/* ingengraph.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: ingengraph.c * * Author: Fasika Aklilu * * Version Creation Date: 8/8/01 * * $Revision: 6.7 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #define ING_MAX_VIEWER_HEIGHT 600 #define SEGMENT_SCALE 2336 #define ARROWS_SCALE 500 #define LABELS_SCALE 100 Boolean IngfeatDefFilter[FEATDEF_MAX];/* filter parameter for SeqMgrExploreFeatures() */ Boolean IngfeatDefTrack2[FEATDEF_MAX];/* used by Ing_AddToOverviewPage() when scale is greater than COMPRESS_SCALE */ Uint1 IngfeatDefTrack[FEATDEF_MAX];/* track features 1=exists 2=exists and is visible */ /******************************************************************************* Static Var and Function Declarations *******************************************************************************/ typedef struct ing_node { Int4 row; Uint4 col; Boolean build; } IngNode, PNTR IngNodePtr; static void Ing_GetNamesZoomedVal(VieweR vNames,Int4Ptr from, Int4Ptr to, Int4Ptr scaleX,Int4 MaxLength); static Uint1 Ing_GetMiscFeatColor(CharPtr str_4); /****************************************************************************** Function : Ing_InitfeatDefFilter(), Ing_AddStringToSad(), Ing_SearchAli(),Ing_GetAlignColor(), Ing_GetCurrentSegment() Purpose : function to retrieve data for drawing *******************************************************************************/ extern void Ing_InitfeatDefFilter(void) { MemSet(IngfeatDefFilter,1,sizeof(Boolean)*(FEATDEF_MAX)); IngfeatDefFilter[FEATDEF_COMMENT]=FALSE; IngfeatDefFilter[FEATDEF_BIOSRC]=FALSE; IngfeatDefFilter[FEATDEF_PUB]=FALSE; IngfeatDefFilter[FEATDEF_ORG]=FALSE; } static Uint1Ptr Ing_GetAlignColor(CharPtr name, Uint1Ptr PNTR pClr) { if (StringCmp(name, "Spidey")==0) return pClr[Ing_SPIDEY]; if (StringCmp(name, "Blast 2 seqs")==0) return pClr[ALIGN_BLAST2SEQ]; if (StringCmp(name, "Blast")==0) return pClr[ALIGN_BLAST]; if (StringCmp(name, "Blast file")==0) return pClr[ALIGN_FILE]; return pClr[ALIGN_ANNOT]; } static CharPtr PNTR Ing_AddStringToSad(CharPtr PNTR names, SeqAnnotPtr sanp, Int4 index) { Int4 i; CharPtr new_name = NULL; CharPtr name = NULL; CharPtr title = NULL; CharPtr PNTR head = NULL; ValNodePtr desc = NULL; Int4 len; if (sanp->name) new_name=sanp->name; else if (sanp->desc) { desc = sanp->desc; while (desc){ if (desc->choice == Annot_descr_name){ if (new_name == NULL) new_name=(CharPtr)sanp->desc->data.ptrvalue; } if (desc->choice == Annot_descr_title){ if (title == NULL) title = (CharPtr)desc->data.ptrvalue; } desc = desc->next; } if(name != NULL) StringNCpy_0(new_name, name, 20); len = StringLen(new_name); if(title != NULL && len < 19) { StringCat(new_name, ":"); ++len; StringNCpy_0(new_name+len, title, 20-len); } } else return NULL; if (names==NULL){ head=(CharPtr PNTR)MemNew(sizeof(CharPtr)); *head=new_name; return head; } else { head=(CharPtr PNTR)MemNew(sizeof(CharPtr)*index); for (i=0; ihidelist; vnp_s = tap->showlist; while (vnp_h){ sap_h = (SeqAlignPtr)vnp_h->data.ptrvalue; if (sap == sap_h) return FALSE; vnp_h = vnp_h->next; } while (vnp_s){ sap_s = (SeqAlignPtr)vnp_s->data.ptrvalue; if (sap == sap_s) return FALSE; vnp_s = vnp_s->next; } return TRUE; } extern void Ing_SearchAli(SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp=NULL; BioseqSetPtr bssp=NULL; SeqAnnotPtr sanp=NULL; SeqAlignPtr salp=NULL; IngSeqAnnotData * sadp=NULL; sadp=(IngSeqAnnotData *)mydata; 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*/ salp=(SeqAlignPtr)sanp->data; if (Ing_shouldIstore(sadp->tap, salp)){ sadp->sindex++; sadp->aln_namelist=Ing_AddStringToSad(sadp->aln_namelist, sanp, sadp->sindex); ValNodeAddPointer(&(sadp->aln_showlist),OBJ_SEQALIGN,(Pointer)salp); } } sanp=sanp->next; } } static SegmenT Ing_GetCurrentSegment(IngPopFeatPtr pfp) { SegmenT CurrentSeg=NULL; if (!(pfp->nPrims%FEATURE_SEGMENT_MAXSIZE)) { if (!(pfp->nLevel2%LEVEL2_MAXNUM)){ if (!(pfp->nLevel1%LEVEL1_MAXNUM)){ pfp->nLevel1++; pfp->seg1=CreateSegment(pfp->pictMain, pfp->nLevel1, 0); } pfp->nLevel2++; pfp->seg2=CreateSegment(pfp->seg1, pfp->nLevel2, 0); } pfp->nLevel3++; CurrentSeg=CreateSegment(pfp->seg2, pfp->nLevel3, 0); pfp->CurrentSeg=CurrentSeg; /* pfp->nSegs=1; */ } else CurrentSeg=pfp->CurrentSeg; return CurrentSeg; } /******************************************************************************* Function : Ing_BigEncodeIdxFeat() Purpose : index data for collision detection *******************************************************************************/ extern Uint8 Ing_BigEncodeIdxFeat (Uint4 val1,Uint4 val2) { Uint4 index_g[2]; index_g[0]=val1; index_g[1]=val2; return *((Uint8Ptr) index_g); } typedef struct ing_pkg { CharPtr title; Int4 row; } IngPkgData, PNTR IngPkgPtr; /******************************************************************************* Function : Ing_BigDecodeIdxFeat() Purpose : retrieve data from index *******************************************************************************/ extern void Ing_BigDecodeIdxFeat (Uint8 index_g, Uint4Ptr val1, Uint4Ptr val2) { Uint4Ptr index_g2; index_g2 = (Uint4Ptr) (&index_g); if (val1) *val1 = (Uint4) index_g2 [0]; if (val2) *val2 = (Uint4) index_g2 [1]; } static IngPkgPtr Ing_EncodeFeatString( Uint4 row, CharPtr title) { IngPkgPtr pkg; pkg = (IngPkgPtr)MemNew(sizeof(IngPkgData)); pkg->title = title; pkg->row = row; return pkg; } static void Ing_DecodeFeatString(IngPkgPtr pkg, Uint4Ptr row, CharPtr PNTR title) { *row = pkg->row; *title = pkg->title; } /******************************************************************************* Function : Ing_PopOverviewPage(), Ing_PopOverviewRuler(), Ing_AddToOverViewPage(), Ing_AddToOverviewPict(), Ing_AddAlignsToOverviewPage(), Ing_AddOneAlignToOverviewPage() Purpose : Top (Overview) viewer drawing functions *******************************************************************************/ extern Boolean Ing_PopOverviewRuler(VieweR vRuler1, SegmenT pictRuler1, BioseqPtr bsp, IngGraphData GrData, Int4 from, Int4 to, Uint1Ptr seqbuf, Int4 scaleX) { IngExploreSegs gpn; Int2 nSegments=0; Boolean bSegmented = FALSE; gpn.seg=pictRuler1; gpn.viewer=vRuler1; gpn.idx=1; gpn.GrData= &GrData; gpn.left=from; gpn.right=to; gpn.seqbuf=seqbuf; gpn.bShowGC = FALSE; gpn.scaleX = scaleX; gpn.bTop = TRUE; gpn.bRegister = FALSE; gpn.bLabels = FALSE; nSegments=SeqMgrExploreSegments(bsp, (Pointer)&gpn, Ing_ExploreSegments); /*this bioseq doesn't have any segments*/ if (nSegments==0){ AddAttribute(pictRuler1, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); AddRectangle(pictRuler1,0,GrData.SegBoxHeight/2 , to - from + 1, -GrData.SegBoxHeight/2, NO_ARROW, TRUE, 2); } else{ bSegmented=TRUE; } Ing_AddRuler(pictRuler1, GrData.SegBoxHeight, from, to, scaleX, 1, TRUE); return bSegmented; } static void Ing_AddOneAlignToOverviewPage(SegmenT seg, SeqAlignPtr sap, Int4 row, Int4 start, Int4 stop) { BioseqPtr bsp=NULL; Uint1 strand; Int4 j; PrimitivE prim; strand=AlnMgr2GetNthStrand(sap, 2); if (strand == Seq_strand_minus) j = -6; else j = 6; prim = AddRectangle(seg, start, (row)*(-20), stop, (row)*(-20)+j, NO_ARROW, FALSE,0); SetPrimitiveIDs(prim, sap->idx.entityID, sap->idx.itemID, OBJ_SEQALIGN, 2); } static Uint4 Ing_AddAlignsToOverviewPage(SegmenT pictTop, SegmenT CurrentSeg, Uint2 nPrims, Uint2 nSegs, SeqEntryPtr sep, SeqAlignPtr sap, Uint4 rowNum, Int4 left, Int4 right, CharPtr name, Uint1Ptr Clr) { SeqAlignPtr salp=NULL; enumPrimAddOrder oldOrder; Boolean NewLine=FALSE; Int4 start; Int4 stop; Int4 len; Int4 offset; Char buf[41]={""}; Char label[41]={""}; len=right-left+1; offset=left; if (sap->segtype==SAS_DISC){ salp=(SeqAlignPtr)sap->segs; } else { salp=sap; } AddAttribute(CurrentSeg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); if (StringHasNoText(name)) sprintf(label, "Alignment"); else { sprintf(label, "%s", name); } AddLabel(CurrentSeg, -15, (rowNum)*(-20)+6, label, SMALL_TEXT, 0, UPPER_RIGHT, 0); AddAttribute(CurrentSeg, COLOR_ATT, (Clr?Clr:BLACK_COLOR), 0, 0, 0, 0); AddLine(CurrentSeg, 0, (rowNum)*(-20), len, (rowNum)*(-20), 0, 0); oldOrder=ChangeAddPrimOrder(ADD_TO_HEAD); while(salp){ AlnMgr2GetNthSeqRangeInSA(salp, 1, &start, &stop); if (start>right || stopnext; continue; } start=MAX(left, start); stop=MIN(right, stop); if (!(nPrims%FEATURE_SEGMENT_MAXSIZE)) { CurrentSeg=CreateSegment(pictTop, nSegs, 0); nSegs++; AddAttribute(CurrentSeg, COLOR_ATT, (Clr?Clr:BLACK_COLOR), 0, 0, 0, 0); } Ing_AddOneAlignToOverviewPage(CurrentSeg, salp, (Int4)rowNum, start-offset, stop-offset); nPrims++; NewLine=TRUE; salp=salp->next; } ChangeAddPrimOrder(oldOrder); return rowNum; } typedef struct ingcontext{ SeqFeatPtr sfp; Int4 left; Int4 right; Uint1 strand; Uint1 featdeftype; Int4 numivals; Int4Ptr ivals; Uint2 entityID; Uint2 itemID; CharPtr name; } IngContext, PNTR IngContextPtr; static void Ing_FreeContext (IngContextPtr context){ if (context->numivals > 1) MemFree(context->ivals); MemFree(context); } static void Ing_AddToOverviewPict(SegmenT seg, IngContextPtr context, Int4 start, Int4 stop, Int4 base) { Int4 j; PrimitivE prim; Int4 left; Int4 right; Int4 offset; if (seg == NULL || context == NULL) return; if (context->strand == Seq_strand_minus) j = -6; else j = 6; offset=start; left=MAX(start, context->left); right=MIN(stop, context->right); prim = AddRectangle(seg, left-offset, base, right-offset, base+j, NO_ARROW, FALSE,0); SetPrimitiveIDs(prim, context->entityID, context->itemID, OBJ_SEQFEAT, 2); } static Uint1 Ing_IsTitleAColor(CharPtr title) { if (StringCmp(title, "red") == 0 || StringCmp(title, "green") == 0 || StringCmp(title, "blue")==0 || StringCmp(title, "cyan") == 0 || StringCmp(title, "magenta") == 0 || StringCmp(title, "yellow") == 0 || StringCmp(title, "grey") == 0 || StringCmp(title, "purple") == 0 || StringCmp(title, "black") == 0) return TRUE; else return FALSE; } static Boolean LIBCALLBACK Ing_DrawOverviewPage(IngPopFeatPtr pfp, IngContextPtr context) { ValNodePtr tmp_vnp = NULL; Int4 leftmargin; Int4 rightmargin; Uint4 rowNum, featdeftype; Boolean bPop=FALSE; Boolean Visible=FALSE; Uint8 idx; Char str[60]={""}; Int4 feat_len; Int4 pict_len; Int4 offset; Boolean index_by_fdtype = TRUE; IngPkgPtr pkg = NULL; CharPtr title = NULL; SeqFeatPtr sfp = NULL; sfp = context->sfp; if (!pfp || !sfp) return (FALSE); if (context->featdeftype == FEATDEF_misc_feature && !StringHasNoText(sfp->comment) && Ing_IsTitleAColor(sfp->title)) index_by_fdtype = FALSE; leftmargin=pfp->left; offset=pfp->left; rightmargin=pfp->right; pict_len=rightmargin-leftmargin+1; if (!(pfp->nPrims%FEATURE_SEGMENT_MAXSIZE)){ pfp->CurrentSeg=CreateSegment(pfp->pictMain, pfp->nLevel1, 0); pfp->nLevel1++; } AddAttribute(pfp->CurrentSeg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); if (index_by_fdtype) AddAttribute(pfp->CurrentSeg, COLOR_ATT, pfp->pClr[context->featdeftype] , 0, 0, 0, 0); else AddAttribute(pfp->CurrentSeg, COLOR_ATT, pfp->pClr[Ing_GetMiscFeatColor(sfp->title)] , 0, 0, 0, 0); if (!pfp->PopRowsList){ rowNum = 0 ; if (index_by_fdtype){ idx=Ing_BigEncodeIdxFeat(rowNum, context->featdeftype); pfp->vnp_last = ValNodeAddBigInt (&pfp->PopRowsList, OBJ_SEQANNOT, idx); pfp->PopRowsList->data.ptrvalue = NULL; } else { pkg = Ing_EncodeFeatString(rowNum, sfp->title); pfp->vnp_last = ValNodeAddPointer(&pfp->PopRowsList, OBJ_SEQFEAT, pkg); } bPop=FALSE; } else{ tmp_vnp = pfp->PopRowsList; while(tmp_vnp){ if (tmp_vnp->choice == OBJ_SEQANNOT){ Ing_BigDecodeIdxFeat((Uint8)tmp_vnp->data.bigintvalue, &rowNum, &featdeftype); if (context->featdeftype == featdeftype){ bPop = TRUE; break; } } else { Ing_DecodeFeatString(tmp_vnp->data.ptrvalue, &rowNum, &title); if (StringCmp(sfp->title, title) == 0){ bPop = TRUE; break; } } tmp_vnp = tmp_vnp->next; } } if (bPop==FALSE){ rowNum = pfp->nPopRows; if (index_by_fdtype){ idx = Ing_BigEncodeIdxFeat(rowNum,context->featdeftype); pfp->vnp_last = ValNodeAddBigInt (&pfp->vnp_last, OBJ_SEQANNOT, idx); } else { pkg = Ing_EncodeFeatString(rowNum, sfp->title); pfp->vnp_last = ValNodeAddPointer(&pfp->vnp_last, OBJ_SEQFEAT, (Pointer)pkg); } pfp->nPopRows++; FeatDefLabel(sfp, str, sizeof(str)-1, OM_LABEL_TYPE); if (Ing_IsTitleAColor(sfp->title) && sfp->comment) StringCat(str, sfp->comment); AddLabel(pfp->pictMain, -15, (rowNum)*(-20)+6, str, SMALL_TEXT, 0, UPPER_RIGHT, 0); AddLine(pfp->CurrentSeg, 0, (rowNum)*(-20), pict_len, (rowNum)*(-20), 0, 0); pfp->nPopRows++; } Ing_AddToOverviewPict(pfp->CurrentSeg, context, leftmargin, rightmargin, rowNum*(-20)); pfp->nPrims++; return (TRUE); } static int LIBCALLBACK Ing_SortByChoice (VoidPtr ptr1, VoidPtr ptr2) { ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; if (vnp1->choice > vnp2->choice) { return 1; } else if (vnp1->choice < vnp2->choice) { return -1; } return 0; } static Boolean LIBCALLBACK Ing_CollectFeatures1(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) { IngPopFeatPtr pfp = NULL; IngContextPtr context = NULL; Int4 feat_len; Boolean index_by_fdtype = TRUE; Int4 scaledLen; Int4 scale; pfp = (IngPopFeatPtr)sfc->userdata; if (!pfp) return (FALSE); if (sfc->featdeftype == FEATDEF_misc_feature && !StringHasNoText(sfp->comment) && Ing_IsTitleAColor(sfp->title)) index_by_fdtype = FALSE; feat_len=sfc->right-sfc->left; scale=pfp->scaleX; if (scale>COMPRESS_SCALE){ scaledLen=feat_len/scale; if (index_by_fdtype){ if (scaledLen<2 && IngfeatDefTrack2[sfc->featdeftype]) return (TRUE); else IngfeatDefTrack2[sfc->featdeftype]=TRUE; } } context = (IngContextPtr)MemNew(sizeof(IngContext)); context->left = sfc->left; context->right = sfc->right; context->featdeftype = sfc->featdeftype; context->sfp = sfc->sfp; context->strand = sfc->strand; context->entityID = sfc->entityID; context->itemID = sfc->itemID; if (!pfp->group1) pfp->group1_last = ValNodeAddPointer(&pfp->group1, sfc->featdeftype, (Pointer)context); else pfp->group1_last = ValNodeAddPointer(&pfp->group1_last, sfc->featdeftype, (Pointer)context); return (TRUE); } static Boolean LIBCALLBACK Ing_CollectFeatures2(SeqFeatPtr sfp, SeqMgrFeatContextPtr sfc) { IngPopFeatPtr pfp = NULL; IngContextPtr context = NULL; Int4 numivals = 0, i; ValNodePtr desc; pfp = (IngPopFeatPtr)sfc->userdata; if (!pfp) return (FALSE); IngfeatDefTrack[sfc->featdeftype] = 2; context = (IngContextPtr)MemNew(sizeof(IngContext)); context->left = sfc->left; context->right = sfc->right; context->featdeftype = sfc->featdeftype; context->sfp = sfc->sfp; context->strand = sfc->strand; context->entityID = sfc->entityID; context->itemID = sfc->itemID; numivals = sfc->numivals; if (numivals > 1){ context->ivals = (Int4Ptr)MemNew(sizeof(Int4)*numivals*2); for (i = 0; i < (numivals*2); i++) context->ivals[i] = sfc->ivals[i]; context->numivals = numivals; } else { context->numivals = 0; } if (sfc->sap->name != NULL){ /* feature was read into file */ context->name = sfc->sap->name; if (!pfp->group3) pfp->group3_last = ValNodeAddPointer(&pfp->group3, sfc->featdeftype, (Pointer)context); else pfp->group3_last = ValNodeAddPointer(&pfp->group3_last, sfc->featdeftype, (Pointer)context); } else if (sfc->featdeftype < 7){ if (!pfp->group1) pfp->group1_last = ValNodeAddPointer(&pfp->group1, sfc->featdeftype, (Pointer)context); else pfp->group1_last = ValNodeAddPointer(&pfp->group1_last, sfc->featdeftype, (Pointer)context); } else { if (!pfp->group2) pfp->group2_last = ValNodeAddPointer(&pfp->group2, sfc->featdeftype, (Pointer)context); else pfp->group2_last = ValNodeAddPointer(&pfp->group2_last, sfc->featdeftype, (Pointer)context); } return (TRUE); } extern Uint4 Ing_PopOverviewPage(BioseqPtr bsp, SegmenT pictTop, Int4 left, Int4 right, Uint1Ptr PNTR pClr, Int4 maxScaleX, IngTrackAlignsPtr tap) { IngPopFeat pf; Uint2 entityID; Int4 i; SeqEntryPtr sep; SeqAnnotPtr sanp=NULL; SeqAlignPtr sap=NULL; SeqLocPtr slp=NULL, whole_slp=NULL; Uint4 nPopRows=0; IngSeqAnnotData sad; SegmenT CurrentSeg; Char buf[50]={""}; Int4 margin, len; Int4 start=0; ValNodePtr slp_list=NULL, slp_head=NULL; ValNodePtr slp_cur = NULL; ValNodePtr vnp = NULL; Uint1Ptr Clr=NULL; CharPtr PNTR names = NULL; Boolean bUpdate = FALSE; IngContextPtr context = NULL; whole_slp=SeqLocIntNew(left, right, Seq_strand_plus, (SeqIdPtr)bsp->id); if (maxScaleX>COMPRESS_SCALE){ start=left; len=right; while (start < len){ slp=SeqLocIntNew(start, start+maxScaleX, Seq_strand_plus, (SeqIdPtr)bsp->id); if (slp_list == NULL) slp_cur = ValNodeAddPointer(&slp_list, OBJ_BIOSEQ, (Pointer)slp); else slp_cur = ValNodeAddPointer(&slp_cur, OBJ_BIOSEQ, (Pointer)slp); start+=maxScaleX; } slp=SeqLocIntNew(start, len-1, Seq_strand_plus, (SeqIdPtr)bsp->id); if (slp_list == NULL) ValNodeAddPointer(&slp_list, OBJ_BIOSEQ, (Pointer)slp); else ValNodeAddPointer(&slp_cur, OBJ_BIOSEQ, (Pointer)slp); MemSet(&pf,0,sizeof(pf)); pf.pictMain=pictTop; pf.pClr=pClr; pf.scaleX=maxScaleX; pf.nPrims=0; pf.nLevel1=1; pf.left=left; pf.right=right; pf.group1 = NULL; pf.group1_last = NULL; pf.PopRowsList=NULL; pf.vnp_last = NULL; slp_head=slp_list; while(slp_list){ slp=slp_list->data.ptrvalue; MemSet((Pointer)IngfeatDefTrack2, 0, sizeof(IngfeatDefTrack2)); SeqMgrExploreFeatures (bsp, (Pointer) &pf, Ing_CollectFeatures2, slp, NULL,IngfeatDefFilter); slp_list=slp_list->next; SeqLocFree(slp); } ValNodeFree(slp_head); } else { MemSet(&pf,0,sizeof(pf)); pf.pictMain=pictTop; pf.pClr=pClr; pf.scaleX=maxScaleX; pf.nPrims=0; pf.nLevel1=1; pf.left=left; pf.right=right; pf.PopRowsList=NULL; pf.group1 = NULL; pf.group1_last = NULL; pf.group2 = NULL; pf.group2_last = NULL; pf.group3 = NULL; pf.group3_last = NULL; SeqMgrExploreFeatures (bsp, (Pointer) &pf,Ing_CollectFeatures2, whole_slp, NULL,IngfeatDefFilter); } /* vnp = ValNodeSort(pf.group1, Ing_SortByChoice); */ if (pf.group1) { for (vnp = pf.group1; vnp != NULL; vnp = vnp->next){ context = (IngContextPtr)vnp->data.ptrvalue; Ing_DrawOverviewPage(&pf, context); Ing_FreeContext(context); } ValNodeFree (pf.group1); pf.group1 = NULL; pf.group1_last = NULL; } if (pf.group2){ for (vnp = pf.group2; vnp != NULL; vnp = vnp->next){ context = (IngContextPtr)vnp->data.ptrvalue; Ing_DrawOverviewPage(&pf, context); Ing_FreeContext(context); } ValNodeFree (pf.group2); pf.group2 = NULL; pf.group2_last = NULL; } if (pf.group3){ for (vnp = pf.group3; vnp != NULL; vnp = vnp->next){ context = (IngContextPtr)vnp->data.ptrvalue; Ing_DrawOverviewPage(&pf, context); Ing_FreeContext(context); } ValNodeFree(pf.group3); pf.group3 = NULL; pf.group3_last = NULL; } if (pf.PopRowsList) ValNodeFree(pf.PopRowsList); pf.PopRowsList = NULL; nPopRows = pf.nPopRows; pf.nLevel1++; CurrentSeg=CreateSegment(pictTop, pf.nLevel1, 0); if (IngfeatDefFilter[0]){ entityID=ObjMgrGetEntityIDForPointer(bsp); sep = GetTopSeqEntryForEntityID(entityID); if (tap && tap->update){ sad.sindex= tap->showindex; sad.hindex= tap->hideindex; sad.aln_showlist = tap->showlist; sad.aln_namelist = tap->namelist; sad.aln_hidelist = tap->hidelist; sad.aln_hnamelist = tap->hnamelist; bUpdate = TRUE; } else if (!tap){ sad.sindex = 0; sad.hindex= 0; sad.aln_showlist = NULL; sad.aln_namelist = NULL; sad.aln_hidelist = NULL; sad.aln_hnamelist = NULL; bUpdate = TRUE; } if (bUpdate){ sad.tap = tap; SeqEntryExplore(sep,(Pointer)&sad, Ing_SearchAli); if (tap){ tap->namelist = sad.aln_namelist; tap->showlist = sad.aln_showlist; tap->hidelist = sad.aln_hidelist; tap->hnamelist = sad.aln_hnamelist; tap->showindex = sad.sindex; tap->hideindex = sad.hindex; tap->update = FALSE; } vnp = sad.aln_showlist; names = sad.aln_namelist; } else { vnp = tap->showlist; names = tap->namelist; } if (!vnp) goto end; IngfeatDefTrack[0]=2; i=0; len=right-left+1; margin=10*maxScaleX; while (vnp){ sap=(SeqAlignPtr)vnp->data.ptrvalue; if (sap->segtype!