TEXT, 0, UPPER_RIGHT, 0); row +=4; strw_orig = last_pos = 0; } } row -= 2; aap->rowNum = row; } static void Ing_PropagateReport(IngAnnotAlignPtr aap, IngProgFeatPtr pfp) { PrimitivE prim; Int4 left = 10; Int4 row; Int4 stringwidth = 0; Int2 winsize, top; Char message[255]={""}, str[255] = {""}; Uint1 ARROW=NO_ARROW; IngGenomeViewerPtr igvp = NULL; Uint1 gray[3]; Uint1 red[3], green[3], dkblue[3]; Uint1Ptr title_clr = NULL; Boolean print_translation = FALSE; RecT rc; enumPrimAddOrder oldOrder; row = aap->rowNum; gray[0] = 100; gray[1] = 100; gray[2] = 100; dkblue[0] = 0; dkblue[1] = 64; dkblue[2] = 194; green[0] = 0; green[1] = 200; green[2] = 12; red[0] = 224; red[1] = 0; red[2] = 64; GetPosition(aap->viewer, &rc); winsize = (rc.right - rc.left) - 3*stdCharWidth; if (pfp->strand == Seq_strand_minus) ARROW = LEFT_ARROW; else ARROW = RIGHT_ARROW; igvp=(IngGenomeViewerPtr)GetObjectExtra((WindoW)ParentWindow(aap->viewer)); if (!igvp) return; if (pfp->status == _success_){ if (pfp->prot_ok){ title_clr = green; sprintf(message, "O.K."); } else { title_clr = red; sprintf(message, "WARNING -- unclassified translation discrepancy -- check CDS coordinates"); print_translation = TRUE; } } else if (pfp->status == _already_exists_ ){ title_clr = BLUE_COLOR; sprintf(message, "Already Exists"); } else if (pfp->status == _failed_to_map_ ){ title_clr = gray; sprintf(message, "Failed to map"); } else { title_clr = BLACK_COLOR; sprintf(message, "??"); } top = row*(-15) + 20; oldOrder = ChangeAddPrimOrder(ADD_TO_HEAD); row += Ing_PrintText(message, aap->seg, row, winsize, WHITE_COLOR, 0); AddAttribute(aap->seg, COLOR_ATT, title_clr , 0, 0, 0, 0); prim= AddRectangle(aap->seg, 0, top, MIN(StringWidth(message) + 2, winsize), (row - 1)*(-15) + 5, NO_ARROW, TRUE, 0); ChangeAddPrimOrder(oldOrder); sprintf(str, "%s", pfp->name); row += Ing_PrintText(str, aap->seg, row, winsize, BLACK_COLOR, 0); if (pfp->new_loc) { sprintf(str, "Genomic: %s", pfp->new_loc); row += Ing_PrintText(str, aap->seg, row, winsize, green, 0); } sprintf(str, "mRNA: %s", pfp->orig_loc); row += Ing_PrintText(str, aap->seg, row, winsize, dkblue, 0); if (print_translation && (!StringHasNoText(pfp->str_prot)) && (!StringHasNoText(pfp->str_new))){ aap->rowNum = row; Ing_PrintCompProteins(aap, pfp); aap->rowNum += 3; } else aap->rowNum = row + 3; } static void Ing_PopulateProgWin(IngAnnotAlignPtr aap){ IngProgFeatPtr pfp; pfp = aap->pfp; aap->rowNum = 0; Reset(aap->viewer); DeletePicture(aap->seg); Update(); aap->seg=CreatePicture(); while (pfp != NULL){ Ing_PropagateReport(aap, pfp); pfp = pfp->next; } AttachPicture (aap->viewer, aap->seg, INT4_MIN, INT4_MAX, UPPER_RIGHT, 1 , 1, NULL); SetViewerProcs(aap->viewer, Ing_PropagateClickProc,NULL,NULL, NULL); } static void Ing_ResizePropagateWin(WindoW w) { IngAnnotAlignPtr aap = NULL; RecT rcW, rcR, rcVsb, rcHsb; Int2 height,width,gap,vsbWidth; Int2 hsbWidth,in; BaR vsb, hsb; aap = (IngAnnotAlignPtr)GetObjectExtra(w); if (!aap) return; ObjectRect(aap->w, &rcW); width= rcW.right-rcW.left; height= rcW.bottom-rcW.top; SafeHide(aap->viewer); Update(); vsb = GetSlateVScrollBar ((SlatE) aap->viewer); hsb = GetSlateHScrollBar ((SlatE) aap->viewer); GetPosition(aap->viewer, &rcR); GetPosition(vsb, &rcVsb); GetPosition(hsb, &rcHsb); vsbWidth=rcVsb.right-rcVsb.left; hsbWidth=rcHsb.right-rcHsb.left; gap=10; in=2; rcR.right=rcR.left+width-in-vsbWidth; rcR.bottom=rcR.top+height-in-gap-hsbWidth; SetPosition(aap->viewer, &rcR); Ing_PopulateProgWin(aap); SafeShow(aap->viewer); Update(); } static SeqLocPtr Ing_MapLocForProp(SeqAlignPtr salp, Boolean gap_split, SeqLocPtr location, Uint1 strand) { SeqLocPtr head = NULL; IngIvalInfoPtr ival; IngIvalInfoPtr ival_head; ValNodePtr vnp_cur = NULL; SeqIntPtr sinp; SeqLocPtr slp; SeqPntPtr spp; SeqIdPtr sip = NULL; Int4 from_row = 2, to_row = 1; Int4 start, stop; sip = AlnMgr2GetNthSeqIdPtr(salp, 1); slp = SeqLocFindNext (location, NULL); while (slp != NULL) { switch (slp->choice) { case SEQLOC_INT : sinp = (SeqIntPtr) slp->data.ptrvalue; if (sinp != NULL) { /* strand = sinp->strand; */ ival_head = (IngIvalInfoPtr)Ing_GetAlignmentIntervals (salp, from_row, to_row, sinp->from, sinp->to, strand); if (!ival_head){ if (head) SeqLocFree(head); return NULL; } ival_head = MergeAdjacentIntervals (ival_head); /* what if one or the other interval maps into a gap? */ if (gap_split) { for (ival = ival_head; ival != NULL; ival = ival->next) { sinp = SeqIntNew (); sinp->from = ival->start2; sinp->to = ival->stop2; sinp->strand = strand; sinp->id = SeqIdDup (sip); if (head == NULL) vnp_cur = ValNodeAddPointer (&head, SEQLOC_INT, (Pointer) sinp); else vnp_cur = ValNodeAddPointer (&vnp_cur, SEQLOC_INT, (Pointer) sinp); } } else { sinp = SeqIntNew (); sinp->from = ival_head->start2; for (ival = ival_head; ival->next != NULL; ival = ival->next) continue; sinp->to = ival->stop2; sinp->strand = strand; sinp->id = SeqIdDup (sip); if (head == NULL) vnp_cur = ValNodeAddPointer (&head, SEQLOC_INT, (Pointer) sinp); else vnp_cur = ValNodeAddPointer (&vnp_cur, SEQLOC_INT, (Pointer) sinp); } Ing_IvalInfoFree (ival_head); } break; case SEQLOC_PNT : spp = (SeqPntPtr) slp->data.ptrvalue; if (spp != NULL) { /* strand = spp->strand; */ ival_head = (IngIvalInfoPtr)Ing_GetAlignmentIntervals (salp, from_row, to_row, spp->point, spp->point, strand); if (!ival_head){ if (head) SeqLocFree(head); return NULL; } spp = SeqPntNew (); spp->point = ival_head->start2; spp->strand = strand; spp->id = SeqIdDup (sip); if (head == NULL) vnp_cur = ValNodeAddPointer (&head, SEQLOC_PNT, (Pointer) spp); else vnp_cur = ValNodeAddPointer (&vnp_cur, SEQLOC_PNT, (Pointer) spp); Ing_IvalInfoFree (ival_head); } break; case SEQLOC_PACKED_PNT : /* not yet implemented */ break; default : break; } slp = SeqLocFindNext (location, slp); } if (head == NULL) return NULL; if (head->next == NULL) return head; slp = ValNodeNew (NULL); slp->choice = SEQLOC_MIX; slp->data.ptrvalue = (Pointer) head; slp->next = NULL; return slp; } static Boolean Ing_KeywordAlreadyInList (ValNodePtr head, CharPtr kwd) { ValNodePtr vnp; if (head == NULL || kwd == NULL) return FALSE; for (vnp = head; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, kwd) == 0) return TRUE; } return FALSE; } static IngProgFeatPtr Ing_AddProgFeat(IngProgFeatPtr head, IngProgFeatPtr pfp) { IngProgFeatPtr tmp; if (head == NULL) return pfp; tmp = head; while (tmp->next != NULL) tmp = tmp->next; tmp->next = pfp; return head; } static IngAnnotAlignPtr Ing_AnnotAlignFree(IngAnnotAlignPtr aap) { IngProgFeatPtr pfp_tmp = NULL, pfp = NULL; IngAnnotAlignPtr aap_tmp = NULL; if (!aap) return NULL; while (aap){ pfp = aap->pfp; while (pfp){ if (pfp->str_new) MemFree(pfp->str_new); if (pfp->str_prot) MemFree(pfp->str_prot); pfp_tmp = pfp; pfp = pfp->next; MemFree(pfp_tmp); } aap_tmp = aap; aap = aap->next; MemFree(aap_tmp); } return NULL; } static Boolean LIBCALLBACK Ing_DoPropagate(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) { BioseqPtr bsp_genome = NULL; IngAnnotAlignPtr aap = NULL; IngProgFeatPtr pfp = NULL; SeqFeatPtr sfp_new = NULL; SeqFeatPtr sfp_genome = NULL; SeqFeatPtr temp = NULL; SeqLocPtr slp = NULL; Char strErr[50]={""}; ByteStorePtr bs=NULL; CharPtr str_new = NULL, str_prot = NULL; CharPtr str = NULL; Int4 len = 0; Uint1 strand_rel_to_genome; Char str_buf[300]={""}; Boolean prot_ok = TRUE; Boolean gap_split; SeqIdPtr sip_prot = NULL; BioseqPtr bsp_prot = NULL; MsgAnswer ans; SeqMgrFeatContext context; aap = (IngAnnotAlignPtr)sfc->userdata; if (!aap) return (FALSE); sfp_genome = aap->sfp_mrna; bsp_genome = BioseqFindFromSeqLoc(sfp_genome->location); /* check if feature is already on NG */ pfp = (IngProgFeatPtr)MemNew(sizeof(IngProgFeat)); FeatDefLabel (sfp, pfp->name, sizeof (pfp->name) - 1, OM_LABEL_BOTH); pfp->type = sfc->featdeftype; pfp->strand = sfc->strand; pfp->orig_loc = SeqLocPrint(sfp->location); pfp->found = FALSE; SeqMgrExploreFeatures(bsp_genome, (Pointer)pfp, Ing_CheckGenFeats, NULL, NULL, mRNAFilter); if (pfp->found) { sprintf (str_buf, "%s already exists. Do you still want to propagate it?", pfp->name); ans = Message (MSG_YN, str_buf); if (ans == ANS_NO) { pfp->status = _already_exists_; pfp->prot_ok = TRUE; Ing_PropagateReport(aap, pfp); aap->pfp = Ing_AddProgFeat(aap->pfp, pfp); return (TRUE); } } /* map location */ if (aap->holes == FALSE) { slp = productLoc_to_locationLoc(sfp_genome, sfp->location); } else { if (GetValue(aap->gap_split) == 1) gap_split = TRUE; else gap_split = FALSE; strand_rel_to_genome = SeqLocStrand(sfp_genome->location); slp = Ing_MapLocForProp(aap->child, gap_split, sfp->location, strand_rel_to_genome); } if (!slp) { pfp->status = _failed_to_map_; pfp->prot_ok = TRUE; Ing_PropagateReport(aap, pfp); aap->pfp = Ing_AddProgFeat(aap->pfp, pfp); return (TRUE); } if (sfp->idx.subtype == FEATDEF_GENE) slp = SeqLocMerge(bsp_genome, slp, NULL, TRUE, FALSE, FALSE); IngfeatDefTrack[sfc->featdeftype] = 2; temp = AsnIoMemCopy(sfp, (AsnReadFunc) SeqFeatAsnRead, (AsnWriteFunc) SeqFeatAsnWrite); /* copy fields from temp to new genomic feature */ sfp_new = CreateNewFeatureOnBioseq(bsp_genome, sfc->seqfeattype, NULL); sfp_new->location = SeqLocFree(sfp_new->location); sfp_new->location = slp; sfp_new->product = AsnIoMemCopy(sfp->product, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); sfp_new->xref = temp->xref; sfp_new->data = temp->data; sfp_new->id = temp->id; sfp_new->idx.subtype = sfp->idx.subtype; sfp_new->partial = temp->partial; sfp_new->excpt = temp->excpt; sfp_new->except_text = temp->except_text; sfp_new->exp_ev = temp->exp_ev; sfp_new->comment = temp->comment; sfp_new->qual = temp->qual; sfp_new->title = temp->title; sfp_new->ext = temp->ext; sfp_new->cit = temp->cit; sfp_new->exp_ev = temp->exp_ev; sfp_new->dbxref = temp->dbxref; sfp_new->xref = temp->xref; sfp_new->pseudo = temp->pseudo; sfp_new->except_text = temp->except_text; pfp->new_loc = SeqLocPrint(sfp_new->location); /* check translated product */ if (sfp->idx.subtype == FEATDEF_CDS){ bs = ProteinFromCdRegionEx(sfp_new, FALSE, TRUE); if (!bs) return (TRUE); str_new = (CharPtr)BSMerge(bs, NULL); BSFree(bs); sip_prot = SeqLocId(sfp_new->product); bsp_prot = BioseqFind(sip_prot); str_prot = (CharPtr)GetSequenceByBsp(bsp_prot); prot_ok = FALSE; if (str_prot == NULL || str_new == NULL){ if (str_prot == NULL) Message (MSG_OK, "Failed to find a protein sequence associated with the mRNA record, cannot check if the protein sequence matches the translated coding region."); else Message (MSG_OK, "Failed to translate the new coding region."); prot_ok = FALSE; } else if ((StringCmp(str_new, str_prot) == 0)) prot_ok = TRUE; if (!prot_ok){ if (sfp_new->excpt && !StringHasNoText(sfp_new->except_text)){ len = StringWidth(sfp_new->except_text) + StringWidth("unclassified translation discrepancy"); str = (CharPtr) MemNew(sizeof(Char)*len); sprintf(str, "%s, unclassified translation discrepancy", sfp_new->except_text); MemFree(sfp_new->except_text); sfp_new->except_text = str; } else { sfp_new->excpt = TRUE; sfp_new->except_text = StringSave("unclassified translation discrepancy"); } } pfp->str_prot = str_prot; pfp->str_new = str_new; } MemFree(temp); /* do not SeqFeatFree */ pfp->status = _success_; pfp->prot_ok = prot_ok; Ing_PropagateReport(aap, pfp); aap->pfp = Ing_AddProgFeat(aap->pfp, pfp); return (TRUE); } static void Ing_ClosePropagateWin(WindoW w) { IngAnnotAlignPtr aap = NULL; aap = (IngAnnotAlignPtr)GetObjectExtra(w); aap = Ing_AnnotAlignFree(aap); Remove(w); } static void Ing_PropagateFeatures(BioseqPtr bsp_genome, IngAnnotAlignPtr aap) { SegmenT seg; aap->viewer = CreateViewer(aap->w, 500 ,150, TRUE, TRUE); aap->seg = CreatePicture(); aap->rowNum = 0; aap->pfp = NULL; SeqMgrExploreFeatures(aap->bsp_mrna, (Pointer)aap, Ing_DoPropagate, NULL, NULL, mRNAFilter); AttachPicture (aap->viewer, aap->seg, INT4_MIN, INT4_MAX, UPPER_RIGHT, 1 , 1, NULL); SetViewerProcs(aap->viewer, Ing_PropagateClickProc,NULL,NULL, NULL); RealizeWindow(aap->w); Ing_ResizePropagateWin(aap->w); Show(aap->w); Update(); } static void Ing_AnnotateAlignmentCancel(ButtoN b) { Remove(ParentWindow(b)); } static void Ing_mRNATrackTomRNAFilter(IngAnnotAlignPtr aap) { Int4 i; for(i=0; inList; i++){ if (GetItemStatus(aap->feat_list, i+1)){ mRNAFilter[mRNALookup[i]]=TRUE; } else { mRNAFilter[mRNALookup[i]]=FALSE; } } } static Boolean Ing_IsSpideyAlign(IngTrackAlignsPtr tap, SeqAlignPtr sap) { Int4 i = 0; SeqAlignPtr sap_list = NULL; ValNodePtr vnp = NULL; vnp = tap->showlist; while (vnp){ sap_list = (SeqAlignPtr) vnp->data.ptrvalue; if (sap_list == sap){ if (StringCmp(tap->namelist[i], "Spidey")==0) return TRUE; else return FALSE; } vnp = vnp->next; i++; } return FALSE; } static void Ing_QuitPropagateWin(IteM i) { Ing_ClosePropagateWin(ParentWindow(i)); } static void Ing_AnnotateAlignmentAccept (ButtoN b) { IngGenomeViewerPtr igvp = NULL; Int2 retval; SelStructPtr ssp = NULL; SeqLocPtr slp_list = NULL; SeqAlignPtr child=NULL, parent=NULL; SeqAlignPtr salp_prev=NULL, salp_head=NULL; SeqAlignPtr salp=NULL; SeqFeatPtr sfp_mrna = NULL; BioseqPtr product = NULL; Boolean found=FALSE, Only_sap=FALSE; SeqEntryPtr sep = NULL; IngAnnotAlignPtr aap = NULL; Int4 value, i; Uint2 itemID; WindoW w; Uint1 seqfeattype=0; Uint1 featdeftype= 0; IngMarkData marked; OMProcControl ompc; Boolean gap_split; MsgAnswer ans; MenU m; ChoicE cg; WatchCursor(); w=ParentWindow(b); igvp = (IngGenomeViewerPtr) GetObjectExtra (w); aap = (IngAnnotAlignPtr)GetObjectExtra(b); if (aap->nList > 0){ aap->w = DocumentWindow(-50, -90 , 550, 250, "Feature Propagation Report", Ing_ClosePropagateWin, Ing_ResizePropagateWin); SetObjectExtra(aap->w, (Pointer)aap, NULL); } else aap->w = NULL; m = PulldownMenu(aap->w, "Window"); CommandItem(m, "Quit", Ing_QuitPropagateWin); product = aap->bsp_mrna; if (igvp==NULL || aap==NULL) goto end; Hide(w); value=GetValue(aap->feat_type); if (value == 1){ seqfeattype = SEQFEAT_RNA; featdeftype = FEATDEF_mRNA; } else if (value==2){ seqfeattype=SEQFEAT_CDREGION; featdeftype = FEATDEF_CDS; } else if (value==3){ seqfeattype=SEQFEAT_GENE; featdeftype = FEATDEF_GENE; } ssp = ObjMgrGetSelected(); while (ssp){ if (ssp == NULL || (ssp->itemtype!=0 && ssp->itemtype != OBJ_SEQALIGN)){ goto next; } child = (SeqAlignPtr)GetPointerForIDs(ssp->entityID, ssp->itemID, OBJ_SEQALIGN); if (!child) goto next; parent=AlnMgr2GetParent(child); if (!dblClick){ ObjMgrDeSelect(ssp->entityID, ssp->itemID, ssp->itemtype, 0, NULL); } /* make seqlocptrs and create new feature */ if (GetValue(aap->gap_split) == 1) gap_split = TRUE; else gap_split = FALSE; if (!igvp->isExons && Ing_IsSpideyAlign(&igvp->talign, parent) && igvp->data){ slp_list = Ing_MakeLocListFromSpidp(igvp->data, parent, gap_split); if (!slp_list) slp_list = Ing_MakeLocListFromSAP(child, gap_split); } else slp_list = Ing_MakeLocListFromSAP(child, gap_split); if (!slp_list) goto next; sfp_mrna = Ing_CreateNewFeature(igvp->entityID, igvp->itemID, product, seqfeattype, featdeftype, NULL, slp_list, NULL); /* copy features from mRNA record */ Ing_mRNATrackTomRNAFilter(aap); if (GetStatus(aap->propc) && aap->w){ if (igvp->data != NULL) aap->holes = Ing_DoesAlignmentCoverAll(igvp->data); aap->child = child; aap->sfp_mrna = sfp_mrna; Ing_PropagateFeatures(igvp->bsp, aap); } /* delete child alignment and reindex parent */ ans = Message (MSG_YN, "Do you want to delete the alignment?"); if (ans == ANS_YES) { if (parent){ salp=(SeqAlignPtr)parent->segs; while (salp && !found) { if (salp == child) found = TRUE; else { if (salp_head) salp_prev = salp; else salp_head = salp_prev = salp; salp = salp->next; } } if (!found) goto next; if (salp_head != NULL) { salp_prev->next = salp->next; salp->next = NULL; SeqAlignFree(salp); } else { if (salp->next==NULL) Only_sap=TRUE; else { salp_head = salp->next; salp->next = NULL; SeqAlignFree(salp); } } if (!Only_sap){ parent->segs = (Pointer)salp_head; if (parent->saip != NULL) AMAlignIndex2Free2(parent); parent->saip=NULL; AlnMgr2IndexLite(parent); marked.parent = parent; marked.idx = 0; marked.bSpidey = FALSE; sep = GetTopSeqEntryForEntityID(igvp->entityID); SeqEntryExplore(sep,(Pointer)&marked, is_parent_spidey); if (marked.bSpidey) Disable(igvp->d_Win->mrnaorexons); } else{ marked.parent = parent; marked.idx = 0; marked.bSpidey = FALSE; sep = GetTopSeqEntryForEntityID(igvp->entityID); SeqEntryExplore(sep,(Pointer)&marked, Ing_MarkSeqAnnot); DeleteMarkedObjects(igvp->entityID, OBJ_SEQENTRY, (Pointer)sep); if (marked.bSpidey){ Disable(igvp->d_Win->mrnaorexons); Ing_DeleteSpidey(igvp, marked.idx); } } } else { marked.parent = parent; marked.idx = 0; marked.bSpidey = FALSE; sep = GetTopSeqEntryForEntityID(igvp->entityID); SeqEntryExplore(sep,(Pointer)&marked, Ing_MarkSeqAnnot); DeleteMarkedObjects(igvp->entityID, OBJ_SEQENTRY, (Pointer)sep); if (marked.bSpidey){ Disable(igvp->d_Win->mrnaorexons); Ing_DeleteSpidey(igvp, marked.idx); } } Ing_InitAlignArrays(&igvp->talign, FALSE); } SeqMgrIndexFeatures(igvp->entityID, NULL); itemID=GetItemIDGivenPointer(igvp->entityID, OBJ_SEQFEAT, (Pointer)sfp_mrna); GatherProcLaunch (OMPROC_EDIT, FALSE, igvp->entityID, itemID, OBJ_SEQFEAT, 0, 0, OBJ_SEQFEAT, 0); ObjMgrSetDirtyFlag (igvp->entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, igvp->entityID, 0, 0); /* BioseqUnlock(aap->bsp_mrna); */ next: ssp = ssp->next; /* aap_old = aap; */ /* aap = aap->next; */ /* MemFree(aap_old); */ } end: Remove(w); ArrowCursor(); return; } static Boolean LIBCALLBACK Ing_SetToPropagateArray(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) { mRNATrack[sfc->featdeftype] = TRUE; return TRUE; } static void Ing_SetFeatList(LisT feat_list, Int4 index) { Int4 i; for(i=0; i < index; i++){ SetItemStatus(feat_list, i+1, TRUE); } } static void Ing_AnnotateAlignmentForm(IteM item) { IngGenomeViewerPtr igvp; GrouP g, g2, g3, g4, g5; ButtoN b1, b2; IngAnnotAlignPtr aap = NULL; IngAnnotAlignPtr aap_head = NULL; IngAnnotAlignPtr aap_new = NULL; BioseqPtr bsp_mrna = NULL; BioseqPtr bsp_genome = NULL; SeqAlignPtr salp = NULL; WindoW w; Int4 i; SelStructPtr ssp = NULL, temp_ssp = NULL; SeqIdPtr sip = NULL; SeqLocPtr slp = NULL; Char str_mrna[100]={""}, buf_mrna[100]={""}; Char str_gen[100]={""}, buf_gen[100]={""}; Boolean bFirst = TRUE; Boolean found = FALSE; ssp = ObjMgrGetSelected(); if (!ssp || ssp->itemtype != OBJ_SEQALIGN) return; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(item)); if (!igvp) return; bsp_genome = igvp->bsp; w = FixedWindow(-50, -33, -10, -10, "Make Feature From Align", StdCloseWindowProc); if (!w) return; SetObjectExtra(w, (Pointer)igvp, NULL); g=HiddenGroup(w, 1, -3, NULL); SetGroupMargins(g, 10, 10); SetGroupSpacing(g, 10, 20); g2 = NormalGroup (g, 1, 2, "New Feature Type", systemFont,NULL); aap=(IngAnnotAlignPtr)MemNew(sizeof(IngAnnotAlign)); aap_head = aap; aap->feat_type = HiddenGroup(g2, 3, 1, NULL); RadioButton (aap->feat_type, "mRNA"); RadioButton (aap->feat_type, "CDS"); RadioButton (aap->feat_type, "Gene"); SetValue (aap->feat_type, 1); aap->gap_split = HiddenGroup(g2, 2, 1, NULL); RadioButton(aap->gap_split, "Split at gaps"); RadioButton(aap->gap_split, "Extend over gaps"); SetValue(aap->gap_split, 1); SetObjectExtra((Handle)aap->feat_type, (Pointer)aap_head, NULL); temp_ssp = ssp; i = 0; while (temp_ssp){ if (temp_ssp->itemtype != 0 && temp_ssp->itemtype == OBJ_SEQALIGN) i++; temp_ssp = temp_ssp->next; } g3 = NormalGroup (g, 1, i, "Features To Propagate", systemFont, NULL); MemSet((Pointer)mRNAFilter, 1, sizeof(mRNAFilter)); i = 0; while (ssp){ if (ssp->itemtype == 0 || ssp->itemtype != OBJ_SEQALIGN) goto next; salp = (SeqAlignPtr)GetPointerForIDs(ssp->entityID, ssp->itemID, OBJ_SEQALIGN); sip = AlnMgr2GetNthSeqIdPtr(salp, 2); bsp_mrna = BioseqLockById (sip); if (!sip || !bsp_mrna) goto next; g4 = HiddenGroup(g3, 1, 2, NULL); g5 = HiddenGroup(g4, 1, 5, NULL); aap->propc = CheckBox(g5, "Propagate Features", NULL); SetStatus(aap->propc, TRUE); SeqIdWrite (bsp_mrna->id, str_mrna, PRINTID_REPORT, sizeof (str_mrna) - 1); sprintf(buf_mrna, "from: %s", str_mrna); MultiLinePrompt(g5, buf_mrna, 350, programFont); SeqIdWrite (bsp_genome->id, str_gen, PRINTID_REPORT, sizeof(str_gen) - 1); sprintf(buf_gen, "to: %s", str_gen); MultiLinePrompt(g5, buf_gen, 350, programFont); MemSet((Pointer)mRNATrack, FALSE, sizeof(mRNATrack)); MemSet((Pointer)mRNALookup, 0, sizeof(mRNALookup)); if (!salp->bounds) SeqMgrExploreFeatures (bsp_mrna, NULL, Ing_SetToPropagateArray, NULL, NULL, mRNAFilter); else while ((slp = SeqLocFindNext(salp->bounds, slp)) != NULL) SeqMgrExploreFeatures (bsp_mrna, NULL, Ing_SetToPropagateArray, slp, NULL, mRNAFilter); if (!bFirst){ aap_new = (IngAnnotAlignPtr)MemNew(sizeof(IngAnnotAlign)); aap_new->feat_type = NULL; aap->next = aap_new; aap = aap_new; } else bFirst = FALSE; aap->bsp_mrna = bsp_mrna; aap->nList=0; aap->feat_list = MultiList(g4, 20, 6, NULL); for (i=0; ifeat_list, IngfeatDefLabels[i]); mRNALookup[aap->nList]=i; aap->nList++; found = TRUE; } } if (found) Ing_SetFeatList(aap->feat_list, aap->nList); else Disable(g3); next: ssp = ssp->next; } g = HiddenGroup(g, 2, 1, NULL); b1 =DefaultButton(g, "Accept", Ing_AnnotateAlignmentAccept); Enable(b1); b2 =PushButton(g, "Cancel", Ing_AnnotateAlignmentCancel); SetObjectExtra(b1, (Pointer)aap_head, NULL); SetObjectExtra(b2, (Pointer)aap_head, NULL); Select(w); Show(w); } /******************************************************************************* Function : Ing_ViewFlatFile() Purpose : view record as flat file *******************************************************************************/ static void Ing_ViewFlatFile(IteM i) { SeqEntryPtr sep = NULL; IngGenomeViewerPtr igvp = NULL; Char path [PATH_MAX]; FILE *fp = NULL; Boolean ok; ErrSev level; igvp = (IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); sep = GetTopSeqEntryForEntityID(igvp->entityID); if (!sep) return; TmpNam(path); fp = FileOpen(path, "w"); if (!fp) return; WatchCursor(); Update(); level = ErrSetMessageLevel (SEV_MAX); ok = SeqEntryToFlat(sep, fp, /* GENBANK_FMT */(Uint1) 0, /* SEQUIN_MODE */(Uint1) 8); ErrSetMessageLevel (level); FileClose(fp); if (ok){ LaunchGeneralTextViewer (path, igvp->title); FileRemove (path); } else FileRemove (path); ArrowCursor(); Update(); } /******************************************************************************* Function : Ing_NewFeatureMenuProc(), Ing_SetupNewFeaturesMenu(), Ing_FeatureFilter() Purpose : create a new feature *******************************************************************************/ static void Ing_NewFeatureMenuProc (IteM i) { MsgAnswer ans; IngGenomeViewerPtr igvp; IngObjectPtr nop; OMProcControl ompc; ObjMgrProcPtr ompp; Int2 retval; nop = (IngObjectPtr) GetObjectExtra (i); if (nop == NULL) return; igvp = nop->igvp; if (igvp == NULL) return; ompp = nop->ompp; if (ompp == NULL || ompp->func == NULL) return; MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl)); ompc.input_entityID = igvp->entityID; ompc.input_itemID = igvp->itemID; ompc.input_itemtype = igvp->itemType; GatherDataForProc (&ompc, FALSE); ompc.proc = ompp; retval = (*(ompp->func)) (&ompc); if (retval == OM_MSG_RET_ERROR) { ErrShow (); } } static Boolean Ing_FeatureFilter(Uint1 featdeftype) { if (featdeftype != FEATDEF_COMMENT && featdeftype!=FEATDEF_BIOSRC && featdeftype!=FEATDEF_PUB && featdeftype!=FEATDEF_ORG) return TRUE; return FALSE; } static void Ing_SetupNewFeaturesMenu(MenU m, IngGenomeViewerPtr igvp) { FeatDispGroupPtr fdgp; FeatDefPtr fdp; IngObjectPtr first; IteM i; Uint1 key; CharPtr label; IngObjectPtr last; IngObjectPtr nop; ObjMgrPtr omp; ObjMgrProcPtr ompp; ObjMgrTypePtr omtp; MenU sub; Uint2 subtype; if (m == NULL) return; omp = ObjMgrGet (); if (omp == NULL) return; ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, 0, 0, NULL); if (ompp == NULL) return; omtp = NULL; first = NULL; last = NULL; while ((omtp = ObjMgrTypeFindNext (omp, omtp)) != NULL) { ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, NULL); if (ompp != NULL) { switch (omtp->datatype) { case OBJ_SEQFEAT : fdgp = NULL; while ((fdgp = DispGroupFindNext (fdgp, &key, &label)) != NULL) { if (fdgp->groupkey != 0 && key!=4) { sub = SubMenu (m, fdgp->groupname); fdp = NULL; label = NULL; while ((fdp = FeatDefFindNext (fdp, &key, &label,fdgp->groupkey, FALSE)) != NULL) { if (Ing_FeatureFilter(key)/* key != FEATDEF_BAD */) { ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { if (ompp->subinputtype == fdp->featdef_key && Ing_FeatureFilter(ompp->subinputtype)/* ompp->subinputtype != FEATDEF_PUB */) { i = CommandItem (sub, ompp->proclabel, Ing_NewFeatureMenuProc); nop = (IngObjectPtr) MemNew (sizeof (IngObjectData)); if (nop != NULL) { nop->kind = 1; /* feature creation item */ nop->ompp = ompp; nop->igvp = igvp; nop->item = i; nop->molgroup = fdp->molgroup; } if (first == NULL) { first = nop; } if (last != NULL) { last->next = nop; } last = nop; nop->igvp=igvp; SetObjectExtra (i, (Pointer) nop, NULL); } } } } } } } } } } /******************************************************************************* Function : Ing_CloseWin(), Ing_CloseProc(), Ing_QuitProc() Purpose : Close window (program is still running) or quit program *******************************************************************************/ static void Ing_CloseWin(WindoW w) { IngGenomeViewerPtr igvp=NULL; igvp=(IngGenomeViewerPtr)GetObjectExtra(w); ObjMgrSendMsg(OM_MSG_FLUSH, igvp->entityID, igvp->itemID, OBJ_BIOSEQ); } static void Ing_CloseProc(IteM