/* gphview.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: gphview.c * * Author: Jonathan Kans * * Version Creation Date: 2/5/97 * * $Revision: 6.45 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include #include #include #include #include #include #include #include #include #include extern SegmenT VSMEntityDraw PROTO((ObjMgrDataPtr omdp, VSMPictPtr vsmpp, VSeqMgrPtr vsmp)); static void InitSelectGraphical (BioseqViewPtr bvp); static void InitSelectDesktop (BioseqViewPtr bvp); static void DrawSelectionRange (VieweR viewer, SegmenT segment); static void PopulateDesktop (BioseqViewPtr bvp); #define MAXZOOMSCALEVAL 22 static Int4 zoomScaleVal [MAXZOOMSCALEVAL] = { 1L, 1L, 2L, 5L, 10L, 20L, 50L, 100L, 200L, 500L, 1000L, 2000L, 5000L, 10000L, 20000L, 50000L, 100000L, 200000L, 500000L, 1000000L, 2000000L, 5000000L }; static Boolean Find_segment_IDs (VieweR viewer, PoinT pt, Uint2Ptr entityID, Uint2Ptr itemID, Uint2Ptr itemType) { SegmenT seg, pseg; Uint2 pID, sID, primID, primCt; if (entityID == NULL || itemID == NULL ||itemType == NULL) return FALSE; seg = FindSegment (viewer, pt, &sID, &primID, &primCt); if (seg == NULL || sID == 0 || primID == 0) return FALSE; pseg = ParentSegment (seg); if (pseg == NULL) return FALSE; pID = SegmentID (pseg); if (pID == 0) return FALSE; *itemType = pID; *entityID = sID; *itemID = primID; return TRUE; } static void get_viewer_position (VieweR viewer, Int4Ptr x, Int4Ptr y) { Int4 scale_x, scale_y; BoxInfo port, world; RecT v_iew; ViewerBox (viewer, &world, &port, &v_iew, &scale_x, &scale_y); *x = (port.left + port.right) / 2; *y = (port.top + port.bottom) / 2; } typedef struct makemultidata { ValNodePtr slp_list; Int4 len; } MakeMultiData, PNTR MakeMultiPtr; static void MakeMultiSlpList (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; Int4 len; MakeMultiPtr mmp; SeqLocPtr slp; if (sep != NULL && sep->choice == 1 && mydata != NULL) { mmp = (MakeMultiPtr) mydata; bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp != NULL && ISA_na (bsp->mol)) { len = bsp->length; slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); ValNodeAddPointer (&(mmp->slp_list), 0, (Pointer) slp); mmp->len = MAX (mmp->len, len); } } } static void FindAlignment (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { SeqAlignPtr align; BioseqPtr bsp; BioseqSetPtr bssp; SeqAnnotPtr sap; SeqAlignPtr PNTR sapp; if (sep != NULL && sep->data.ptrvalue != NULL && mydata != NULL) { sapp = (SeqAlignPtr PNTR) mydata; sap = NULL; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; } else { return; } while (sap != NULL) { if (sap->type == 2) { align = sap->data; if (align != NULL && *sapp == NULL) { *sapp = align; } } sap = sap->next; } } } static void CommonFrameProc (VieweR vwr, BioseqViewPtr bvp) { RecT dr; RecT or; RecT r; if (vwr == NULL || bvp == NULL) return; Dotted (); ObjectRect (vwr, &or); InsetRect (&or, 2, 2); LoadRect (&r, bvp->pnt_start.x, bvp->pnt_start.y, bvp->pnt_stop.x, bvp->pnt_stop.y); SectRect (&r, &or, &dr); FrameRect (&dr); } static void ClickMap (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; bvp->wasDoubleClick = dblClick; bvp->wasShiftKey = shftKey; if (bvp->old_rect_shown) { InvertMode (); CommonFrameProc (vwr, bvp); } bvp->old_rect_shown = FALSE; bvp->pnt_start = pt; bvp->pnt_stop = pt; InvertMode (); CommonFrameProc (vwr, bvp); } static void DragMap (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; if(bvp->wasDoubleClick || bvp->wasShiftKey) return; InvertMode (); CommonFrameProc (vwr, bvp); bvp->pnt_stop = pt; CommonFrameProc (vwr, bvp); } static void ReleaseMap (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; Uint2 entityID; Uint2 itemID; Uint2 itemtype; SeqEntryPtr sep; PntInfo start_info, stop_info; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; if (bvp->wasDoubleClick) { if (Find_segment_IDs (vwr, pt, &entityID, &itemID, &itemtype)) { sep = GetTopSeqEntryForEntityID (entityID); if (bvp->launchSubviewers) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); } else if (LaunchViewerNotEditor (bvp, sep, entityID, itemID, itemtype)) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); } return; } if (! bvp->sendSelectMessages) return; if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (bvp->sendSelectMessages) { if (Find_segment_IDs (vwr, pt, &entityID, &itemID, &itemtype)) { if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (! bvp->wasShiftKey) { ObjMgrDeSelect (0, 0, 0, 0, NULL); } } if (bvp->gdraw_p != NULL) { bvp->old_rect_shown = TRUE; if (bvp->slp_list != NULL) { free_slp_list (bvp->slp_list); } bvp->slp_list = NULL; if (bvp->anp_node != NULL) { FreeAlignNode (bvp->anp_node); } bvp->anp_node = NULL; bvp->scaleNotCalculated = TRUE; MapViewerToWorld(bvp->vwr, bvp->pnt_start, &start_info); MapViewerToWorld(bvp->vwr, bvp->pnt_stop, &stop_info); bvp->slp_list = find_map_pos (bvp->gdraw_p, start_info, stop_info); } } static void PopulateMap (BioseqViewPtr bvp) { Uint2 entityID; Int2 oldstyle; RecT r; SeqEntryPtr sep; Int2 style; if (bvp == NULL) return; WatchCursor (); oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); bvp->pict = DeletePicture (bvp->pict); entityID = ObjMgrGetEntityIDForPointer (bvp->bsp); sep = GetTopSeqEntryForEntityID (entityID); if (bvp->gdraw_p == NULL) { bvp->pict = SequinGlobalPicture (sep, r.right - r.left, r.bottom - r.top, bvp->g_list, &(bvp->gdraw_p), FALSE); } else { bvp->pict = GlobalPictureUpdate (bvp->gdraw_p, bvp->g_list, r.right - r.left, r.bottom - r.top); } if (bvp->gdraw_p != NULL && bvp->pict != NULL) { if (bvp->gdraw_p->is_circle) { AttachPicture (bvp->vwr, bvp->pict, 0, 0, UPPER_LEFT, 1, 1, NULL); } else { AttachPicture (bvp->vwr, bvp->pict, INT4_MIN, 0, UPPER_LEFT, 1, 1, NULL); } SetViewerProcs (bvp->vwr, ClickMap, DragMap, ReleaseMap, NULL); } SetMuskCurrentSt (GetMuskStyleName (oldstyle)); ArrowCursor (); } static void ClickGraphic (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; bvp->wasDoubleClick = dblClick; bvp->wasShiftKey = shftKey; bvp->old_rect_shown = FALSE; bvp->pnt_start = pt; bvp->pnt_stop = pt; } static void ReleaseGraphic (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; Uint2 entityID; Uint2 itemID; Uint2 itemtype; SeqEntryPtr sep; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; if (bvp->wasDoubleClick) { if (Find_segment_IDs (vwr, pt, &entityID, &itemID, &itemtype)) { sep = GetTopSeqEntryForEntityID (entityID); if (bvp->launchSubviewers) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); return; } else if (LaunchViewerNotEditor (bvp, sep, entityID, itemID, itemtype)) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); return; } else if (bvp->launchEditors) { WatchCursor (); Update (); GatherProcLaunch (OMPROC_EDIT, FALSE, entityID, itemID, itemtype, 0, 0, itemtype, 0); ArrowCursor (); Update (); return; } else { return; } } if (! bvp->sendSelectMessages) return; if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (bvp->sendSelectMessages) { if (Find_segment_IDs (vwr, pt, &entityID, &itemID, &itemtype)) { if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (! bvp->wasShiftKey) { ObjMgrDeSelect (0, 0, 0, 0, NULL); } } } static SegmenT DrawCompressNoAlignment (SeqLocPtr m_loc, ValNodePtr PNTR anp_list, Uint2Ptr seq_entityID, Boolean flat_insert, Int4 width, Int4Ptr p_scale, Int4Ptr p_maxwidth) { Int2 styleNum; CharPtr old_style; Int4 scale; SegmenT pic; ValNode vn; Int4 max_width; Int4 y_pos; ValNodePtr anp_node; Int4 len; Uint2 entityID; anp_node = collect_alignnode_from_slp(m_loc, &entityID, flat_insert); if(anp_node == NULL) return NULL; vn.data.ptrvalue = m_loc; vn.next = NULL; max_width = CountMaxSeqLabel(&vn); scale = FigureMaxScale(&vn, (Int2)width, max_width); if(scale <=0) return NULL; pic = CreatePicture(); len = slp_list_len(m_loc); /*set up the sepcial style */ styleNum = GetMuskCurrentSt(); old_style = GetMuskStyleName(styleNum); SetMuskCurrentSt("StyleX"); y_pos = 0; DrawMPAlignment(anp_node, 0, len-1, m_loc, entityID, scale, &y_pos, MSM_MPAIR, FALSE, pic); *p_scale = scale; *p_maxwidth = max_width; SetMuskCurrentSt(old_style); if(seq_entityID != NULL) *seq_entityID = entityID; if(anp_list != NULL) *anp_list = anp_node; else FreeAlignNode(anp_node); return pic; } static void PopulateCompressedNoAlignment (BioseqViewPtr bvp) { ValNodePtr anp_list; BioseqPtr bsp; Uint2 entityID; SeqLocPtr m_loc; Int4 max_width; RecT r; Int4 scale; Int4 X_VIEW; if (bvp == NULL) return; bsp = bvp->bsp; if (bsp == NULL) return; m_loc = SeqLocIntNew (0, bsp->length - 1, 0, bsp->id); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); X_VIEW = r.right - r.left; bvp->pict = DrawCompressNoAlignment (m_loc, &(anp_list), &(entityID), FALSE, X_VIEW, &scale, &max_width); if (bvp->pict != NULL) { max_width += 2; max_width *= scale; AttachPicture (bvp->vwr, bvp->pict, INT4_MIN, 0, UPPER_LEFT, scale, 1, NULL); SetViewerProcs (bvp->vwr, ClickGraphic, NULL, ReleaseGraphic, NULL); } FreeAlignNode (anp_list); SeqLocFree (m_loc); ArrowCursor (); } static void PopulateCompressed (BioseqViewPtr bvp) { ValNodePtr anp_list; BioseqPtr bsp; Uint2 entityID; SeqLocPtr m_loc; Int4 max_width; RecT r; Int4 scale; SeqEntryPtr sep; Int4 X_VIEW; if (bvp == NULL) return; WatchCursor (); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); bsp = bvp->bsp; if (bsp == NULL) return; sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); if (! SeqEntryHasAligns (entityID, sep)) { PopulateCompressedNoAlignment (bvp); return; } anp_list = MakeCompressAlignList (bvp->bsp, NULL, &entityID); if (anp_list == NULL) { PopulateCompressedNoAlignment (bvp); return; } m_loc = SeqLocIntNew (0, bsp->length - 1, 0, bsp->id); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); X_VIEW = r.right - r.left; bvp->pict = DrawCompressAlignment (anp_list, m_loc, X_VIEW, &scale, &max_width, entityID, NULL); if (bvp->pict != NULL) { max_width += 2; max_width *= scale; AttachPicture (bvp->vwr, bvp->pict, INT4_MIN, 0, UPPER_LEFT, scale, 1, NULL); SetViewerProcs (bvp->vwr, ClickGraphic, NULL, ReleaseGraphic, NULL); } FreeAlignNode (anp_list); SeqLocFree (m_loc); ArrowCursor (); } typedef struct gphfinddata { ValNodePtr vnp; SeqLocPtr slp; Int4 start; Int4 stop; BioseqPtr bsp; } GphFindData, PNTR GphFindPtr; static Boolean GraphFindFunc (GatherContextPtr gcp) { GphFindPtr gfp; SeqGraphPtr sgp; Int4 left; Int4 right; if (gcp == NULL) return TRUE; gfp = (GphFindPtr) gcp->userdata; if (gfp == NULL ) return TRUE; if (gcp->thistype == OBJ_SEQGRAPH) { sgp = (SeqGraphPtr) gcp->thisitem; if (sgp != NULL) { if (SeqIdForSameBioseq (SeqLocId (sgp->loc), SeqLocId (gfp->slp))) { left = GetOffsetInBioseq (sgp->loc, gfp->bsp, SEQLOC_LEFT_END); right = GetOffsetInBioseq (sgp->loc, gfp->bsp, SEQLOC_RIGHT_END); if (left == -1 || right == -1) return TRUE; if (left >= gfp->start && right <= gfp->stop) { ValNodeAddPointer (&(gfp->vnp), 0, (Pointer) sgp); } } } } return TRUE; } static ValNodePtr CollectGraphs (Uint2 entityID, BioseqPtr bsp, Int4 start, Int4 stop) { GphFindData gfd; GatherScope gs; ValNode vn; gfd.vnp = NULL; vn.choice = SEQLOC_WHOLE; vn.data.ptrvalue = (Pointer) bsp->id; gfd.slp = &vn; gfd.start = start; gfd.stop = stop; gfd.bsp = bsp; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof (Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQGRAPH] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; GatherEntity (entityID, (Pointer) &gfd, GraphFindFunc, &gs); return gfd.vnp; } static void PopulateSimpleGraphic (BioseqViewPtr bvp) { BoxInfo box; BioseqPtr bsp; Uint2 entityID; GeneDataPtr gdata; ValNodePtr graphs; Int2 i; Int4 labelWid; Int4 len; Int4 max; Int4 min; MakeMultiData mmd; SeqEntryPtr oldscope = NULL; Int2 oldstyle; RecT r; Int4 scaleX; Int4 scaleY; SeqEntryPtr sep; SeqGraphPtr sgp; ValNodePtr slp_list; SeqLocPtr slp; Char str [32]; Int2 style; ValNodePtr vnp; Int4 vwr_x; Int4 vwr_y; Int2 vwr_align; if (bvp == NULL) return; WatchCursor (); vwr_x = INT4_MIN; vwr_y = INT4_MAX; vwr_align = UPPER_LEFT; if (bvp->moveToOldPos) { if (bvp->pict != NULL) { get_viewer_position (bvp->vwr, &(vwr_x), &(vwr_y)); vwr_align = MIDDLE_CENTER; } bvp->moveToOldPos = FALSE; } Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); Update (); if (bvp->isGenome && bvp->slp_list == NULL) return; bsp = bvp->bsp; if (bsp != NULL) { scaleY = 1; len = 0; if (! bvp->isGenome) { slp_list = NULL; sep = NULL; len = 0; if (bvp->viewWholeEntity) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); sep = GetTopSeqEntryForEntityID (entityID); mmd.slp_list = NULL; mmd.len = 0; BioseqExplore (sep, (Pointer) &mmd, MakeMultiSlpList); slp_list = mmd.slp_list; len = mmd.len; } else { sep = SeqMgrGetSeqEntryForData (bsp); len = bsp->length; slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); ValNodeAddPointer (&slp_list, 0, (Pointer) slp); } if (bvp->slp_list != NULL) { free_slp_list (bvp->slp_list); bvp->slp_list = NULL; } bvp->slp_list = slp_list; } oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); if (bvp->scaleNotCalculated) { SafeHide (bvp->scale); Reset (bvp->scale); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); labelWid = CountMaxSeqLabel (bvp->slp_list) + 2; if (r.right - r.left < 2 * labelWid) { labelWid = 0; } if (bvp->isGenome) { slp = (SeqLocPtr) bvp->slp_list->data.ptrvalue; len = slp_list_len (slp); } max = (Int4) MAX (len / (Int4) (r.right - r.left - labelWid), 1) + 2; max = (Int4) MIN (max, 50000L); min = (Int4) MAX (len / 320000L, 1L); bvp->maxScale = max; i = 1; while (i < MAXZOOMSCALEVAL && min > zoomScaleVal [i]) { i++; } bvp->minIndex = i; while (i < MAXZOOMSCALEVAL && max > zoomScaleVal [i - 1]) { sprintf (str, "%ld", (long) (zoomScaleVal [i])); if (max < zoomScaleVal [i]) { sprintf (str, "%ld", (long) zoomScaleVal [i]); } PopupItem (bvp->scale, str); i++; } SetValue (bvp->scale, MAX (i - bvp->minIndex, 1)); bvp->scaleNotCalculated = FALSE; } SafeShow (bvp->scale); i = GetValue (bvp->scale) - 1 + bvp->minIndex; if (i < MAXZOOMSCALEVAL && i > 0) { scaleX = MIN (zoomScaleVal [i], bvp->maxScale); } else { scaleX = bvp->minIndex; } sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); if (entityID > 0) { sep = GetBestTopParentForData (entityID, bsp); oldscope = SeqEntrySetScope (sep); } gdata = make_gene_data (bvp->g_list); bvp->ftype_list = ValNodeFree (bvp->ftype_list); bvp->pict = DrawSequinMapEx (bvp->slp_list, sep, scaleX, gdata, &(bvp->ftype_list), FALSE, bvp->tempResultList); GeneDataFree (gdata); graphs = CollectGraphs (entityID, bsp, 0, bsp->length - 1); if (graphs != NULL) { SegmentBox (bvp->pict, &box); for (vnp = graphs; vnp != NULL; vnp = vnp->next) { sgp = (SeqGraphPtr) vnp->data.ptrvalue; AddGraphSentinelToPicture (sgp, bsp, bvp->pict, scaleX, box.bottom - 10, 0, NULL); } } if (entityID > 0) { SeqEntrySetScope (oldscope); } AttachPicture (bvp->vwr, bvp->pict, vwr_x, vwr_y, vwr_align, scaleX, scaleY, bvp->highlightSelections ? DrawSelectionRange : NULL); SetViewerProcs (bvp->vwr, ClickGraphic, NULL, ReleaseGraphic, NULL); SetMuskCurrentSt (GetMuskStyleName (oldstyle)); InitSelectGraphical (bvp); } ArrowCursor (); } /* functions copied from glbpic.c */ static Int4 