=SAS_DISC && StringCmp(names[i], "Spidey")==0) goto skipindex; AMAlignIndexFreeEitherIndex(sap); AlnMgr2IndexLite(sap); AlnMgr2SortAlnSetByNthRowPos(sap, 1); skipindex: AssignIDsInEntity(entityID, OBJ_SEQALIGN, (Pointer)sap); Clr=Ing_GetAlignColor(names[i], pClr); nPopRows=Ing_AddAlignsToOverviewPage(pictTop, CurrentSeg, 0, pf.nLevel1, sep, sap, nPopRows, left, right, names[i], Clr); vnp=vnp->next; nPopRows+=2; i++; } } end: SeqLocFree(whole_slp); return (nPopRows); } /******************************************************************************* Function : Ing_PopDetailedPage(), Ing_AddToDetailedPage(), Ing_AddToDetailedPict(), Ing_AddAlignsToDetailedPage(), Ing_AddOneAlignToDetailedPage() Purpose : Bottom (Detailed) viewer drawing functions *******************************************************************************/ static void Ing_AddOneAlignToDetailedPage(SegmenT seg, SeqAlignPtr sap, Int4 row, Int4 start, Int4 stop, Int4 offset, Int4 scale, Uint2 alignID) { Uint1 strand; Int4 i=0; PrimitivE prim; Int4 numivals; AlnMsg2Ptr amp1 = NULL; AlnMsg2Ptr amp2 = NULL; SegmenT subSeg; Boolean more; Uint1 ARROW=NO_ARROW; Int4 half; half = Ing_FEAT_HEIGHT/2; strand=AlnMgr2GetNthStrand(sap, 2); numivals= AlnMgr2GetNumSegs(sap); if (numivals>1){ subSeg=CreateSegment(seg, alignID, 0); 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; i=1; while((Boolean) (more = AlnMgr2GetNextAlnBit(sap, amp2))){ AlnMgr2GetNextAlnBit(sap, amp1); if (amp2->type == AM_SEQ){ if (scalefrom_row>stop || amp1->to_rowfrom_row)-offset, (row)*(-20), MIN(stop, amp1->to_row)-offset, (row)*(-20)-Ing_FEAT_HEIGHT, ARROW, TRUE,0); SetPrimitiveIDs(prim, sap->idx.entityID, sap->idx.itemID, OBJ_SEQALIGN, 0); } i++; } AlnMsgFree2(amp1); AlnMsgFree2(amp2); AddLine(subSeg, start-offset, (row)*(-20)-half, stop-offset, (row)*(-20)-half, 0, 0); } else { if (scaleidx.entityID, sap->idx.itemID, OBJ_SEQALIGN, alignID); } } static Uint4 Ing_NextExon(Uint4 exon, Uint1 strand) { if (strand==Seq_strand_plus) exon++; else exon--; return exon; } /* typedef struct ing_rowdata{ Int4 index; Int4 start_row; Int4Ptr cols; }IngRowData, PNTR IngRowDataPtr; static IngRowDataPtr rdp = NULL; static Boolean Ing_WhichRow(Int4 from, Int4 to, Uint4Ptr rowp) { Int4 i, index; Int4Ptr cols, tmp; if (!rdp) return -1; index = rdp->index + 1; cols = rdp->cols; for (i = 0; i < index; i++){ if (cols[i] < from){ cols[i] = to; *rowp = (Uint4)rdp->start_row + i; return (TRUE); } } tmp = (Int4Ptr)MemNew(sizeof(Int4)*index+1); for (i = 0; i < index; i++){ tmp[i] = cols[i]; } tmp[index] = to; rdp->cols = tmp; rdp->index++; MemFree(cols); return (FALSE); } */ static Uint4 Ing_AddAlignsToDetailedPage(SegmenT pictBottom, IngPopFeatPtr pfp, SeqEntryPtr sep, SeqAlignPtr sap, Uint4 rowNum, Int4 left, Int4 right, Uint1Ptr Clr, Uint4 scaleX, CharPtr name, Uint2 alignID, Boolean isExons) { Char buf[41]={""}; Char label[41]={""}; Uint4 top, bottom; enumPrimAddOrder oldOrder; SeqIdPtr sip=NULL; Uint8 idx; Boolean NewLine=FALSE; Uint4 rowCnt=0; Uint4 ColStart; Int4 start, stop; Int4 i; AMAlignIndex2Ptr amaip=NULL; Int4 len; Int4 len_diff; Int4 bExonlabels=FALSE; Int4 label_len; Int4 feat_len; Boolean labels=TRUE; Boolean bDraw = FALSE; Boolean bOver_the_edge = FALSE; Boolean bSaved = FALSE, bTrim = FALSE; Int4 offset; Uint4 exon=0; Uint1 strand=0; SegmenT CurrentSeg=NULL; ValNodePtr vnp_head = NULL; ValNodePtr tmp_vnp = NULL; ValNodePtr vnp_half = NULL; ValNodePtr vnp_cur = NULL; amaip = (AMAlignIndex2Ptr)(sap->saip); if (!amaip) return rowNum; len=right-left+1; offset=left; if ((StringCmp(name, "Spidey")==0) && isExons){ bExonlabels=TRUE; strand=AlnMgr2GetNthStrand(amaip->saps[0], 2); if (strand==Seq_strand_minus) exon=amaip->numsaps; else exon=1; } if (scaleX > LABELS_SCALE) labels=FALSE; oldOrder=ChangeAddPrimOrder(ADD_TO_HEAD); top=(rowNum)*(-20); rowNum++; rowCnt=rowNum; for(i=0; inumsaps; i++){ AlnMgr2GetNthSeqRangeInSA(amaip->saps[i], 1, &start, &stop); if (start>right || stopshowLabels) { /* SetSmallFont(); */ if (bExonlabels){ sprintf(label, "Exon %u", exon); exon = Ing_NextExon(exon, strand); } else { sip=AlnMgr2GetNthSeqIdPtr(amaip->saps[i], 2); SeqIdWrite(sip, buf, PRINTID_REPORT, 41); sprintf(label,"gi|%s", buf); } label_len=(StringWidth(label)+2)*scaleX; feat_len=stop-start-1; if (feat_lendata.bigintvalue, &rowCnt, &ColStart); if (ColStart < MAX(0, start-len_diff)){ ColStart=stop+len_diff; tmp_vnp->data.bigintvalue=Ing_BigEncodeIdxFeat(rowCnt,ColStart); NewLine=FALSE; break; } tmp_vnp=tmp_vnp->next; } } if (NewLine){ rowNum++; ColStart=stop+len_diff; idx=Ing_BigEncodeIdxFeat(rowNum, ColStart); vnp_cur = ValNodeAddBigInt(&vnp_cur, 5, idx); /* start triming list(#rows) if it grows beyond 100 */ if (!(rowCnt % 10)){ if (!(rowCnt % 120)) bTrim = TRUE; if (!bSaved){ vnp_half = vnp_cur; bSaved = TRUE; } else if (bTrim){ vnp_half->next = NULL; ValNodeFree(vnp_head); vnp_head = vnp_cur; bSaved = FALSE; } } rowCnt=rowNum; } if (labels && pfp->showLabels){ AddAttribute(CurrentSeg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); if (bOver_the_edge) AddLabel(CurrentSeg, start - offset, rowCnt*(-20), label, SMALL_TEXT, 0, UPPER_RIGHT, 0); else AddLabel (CurrentSeg, start - offset + (stop-start)/2, rowCnt*(-20), label, SMALL_TEXT, 0, UPPER_CENTER, 0); } AddAttribute(CurrentSeg, COLOR_ATT, Clr, 0, 0, 0, 0); Ing_AddOneAlignToDetailedPage(CurrentSeg, amaip->saps[i], (Int4)rowCnt, start, stop, offset, scaleX, alignID); pfp->nPrims++; NewLine = TRUE; bDraw = TRUE; } if (bDraw){ CurrentSeg = Ing_GetCurrentSegment(pfp); if (!CurrentSeg) return (FALSE); AddAttribute(CurrentSeg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); if (StringHasNoText(name)) sprintf(label, "Alignment"); else { sprintf(label, "%s", name); } AddAttribute(CurrentSeg, COLOR_ATT, BLUE_COLOR, 0, 0, 0, 0); AddLabel(CurrentSeg, (len/2)+(10*scaleX), top+6, label, SMALL_TEXT, 0, UPPER_CENTER, 0); rowNum++; bottom=(rowNum)*(-20); AddAttribute(CurrentSeg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); AddRectangle(CurrentSeg, (-10)*scaleX, top, len+(10*scaleX), bottom, NO_ARROW, FALSE,0); ChangeAddPrimOrder(oldOrder); } else { rowNum-=3; } return rowNum; } static void Ing_AddToDetailedPict(SegmenT Seg, IngContextPtr context, Int4 yBase, Uint4Ptr subSegID, Int4 start, Int4 stop, Int4 scale) { PrimitivE prim; Int4 left_end, right_end; Uint1 strand; Int4 fhalf; Int4 numivals, max, i; Int4 left, right; Int4Ptr ivals; SegmenT subSeg; SeqFeatPtr sfp; Uint1 ARROW=NO_ARROW; Int4 offset; if (Seg == NULL || context == NULL) return; fhalf=Ing_FEAT_HEIGHT/2; strand=context->strand; offset=start; left=MAX(start, context->left); right=MIN(stop, context->right); ivals=context->ivals; numivals=context->numivals; if (numivals>1){ subSeg=CreateSegment(Seg, *subSegID, 0); (*subSegID)++; sfp=(SeqFeatPtr)context->sfp; /* draw a line thought segmented feature */ left_end=(strand == Seq_strand_minus ? ivals[2*numivals-1] : ivals[0]); right_end=(strand == Seq_strand_minus ? ivals[0] : ivals[2*numivals-1]); if (!