i) { Ing_CloseWin(ParentWindow(i)); } static void Ing_QuitProc(IteM i) { IngGenomeViewerPtr igvp; WindoW w; w=ParentWindow(i); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); if (igvp->bspIsLocked) BioseqUnlock(igvp->bsp); Ing_MainDataFree(igvp); Remove(w); QuitProgram(); } /******************************************************************************* Function : Ing_DoSave(), Ing_SaveProc() Purpose : saving functions *******************************************************************************/ static void Ing_DoSave(ButtoN b) { BioseqPtr bsp; SeqEntryPtr sep; AsnIoPtr aip; Char filename[21]; WindoW w; IngSaveInfoPtr igsi; w=ParentWindow(b); igsi=(IngSaveInfoPtr)GetObjectExtra(b); bsp=(BioseqPtr)GetObjectExtra(w); GetTitle(igsi->text, filename, 20); sep=GetTopSeqEntryForEntityID(ObjMgrGetEntityIDForPointer(bsp)); aip = AsnIoOpen(filename, "w"); SeqEntryAsnWrite(sep, aip, NULL); aip = AsnIoClose(aip); Remove(w); } static void Ing_SaveProc(IteM i) { IngGenomeViewerPtr igvp; WindoW w; GrouP g, g1, g3; ButtoN b; IngSaveInfoPtr igsi; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); igsi =(IngSaveInfoPtr)MemNew(sizeof(IngSaveInfo)); w = FixedWindow(-50, -33, -10, -10,"SAVE - ASN.1 format", StdCloseWindowProc); g = HiddenGroup(w, 1, 3, NULL); g1 = HiddenGroup(g, 1, 2, NULL); StaticPrompt(g1, "File name: ", 0, 0, systemFont, 'l'); igsi->text = DialogText(g1, "UNTITLED", 20, NULL); g3= HiddenGroup(g, 2, 1, NULL); b = DefaultButton(g3, "Save", Ing_DoSave); SetObjectExtra(b, (Pointer)igsi, StdCleanupExtraProc); Enable(b); PushButton(g3, "Cancel", Ing_GenericCancelButton); SetObjectExtra(w, (Pointer)igvp->bsp, NULL); Select(w); Show(w); return; } /******************************************************************************* Function : Ing_PrintProc(), Ing_DoPrint() Purpose : print viewer *******************************************************************************/ typedef struct ing_printinfo{ ButtoN top; ButtoN bottom; ButtoN report; TexT toptext; TexT bottomtext; TexT reporttext; } IngPrintInfo, PNTR IngPrintInfoPtr; static void Ing_DoPrint(ButtoN b) { MsgAnswer ans; WindoW dlg; IngGenomeViewerPtr igvp; IngPrintInfoPtr pinfo = NULL; dlg = ParentWindow(b); Hide(dlg); igvp=(IngGenomeViewerPtr)GetObjectExtra(dlg); pinfo = (IngPrintInfoPtr)GetObjectExtra(b); if (igvp == NULL || igvp->vTop == NULL || igvp->vBottom == NULL || pinfo == NULL) return; /* -- cannot create gif files from vibrant program -- #ifdef WIN_MOTIF {{ Boolean print_top_failed = FALSE; Boolean print_bot_failed = FALSE; Boolean print_report_failed = FALSE; FILE *f = NULL; Char filename[21]={""}; IngReportPtr Report = NULL; BoxInfo pBox; Int2 width = 700, height = 710; SegmenT pic = NULL; gdImage* im = NULL; SetUpDrawingTools(); Nlm_InitMuskStyles (); Nlm_SetMuskCurrentSt("style6"); if (GetStatus(pinfo->top)){ pic = igvp->pictTop; ASSERT(pic); SegmentBox (pic, &pBox); width = (Int2)pBox.right - pBox.left; height = (Int2)pBox.top - pBox.bottom; GetTitle(pinfo->toptext, filename, 20); f = FileOpen(filename, "wb"); ASSERT(f); im = gdImageCreate(width, height); if (!Nlm_Picture2gdImage (im, pic, -10, -10, LOWER_LEFT, 1, 1)) print_top_failed = TRUE; gdImageGif(im, f); FileClose(f); f = NULL; } if (GetStatus(pinfo->bottom)){ GetTitle(pinfo->bottomtext, filename, 20); pic = igvp->pictBottom; RecalculateSegment(pic, 1, 1); SegmentBox (pic, &pBox); f = FileOpen(filename, "wb"); if (f){ if (!Nlm_PictureToGIF(f, width, height, igvp->pictBottom, -10, -10, LOWER_LEFT, igvp->scaleX, 1, FALSE)) print_bot_failed = TRUE; } else print_bot_failed = TRUE; FileClose(f); f = NULL; } if (GetStatus(pinfo->report)){ Report = (IngReportPtr)GetObjectExtra(igvp->hReport); if (Report){ pic = Report->Picture; RecalculateSegment(pic, 1, 1); SegmentBox (pic, &pBox); GetTitle(pinfo->reporttext, filename, 20); f = FileOpen(filename, "wb"); if (f){ if (!Nlm_PictureToGIF(f, width, height, pic, -10, -10, LOWER_LEFT, 1, 1, FALSE)) print_report_failed = TRUE; } else print_report_failed = TRUE; FileClose(f); } } }} Remove(dlg); if (print_top_failed) Message (MSG_OK, "Printing overview (top viewer) failed."); if (print_bot_failed) Message (MSG_OK, "Printing detailed view (bottom viewer) failed."); if (print_report_failed) Message (MSG_OK, "Printing report window failed."); Nlm_ExitMuskStyles(); */ Remove(dlg); ans = Message (MSG_YN, "Do you want to print just the visible area?"); if (ans == ANS_YES) { PrintViewer (igvp->vTop); PrintViewer (igvp->vBottom); } else { PrintAllViewer(igvp->vTop); PrintAllViewer(igvp->vBottom); } } static void Ing_PrintProc(IteM i) { IngGenomeViewerPtr igvp; WindoW w; GrouP g, g1, g2, g3; ButtoN b; IngPrintInfoPtr pinfo = NULL; IngReportPtr Report = NULL; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); pinfo =(IngPrintInfoPtr)MemNew(sizeof(IngPrintInfo)); if (igvp->hReport) Report = (IngReportPtr)GetObjectExtra(igvp->hReport); w = FixedWindow(-50, -33, -10, -10,"Print Window", StdCloseWindowProc); SetObjectExtra(w, (Pointer)igvp, NULL); g = HiddenGroup(w, 1, 3, NULL); SetGroupMargins(g, 10, 10); SetGroupSpacing(g, 10, 20); g1 = HiddenGroup(g, 3, 2, NULL); pinfo->top = CheckBox(g1, "Overview (top)", NULL); SetStatus(pinfo->top, TRUE); StaticPrompt(g1, "Filename: ", 0, 0, systemFont, 'l'); pinfo->toptext = DialogText(g1, "overview.gif", 20, NULL); pinfo->bottom = CheckBox(g1, "Detailed (bottom)", NULL); SetStatus(pinfo->bottom, TRUE); StaticPrompt(g1, "Filename: ", 0, 0, systemFont, 'l'); pinfo->bottomtext = DialogText(g1, "detail.gif", 20, NULL); g2 = HiddenGroup(g, 1, 3, NULL); pinfo->report = CheckBox(g2, "Report", NULL); SetStatus(pinfo->report, TRUE); StaticPrompt(g2, "Filename: ", 0, 0, systemFont, 'l'); pinfo->reporttext = DialogText(g2, "report.gif", 20, NULL); if (Report == NULL){ SetStatus(pinfo->report, FALSE); Disable(g2); } g3= HiddenGroup(g, 2, 1, NULL); b = DefaultButton(g3, "Print", Ing_DoPrint); SetObjectExtra((Handle)b, pinfo, StdCleanupExtraProc); PushButton(g3, "Cancel", Ing_GenericCancelButton); Select(w); Show(w); return; } /******************************************************************************* Function : Ing_SetupMenus() Purpose : *******************************************************************************/ void Ing_SetupMenus () { MenU m; #ifdef WIN_MAC m = AppleMenu (NULL); DeskAccGroup (m); #endif } /******************************************************************************* Function : Ing_TargetAccept(), Ing_CreateTargetList(), Ing_ChangeTarget(), Ing_BspListProc(), Ing_LocalFileProc() Purpose : view a new sequence *******************************************************************************/ static void Ing_TargetAccept(ButtoN b) { Int4 i, value; IngGenomeViewerPtr igvp=NULL; BioseqPtr bsp=NULL; SeqEntryPtr sep=NULL; SeqIdPtr sip=NULL; ValNode *pvn=NULL; WindoW hTarget; hTarget=ParentWindow(b); igvp=(IngGenomeViewerPtr)GetObjectExtra(b); if (!igvp) return; Hide(hTarget); sep=GetTopSeqEntryForEntityID(igvp->entityID); value=GetValue(igvp->bsp_list); for(i = 1, pvn=igvp->entity_list->Sips; i <= value; i++, pvn=pvn->next) { if(i==value) { sip=(SeqId*)pvn->data.ptrvalue; bsp = BioseqFindInSeqEntry(sip, sep); igvp->cur_sip=sip; igvp->cur_target=value; } } if (bsp){ Ing_RunIngenue(igvp, bsp, igvp->entityID); Remove(hTarget); } else { Select(hTarget); Show(hTarget); } } static void Ing_CreateTargetList(IngGenomeViewerPtr igvp) { ValNode *pvn; Char szName[31]={""}; ButtoN b; WindoW d; GrouP h, h2; IngEntityPtr e_list; if (!igvp) return; igvp->numseqs=0; d = MovableModalWindow(-50, -33 ,-10, -10, "Get Sequence from Memory", NULL); h = HiddenGroup(d, 1, 2, NULL); igvp->bsp_list = SingleList(h,20,6,NULL); for (e_list=igvp->entity_list; e_list!=NULL; e_list=e_list->next){ for(pvn = e_list->Sips; pvn != NULL; pvn = pvn->next) { SeqIdWrite((SeqId *)pvn->data.ptrvalue,szName, PRINTID_FASTA_LONG,30); igvp->numseqs++; ListItem(igvp->bsp_list, szName); } } h2 = HiddenGroup(h, 2, 1, NULL); b= DefaultButton(h2, "Accept", Ing_TargetAccept); SetObjectExtra(b, (Pointer)igvp, NULL); Enable(b); PushButton(h2, "Cancel", Ing_GenericCancelButton); SetValue(igvp->bsp_list, igvp->cur_target); SetObjectExtra (d, (Pointer) igvp, NULL); RealizeWindow(d); Select(d); Show(d); } static void Ing_ChangeTarget(IteM i) { IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); Ing_CreateTargetList(igvp); } static void Ing_BspListProc(IteM i) { IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(i)); Ing_CreateTargetList(igvp); } static void Ing_LocalFileProc(IteM i) { IngGenomeViewerPtr igvp_new=NULL; if (!