get_min_size(Int4 seq_len) { if(seq_len <= 350000) return seq_len; return MAX(350000, seq_len/8); } static SeqLocPtr load_seq_loc(Int4 val_1, Int4 val_2, Int4 seq_len, Boolean has_zero, SeqIdPtr sip, BoolPtr show_msg, Boolean add_interval) { Int4 m_start, m_stop; Uint1 m_strand = Seq_strand_plus; SeqLocPtr slp = NULL, loc; Int4 min_len; Int4 temp; Int4 len; min_len = get_min_size(seq_len); if(has_zero) { if(val_1 < val_2) { temp = val_2; val_2 = val_1; val_1 = temp; } if(add_interval) { val_1 -= seq_len/20; val_2 += seq_len/20; } len = (seq_len - 1 - val_1 +1 + val_2 +1); if(len > min_len) { if(*show_msg) Message(MSG_OK, "The selected region is too large. Reduced to %ld base pairs", min_len); val_1 = seq_len - 1 - min_len/2; val_2= min_len/2 -1; } m_start = val_1; m_stop = seq_len -1; loc = SeqLocIntNew(m_start, m_stop, m_strand, sip); m_start = 0; m_stop = val_2; loc->next = SeqLocIntNew(m_start, m_stop, m_strand, sip); slp = loc; } else { m_start = MIN(val_1, val_2); m_start = MAX(0, m_start); m_stop = MAX(val_1, val_2); m_stop = MIN(seq_len-1, m_stop); len = m_stop - m_start + 1; if(add_interval) { len += seq_len/10; m_start = MAX(0, (m_start - seq_len/20)); m_stop = m_start + len -1; } /* if(len > min_len) { if(*show_msg) Message(MSG_OK, "The selected region is too large. Reduced to %ld base pairs", min_len); center = (m_start + m_stop)/2; m_start = center - min_len/2; m_stop = m_start + min_len -1; } */ slp = SeqLocIntNew(m_start, m_stop, m_strand, sip); } *show_msg = FALSE; return slp; } typedef struct sentineldata { BioseqViewPtr bvp; SegmenT seg; PrimitivE snt; Int4 start; Int4 stop; Boolean fetched; } SentinelData, PNTR SentinelPtr; static Boolean AddToEntityList (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { BioseqViewPtr bvp; BaseFormPtr bfp; Uint2 entityID; OMUserDataPtr omudp; bvp = (BioseqViewPtr) userdata; entityID = segID; if (bvp == NULL || entityID == 0) return TRUE; bfp = (BaseFormPtr) GetObjectExtra (bvp->form); if (bfp == NULL || entityID == bfp->input_entityID) return TRUE; if (! InBioseqViewEntityList (entityID, bvp)) { ValNodeAddInt (&(bvp->entityList), 0, (Int4) entityID); omudp = ObjMgrAddUserData (entityID, bfp->procid, OMPROC_VIEW, bfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) bfp; omudp->messagefunc = BioseqViewMsgFunc; } } return TRUE; } static void GenomicSentinelProc (BigScalar calldata, PrimDrawContext pdc) { BoxInfo box; BioseqPtr bsp; BioseqViewPtr bvp; ValNodePtr curr; Uint2 entityID; Boolean forceSeglevelsTo1 = TRUE; GlobalBspPtr gbp; ValNodePtr graphs; /* SeqEntryPtr oldscope; */ Int2 oldstyle; SegmenT pic; BasePPtr prim; Int4 scaleX; Int4 scaleY; SeqEntryPtr sep; Int4 seq_len; SeqGraphPtr sgp; Boolean show_msg = FALSE; ValNodePtr slp_list; SeqLocPtr slp; SentinelPtr sp; Int2 style; ValNodePtr vnp; BoxInfo world; sp = (SentinelPtr) calldata; if (sp == NULL) return; if (sp->fetched) return; sp->fetched = TRUE; bvp = sp->bvp; bsp = bvp->bsp; slp_list = NULL; if (bvp->isGenome && bvp->gdraw_p != NULL) { slp_list = NULL; for (curr = bvp->gdraw_p->gbp_list; curr !=NULL; curr = curr->next) { gbp = curr->data.ptrvalue; bsp = gbp->bsp; seq_len = bsp->length; slp = load_seq_loc (sp->start, sp->stop, seq_len, FALSE, SeqIdFindBest (bsp->id, 0), &show_msg, FALSE); if (slp != NULL) { ValNodeAddPointer ((Pointer) &slp_list, (Uint1) (gbp->priority), slp); } } } else { bsp = bvp->bsp; slp = SeqLocIntNew (sp->start, sp->stop, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); ValNodeAddPointer (&slp_list, 0, (Pointer) slp); } oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); bsp = bvp->bsp; sep = SeqMgrGetSeqEntryForData (bsp); if (IsADeltaBioseq (sep)) { forceSeglevelsTo1 = FALSE; } entityID = ObjMgrGetEntityIDForChoice (sep); if (entityID > 0) { sep = GetBestTopParentForData (entityID, bsp); /* oldscope = SeqEntrySetScope (sep); */ } ViewerBox (bvp->vwr, NULL, NULL, NULL, &scaleX, &scaleY); pic = DrawSequinMapEx (slp_list, sep, scaleX, NULL, NULL, forceSeglevelsTo1, bvp->tempResultList); ChangeAddPrimOrder (ADD_TO_TAIL); prim = (BasePPtr) pic; prim->code = SEGMENT; OffsetSegment (pic, sp->start, 0); ExploreSegment (pic, (Pointer) bvp, AddToEntityList); graphs = CollectGraphs (entityID, bsp, sp->start, sp->stop); if (graphs != NULL) { SegmentBox (pic, &box); for (vnp = graphs; vnp != NULL; vnp = vnp->next) { sgp = (SeqGraphPtr) vnp->data.ptrvalue; AddGraphSentinelToPicture (sgp, bsp, pic, scaleX, box.bottom - 10, /* sp->start */ 0, NULL); } } LinkSegment (bvp->pict, pic); RecalculateSegment (pic, scaleX, scaleY); ViewerBox (bvp->vwr, &world, NULL, NULL, &scaleX, &scaleY); for (vnp = bvp->sentinelList; vnp != NULL; vnp = vnp->next) { sp = (SentinelPtr) vnp->data.ptrvalue; if (sp != NULL) { if (PrimitiveBox (sp->snt, scaleX, scaleY, &box)) { ChangeSentinelRectangle (sp->snt, box.left, world.top, box.right, world.bottom); } } } /* if (entityID > 0) { SeqEntrySetScope (oldscope); } */ SetMuskCurrentSt (GetMuskStyleName (oldstyle)); } static void PopulateGraphic (BioseqViewPtr bvp) { BioseqPtr