(right_end < offset)){ left_end=MAX(left_end, offset); prim=AddLine(subSeg, left_end-offset, yBase-fhalf, right_end-offset, yBase-fhalf, FALSE, 0); SetPrimitiveIDs(prim, context->entityID, context->itemID, sfp->idx.itemtype, 0); } /* far left ivals */ left_end=(strand == Seq_strand_minus ? ivals[2*numivals-1] : ivals[0]); right_end=(strand == Seq_strand_minus ? ivals[2*numivals-2] : ivals[1]); if (!(right_end < offset)){ left_end=MAX(left_end, offset); if (scale < ARROWS_SCALE){ ARROW = (strand == Seq_strand_minus)?LEFT_ARROW:NO_ARROW; } else { ARROW = NO_ARROW; } prim = AddRectangle(subSeg, left_end-offset, yBase, right_end-offset, yBase-Ing_FEAT_HEIGHT, ARROW, TRUE, 0); SetPrimitiveIDs(prim, context->entityID, context->itemID, sfp->idx.itemtype, 0); } /* middle ivals */ if (numivals>2){ if (strand==Seq_strand_minus){ for (i = 2*numivals-4 ; i > 1 ; i -= 2){ left_end=MIN(ivals[i], ivals[i+1]); right_end=MAX(ivals[i], ivals[i+1]); if ((!(left_endstop && right_end>stop))){ prim = AddRectangle(subSeg,MAX(start, left_end)-offset, yBase, MIN(stop, right_end)-offset,yBase-Ing_FEAT_HEIGHT,NO_ARROW,TRUE,0); SetPrimitiveIDs(prim, context->entityID, context->itemID, sfp->idx.itemtype, 0); } } } else{ max=2*numivals-2; for (i = 2 ; i < max ; i += 2){ left_end=MIN(ivals[i], ivals[i+1]); right_end=MAX(ivals[i], ivals[i+1]); if ((!(left_endstop && right_end>stop))){ prim = AddRectangle(subSeg, MAX(start, left_end)-offset,yBase, MIN(stop, right_end)-offset, yBase-Ing_FEAT_HEIGHT, NO_ARROW, TRUE, 0); SetPrimitiveIDs(prim, context->entityID, context->itemID, sfp->idx.itemtype, 0); } } } } /* far right ivals*/ left_end=(strand == Seq_strand_minus ? ivals[0] : ivals[2*numivals-2]); right_end=(strand == Seq_strand_minus ?ivals[1] : ivals[2*numivals-1]); if (!(left_end>right && right_end>right)){ if (scale < ARROWS_SCALE){ ARROW = (strand == Seq_strand_minus)?NO_ARROW:RIGHT_ARROW; } else { ARROW = NO_ARROW; } prim = AddRectangle(subSeg, MAX(start, left_end)-offset, yBase, MIN(stop, right_end)-offset, yBase-Ing_FEAT_HEIGHT, ARROW, TRUE, 0); SetPrimitiveIDs(prim, context->entityID, context->itemID, sfp->idx.itemtype, 0); } } else { if (scale < ARROWS_SCALE){ prim = AddRectangle(Seg, left-offset, yBase, right-offset, yBase-Ing_FEAT_HEIGHT, (strand == Seq_strand_minus ?LEFT_ARROW:RIGHT_ARROW), TRUE, 0); } else { prim= AddRectangle(Seg, left-offset, yBase, right-offset, yBase-2, NO_ARROW, TRUE, 0); } SetPrimitiveIDs(prim, context->entityID, context->itemID, OBJ_SEQFEAT, OBJ_SEQFEAT); } } static void Ing_DrawDetailedPage(IngPopFeatPtr pfp, IngContextPtr context) { ValNodePtr tmp_vnp = NULL; Int4 leftmargin; Int4 rightmargin; Int4 left; Int4 right; Uint4 rowNum; Boolean bPop=FALSE; Uint8 idx; Uint4 ColStart; Char str[60]={""}; Int4 scaleX; Int4 label_len, len_diff; Int4 feat_len; Boolean labels=TRUE; Boolean over_the_edge=FALSE; SegmenT CurrentSeg=NULL; SeqFeatPtr sfp = NULL; sfp = context->sfp; if (!pfp || !sfp) return; scaleX=pfp->scaleX; leftmargin=pfp->left; rightmargin=pfp->right; left=MAX(leftmargin, context->left); right=MIN(rightmargin, context->right); feat_len=right-left; if (scaleX>LABELS_SCALE){ labels=FALSE; } if (labels && pfp->showLabels){ FeatDefLabel (sfp, str, sizeof (str) - 1, OM_LABEL_CONTENT); label_len=(StringWidth(str))*scaleX; if (label_len > feat_len){ if ((left - (label_len - feat_len)/2)<0) over_the_edge = TRUE; if (over_the_edge) len_diff = ((label_len - feat_len)+scaleX); else len_diff= ((label_len-feat_len)/2)+(1*scaleX); } else len_diff=1*scaleX; } else{ len_diff=1*scaleX; } CurrentSeg=Ing_GetCurrentSegment(pfp); if (!CurrentSeg) return; if (context->featdeftype == FEATDEF_misc_feature && !StringHasNoText(sfp->comment) && Ing_IsTitleAColor(sfp->title)){ AddAttribute(pfp->CurrentSeg, COLOR_ATT, pfp->pClr[Ing_GetMiscFeatColor(sfp->title)] , 0, 0, 0, 0); } else { AddAttribute(pfp->CurrentSeg, COLOR_ATT, pfp->pClr[context->featdeftype] , 0, 0, 0, 0); } if (!pfp->PopRowsList){ rowNum = pfp->nPopRows; ColStart=context->right+len_diff; idx=Ing_BigEncodeIdxFeat(rowNum, ColStart); pfp->vnp_last = ValNodeAddBigInt (&pfp->PopRowsList, 5, idx); bPop=TRUE; pfp->nPopRows++; } else{ tmp_vnp=pfp->PopRowsList; while(tmp_vnp){ Ing_BigDecodeIdxFeat((Uint8)tmp_vnp->data.bigintvalue,&rowNum,&ColStart); if (ColStart < MAX(0, left-len_diff)){ ColStart=context->right+len_diff; tmp_vnp->data.bigintvalue=Ing_BigEncodeIdxFeat(rowNum,ColStart); bPop=TRUE; break; } tmp_vnp = tmp_vnp->next; } } if (bPop==FALSE){ rowNum = pfp->nPopRows; ColStart=context->right+len_diff; idx = Ing_BigEncodeIdxFeat(rowNum, ColStart); pfp->vnp_last = ValNodeAddBigInt (&pfp->vnp_last, 5, idx); /* start triming list(#rows) if it grows beyond 100 */ if (!(rowNum % 10)){ if (!(rowNum % 120)) pfp->bTrim = TRUE; if (!pfp->bSaved){ pfp->vnp_top10 = pfp->vnp_last; pfp->bSaved = TRUE; } else if (pfp->bTrim){ pfp->vnp_top10->next = NULL; ValNodeFree(pfp->PopRowsList); pfp->PopRowsList = pfp->vnp_last; pfp->bSaved = FALSE; } } pfp->nPopRows++; } Ing_AddToDetailedPict(pfp->CurrentSeg, context, rowNum*(-20), &pfp->nSegs, leftmargin, rightmargin, scaleX); if (labels && pfp->showLabels){ AddAttribute(pfp->CurrentSeg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); if (over_the_edge) AddLabel (pfp->CurrentSeg, left -leftmargin, rowNum*(-20), str, SMALL_TEXT, 0, UPPER_RIGHT, 0); else AddLabel (pfp->CurrentSeg, left -leftmargin + (right-left)/2, rowNum*(-20), str, SMALL_TEXT, 0, UPPER_CENTER, 0); } pfp->nPrims++; return; } extern Uint4 Ing_PopDetailedPage(BioseqPtr bsp, SegmenT pictBottom, Int4 left, Int4 right, Uint1Ptr PNTR pClr, Int4 scaleX, Int4 start_row, Boolean Labels, Boolean isExons, IngTrackAlignsPtr tap) { IngPopFeat pf; Uint2 entityID; SeqEntryPtr sep; ValNodePtr vnp=NULL; SeqAlignPtr sap=NULL; SeqLocPtr