(igvp_new=Ing_MainDataNew())) return; Ing_FileOpenProc(igvp_new, ParentWindow(i)); } /******************************************************************************* Function : Ing_CreateReOrderAlignForm(), Ing_AddAlignList(), Ing_RemoveAlignList(), Ing_AlignListAccept(), Ing_ResetAlignList(), Ing_UpdateNamelists(), Ing_RemoveNode(), Ing_AddNode() Purpose : change the order of alignments in display *******************************************************************************/ typedef struct ing_seqform { LisT feat_list; LisT feat_list2; Int4 nList; Int4 nList2; } IngseqForm, PNTR IngseqFormPtr; static ValNodePtr vnp_left = NULL; static ValNodePtr vnp_right = NULL; static CharPtr PNTR namelist_left = NULL; static CharPtr PNTR namelist_right = NULL; static Int4 index1=0; static Int4 index2=0; static void Ing_ResetAlignList(IngseqFormPtr sformp) { ValNodePtr vnp = NULL; Int4 i = 0; AMAlignIndex2Ptr amaip = NULL; SeqAlignPtr sap = NULL; SeqIdPtr sip = NULL; Char str[41] = {""}, buf[60]={""}; Reset(sformp->feat_list); sformp->nList = 0; vnp = vnp_left; while (vnp){ sap = (SeqAlignPtr)vnp->data.ptrvalue; amaip = (AMAlignIndex2Ptr) sap->saip; sip=AlnMgr2GetNthSeqIdPtr(amaip->saps[0], 2); SeqIdWrite(sip, str, PRINTID_FASTA_LONG, 41); sprintf(buf, "%s: ", namelist_left[i]); StringCat(buf, str); ListItem(sformp->feat_list, buf); sformp->nList++; vnp = vnp->next; i++; } Reset(sformp->feat_list2); sformp->nList2 = 0; vnp = vnp_right; i = 0; while(vnp){ sap = (SeqAlignPtr)vnp->data.ptrvalue; amaip = (AMAlignIndex2Ptr) sap->saip; sip=AlnMgr2GetNthSeqIdPtr(amaip->saps[0], 2); SeqIdWrite(sip, str, PRINTID_FASTA_LONG, 41); sprintf(buf, "%s: ", namelist_right[i]); StringCat(buf, str); ListItem(sformp->feat_list2, buf); sformp->nList2++; vnp = vnp->next; i++; } } static void Ing_UpdateNamelists(Int2 list, Int4 index) { Int4 i, j; CharPtr PNTR tmplist = NULL; if (list == 1){ /* add name to left list */ if (namelist_left == NULL){ /* index1 == 0 */ namelist_left = (CharPtr PNTR)MemNew(sizeof(CharPtr)); namelist_left[0] = namelist_right[index]; } else { tmplist = (CharPtr PNTR)MemNew(sizeof(CharPtr)*index1); for (i = 0; i < index1-1; i++) tmplist[i] = namelist_left[i]; tmplist[index1-1]=namelist_right[index]; MemFree(namelist_left); namelist_left = tmplist; } /* remove name from right list */ if (index2 == 0){ MemFree(namelist_right); namelist_right = NULL; } else { tmplist = (CharPtr PNTR)MemNew(sizeof(CharPtr)*index2); for (i = 0, j = 0; i < index2; i++, j++){ if (j == index2-1) j++; tmplist[i] = namelist_right[j]; } MemFree(namelist_right); namelist_right = tmplist; } } else { /* add name to right list */ if (namelist_right == NULL){ /* index2 == 0 */ namelist_right = (CharPtr PNTR)MemNew(sizeof(CharPtr)); namelist_right[0] = namelist_left[index]; } else { tmplist = (CharPtr PNTR)MemNew(sizeof(CharPtr)*index2); for (i = 0; i < index2-1; i++) tmplist[i] = namelist_right[i]; tmplist[index2-1]=namelist_left[index]; MemFree(namelist_right); namelist_right = tmplist; } /* remove name from left list */ if (index1 == 0){ MemFree(namelist_left); namelist_left = NULL; } else { tmplist = (CharPtr PNTR)MemNew(sizeof(CharPtr)*index1); for (i = 0, j = 0; i < index1; i++, j++){ if (j == index1-1) j++; tmplist[i] = namelist_left[j]; } MemFree(namelist_left); namelist_left = tmplist; } } } static void Ing_RemoveNode (SeqAlignPtr salp, Int2 list) { ValNodePtr vnp_cur = NULL; ValNodePtr vnp_prev = NULL; SeqAlignPtr salp2 = NULL; if (list == 1) vnp_cur = vnp_left; else vnp_cur = vnp_right; while (vnp_cur){ salp2 = (SeqAlignPtr)vnp_cur->data.ptrvalue; if (salp2 == salp){ if (!vnp_prev){ if (list == 1) vnp_left = vnp_cur->next; else vnp_right = vnp_cur->next; vnp_cur->next = NULL; ValNodeFree(vnp_cur); } else { vnp_prev->next = vnp_cur->next; vnp_cur->next = NULL; ValNodeFree(vnp_cur); } return; } vnp_prev = vnp_cur; vnp_cur = vnp_cur->next; } } static void Ing_AddNode (SeqAlignPtr salp, Int2 list, Int4 i) { Ing_UpdateNamelists(list, i); if (list == 1) ValNodeAddPointer(&vnp_left, OBJ_SEQALIGN, (Pointer)salp); else ValNodeAddPointer(&vnp_right, OBJ_SEQALIGN, (Pointer)salp); } static void Ing_AddAlignList(ButtoN b) { Int4 i = 0; Int4 j = 0; ValNodePtr vnp = NULL; IngseqFormPtr sformp = NULL; SeqAlignPtr sap = NULL; sformp = (IngseqFormPtr)GetObjectExtra(ParentWindow(b)); if (!sformp) return; vnp = vnp_left; while (vnp){ if (GetItemStatus(sformp->feat_list, i+1)){ /* copy the contents of vnp1 to vnp2 */ sap = (SeqAlignPtr)vnp->data.ptrvalue; index1--; index2++; vnp = vnp->next; Ing_AddNode(sap, 2, i-j); Ing_RemoveNode(sap, 1); i++; j++; continue; } i++; vnp = vnp->next; } Ing_ResetAlignList (sformp); } static void Ing_RemoveAlignList(ButtoN b) { Int4 i = 0; Int4 j = 0; ValNodePtr vnp = NULL; IngseqFormPtr sformp = NULL; SeqAlignPtr sap = NULL; sformp = (IngseqFormPtr)GetObjectExtra(ParentWindow(b)); if (!sformp) return; vnp = vnp_right; while (vnp){ if (GetItemStatus(sformp->feat_list2, i+1)){ sap = (SeqAlignPtr)vnp->data.ptrvalue; index1++; index2--; vnp = vnp->next; Ing_AddNode(sap, 1, i-j); Ing_RemoveNode(sap , 2); i++; j++; continue; } i++; vnp = vnp->next; } Ing_ResetAlignList(sformp); } static void Ing_AlignListAccept(ButtoN b) { IngGenomeViewerPtr igvp=NULL; IngseqFormPtr sformp=NULL; WindoW w; w=ParentWindow(b); sformp=(IngseqFormPtr)GetObjectExtra(w); igvp= (IngGenomeViewerPtr) GetObjectExtra (b); if (!sformp || !igvp) return; Hide (w); /* update global vars */ Ing_InitAlignArrays(&igvp->talign, FALSE); igvp->talign.showlist = vnp_right; igvp->talign.namelist = namelist_right; igvp->talign.hidelist = vnp_left; igvp->talign.hnamelist = namelist_left; igvp->talign.hideindex = index1; igvp->talign.showindex = index2; Ing_PopulateOverviewPage((Pointer)igvp, FALSE); Ing_PopulateDetailedPage((Pointer)igvp); Remove(w); } static ValNodePtr Ing_ValNodeCopy (ValNodePtr vnp) { ValNodePtr vnp_copy = NULL; ValNodePtr vnp_tmp = NULL; SeqAlignPtr sap = NULL; vnp_tmp = vnp; while(vnp_tmp){ sap = (SeqAlignPtr)vnp_tmp->data.ptrvalue; ValNodeAddPointer(&vnp_copy, OBJ_SEQALIGN, sap); vnp_tmp = vnp_tmp->next; } return vnp_copy; } static CharPtr PNTR Ing_CharPtrCopy(CharPtr PNTR names, Int4 n) { CharPtr PNTR names_copy = NULL; Int4 i; names_copy = (CharPtr PNTR) MemNew(sizeof(CharPtr)*n); for (i= 0; italign.showlist && !igvp->talign.hidelist) return; d = MovableModalWindow(-50, -33 ,-10, -10, "Change Alignment Order", NULL); g = HiddenGroup(d, 1, 2, NULL); h = HiddenGroup(g, 2, 2, NULL); sformp=(IngseqFormPtr)MemNew(sizeof(IngseqForm)); StaticPrompt (h, "Hide", 0, LineHeight() , systemFont, 'c'); StaticPrompt (h, "Show", 0, LineHeight() , systemFont, 'c'); sformp->feat_list = MultiList(h, 15, 10, NULL); sformp->nList=0; i = 0; vnp = igvp->talign.hidelist; while(vnp){ sap = (SeqAlignPtr)vnp->data.ptrvalue; amaip = (AMAlignIndex2Ptr)sap->saip; sip=AlnMgr2GetNthSeqIdPtr(amaip->saps[0], 2); SeqIdWrite(sip, str, PRINTID_FASTA_LONG, 41); sprintf(buf, "%s", igvp->talign.hnamelist[i]); StringCat(buf, str); ListItem(sformp->feat_list, buf); sformp->nList++; vnp = vnp->next; i++; } index1 = i; vnp_left = Ing_ValNodeCopy(igvp->talign.hidelist); namelist_left = Ing_CharPtrCopy(igvp->talign.hnamelist, index1); /* get visible alignments if any */ sformp->feat_list2 = MultiList(h, 15, 10, NULL); sformp->nList2 = 0; i = 0; vnp = igvp->talign.showlist; while (vnp){ sap = (SeqAlignPtr)vnp->data.ptrvalue; amaip = (AMAlignIndex2Ptr)sap->saip; sip=AlnMgr2GetNthSeqIdPtr(amaip->saps[0], 2); SeqIdWrite(sip, str, PRINTID_FASTA_LONG, 41); sprintf(buf, "%s: ", igvp->talign.namelist[i]); StringCat(buf, str); ListItem(sformp->feat_list2, buf); sformp->nList2++; vnp = vnp->next; i++; } index2 = i; vnp_right = Ing_ValNodeCopy(igvp->talign.showlist); namelist_right = Ing_CharPtrCopy(igvp->talign.namelist, index2); h2 = HiddenGroup(g, 4, 1, NULL); b = PushButton(h2, "Add", Ing_AddAlignList); SetObjectExtra(b, (Pointer) igvp, NULL); b = PushButton(h2, "Remove", Ing_RemoveAlignList); SetObjectExtra(b, (Pointer) igvp, NULL); b= DefaultButton(h2, "Accept", Ing_AlignListAccept); SetObjectExtra(b, (Pointer)igvp, NULL); Enable(b); PushButton(h2, "Cancel", Ing_GenericCancelButton); SetObjectExtra (d, (Pointer) sformp, StdCleanupExtraProc); RealizeWindow(d); Select(d); Show(d); } /******************************************************************************* Function : Ing_SetShowList(), Ing_TrackToFilter(), Ing_ShowListAccept(), Ing_LabelsProc(), Ing_CreateShowListForm() Purpose : create a window to choose whether to show or hide specific features *******************************************************************************/ static void Ing_SetShowList(LisT feat_list, Int4 nList) { Int4 i; for(i=0; inList; i++){ if (GetItemStatus(sformp->feat_list, i+1)){ IngfeatDefFilter[fDefLookup[i]]=TRUE; IngfeatDefTrack[fDefLookup[i]]=2; } else { IngfeatDefFilter[fDefLookup[i]]=FALSE; IngfeatDefTrack[fDefLookup[i]]=1; } } } static void Ing_ShowListAccept(ButtoN b) { IngGenomeViewerPtr igvp=NULL; IngseqFormPtr sformp=NULL; WindoW w; w=ParentWindow(b); sformp=(IngseqFormPtr)GetObjectExtra(w); igvp= (IngGenomeViewerPtr) GetObjectExtra (b); if (!sformp || !igvp) return; Hide (w); Ing_TrackToFilter(sformp); Ing_PopulateOverviewPage((Pointer)igvp, FALSE); Ing_PopulateDetailedPage((Pointer)igvp); Remove(w); } static void Ing_LabelsProc(IteM item) { IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(item)); if (igvp->bLabels){ igvp->bLabels=FALSE; SetTitle(igvp->d_Win->labels, "Show Labels"); } else { igvp->bLabels=TRUE; SetTitle(igvp->d_Win->labels, "Hide Labels"); } Ing_PopulateDetailedPage((Pointer)igvp); } typedef struct ing_simplepopup { PopuP pop; TexT text; } IngSimplePopup, PNTR IngSimplePopupPtr; static void Ing_AdjustTopHeight(ButtoN b) { IngGenomeViewerPtr igvp = NULL; IngSimplePopupPtr spp = NULL; Char str[20] ={""}; WindoW Dlg; Dlg = ParentWindow(b); spp = (IngSimplePopupPtr)GetObjectExtra(b); igvp = (IngGenomeViewerPtr)GetObjectExtra(Dlg); if (!spp || !igvp) return; Hide(Dlg); GetTitle(spp->text, str, sizeof(str)); igvp->TopHeight = atoi(str); Ing_ResizeWin(igvp->hMain); Remove(Dlg); } static void Ing_TopHeightProc(IteM item) { IngGenomeViewerPtr igvp; WindoW w; GrouP g; Char str[20] = {""}; IngSimplePopupPtr spp; ButtoN b; igvp = GetObjectExtra (ParentWindow(item)); if (!igvp) return; w = FixedWindow(-50, -33, -10, -10, "Overview Height", StdCloseWindowProc); SetObjectExtra(w, igvp, NULL); spp = (IngSimplePopupPtr)MemNew(sizeof(IngSimplePopup)); g = HiddenGroup(w, -2, 0, NULL); SetGroupMargins(g, 10, 10); SetGroupSpacing(g, 10, 20); StaticPrompt(g, "New Height: ", 0, 0, systemFont, 'l'); sprintf(str, "%d", igvp->TopHeight); spp->text = DialogText(g, str, 10, NULL); b = DefaultButton(g, "OK", Ing_AdjustTopHeight); SetObjectExtra(b, (Pointer)spp, StdCleanupExtraProc); PushButton(g, "Cancel", Ing_GenericCancelButton); Select(w); Show(w); } static void Ing_CreateShowListForm(IteM item) { ButtoN b; WindoW d; GrouP h, h2; Int4 i; IngseqFormPtr sformp; IngGenomeViewerPtr igvp=NULL; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(item)); if (!igvp) return; d = MovableModalWindow(-50, -33 ,-10, -10, "Show or Hide Features", NULL); h = HiddenGroup(d, 1, 2, NULL); sformp=(IngseqFormPtr)MemNew(sizeof(IngseqForm)); sformp->nList=0; sformp->feat_list = MultiList(h, 20, 6, NULL); for (i=0; ifeat_list, IngfeatDefLabels[i]); fDefLookup[sformp->nList]=i; sformp->nList++; } } Ing_SetShowList(sformp->feat_list, sformp->nList); h2 = HiddenGroup(h, 2, 1, NULL); b= DefaultButton(h2, "Accept", Ing_ShowListAccept); SetObjectExtra(b, (Pointer)igvp, NULL); Enable(b); PushButton(h2, "Cancel", Ing_GenericCancelButton); SetObjectExtra (d, (Pointer) sformp, StdCleanupExtraProc); RealizeWindow(d); Select(d); Show(d); } /******************************************************************************* Function : Ing_SearchandSelect(), Ing_SearchOK(), Ing_SearchCancel(), Ing_CreateSearchForm() Purpose : create a window to choose whether to show or hide specific features *******************************************************************************/ typedef struct search { VieweR v; SegmenT pict; Boolean selected; CharPtr name; } IngSearch, PNTR IngSearchPtr; static Boolean LIBCALLBACK Ing_SearchandSelect(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) { IngSearchPtr searchp=NULL; Char str[100]={""}; searchp=(IngSearchPtr)sfc->userdata; if (!searchp || StringHasNoText(searchp->name)) return FALSE; FeatDefLabel (sfp, str, sizeof (str) - 1, OM_LABEL_CONTENT); if (StrStr(str, searchp->name)){ msg.segID=0; msg.labelmsg=0; if (searchp->selected){ ObjMgrAlsoSelect(sfc->entityID, sfc->itemID, OBJ_SEQFEAT, 0, NULL); } else { ObjMgrSelect(sfc->entityID, sfc->itemID, OBJ_SEQFEAT, 0, NULL); searchp->selected=TRUE; } } return TRUE; } static void Ing_SearchOK(ButtoN b) { IngSimplePopupPtr ipp=NULL; IngGenomeViewerPtr igvp=NULL; WindoW w; IngSearch search; Char str[255]={""}; Char strErr[50]={""}; ipp=(IngSimplePopupPtr)GetObjectExtra(b); w=ParentWindow(b); igvp=(IngGenomeViewerPtr)GetObjectExtra(w); Hide(w); GetTitle(ipp->text, str, sizeof(str)); search.v = igvp->vBottom; search.pict = igvp->pictBottom; search.name = StringSave(str); search.selected = FALSE; SeqMgrExploreFeatures (igvp->bsp, (Pointer) &search, Ing_SearchandSelect, igvp->slp, NULL, IngfeatDefFilter); if (!search.selected){ sprintf(strErr, "%s was not found in record", str); Message (MSG_OK, strErr); Show(w); return; } MemFree(search.name); Remove(w); } static void Ing_SearchCancel(ButtoN b) { Remove(ParentWindow(b)); } static void Ing_CreateSearchForm(IteM item) { IngGenomeViewerPtr igvp=NULL; WindoW d; GrouP g; IngSimplePopupPtr ipp=NULL; ButtoN b; Int4 i; igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(item)); d = MovableModalWindow(-50, -33 ,-10, -10, "Find Feature", NULL); ipp=(IngSimplePopupPtr)MemNew(sizeof(IngSimplePopup)); g = HiddenGroup(d, -2, -2, NULL); StaticPrompt (g, "Keyword: ", 0, LineHeight() , systemFont, 'l'); ipp->text = DialogText(g, "", 15, NULL); b = DefaultButton(g, "OK", Ing_SearchOK); PushButton(g, "Cancel", Ing_SearchCancel); SetObjectExtra(b, (Pointer)ipp, StdCleanupExtraProc); SetObjectExtra(d, (Pointer)igvp, NULL); RealizeWindow(d); Select(d); Show(d); } /******************************************************************************* Function : Ing_GetBspFromGIOrAcc(), Ing_NetOpen_okProc(), Ing_NetOpen_cancelProc(), Ing_GetFromNetwork(), Ing_ItemToNetwork() Purpose : retrieve sequence from network *******************************************************************************/ extern BioseqPtr Ing_GetBspFromGIOrAcc(CharPtr str) { BioseqPtr bsp; Int4 gi; Char ptr; SeqIdPtr sip; ValNode vn; str = TrimSpacesAroundString(str); ptr = *str; if (IS_ALPHA(ptr)) /* accession */ { sip = SeqIdFromAccessionDotVersion(str); bsp = BioseqLockById(sip); } else /* it's a GI */ { gi = atoi(str); vn.choice = SEQID_GI; vn.data.intvalue = gi; vn.next = NULL; bsp = BioseqLockById(&vn); } return bsp; } static void Ing_NetOpen_okProc(ButtoN b) { BioseqPtr bsp=NULL; WindoW w; IngFileOpenDataPtr dfodp=NULL; IngGenomeViewerPtr igvp=NULL; Char str[50]={""}; Uint2 entityID; SeqEntryPtr sep=NULL; w=(WindoW)ParentWindow(b); if (!w) return; dfodp=(IngFileOpenDataPtr)GetObjectExtra(b); igvp=(IngGenomeViewerPtr)GetObjectExtra(ParentWindow(b)); if (!dfodp || !igvp) return; Hide(w); /*retrieve a Gi*/ GetTitle(dfodp->GI, str, sizeof(str)); if (StringHasNoText (str)) { Message (MSG_OK, "Enter GI or Accession number"); Show (w); Select (w); Select (dfodp->GI); return; } WatchCursor(); Ing_ProgressNew(igvp, "Fetching your record....."); bsp=Ing_GetBspFromGIOrAcc(str); if (!bsp){ Ing_ProgressEnd(igvp); ArrowCursor(); Message (MSG_OK, "Unable to find your record in the database."); Select (w); Show (w); Select (dfodp->GI); return; } igvp->bspIsLocked=TRUE; entityID=ObjMgrGetEntityIDForPointer((Pointer)bsp); sep=GetTopSeqEntryForEntityID(entityID); sep = SeqMgrGetSeqEntryForData (bsp); igvp->entity_list=(IngEntityPtr)MemNew(sizeof(IngEntity)); igvp->entity_list->entityID=entityID; igvp->entity_list->itemID=1; igvp->entity_list->bspcount=Ing_AllButPartsCount(sep, NULL, NULL, 0, 0); igvp->entity_list->Sips=SAM_ExtractSips(sep); igvp->cur_sip=(SeqId *)igvp->entity_list->Sips->data.ptrvalue; igvp->cur_target=1; ArrowCursor(); Ing_ProgressEnd(igvp); if (dfodp->hStart){ Remove(dfodp->hStart); dfodp->hStart=NULL; } Remove(w); if (entityID!