bsp; BioseqSetPtr bssp; DeltaSeqPtr dsp; Uint2 entityID; Int2 i; Boolean isGenome; Int4 labelWid; Int4 len; SeqLocPtr loc; Int4 max; Int4 min; MakeMultiData mmd; Int2 oldstyle; RecT r; Int4 scaleX; Int4 scaleY; SeqEntryPtr sep; SeqLocPtr slp; ValNodePtr slp_list; SentinelPtr sp; Int4 start; Char str [32]; Int2 style; ValNode vn; ValNodePtr vnp; Int4 vwr_x; Int4 vwr_y; Int2 vwr_align; if (bvp == NULL) return; sep = SeqMgrGetSeqEntryForData (bvp->bsp); entityID = ObjMgrGetEntityIDForChoice (sep); sep = GetBestTopParentForData (entityID, bvp->bsp); if (! bvp->hasTargetControl) { PopulateSimpleGraphic (bvp); /* Nentrez should do this until more work is done */ return; } isGenome = FALSE; if (IsAGenomeRecord (sep) || IsSegmentedBioseqWithoutParts (sep)) { isGenome = TRUE; if (bvp->isGenome) { if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == BioseqseqSet_class_equiv) { PopulateSimpleGraphic (bvp); return; } } } } else if (IsADeltaBioseq (sep)) { /* isGenome = FALSE; if (bvp->isGenome) { if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == BioseqseqSet_class_equiv) { PopulateSimpleGraphic (bvp); return; } } } */ PopulateSimpleGraphic (bvp); return; } else { PopulateSimpleGraphic (bvp); return; } WatchCursor (); vwr_x = INT4_MIN; vwr_y = INT4_MAX; vwr_align = UPPER_LEFT; if (bvp->moveToOldPos) { if (bvp->pict != NULL) { get_viewer_position (bvp->vwr, &(vwr_x), &(vwr_y)); vwr_align = MIDDLE_CENTER; } bvp->moveToOldPos = FALSE; } Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); Update (); if (bvp->isGenome && bvp->gdraw_p == NULL) { PopulateMap (bvp); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); Update (); } bsp = bvp->bsp; if (bsp != NULL) { scaleY = 1; len = 0; if (bvp->sentinelList != NULL) { bvp->sentinelList = ValNodeFreeData (bvp->sentinelList); } if (bvp->sentinelList == NULL) { sep = SeqMgrGetSeqEntryForData (bsp); if (bsp->repr == Seq_repr_raw) { sp = MemNew (sizeof (SentinelData)); if (sp != NULL) { sp->bvp = bvp; sp->start = 0; sp->stop = bsp->length - 1; sp->fetched = FALSE; ValNodeAddPointer (&(bvp->sentinelList), 0, (Pointer) sp); } } else if (bsp->repr == Seq_repr_seg) { vn.choice = SEQLOC_MIX; vn.next = NULL; vn.data.ptrvalue = bsp->seq_ext; start = 0; slp = SeqLocFindNext (&vn, NULL); while (slp != NULL) { if (slp->choice != SEQLOC_NULL) { len = SeqLocLen (slp); if (len > 0) { sp = MemNew (sizeof (SentinelData)); if (sp != NULL) { sp->bvp = bvp; sp->start = start; sp->stop = start + len - 1; sp->fetched = FALSE; ValNodeAddPointer (&(bvp->sentinelList), 0, (Pointer) sp); start += len; } } } slp = SeqLocFindNext (&vn, slp); } } else if (bsp->repr == Seq_repr_delta && bsp->seq_ext_type == 4) { dsp = (DeltaSeqPtr) bsp->seq_ext; loc = DeltaSeqsToSeqLocs (dsp); start = 0; slp = SeqLocFindNext (loc, NULL); while (slp != NULL) { if (slp->choice != SEQLOC_NULL) { len = SeqLocLen (slp); if (len > 0) { sp = MemNew (sizeof (SentinelData)); if (sp != NULL) { sp->bvp = bvp; sp->start = start; sp->stop = start + len - 1; sp->fetched = FALSE; ValNodeAddPointer (&(bvp->sentinelList), 0, (Pointer) sp); start += len; } } } slp = SeqLocFindNext (loc, slp); } SeqLocFree (loc); } else if (bsp->repr == Seq_repr_map) { if (bsp->length > 100000000) { len = 10000000; } else if (bsp->length > 10000000) { len = 1000000; } else if (bsp->length > 1000000) { len = 100000; } else if (bsp->length > 100000) { len = 10000; } else { len = bsp->length; } start = 0; while (start < bsp->length) { sp = MemNew (sizeof (SentinelData)); if (sp != NULL) { sp->bvp = bvp; sp->start = start; if (start + len - 1 > bsp->length) { len = bsp->length - start; } sp->stop = start + len - 1; sp->fetched = FALSE; ValNodeAddPointer (&(bvp->sentinelList), 0, (Pointer) sp); start += len; } } } } len = 0; if (! bvp->isGenome) { slp_list = NULL; sep = NULL; len = 0; if (bvp->viewWholeEntity) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); sep = GetTopSeqEntryForEntityID (entityID); mmd.slp_list = NULL; mmd.len = 0; BioseqExplore (sep, (Pointer) &mmd, MakeMultiSlpList); slp_list = mmd.slp_list; len = mmd.len; } else { sep = SeqMgrGetSeqEntryForData (bsp); len = bsp->length; slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); ValNodeAddPointer (&slp_list, 0, (Pointer) slp); } if (bvp->slp_list != NULL) { free_slp_list (bvp->slp_list); bvp->slp_list = NULL; } bvp->slp_list = slp_list; } if (bvp->scaleNotCalculated) { SafeHide (bvp->scale); Reset (bvp->scale); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); labelWid = CountMaxSeqLabel (bvp->slp_list) + 2; SetMuskCurrentSt (GetMuskStyleName (oldstyle)); if (r.right - r.left < 2 * labelWid) { labelWid = 0; } if (isGenome) { if (bsp->length > 100000000) { max = 49999L; } else if (bsp->length > 10000000) { max = 4999L; } else if (bsp->length > 1000000) { max = 499L; } else if (bsp->length > 100000) { max = 49L; } else if (bsp->length > 10000) { max = 19L; } else if (bsp->length > 1000) { max = 9L; } else { max = 4L; } min = (Int4) 1; } else { max = (Int4) MAX (len / (Int4) (r.right - r.left - labelWid), 1) + 