slp=NULL; Uint4 nPopRows=0; Int4 i; Int4 alignID; Int4 top = 0; Int4 len; IngSeqAnnotData sad; SegmenT CurrentSeg=NULL; Uint1Ptr Clr=NULL; CharPtr PNTR names = NULL; Boolean bUpdate = FALSE; IngContextPtr context = NULL; enumPrimAddOrder oldOrder; memset(&pf,0,sizeof(pf)); pf.pictMain=pictBottom; pf.pClr=pClr; pf.scaleX=scaleX; pf.nPrims=0; pf.nLevel1=0; pf.nLevel2=0; pf.nLevel3=0; pf.left=left; pf.right=right; pf.showLabels=Labels; pf.bSaved = FALSE; pf.bTrim = FALSE; pf.nPopRows=start_row; pf.PopRowsList = NULL; pf.group1 = NULL; pf.group1_last = NULL; pf.group2 = NULL; pf.group2_last = NULL; pf.group3 = NULL; pf.group3_last = NULL; pf.vnp_top10 = NULL; pf.vnp_last = NULL; slp=SeqLocIntNew(left, right, Seq_strand_plus, (SeqIdPtr)bsp->id); SeqMgrExploreFeatures (bsp, (Pointer) &pf,Ing_CollectFeatures2, slp, NULL, IngfeatDefFilter); if (pf.group1) { for (vnp = pf.group1; vnp != NULL; vnp = vnp->next){ context = (IngContextPtr)vnp->data.ptrvalue; Ing_DrawDetailedPage(&pf, context); Ing_FreeContext(context); } ValNodeFree (pf.group1); pf.group1 = NULL; pf.group1_last = NULL; } if (pf.PopRowsList) ValNodeFree(pf.PopRowsList); pf.PopRowsList = NULL; if (pf.group2){ for (vnp = pf.group2; vnp != NULL; vnp = vnp->next){ context = (IngContextPtr)vnp->data.ptrvalue; Ing_DrawDetailedPage(&pf, context); Ing_FreeContext(context); } ValNodeFree (pf.group2); pf.group2 = NULL; pf.group2_last = NULL; } if (pf.PopRowsList) ValNodeFree(pf.PopRowsList); pf.PopRowsList = NULL; if (pf.group3){ top = pf.nPopRows; pf.nPopRows++; oldOrder=ChangeAddPrimOrder(ADD_TO_HEAD); for (vnp = pf.group3; vnp != NULL; vnp = vnp->next){ context = (IngContextPtr)vnp->data.ptrvalue; Ing_DrawDetailedPage(&pf, context); Ing_FreeContext(context); } len = right-left+1; ValNodeFree(pf.group3); pf.group3 = NULL; pf.group3_last = NULL; AddAttribute(pictBottom, COLOR_ATT, BLUE_COLOR, 0, 0, 0, 0); AddLabel(pictBottom, len/2 + (10*scaleX), top*(-20), context->name, SMALL_TEXT, 0, UPPER_CENTER, 0); AddAttribute(pictBottom, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); AddRectangle(pictBottom, (-10)*scaleX, top*(-20), len+(10*scaleX), pf.nPopRows*(-20), NO_ARROW, FALSE,0); ChangeAddPrimOrder(oldOrder); } if (pf.PopRowsList) ValNodeFree(pf.PopRowsList); pf.PopRowsList = NULL; CurrentSeg=CreateSegment(pictBottom,pf.nLevel1+1, 0); nPopRows=pf.nPopRows; /* get alignments */ if (IngfeatDefFilter[0]){ nPopRows+=2; entityID=ObjMgrGetEntityIDForPointer(bsp); sep = GetTopSeqEntryForEntityID(entityID); if (tap && tap->update){ sad.sindex= tap->showindex; sad.hindex= tap->hideindex; sad.aln_showlist = tap->showlist; sad.aln_namelist = tap->namelist; sad.aln_hidelist = tap->hidelist; sad.aln_hnamelist = tap->hnamelist; bUpdate = TRUE; } else if (!tap){ sad.sindex = 0; sad.hindex= 0; sad.aln_showlist = NULL; sad.aln_namelist = NULL; sad.aln_hidelist = NULL; sad.aln_hnamelist = NULL; bUpdate = TRUE; } if (bUpdate){ sad.tap = tap; SeqEntryExplore(sep,(Pointer)&sad, Ing_SearchAli); vnp = sad.aln_showlist; names = sad.aln_namelist; if (tap){ tap->namelist = sad.aln_namelist; tap->showlist = sad.aln_showlist; tap->hidelist = sad.aln_hidelist; tap->hnamelist = sad.aln_hnamelist; tap->showindex = sad.sindex; tap->hideindex = sad.hindex; tap->update = FALSE; } } else { vnp = tap->showlist; names = tap->namelist; } if (!vnp) goto end; IngfeatDefTrack[0]=2; i=0; alignID=1; /* alignID is same as segID in Spidey Report */ while(vnp){ sap=(SeqAlignPtr)vnp->data.ptrvalue; AMAlignIndexFreeEitherIndex(sap); AlnMgr2IndexLite(sap); AlnMgr2SortAlnSetByNthRowPos(sap, 1); AssignIDsInEntity(entityID, OBJ_SEQALIGN, (Pointer)sap); Clr=Ing_GetAlignColor(names[i], pClr); nPopRows=Ing_AddAlignsToDetailedPage(pictBottom, &pf, sep, sap, nPopRows, left, right, Clr, scaleX, names[i], alignID, isExons); nPopRows+=2; i++; alignID++; vnp=vnp->next; } } end: SeqLocFree(slp); return (nPopRows); } /******************************************************************************* Function : Ing_GetValue() Purpose : returns int value given TexT *******************************************************************************/ extern Int4 Ing_GetValue (TexT t) { Char str[20]; Int4 val; GetTitle (t, str, sizeof(str)); if (StringHasNoText(str)) { ErrPostEx (SEV_WARNING, 0, 0, "%s", "missing parameter(s)"); return 0; } val=atoi(str); return val; } /***************************************************************************** Function: Ing_PutColor(), Ing_FreeColor(), Ing_BuildColorTable(), Ing_FreeColorTable(), Ing_GetMiscFeatColor(), Purpose: color functions *****************************************************************************/ extern Uint1Ptr Ing_PutColor(Uint1 r, Uint1 g, Uint1 b) { Uint1Ptr Clr; Clr = (Uint1Ptr)MemNew(sizeof(Uint1)*3); Clr[0]=r; Clr[1]=g; Clr[2]=b; return (Clr); } static Uint1Ptr Ing_FreeColor(Uint1Ptr Clr) { MemFree(Clr); return NULL; } static Uint1 Ing_GetMiscFeatColor(CharPtr str_4) { if (StringCmp(str_4, "red") == 0) return Ing_red; else if (StringCmp(str_4, "green") == 0) return Ing_green; else if (StringCmp(str_4, "blue")==0) return Ing_blue; else if (StringCmp(str_4, "cyan") == 0) return Ing_cyan; else if (StringCmp(str_4, "magenta") == 0) return Ing_magenta; else if (StringCmp(str_4, "yellow") == 0) return Ing_yellow; else if (StringCmp(str_4, "grey") == 0) return Ing_grey; else if (StringCmp(str_4, "purple") == 0) return Ing_purple; return Ing_black; /* default is black */ } extern Uint1Ptr PNTR Ing_BuildColorTable(void) { Uint1Ptr PNTR pClr; pClr=(Uint1Ptr PNTR)MemNew(Ing_MAX*sizeof(Uint1Ptr)); if (!pClr) return(NULL); pClr[FEATDEF_GENE]=Ing_PutColor(204,45,61); /*deep red*/ pClr[FEATDEF_precursor_RNA]=Ing_PutColor(128,128,128);/*grey*/ pClr[FEATDEF_misc_RNA]=Ing_PutColor(128,128,128);/*grey*/ pClr[FEATDEF_preRNA]=Ing_PutColor(128, 128,128);/*grey*/ pClr[FEATDEF_mRNA]=Ing_PutColor(0,127,0);/*green*/ pClr[FEATDEF_tRNA]=Ing_PutColor(224,95,39);/* orange*/ pClr[FEATDEF_rRNA]=Ing_PutColor(157,34, 28);/*sienna*/ pClr[FEATDEF_snRNA]=Ing_PutColor(127,0,0);/* burnt sienna */ pClr[FEATDEF_scRNA]=Ing_PutColor(119,45,0);/*brown*/ pClr[FEATDEF_otherRNA]=Ing_PutColor(128,0,0);/*grey*/ pClr[FEATDEF_prim_transcript]=Ing_PutColor(0,74, 0);/*green*/ pClr[FEATDEF_polyA_signal]=Ing_PutColor(0,174, 0);/*green*/ pClr[FEATDEF_polyA_site]=Ing_PutColor(0,200, 12);/*green*/ pClr[FEATDEF_repeat_region]=Ing_PutColor(114,204,0)/* dk lime *//* (0,155,220) */;/*cyan*/ pClr[FEATDEF_CDS]=Ing_PutColor(235, 150, 235); /*pink*/ pClr[FEATDEF_exon]=Ing_PutColor(192,50,150); /*fuschia */ pClr[FEATDEF_intron]=Ing_PutColor(255,170,170);/* pale pink*/ pClr[FEATDEF_PROT]=Ing_PutColor(0,0,128); /*v dk blue*/ pClr[FEATDEF_mat_peptide]=Ing_PutColor(64, 128, 192);/*pale blue*/ pClr[FEATDEF_sig_peptide]=Ing_PutColor(204,0,61);/* dk red */ pClr[FEATDEF_transit_peptide]=Ing_PutColor(224,224,0);/* lime */ pClr[FEATDEF_preprotein]=Ing_PutColor(0, 19, 127);/*dk blue */ pClr[FEATDEF_mat_peptide_aa]=Ing_PutColor(64, 128, 192);/*pale blue*/ pClr[FEATDEF_sig_peptide_aa]=Ing_PutColor(63, 52, 90);/* indigo */ pClr[FEATDEF_transit_peptide_aa]=Ing_PutColor(224,224,0);/* lime */ pClr[FEATDEF_misc_feature]= Ing_PutColor(210, 154, 14 );/* curry */ pClr[FEATDEF_SITE]=Ing_PutColor(255,0,0); /*red*/ pClr[FEATDEF_REGION]=Ing_PutColor(210,154,14); /*orange*/ pClr[FEATDEF_mutation]=Ing_PutColor(210,154,14); pClr[FEATDEF_variation]=Ing_PutColor(210,154,14); pClr[FEATDEF_PSEC_STR]=Ing_PutColor(104,201,220); /*cyan*/ pClr[FEATDEF_STS]=Ing_PutColor(203, 52, 220); /*pale purple*/ pClr[FEATDEF_HET]=Ing_PutColor(128,128,0); /*yellow*/ pClr[FEATDEF_BOND]=Ing_PutColor(255,92,255); /*pink*/ pClr[FEATDEF_unsure]=Ing_PutColor(104, 0, 40);/* dkred */ pClr[FEATDEF_IMP]=Ing_PutColor(104, 0, 40);/* dkred */ /* user defined */ pClr[Ing_SPIDEY]=Ing_PutColor(0,200,112);/*green*/ pClr[ALIGN_BLAST]=Ing_PutColor(155,145,0); pClr[ALIGN_FILE]=Ing_PutColor(145,155,255); pClr[ALIGN_ANNOT]=Ing_PutColor(255,92,55); pClr[ALIGN_BLAST2SEQ]=Ing_PutColor(25,92,255); pClr[Ing_GENSCAN]=Ing_PutColor(204,45,61)/* (224,224,0) */; pClr[Ing_FEAT_TABLE]=Ing_PutColor(0,224,0); pClr[Ing_TBDL]=Ing_PutColor(0,224,155); /* extras */ pClr[Ing_black]=Ing_PutColor(0,0,0); pClr[Ing_red]=Ing_PutColor(224, 0, 60); pClr[Ing_blue]=Ing_PutColor(0, 0, 255); pClr[Ing_cyan]=Ing_PutColor(0, 235, 245); pClr[Ing_yellow]=Ing_PutColor(235, 245, 0); pClr[Ing_grey]=Ing_PutColor(127, 127, 127); pClr[Ing_green] = Ing_PutColor(0,200,112); pClr[Ing_purple]=Ing_PutColor(163, 52, 190); return(pClr); } extern Uint1Ptr PNTR Ing_FreeColorTable(Uint1Ptr PNTR pClr) { if (!pClr) return(NULL); Ing_FreeColor(pClr[FEATDEF_GENE]); Ing_FreeColor(pClr[FEATDEF_precursor_RNA]); Ing_FreeColor(pClr[FEATDEF_misc_RNA]); Ing_FreeColor(pClr[FEATDEF_preRNA]); Ing_FreeColor(pClr[FEATDEF_mRNA]); Ing_FreeColor(pClr[FEATDEF_tRNA]); Ing_FreeColor(pClr[FEATDEF_rRNA]); Ing_FreeColor(pClr[FEATDEF_snRNA]); Ing_FreeColor(pClr[FEATDEF_scRNA]); Ing_FreeColor(pClr[FEATDEF_otherRNA]); Ing_FreeColor(pClr[FEATDEF_prim_transcript]); Ing_FreeColor(pClr[FEATDEF_polyA_signal]); Ing_FreeColor(pClr[FEATDEF_polyA_site]); Ing_FreeColor(pClr[FEATDEF_repeat_region]); Ing_FreeColor(pClr[FEATDEF_CDS]); Ing_FreeColor(pClr[FEATDEF_exon]); Ing_FreeColor(pClr[FEATDEF_intron]); Ing_FreeColor(pClr[FEATDEF_PROT]); Ing_FreeColor(pClr[FEATDEF_mat_peptide]); Ing_FreeColor(pClr[FEATDEF_sig_peptide]); Ing_FreeColor(pClr[FEATDEF_transit_peptide]); Ing_FreeColor(pClr[FEATDEF_preprotein]); Ing_FreeColor(pClr[FEATDEF_mat_peptide_aa]); Ing_FreeColor(pClr[FEATDEF_sig_peptide_aa]); Ing_FreeColor(pClr[FEATDEF_transit_peptide_aa]); Ing_FreeColor(pClr[FEATDEF_misc_feature]); Ing_FreeColor(pClr[FEATDEF_SITE]); Ing_FreeColor(pClr[FEATDEF_REGION]); Ing_FreeColor(pClr[FEATDEF_mutation]); Ing_FreeColor(pClr[FEATDEF_variation]); Ing_FreeColor(pClr[FEATDEF_PSEC_STR]); Ing_FreeColor(pClr[FEATDEF_STS]); Ing_FreeColor(pClr[FEATDEF_HET]); Ing_FreeColor(pClr[FEATDEF_BOND]); Ing_FreeColor(pClr[FEATDEF_unsure]); Ing_FreeColor(pClr[Ing_ORF]); Ing_FreeColor(pClr[Ing_SPIDEY]); Ing_FreeColor(pClr[ALIGN_BLAST]); Ing_FreeColor(pClr[ALIGN_FILE]); Ing_FreeColor(pClr[ALIGN_ANNOT]); Ing_FreeColor(pClr[ALIGN_BLAST2SEQ]); Ing_FreeColor(pClr[Ing_GENSCAN]); Ing_FreeColor(pClr[Ing_FEAT_TABLE]); Ing_FreeColor(pClr[Ing_TBDL]); Ing_FreeColor(pClr[Ing_black]); Ing_FreeColor(pClr[Ing_red]); Ing_FreeColor(pClr[Ing_blue]); Ing_FreeColor(pClr[Ing_cyan]); Ing_FreeColor(pClr[Ing_yellow]); Ing_FreeColor(pClr[Ing_grey]); Ing_FreeColor(pClr[Ing_purple]); MemFree(pClr); return NULL; } /************************************************* Function : Ing_ExploreSegments() Purpose : draw callback for SeqMgrExploreSegments() **************************************************/ extern Boolean LIBCALLBACK Ing_ExploreSegments(SeqLocPtr slp, SeqMgrSegmentContextPtr context) { IngExploreSegsPtr gpnp; Int4 left,top,right,bottom; Int4 left_ex, right_ex; Uint1 indigo[3], lime[3]; Uint1 orange[3], black[3]; Uint1 strand; GBBlockPtr gbp = NULL; ValNodePtr vnp = NULL; SeqIdPtr sip = NULL; Boolean isDraft = FALSE; Uint2 entityID = 0; Uint2 itemID = 0; OMUserDataPtr omudp; Boolean needs_label = TRUE; orange[0]= 210; orange[1]= 154; orange[2]= 14; black[0] = 0; black[1] = 0; black[2] = 0; indigo[0] = 163; indigo[1] = 52; indigo[2] = 90; lime[0] = 124; lime[1] = 224; lime[2] = 2; gpnp=(IngExploreSegsPtr)context->userdata; if (gpnp->idx) gpnp->idx++; left=context->from; right=context->to-left+context->cumOffset; left=context->cumOffset; if (!(gpnp->left==0 && gpnp->right==0)){ left_ex=gpnp->left; right_ex=gpnp->right; if ((leftright_ex && right>right_ex)){ return (TRUE); } else { left=MAX(left, left_ex)-left_ex; right=MIN(right, right_ex)-left_ex; } } slp = context->slp; strand=SeqLocStrand(slp); if (strand==Seq_strand_minus){ AddAttribute(gpnp->seg, COLOR_ATT, orange, 0, 0, 0, 0); } else{ AddAttribute(gpnp->seg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); } top=gpnp->GrData->SegBoxHeight; if (gpnp->idx % 2) top-=gpnp->GrData->SegBoxHeight; bottom=top-gpnp->GrData->SegBoxHeight; sip = SeqLocId(slp); /* attach seqid to proc*/ if ((sip != NULL) && gpnp->bRegister) { entityID = ObjMgrRegister(OBJ_SEQID, (Pointer)sip); itemID = GetItemIDGivenPointer (entityID, OBJ_SEQID, (Pointer) sip); omudp = ObjMgrAddUserData (entityID, gpnp->procID, OMPROC_VIEW, gpnp->userKey); omudp->messagefunc = gpnp->messagefunc; omudp->userdata.ptrvalue = gpnp->data; omudp->procid = gpnp->procID; } if (gpnp->bLabels == FALSE || gpnp->bTop != FALSE || gpnp->scaleX > SEGMENT_SCALE){ needs_label = FALSE; } Ing_AddGCRect(gpnp->seg, sip, entityID, itemID, OBJ_SEQID, gpnp->seqbuf, left, top, right, bottom, gpnp->scaleX, strand, needs_label, gpnp->bRegister, gpnp->idx, gpnp->bShowGC); return(TRUE); } static void Ing_GetLeftandRight(BioseqPtr bsp, SeqLocPtr slp, Int4Ptr left, Int4Ptr right) { if (slp){ *left=GetOffsetInBioseq(slp, bsp, SEQLOC_LEFT_END); *right=GetOffsetInBioseq(slp, bsp, SEQLOC_RIGHT_END); } else{ *left=0; *right=bsp->length-1; } } extern