=0){ Ing_RunIngenue(igvp, bsp, entityID); } } static void Ing_NetOpen_cancelProc(ButtoN b) { IngFileOpenDataPtr dfodp=NULL; dfodp=(IngFileOpenDataPtr)GetObjectExtra(b); if (dfodp && dfodp->hStart){ Select(dfodp->hStart); Show(dfodp->hStart); } Remove(ParentWindow(b)); } extern void Ing_GetFromNetwork(IngGenomeViewerPtr igvp, WindoW hStart) { WindoW w; GrouP g, c; ButtoN b; Char szAppName [10]={"Ingenue"}; IngFileOpenDataPtr dfodp=NULL; dfodp=(IngFileOpenDataPtr)MemNew(sizeof(IngFileOpenData)); w = MovableModalWindow (-50, -33, -10, -10, "Download From NCBI", NULL); SetObjectExtra(w, (Pointer)igvp, NULL); if (w==NULL) return; SetGroupSpacing (w, 10, 10); /*accesion*/ g = NormalGroup (w, 3, 0, "GI or Accession", systemFont,NULL); dfodp->GI=DialogText (g, "", 10, Ing_NetOpen_access); SetObjectExtra(dfodp->GI, (Pointer)dfodp, StdCleanupExtraProc); /*retrieve - cancel*/ c = HiddenGroup (g, 4, 0, NULL); SetGroupSpacing (c, 10, 2); dfodp->OK=DefaultButton (c, "Retrieve", Ing_NetOpen_okProc); SetObjectExtra(dfodp->OK, (Pointer)dfodp, NULL); Disable(dfodp->OK); b=PushButton (c, "Cancel", Ing_NetOpen_cancelProc); SetObjectExtra(b, (Pointer)dfodp, NULL); dfodp->hStart=hStart; /* SetObjectExtra (w, (Pointer) unop, StdCleanupExtraProc); */ /*display*/ AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); Select (w); Show (w); Update (); } static void Ing_ItemtoNetwork(IteM i){ IngGenomeViewerPtr igvp_new=NULL; if (!(igvp_new=Ing_MainDataNew())) return; Ing_GetFromNetwork(igvp_new, NULL); } /******************************************************************************* Function : Ing_FileOpenFromCommandline(), Ing_NetOpenFromCommandline() Purpose : retrieve a sequence from the commandline *******************************************************************************/ extern void Ing_FileOpenFromCommandline(CharPtr filename, Int4 start, Int4 stop, Int4 spi_job, CharPtr spi_f, CharPtr spi_gilist, CharPtr spi_seqidfile, Int4 b2s_job, CharPtr b2s_f, CharPtr b2s_gilist, CharPtr b2s_seqidfile) { IngGenomeViewerPtr igvp=NULL; if (StringHasNoText (filename)) { Message (MSG_OK, "Enter File name"); return; } igvp=(IngGenomeViewerPtr)MemNew(sizeof(IngGenomeViewer)); if (!igvp) return; Ing_InitMainDataPtr(igvp); igvp->from=start; igvp->to=stop; igvp->filetype=1; Ing_FileOpenMain(filename, igvp); if (spi_job != 0){ igvp->filetype=spi_job; if (spi_f) Ing_FileOpenSpecial(igvp, spi_f, NULL); else if (spi_seqidfile) Ing_FileOpenSpecial(igvp, spi_seqidfile, NULL); else if (spi_gilist) Ing_FileOpenSpecial(igvp, NULL, spi_gilist); } if (b2s_job !=0){ igvp->filetype=b2s_job; if (b2s_f) Ing_FileOpenSpecial(igvp, b2s_f, NULL); else if (b2s_seqidfile) Ing_FileOpenSpecial(igvp, b2s_seqidfile, NULL); else if (b2s_gilist) Ing_FileOpenSpecial(igvp, NULL, b2s_gilist); } ProcessEvents(); } extern void Ing_NetOpenFromCommandline(CharPtr txt, Int4 start, Int4 stop, Int4 spi_job, CharPtr spi_f, CharPtr spi_gilist, CharPtr spi_seqidfile, Int4 b2s_job, CharPtr b2s_f, CharPtr b2s_gilist, CharPtr b2s_seqidfile) { BioseqPtr bsp=NULL; SeqEntryPtr sep; Uint2 entityID; IngGenomeViewerPtr igvp=NULL; Char strErr[50]={""}; if (StringHasNoText (txt)) { Message (MSG_OK, "Enter GI or Accession number"); return; } WatchCursor(); igvp=(IngGenomeViewerPtr)MemNew(sizeof(IngGenomeViewer)); if (!igvp) return; Ing_InitMainDataPtr(igvp); igvp->filetype=1; igvp->from=start; igvp->to=stop; bsp=Ing_GetBspFromGIOrAcc(txt); if (!bsp){ sprintf(strErr, "Ingenue can't find your record %s", txt); Message (MSG_OK, strErr); Ing_MainDataFree(igvp); MemFree(txt); ArrowCursor(); return; } Ing_ProgressNew(igvp, "Fetching your record..."); MemFree(txt); if (igvp->to == 0) igvp->to=bsp->length-1; entityID=ObjMgrGetEntityIDForPointer((Pointer)bsp); sep = GetTopSeqEntryForEntityID(entityID); /* sep = SeqMgrGetSeqEntryForData (bsp); */ igvp->entity_list=(IngEntityPtr)MemNew(sizeof(IngEntity)); igvp->entity_list->entityID=entityID; igvp->entity_list->itemID=1; igvp->entity_list->bspcount=Ing_AllButPartsCount(sep, NULL, NULL, 0, 0); igvp->entity_list->Sips=SAM_ExtractSips(sep); igvp->cur_sip=(SeqId *)igvp->entity_list->Sips->data.ptrvalue; igvp->cur_target=1; ArrowCursor(); Ing_ProgressEnd(igvp); if (entityID!=0){ Ing_RunIngenue(igvp, bsp, entityID); } if (spi_job != 0){ igvp->filetype=spi_job; if (spi_f) Ing_FileOpenSpecial(igvp, spi_f, NULL); else if (spi_seqidfile) Ing_FileOpenSpecial(igvp, spi_seqidfile, NULL); else if (spi_gilist) Ing_FileOpenSpecial(igvp, NULL, spi_gilist); } if (b2s_job !=0){ igvp->filetype=b2s_job; if (b2s_f) Ing_FileOpenSpecial(igvp, b2s_f, NULL); else if (b2s_seqidfile) Ing_FileOpenSpecial(igvp, b2s_seqidfile, NULL); else if (b2s_gilist) Ing_FileOpenSpecial(igvp, NULL, b2s_gilist); } ProcessEvents(); } /******************************************************************************* Function : Ing_WinTimerProc(), Ing_ProgressNew(), Ing_ProgressEnd() Purpose : signal that the program is preforming a task (has not stalled) *******************************************************************************/ extern void Ing_WinTimerProc(WindoW progressW) { IngGenomeViewerPtr igvp; igvp=(IngGenomeViewerPtr)GetObjectExtra(progressW); if (igvp->progress_running){ igvp->progress_string=Ing_StringCat(igvp->progress_string, ".."); if (StringHasNoText(igvp->progress_counter)) SetTitle(igvp->progress_prompt, igvp->progress_string); else SetTitle(igvp->progress_prompt, igvp->progress_counter); Select(progressW); Update(); } else { igvp->progress_timer=0; SetTitle(igvp->progress_prompt, "Ready !"); MemFree(igvp->progress_string); igvp->progress_string=NULL; Select(progressW); Update(); } } extern void Ing_ProgressNew(IngGenomeViewerPtr igvp, CharPtr name) { WindoW tmpMain = NULL; if (igvp->hMain == NULL){ tmpMain = MovableModalWindow(-30, -20, -10, -10, "Ingenue - Get Sequence", NULL); igvp->progress_prompt = StaticPrompt(tmpMain, "", 25*MaxCharWidth(), LineHeight(), systemFont, 'l'); SetObjectExtra(tmpMain, (Pointer)igvp, NULL); igvp->hMain = tmpMain; Select(tmpMain); Show(tmpMain); } SetTitle(igvp->progress_prompt, name); igvp->progress_string=StringSave(name); igvp->progress_running=TRUE; Select(igvp->hMain); Update(); } extern void Ing_ProgressEnd(IngGenomeViewerPtr igvp) { igvp->progress_running=FALSE; MemSet((Pointer)igvp->progress_counter, '\0', sizeof(igvp->progress_counter)); Ing_WinTimerProc(igvp->hMain); } /******************************************************************************* Function : Ing_SetupMainWindow(), Ing_BuildMainGui() Purpose : create the main window *******************************************************************************/ static void Ing_SetupMainWindow(IngGenomeViewerPtr PNTR real_igvp) { WindoW hMain; GrouP g, g1, g2, g3, subg2; VieweR v1,v2; IteM i; ButtoN b1, b2; SegmenT seg1, pict; ChoicE ch; MenU m1, m2, m3, m4, m5, m6, m7, m8; MenU submenu1, submenu2, submenu3; Char title[100]={""}, str1[20]={""}, str2[20]={""}; Char szAppName [10]={"Ingenue"}; FonT hFnt; Int2 cxChar,cyChar; IngRangePtr rnp; IngGenomeViewerPtr igvp; RecT rcg; Int4 Fh; Int4 j; igvp=*real_igvp; #ifdef WIN_MAC Ing_SetupMenus (); #endif hMain = DocumentWindow( 5*stdCharWidth, -5*stdCharWidth, 600, 900, igvp->title,Ing_CloseWin,Ing_ResizeWin); if (!hMain) return; #ifndef WIN_MAC Ing_SetupMenus (); #endif SetObjectExtra (hMain, (Pointer) igvp, NULL); m1 = PulldownMenu (hMain, "File"); submenu1=SubMenu(m1,"New Sequence"); #ifdef USE_ENTREZ CommandItem(submenu1, "Network...", Ing_ItemtoNetwork); #endif SetWindowTimer(hMain, IngenueCheckSocketsProc); igvp->d_Win=(IngWinDataPtr)MemNew(sizeof(IngWinData)); CommandItem(submenu1, "File...", Ing_LocalFileProc); /* igvp->imemory=CommandItem(submenu1, "Memory...", Ing_BspListProc); */ /* Disable(igvp->imemory); */ submenu2=SubMenu(m1, "Annotate"); igvp->d_Win->Feat=submenu2; Disable(submenu2); CommandItem(submenu2, "Genscan File..", Ing_OpenGenscan); CommandItem(submenu2, "Blast File..", Ing_OpenBlast); CommandItem(submenu2, "Feature Table..", Ing_OpenFeatTable); CommandItem(submenu2, "Tab Delimited..", Ing_OpenTabDel); SeparatorItem(m1); CommandItem(m1, "Show as Flat File", Ing_ViewFlatFile); i=CommandItem(m1, "Switch target", Ing_ChangeTarget); if (igvp->entity_list->bspcount<2) Disable(i); SeparatorItem(m1); CommandItem(m1, "Save", Ing_SaveProc); CommandItem(m1, "Print", Ing_PrintProc); CommandItem (m1, "Close Window", Ing_CloseProc); SeparatorItem(m1); CommandItem (m1, "Exit", Ing_QuitProc); m2 = PulldownMenu (hMain, "Edit"); CommandItem(m2, "Edit Feature", Ing_EditFeature); CommandItem(m2, "Delete Feature", Ing_DeleteFeature); m3 = PulldownMenu (hMain, "Features"); submenu2=SubMenu(m3, "Annotate New Feature"); Ing_SetupNewFeaturesMenu(submenu2, igvp); igvp->d_Win->Annotate=m3; CommandItem(m3, "Edit Feature", Ing_EditFeature); CommandItem (m3, "Show or Hide Feature", Ing_CreateShowListForm); CommandItem(m3, "Search ..", Ing_CreateSearchForm); m4 = PulldownMenu(hMain, "Alignments"); CommandItem(m4, "Annotate Alignment", Ing_AnnotateAlignmentForm); CommandItem(m4, "Replace