void Ing_AddGCRect(SegmenT seg, SeqIdPtr sip, Uint2 entityID, Uint2 itemID, Uint2 itemtype, Uint1Ptr seq, Int4 left, Int4 top, Int4 right, Int4 bottom, Int4 scaleX, Uint1 strand, Boolean needs_label, Boolean clickable, Int4 idx, Boolean bShowGC) { Int4 a1, a2; Int4 c1, c2; Int4 g1, g2, t1, t2; Int4 gc_av, at_av, loopexit; Int4 i; Int4 j1, j2; Int4 len, length, start; Int4 n1, n2; FloatHi comp2, comp_prev; FloatHi comp_av; Char szBuf[15]={""}; Int4 pos, temp; Int4 window; Uint1Ptr Clr; PrimitivE prim; Boolean is_loopexit =FALSE; a1 = a2 = c1 = c2 = g1 = g2 = t1 = t2 = n1= n2 = 0; comp2 = comp_av = comp_prev = 0; window= scaleX*2 ; start= left; length=right; if (start>length) { temp=start; start=length; length=temp; } if (needs_label){ if (sip){ /* sip = GetSeqIdForGI(GetGIForSeqId(sip)); */ sip = SeqIdFindBest(sip, SEQID_GENBANK); if (!sip) sip = SeqIdFindBest(sip, 0); SeqIdWrite(sip, szBuf,PRINTID_TEXTID_ACCESSION, 14); } else{ sprintf(szBuf,"%d",idx); } if (idx % 2){ AddLabel (seg, (idx==2 ? left : left+(right-left)/2), bottom, szBuf, SMALL_TEXT, 0, (idx==2 ? LOWER_RIGHT: LOWER_CENTER), 0); } else{ AddLabel (seg, (idx==2 ? left : left+(right-left)/2), top, szBuf, SMALL_TEXT, 0, (idx==2 ? UPPER_RIGHT: UPPER_CENTER), 0); } } if (seq==NULL || !bShowGC){ prim=AddRectangle (seg, left, top , right, bottom , NO_ARROW, TRUE, 0); /* clickable only on bottom panel */ if (clickable) SetPrimitiveIDs(prim, entityID, itemID, itemtype, itemtype); } else{ pos = j1 = j2 = 0; at_av = 0; gc_av = 0; loopexit=length; for (i=start; i165?255:gc_av; /* gc > 65% */ Clr=Ing_PutColor(0, gc_av, 0); if(Clr==NULL) Clr=Ing_PutColor(128, 128, 128); AddAttribute(seg, COLOR_ATT, (Clr?Clr:BLACK_COLOR), 0, 0, 0, 0); prim=AddRectangle (seg, left+(pos-j1), top , left+pos, bottom , 0, TRUE, 0); SetPrimitiveIDs(prim, entityID, itemID, itemtype, idx); MemFree(Clr); a1 = c1 = t1 = g1 = n1 = 0; gc_av = at_av = 0; j1 = 0; } } } } extern void Ing_AddRuler(SegmenT seg, Int4 height, Int4 xstart,Int4 xstop, Int4 scaleX, Int4 scaleY, Boolean add_whitespace) { Int4 pos; Int4 xlen, x, y; Int4 scale_pos, i, j; Int4 bigtick, midtick, smalltick; Int4 line_Y; Int4 pos_2; Int4 pos_10; Int4 yBase; Char scale_buf[35] = {""}; /*scale value*/ Boolean Decrement=FALSE; Int4 label; Int4 SeqLength; if (xstart>xstop) Decrement=TRUE; if (scaleX==0) scaleX=1; if (scaleY==0) scaleY=1; pos=100*scaleX; pos_2=pos/2; pos_10=pos/10; SeqLength=ABS(xstop-xstart)+1; bigtick=10*scaleY; midtick=7*scaleY; smalltick=5*scaleY; label=12*scaleY; line_Y=height+2*bigtick; xlen=ABS(xstop-xstart)+1; yBase = (-10)*FontHeight(); AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); AddLine(seg, 0, line_Y, SeqLength, line_Y, FALSE,-1); if (add_whitespace){ AddAttribute(seg, COLOR_ATT, WHITE_COLOR, 0,0,0,0); AddLine(seg, 0, yBase, SeqLength, yBase, FALSE,0); } sprintf(scale_buf, "len = %d", xlen); AddAttribute(seg, COLOR_ATT, RED_COLOR, 0,0,0,0); AddLabel(seg, xlen+4*scaleY, line_Y, scale_buf, SMALL_TEXT, 0, LOWER_LEFT, 0); AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); if (!Decrement) { for (scale_pos = 0, i=0; scale_pos <= xlen; scale_pos+=pos_10, i+=pos_10) { if (!(scale_pos % pos)) { x = i; y = line_Y; AddLine(seg, x, y, x, y+bigtick, FALSE,-1); if (scale_pos != 0) sprintf(scale_buf, "%d", (scale_pos+xstart)); else sprintf(scale_buf, "1"); AddAttribute(seg, COLOR_ATT, BLUE_COLOR, 0,0,0,0); AddLabel(seg, x, y+label, scale_buf, SMALL_TEXT, 0, UPPER_CENTER, 0); AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); } else if (!(scale_pos % (pos_2))) { x = i; y = line_Y; AddLine(seg, x, y, x, y+midtick, FALSE,-1); } else if (!(scale_pos % (pos_10))) { x = i; y = line_Y; AddLine(seg, x, y, x, y+smalltick, FALSE,-1); } } } else { for (scale_pos = 0, i=0, j=xstart; scale_pos <= xlen; scale_pos+=pos_10, i+=pos_10, j-=pos_10) { if (!(scale_pos % pos)) { x = i; y = line_Y; AddLine(seg, x, y, x, y+bigtick, FALSE,-1); sprintf(scale_buf, "%d", j); AddAttribute(seg, COLOR_ATT, BLUE_COLOR, 0,0,0,0); AddLabel(seg, x, y+label, scale_buf, SMALL_TEXT, 0, UPPER_CENTER, 0); AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0,0,0,0); } else if (!(scale_pos % (pos_2))) { x = i; y = line_Y; AddLine(seg, x, y, x, y+midtick, FALSE,-1); } else if (!(scale_pos % (pos_10))) { x = i; y = line_Y; AddLine(seg, x, y, x, y+smalltick, FALSE,-1); } } } } /******************************************************************************* Function : Ing_InitGrData() Purpose : initialize graphic objects *******************************************************************************/ static FonT Ing_InitFont (void) { FonT f = NULL; #ifdef WIN_MAC f = ParseFont ("Monaco, 9"); #endif #ifdef WIN_MSWIN f = ParseFont ("Courier, 7"); #endif #ifdef WIN_MOTIF f = ParseFont ("fixed, 12"); #endif return (f); } extern void Ing_InitGrData(IngGraphDataPtr gdp) { FonT f = NULL; /*font size*/ /* f = SetSmallFont(); */ f = Ing_InitFont(); if (f==NULL){ gdp->cyChar=16; gdp->cxChar=8; } else{ SelectFont(f); gdp->hFnt = f; gdp->cxChar=MaxCharWidth(); gdp->cyChar=LineHeight(); } /*values used to draw the rulers*/ gdp->SegBoxHeight=gdp->cyChar/2; gdp->SegRulerTick=gdp->cyChar/2; gdp->SegRulerIn=3; /*colors*/ gdp->pClr=Ing_BuildColorTable(); } /******************************************************************************* Function : Ing_PopulateSequinGraphic() Purpose : populate sequin viewer *******************************************************************************/ extern SegmenT Ing_PopulateSequinGraphic(SegmenT seg, BioseqPtr bsp, Uint2 entityID, Uint2 itemID, Int4 scaleX) { IngExploreSegs gpn; Int2 nSegments; PrimitivE prim; IngGraphData GrData; Int4 left, right; WatchCursor(); Ing_InitGrData(&GrData); Ing_InitfeatDefFilter(); gpn.seg=seg; gpn.viewer=NULL; gpn.idx=1; gpn.GrData=&GrData; Ing_GetLeftandRight(bsp, NULL, &left, &right); gpn.left=left; gpn.right=right; gpn.scaleX=scaleX; gpn.seqbuf=NULL; gpn.bTop = FALSE; gpn.bRegister = FALSE; gpn.bLabels = TRUE; nSegments=SeqMgrExploreSegments(bsp, (Pointer)&gpn, Ing_ExploreSegments); /*this bioseq doesn't have any segments*/ if (nSegments==0){ AddAttribute(seg, COLOR_ATT, BLACK_COLOR, 0, 0, 0, 0); prim=AddRectangle(seg,0, GrData.SegBoxHeight, bsp->length, 0,NO_ARROW,TRUE, 2); SetPrimitiveIDs(prim, entityID, itemID, OBJ_BIOSEQ, 2); } Ing_AddRuler(seg, 2*GrData.SegBoxHeight, left, right, scaleX, 1, FALSE); Ing_PopDetailedPage(bsp, seg, left, right, GrData.pClr, scaleX, 2, TRUE, FALSE, NULL); ArrowCursor(); return (seg); }