Mismatches..", Ing_ReplaceAllMismatched); CommandItem(m4, "Print Report", Ing_ReportWindow); igvp->d_Win->mrnaorexons = CommandItem(m4, "Spidey - as Exons", Ing_mRNAOrExons); Disable(igvp->d_Win->mrnaorexons); CommandItem (m4, "Switch Order", Ing_CreateReOrderAlignForm); m5 = PulldownMenu (hMain, "Options"); igvp->d_Win->labels=CommandItem(m5, "Hide Labels", Ing_LabelsProc); CommandItem(m5, "Overview Height", Ing_TopHeightProc); m6 = PulldownMenu(hMain, "Tools"); CommandItem(m6, "View Sequence", Ing_OpenUDV); CommandItem (m6, "View Aligns as Diags", Ing_DotDiagProc); /* do analysis */ m7 = PulldownMenu (hMain, "Analysis"); CommandItem(m7, "Spidey...", Ing_GetFileForSpidey); SeparatorItem(m7); CommandItem(m7, "Blast 2 Sequences...", Ing_Blast2SeqsProc); CommandItem(m7, "QBlast...", Ing_QBlastProc); SeparatorItem(m7); CommandItem(m7, "Dot-Matrix", Ing_DotMatrixProc); Disable(m7); igvp->d_Win->Analysis=m7; /* find motifs */ m8 = PulldownMenu (hMain, "Motifs"); CommandItem(m8, "CpG islands", Ing_CpGProc); i = CommandItem(m8, "Poly-A sites", Ing_PolyAProc); Disable(i); /* sarah needs to fix this */ CommandItem(m8, "Repeats", Ing_RepeatsProc); CommandItem(m8, "Signal Peptide", Ing_SignalPeptideProc); i = CommandItem(m8, "Kozak", Ing_KozakProc); Disable(i); /* sarah needs to fix this */ CommandItem(m8, "User Defined", Ing_UserMotifProc); SeparatorItem(m8); igvp->d_Win->GC = CommandItem(m8, "Show GC content", Ing_ShowGCContent); CommandItem(m8, "Find low complexity", Ing_ShowComplexity); CommandItem(m8, "Find ORF", Ing_RunORFinder); SeparatorItem(m8); Ing_tRNAscanMenu(m8); g=HiddenGroup(hMain,0,7,NULL); igvp->gMain=g; hFnt = igvp->GrData.hFnt; SelectFont(hFnt); cxChar=igvp->GrData.cxChar; cyChar=igvp->GrData.cyChar; rnp=(IngRangePtr)MemNew(sizeof(IngRange)); g1 = HiddenGroup (g, -2, -1, NULL); g2 = HiddenGroup (g1, -1, -3, NULL); g3=HiddenGroup(g2, -6, -2, NULL); SetGroupSpacing (g3, 10, 20); igvp->d_Win->Goto=g3; StaticPrompt (g3, "show ONLY from:", 0, 3*cyChar/2, hFnt, 'l'); rnp->left = DialogText (g3, "0", (Int2)4, NULL); StaticPrompt (g3, "to:", 0, 3*cyChar/2, hFnt, 'l'); rnp->right = DialogText (g3, "0", (Int2)4, NULL); b1=DefaultButton (g3, "OK", Ing_GotoProc); b2=PushButton (g3, "show ALL", Ing_ShowALLProc); SetObjectExtra(b1, (Pointer)rnp, StdCleanupExtraProc); SetObjectExtra(b2, (Pointer)rnp, NULL); subg2=HiddenGroup(g2, 1, 3, NULL); igvp->deflineg=subg2; for (j = 0; j < 4; j++) igvp->featInfo[j]= StaticPrompt(subg2, "", 30*cxChar, cyChar , programFont, 'l'); igvp->vZoom=CreateViewer(g1, 75, 100,FALSE,FALSE); igvp->pictZoom=CreatePicture(); if (igvp->hMain){ Remove(igvp->hMain); } igvp->hMain=hMain; *real_igvp=igvp; } static WindoW Ing_BuildMainGui(IngGenomeViewerPtr igvp, Int2 numrows) { WindoW hMain; GrouP g; IteM i; SegmenT seg1,seg2; Int2 Margins; ChoicE ch; MenU m1, m2, m3, m4, m5, m6, submenu1, submenu2; Char title[100]; if (!igvp) return(NULL); Ing_InitfeatDefFilter(); Ing_SetupMainWindow(&igvp); Enable(igvp->d_Win->Goto); Enable(igvp->d_Win->Feat); Enable(igvp->imemory); hMain=igvp->hMain; g = igvp->gMain; igvp->vRuler1= CreateViewer(g,300,(RULERDEFHEIGHT*igvp->GrData.cyChar),FALSE,FALSE); igvp->pictRuler1 = CreatePicture(); igvp->vTop = CreateViewer(g, 300 ,300, TRUE, TRUE); igvp->pictTop=CreatePicture(); igvp->vRuler2= CreateViewer(g,300,(RULERDEFHEIGHT*igvp->GrData.cyChar)*2,FALSE,FALSE); igvp->pictRuler2 = CreatePicture(); igvp->vBottom = CreateViewer(g, 300 ,300, TRUE, TRUE); igvp->pictBottom=CreatePicture(); igvp->progress_prompt = StaticPrompt (g, "Ready !", 100, LineHeight(), programFont, 'l'); AlignObjects(ALIGN_JUSTIFY, (HANDLE) igvp->deflineg, (HANDLE) g, NULL , NULL); return(hMain); } /******************************************************************************* Function : Ing_AttachMessageProc() Purpose : registered message callback *******************************************************************************/ extern Boolean Ing_AttachMessageProc(IngGenomeViewerPtr igvp, Uint2 procID, Uint2 eID) { OMUserDataPtr omudp; Uint2 userkey; igvp->userKey=OMGetNextUserKey(); igvp->procID=procID; omudp = ObjMgrAddUserData (eID, procID, OMPROC_VIEW, igvp->userKey); if (omudp == NULL) return(FALSE); omudp->messagefunc = Ing_OM_MsgFunc; omudp->userdata.ptrvalue = (Pointer)igvp; return(TRUE); } /******************************************************************************* Function : Ing_GetSeqLocations() Purpose : Store sequence coordinates *******************************************************************************/ static void Ing_GetSeqLocations(IngGenomeViewerPtr igvp, BioseqPtr bsp) { Int4 start, stop; start=igvp->from; stop=igvp->to; if (stop !=0 && stop<= bsp->length-1 && (startslp=SeqLocIntNew(start, stop, (bsp->strand==Seq_strand_plus?1:2), bsp->id); igvp->SeqLength=stop-start+1; } else if (start==0 && stop==0){ igvp->to=bsp->length-1; igvp->SeqLength = bsp->length; } igvp->bspLength=bsp->length; } /******************************************************************************* Function : Ing_LoadViewer() Purpose : retrieve data from object manager, start up a new window *******************************************************************************/ static IngGenomeViewerPtr Ing_LoadViewer(IngGenomeViewerPtr igvp, BioseqPtr bsp, Uint2 itemType, Int2 numrows) { WindoW hMain; Boolean bRet; Int4 from,to,scaleX, diff; Uint2 entityID, itemID; WatchCursor(); /*BioSeq ?*/ if (itemType!=OBJ_BIOSEQ) { ErrPostEx(SEV_ERROR, 0, 0, szErrMsg1); bRet=FALSE; goto fin; } /*get the BioSeq Pointer*/ if (bsp==NULL){ ErrPostEx(SEV_ERROR, 0, 0, szErrMsg4); bRet=FALSE; goto fin; } /*check the sequence length; could be undef.*/ if (bsp->length==(Int4)-1){ ErrPostEx(SEV_ERROR, 0, 0, szErrMsg5); bRet=FALSE; goto fin; } /*save the BioSeq ids*/ entityID=ObjMgrGetEntityIDForPointer((Pointer)bsp); if (SeqMgrFeaturesAreIndexed (entityID) == 0) { SeqMgrIndexFeatures (entityID, NULL); } itemID=GatherItemIDByData(entityID, itemType, (Pointer)bsp); igvp->entityID = entityID; igvp->itemID = itemID; igvp->itemType=itemType; igvp->bsp = bsp; /* get seq loc coordinates if specified */ Ing_GetSeqLocations(igvp, bsp); SeqIdWrite(bsp->id, igvp->title, PRINTID_FASTA_LONG, 41); SetTitle(igvp->hMain, igvp->title); /*build the GUI*/ Ing_InitGrData(&igvp->GrData); hMain = Ing_BuildMainGui(igvp, numrows); igvp->hMain=hMain; if (hMain==NULL) { ErrPostEx(SEV_ERROR, 0, 0, szErrMsg3); bRet=FALSE; goto fin; } igvp->xposition=0; RealizeWindow(hMain); Ing_ResizeMainWindow(igvp,hMain, TRUE); if (Ing_PopulateZoomer(igvp)==FALSE) { ErrPostEx(SEV_ERROR, 0, 0, szErrMsg2); bRet=FALSE; goto fin; } if ((Ing_BuildStartupPage(igvp))==FALSE) { ErrPostEx(SEV_ERROR, 0, 0, szErrMsg2); bRet=FALSE; goto fin; } Ing_GetNamesZoomedVal(igvp->vRuler2,&from,&to,&scaleX,igvp->SeqLength); Ing_MoveCursor(igvp,from,to, TRUE); igvp->xposition=from; Show(hMain); bRet=TRUE; fin: if (bRet==FALSE){ if (igvp){ if (igvp->bspIsLocked) BioseqUnlock(igvp->bsp); igvp=Ing_MainDataFree(igvp); MemFree(igvp); } } ArrowCursor(); return(igvp); } /******************************************************************************* Function : Ing_RegIngenueProc() Purpose : registered ingenue function *******************************************************************************/ NLM_EXTERN Int2 LIBCALLBACK Ing_RegIngenueProc(Pointer data) { IngGenomeViewerPtr igvp; OMProcControlPtr ompcp; BioseqPtr bsp; SeqEntryPtr sep; ompcp = (OMProcControlPtr) data; if (ompcp == NULL || ompcp->proc == NULL) { ErrPostEx (SEV_ERROR, 0, 0, "Data NULL [1]"); return OM_MSG_RET_ERROR; } switch (ompcp->input_itemtype) { case OBJ_BIOSEQ : bsp = (BioseqPtr) ompcp->input_data; break; case 0 : return OM_MSG_RET_ERROR; default : return OM_MSG_RET_ERROR; } if (bsp == NULL) { ErrPostEx (SEV_ERROR, 0, 0, "Input Data NULL"); return OM_MSG_RET_ERROR; } igvp=(IngGenomeViewerPtr)ompcp->input_choice; if (igvp == NULL) { igvp = Ing_MainDataNew(); sep = GetTopSeqEntryForEntityID(ompcp->input_entityID); igvp->entity_list=(IngEntityPtr)MemNew(sizeof(IngEntity)); igvp->entity_list->entityID= ompcp->input_entityID; igvp->entity_list->itemID= ompcp->input_itemID; igvp->entity_list->bspcount=Ing_AllButPartsCount(sep, NULL, NULL, 0, 0); igvp->entity_list->Sips=SAM_ExtractSips(sep); igvp->cur_sip=(SeqId *)igvp->entity_list->Sips->data.ptrvalue; igvp->cur_target=1; } Ing_LoadViewer(igvp, bsp, OBJ_BIOSEQ, 0); if (!igvp) return(OM_MSG_RET_ERROR); Ing_AttachMessageProc(igvp,ompcp->proc->procid,ompcp->input_entityID); return(OM_MSG_RET_DONE); }