2; max = (Int4) MIN (max, 50000L); min = (Int4) MAX (len / 320000L, 1L); } bvp->maxScale = max; i = 1; while (i < MAXZOOMSCALEVAL && min > zoomScaleVal [i]) { i++; } bvp->minIndex = i; while (i < MAXZOOMSCALEVAL && max > zoomScaleVal [i - 1]) { sprintf (str, "%ld", (long) (zoomScaleVal [i])); if (max < zoomScaleVal [i]) { sprintf (str, "%ld", (long) zoomScaleVal [i]); } PopupItem (bvp->scale, str); i++; } SetValue (bvp->scale, MAX (i - bvp->minIndex - 3, 1)); bvp->scaleNotCalculated = FALSE; } SafeShow (bvp->scale); i = GetValue (bvp->scale) - 1 + bvp->minIndex; if (i < MAXZOOMSCALEVAL && i > 0) { scaleX = MIN (zoomScaleVal [i], bvp->maxScale); } else { scaleX = bvp->minIndex; } bvp->pict = CreatePicture (); for (vnp = bvp->sentinelList; vnp != NULL; vnp = vnp->next) { sp = (SentinelPtr) vnp->data.ptrvalue; if (sp != NULL) { sp->seg = CreateSegment (bvp->pict, 0, 0); sp->snt = AddSntRectangle (bvp->pict, sp->start, -35, sp->stop, -40, GenomicSentinelProc, (BigScalar) sp, NULL, 0); /* AddRectangle (bvp->pict, sp->start, -35, sp->stop, -40, 0, FALSE, 0); */ } } AttachPicture (bvp->vwr, bvp->pict, vwr_x, vwr_y, vwr_align, scaleX, scaleY, bvp->highlightSelections ? DrawSelectionRange : NULL); SetViewerProcs (bvp->vwr, ClickGraphic, NULL, ReleaseGraphic, NULL); /* InitSelectGraphical (bvp); */ } ArrowCursor (); } static void ClickAlignment (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; bvp->wasDoubleClick = dblClick; bvp->wasShiftKey = shftKey; bvp->old_rect_shown = FALSE; bvp->pnt_start = pt; bvp->pnt_stop = pt; InvertMode (); CommonFrameProc (vwr, bvp); } static void DragAlignment (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; if(bvp->wasDoubleClick || bvp->wasShiftKey) return; InvertMode (); CommonFrameProc (vwr, bvp); bvp->pnt_stop = pt; CommonFrameProc (vwr, bvp); } static void ReleaseAlignment (VieweR vwr, SegmenT seg, PoinT pt) { BioseqViewPtr bvp; Uint2 entityID; FILE *fp; Uint2 itemID; Uint2 itemtype; Int4 left, right; Uint4 option = TXALIGN_MISMATCH; Char path [PATH_MAX]; SeqEntryPtr sep; SeqLocPtr slp; PntInfo start_info, stop_info; Char title [64]; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; if (bvp->wasDoubleClick) { if (Find_segment_IDs (vwr, pt, &entityID, &itemID, &itemtype)) { sep = GetTopSeqEntryForEntityID (entityID); if (bvp->launchSubviewers) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); } else if (LaunchViewerNotEditor (bvp, sep, entityID, itemID, itemtype)) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); } else if (bvp->launchEditors) { WatchCursor (); Update (); GatherProcLaunch (OMPROC_EDIT, FALSE, entityID, itemID, itemtype, 0, 0, itemtype, 0); ArrowCursor (); Update (); return; } else { return; } } if (! bvp->sendSelectMessages) return; if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (bvp->sendSelectMessages) { if (Find_segment_IDs (vwr, pt, &entityID, &itemID, &itemtype)) { if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (! bvp->wasShiftKey) { ObjMgrDeSelect (0, 0, 0, 0, NULL); } } if (bvp->slp_list != NULL && bvp->anp_node != NULL) { InvertMode (); CommonFrameProc (vwr, bvp); bvp->pnt_stop = pt; if (ABS (bvp->pnt_start.x - bvp->pnt_stop.x) > 5) { WatchCursor (); Update (); GetTitle (ParentWindow (vwr), title, sizeof (title) - 1); MapViewerToWorld(vwr, bvp->pnt_start, &start_info); MapViewerToWorld(vwr, bvp->pnt_stop, &stop_info); left = MIN(start_info.x, stop_info.x); right = MAX(start_info.x, stop_info.x); StringCat (title, " alignment"); TmpNam (path); fp = FileOpen(path, "w"); if (fp != NULL) { slp = bvp->slp_list->data.ptrvalue; if (ShowAlignNodeText (bvp->anp_node, -1, 40, fp, left, right, option, NULL, NULL)) FileClose(fp); else FileClose(fp); } LaunchGeneralTextViewer (path, title); } FileRemove (path); ArrowCursor (); Update (); } } static void DrawAlignOnAllSequences (BioseqViewPtr bvp, SeqAlignPtr align, Int2 scaleX) { ValNode vn; Int4 y_pos = 0; Int4 value, style; SeqIdPtr m_sip; BioseqPtr mbsp; SeqLocPtr m_loc; Int4 start, stop; CollectSeqOption cs_option; CollectAlignOption ca_option; SeqEntryPtr sep; Uint2 entityID; if (bvp == NULL || align == NULL) return; sep = SeqMgrGetSeqEntryForData (bvp->bsp); entityID = ObjMgrGetEntityIDForChoice (sep); m_sip = make_master(align); if(m_sip == NULL) { Message(MSG_ERROR, "Fail to get the master id"); return; } mbsp = BioseqLockById(m_sip); if(mbsp == NULL) { get_boundary(m_sip, &start, &stop, align); m_loc = SeqLocIntNew(start, stop, Seq_strand_plus, m_sip); } else m_loc = SeqLocIntNew(0, mbsp->length-1, Seq_strand_plus, m_sip); vn.data.ptrvalue = m_loc; vn.next = NULL; if(scaleX <=0) { if(mbsp != NULL) BioseqUnlock(mbsp); SeqLocFree(m_loc); return; } style= GetMuskCParam(MSM_ALIGNMENT, 0, MSM_STYLE); if(style== MSM_MDIM) { if(!use_multiple_dimension(align)) style= MSM_MPAIR; } else style= MSM_MPAIR; load_align_option_for_graphic(&ca_option, &cs_option, style, FALSE); if(mbsp == NULL) ca_option.show_mismatch = FALSE; ca_option.csop = &cs_option; if(style== MSM_MDIM) value = COLLECT_MD; else value = COLLECT_MP; if (bvp->anp_node != NULL) { bvp->anp_node = FreeAlignNode (bvp->anp_node); } bvp->anp_node = collect_anpnode_with_option(&ca_option, m_loc, entityID, value, OBJ_SEQALIGN, NULL, NULL, TRUE); if(bvp->anp_node == NULL) { if(mbsp != NULL) BioseqUnlock(mbsp); SeqLocFree(m_loc); return; } bvp->pict = CreatePicture(); DrawMPAlignment(bvp->anp_node, 0, SeqLocLen(m_loc)-1, m_loc, entityID, scaleX, &y_pos, (Uint1)style, FALSE, bvp->pict); if(mbsp != NULL) BioseqUnlock(mbsp); SeqLocFree(m_loc); } static void PopulateAlignment (BioseqViewPtr bvp) { SeqAlignPtr align; BioseqPtr bsp; BioseqSetPtr bssp; Uint2 entityID; Int2 i; Int4 labelWid; Int4 len; Int4 max; Int4 min; MakeMultiData mmd; SeqEntryPtr oldscope = NULL; Int2 oldstyle; RecT r; Int4 scaleX; Int4 scaleY; SeqEntryPtr sep; ValNodePtr slp_list; SeqLocPtr slp; Char str [32]; Int2 style; Int4 vwr_x; Int4 vwr_y; Int2 vwr_align; Int4 y_pos = 0; if (bvp == NULL) return; WatchCursor (); vwr_x = INT4_MIN; vwr_y = INT4_MAX; vwr_align = UPPER_LEFT; if (bvp->moveToOldPos) { if (bvp->pict != NULL) { get_viewer_position (bvp->vwr, &(vwr_x), &(vwr_y)); vwr_align = MIDDLE_CENTER; } bvp->moveToOldPos = FALSE; } Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); Update (); if (bvp->isGenome && bvp->slp_list == NULL) return; bsp = bvp->bsp; if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); sep = GetBestTopParentForData (entityID, bsp); if (sep != NULL && sep->choice == 2) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == 10) { ArrowCursor (); return; } } scaleY = 1; len = 0; slp = NULL; if (! bvp->isGenome) { slp_list = NULL; sep = NULL; len = 0; if (bvp->viewWholeEntity) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); sep = GetTopSeqEntryForEntityID (entityID); mmd.slp_list = NULL; mmd.len = 0; BioseqExplore (sep, (Pointer) &mmd, MakeMultiSlpList); slp_list = mmd.slp_list; len = mmd.len; } else { sep = SeqMgrGetSeqEntryForData (bsp); len = bsp->length; slp = SeqLocIntNew (0, len-1, Seq_strand_plus, SeqIdFindBest (bsp->id, 0)); ValNodeAddPointer (&slp_list, 0, (Pointer) slp); } if (bvp->slp_list != NULL) { free_slp_list (bvp->slp_list); bvp->slp_list = NULL; } bvp->slp_list = slp_list; } oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); if (bvp->scaleNotCalculated) { SafeHide (bvp->scale); Reset (bvp->scale); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); labelWid = CountMaxSeqLabel (bvp->slp_list) + 2; if (r.right - r.left < 2 * labelWid) { labelWid = 0; } if (bvp->isGenome) { slp = (SeqLocPtr) bvp->slp_list->data.ptrvalue; len = slp_list_len (slp); } max = (Int4) MAX (len / (Int4) (r.right - r.left - labelWid), 1) + 2; max = (Int4) MIN (max, 50000L); min = (Int4) MAX (len / 320000L, 1L); bvp->maxScale = max; i = 1; while (i < MAXZOOMSCALEVAL && min > zoomScaleVal [i]) { i++; } bvp->minIndex = i; while (i < MAXZOOMSCALEVAL && max > zoomScaleVal [i - 1]) { sprintf (str, "%ld", (long) (zoomScaleVal [i])); if (max < zoomScaleVal [i]) { sprintf (str, "%ld", (long) zoomScaleVal [i]); } PopupItem (bvp->scale, str); i++; } SetValue (bvp->scale, MAX (i - bvp->minIndex, 1)); bvp->scaleNotCalculated = FALSE; } SafeShow (bvp->scale); i = GetValue (bvp->scale) - 1 + bvp->minIndex; if (i < MAXZOOMSCALEVAL && i > 0) { scaleX = MIN (zoomScaleVal [i], bvp->maxScale); } else { scaleX = bvp->minIndex; } sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); if (entityID > 0) { sep = GetBestTopParentForData (entityID, bsp); oldscope = SeqEntrySetScope (sep); } if (bvp->viewWholeEntity) { align = NULL; sep = GetTopSeqEntryForEntityID (entityID); SeqEntryExplore (sep, &align, FindAlignment); DrawAlignOnAllSequences (bvp, align, scaleX); } else if (bvp->anp_node == NULL) { Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); slp = (SeqLocPtr) bvp->slp_list->data.ptrvalue; bvp->pict = DrawSeqHistoryAlignment (slp, scaleX, &(bvp->anp_node), &(bvp->seq_entityID), FALSE); } else if (bvp->seq_entityID > 0) { bvp->pict = CreatePicture (); slp = (SeqLocPtr) bvp->slp_list->data.ptrvalue; DrawMPAlignment (bvp->anp_node, 0, SeqLocLen (slp), slp, bvp->seq_entityID, scaleX, &y_pos, MSM_MPAIR, FALSE, bvp->pict); } else { if (entityID > 0) { SeqEntrySetScope (oldscope); } ArrowCursor (); return; } if (entityID > 0) { SeqEntrySetScope (oldscope); } AttachPicture (bvp->vwr, bvp->pict, vwr_x, vwr_y, vwr_align, scaleX, scaleY, NULL); SetViewerProcs (bvp->vwr, ClickAlignment, DragAlignment, ReleaseAlignment, NULL); SetMuskCurrentSt (GetMuskStyleName (oldstyle)); InitSelectGraphical (bvp); } ArrowCursor (); } static void ClickSalsa (PaneL pnl, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (pnl); if (bvp == NULL) return; bvp->wasDoubleClick = dblClick; bvp->wasShiftKey = shftKey; } static void ReleaseSalsa (PaneL pnl, PoinT pt) { BioseqViewPtr bvp; Uint2 entityID; Uint2 itemID; Uint2 itemtype; SeqEntryPtr sep; bvp = (BioseqViewPtr) GetObjectExtra (pnl); if (bvp == NULL) return; if (bvp->wasDoubleClick) { if (FindIdsInSalsaPanel (pnl, pt, &entityID, &itemID, &itemtype)) { sep = GetTopSeqEntryForEntityID (entityID); if (bvp->launchSubviewers) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); return; } else if (LaunchViewerNotEditor (bvp, sep, entityID, itemID, itemtype)) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); return; } else if (bvp->launchEditors) { WatchCursor (); Update (); GatherProcLaunch (OMPROC_EDIT, FALSE, entityID, itemID, itemtype, 0, 0, itemtype, 0); ArrowCursor (); Update (); return; } else { return; } } if (! bvp->sendSelectMessages) return; if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (bvp->sendSelectMessages) { if (FindIdsInSalsaPanel (pnl, pt, &entityID, &itemID, &itemtype)) { if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } else if (! bvp->wasShiftKey) { ObjMgrDeSelect (0, 0, 0, 0, NULL); } } } static void PopulateSalsa (BioseqViewPtr bvp) { BioseqPtr bsp; Uint2 entityID; Uint1 numbering; Int2 oldstyle; RecT r; SeqEntryPtr sep; Uint1 sequence_shown; Uint1 show_feat; Int2 style; WindoW tempPort; Int2 val; if (bvp == NULL) return; WatchCursor (); Reset (bvp->pnl); SetPanelClick (bvp->pnl, NULL, NULL, NULL, NULL); Update (); bsp = bvp->bsp; if (bsp != NULL) { oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); sep = SeqMgrGetSeqEntryForData (bsp); if (bvp->viewWholeEntity) { entityID = ObjMgrGetEntityIDForChoice (sep); sep = GetTopSeqEntryForEntityID (entityID); } val = GetValue (bvp->seqControl); switch (val) { case 1 : sequence_shown = SEQ_SHOW1; break; case 2 : sequence_shown = SEQ_SHOWALG; break; default : sequence_shown = SEQ_SHOW1; break; } val = GetValue (bvp->featControl); switch (val) { case 1 : show_feat = SEQ_FEAT0; break; case 2 : show_feat = SEQ_FEAT1; break; case 3 : show_feat = SEQ_FEATALL; break; default : show_feat = SEQ_FEAT1; break; } val = GetValue (bvp->numControl); switch (val) { case 1 : numbering = SEQ_NUM0; break; case 2 : numbering = SEQ_NUM1; break; case 3 : numbering = SEQ_NUM2; break; default : numbering = SEQ_NUM2; break; } PopulateSalsaPanel (bvp->pnl, sep, bvp->viewWholeEntity, sequence_shown, show_feat, numbering, bvp->displayFont); SetPanelClick (bvp->pnl, ClickSalsa, NULL, NULL, ReleaseSalsa); SetMuskCurrentSt (GetMuskStyleName (oldstyle)); if (Visible (bvp->pnl) && AllParentsVisible (bvp->pnl)) { tempPort = SavePort (bvp->pnl); ResetClip (); Select (bvp->pnl); ObjectRect (bvp->pnl, &r); InsetRect (&r, 1, 1); InvalRect (&r); RestorePort (tempPort); } } ArrowCursor (); } #define VSM_PICT_UP_BUTTON 65001 #define VSM_PICT_DOWN_BUTTON 65002 static void ClickDesktop (VieweR vwr, SegmenT s, PoinT pt) { BioseqViewPtr bvp; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; bvp->wasDoubleClick = dblClick; bvp->wasShiftKey = shftKey; } static void ReleaseDesktop (VieweR vwr, SegmenT s, PoinT pt) { BioseqPtr bsp; BioseqViewPtr bvp; Uint2 entityID; Int2 expand = 0; Uint2 itemID; Uint2 itemtype; Uint2 primID; SegmenT seg; Uint2 segID; SeqEntryPtr sep; bvp = (BioseqViewPtr) GetObjectExtra (vwr); if (bvp == NULL) return; bsp = bvp->bsp; if (bsp == NULL) return; sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); seg = FindSegment (vwr, pt, &segID, &primID, NULL); itemID = primID; itemtype = segID; if (primID == 0 || segID == 0) { if (! bvp->wasShiftKey) { ObjMgrDeSelect (0, 0, 0, 0, NULL); } return; } if (itemID == VSM_PICT_UP_BUTTON) { expand = 1; } else if (itemID == VSM_PICT_DOWN_BUTTON) { expand = -1; } if (expand != 0) { bvp->expansion += expand; Hide (vwr); ResetClip (); Update (); PopulateDesktop (bvp); Show (vwr); Update (); return; } if (bvp->wasDoubleClick) { sep = GetTopSeqEntryForEntityID (entityID); if (bvp->launchSubviewers) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); return; } else if (LaunchViewerNotEditor (bvp, sep, entityID, itemID, itemtype)) { WatchCursor (); Update (); LaunchNewBioseqViewer (bvp->bsp, entityID, itemID, itemtype); ArrowCursor (); Update (); return; } else if (bvp->launchEditors) { WatchCursor (); Update (); GatherProcLaunch (OMPROC_EDIT, FALSE, entityID, itemID, itemtype, 0, 0, itemtype, 0); ArrowCursor (); Update (); return; } else { return; } } else if (bvp->sendSelectMessages) { if (bvp->wasShiftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } } static void PopulateDesktop (BioseqViewPtr bvp) { BioseqPtr bsp; Uint2 entityID; Boolean oldExtraLevel; ObjMgrDataPtr omdp; SegmenT seg; SeqEntryPtr sep; FonT tempfont; VSeqMgrPtr vsmp; VSMPictPtr vsmpp; Int4 vwr_x; Int4 vwr_y; Int2 vwr_align; if (bvp == NULL) return; WatchCursor (); vwr_x = INT4_MIN; vwr_y = INT4_MAX; vwr_align = UPPER_LEFT; if (bvp->moveToOldPos) { if (bvp->pict != NULL) { get_viewer_position (bvp->vwr, &(vwr_x), &(vwr_y)); vwr_align = MIDDLE_CENTER; } bvp->moveToOldPos = FALSE; } Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); Update (); bsp = bvp->bsp; if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); omdp = ObjMgrGetData (entityID); vsmpp = MemNew (sizeof (VSMPict)); if (vsmpp != NULL) { vsmpp->expansion = bvp->expansion; vsmp = VSeqMgrGet (); if (vsmp != NULL) { oldExtraLevel = vsmp->extraLevel; vsmp->extraLevel = TRUE; tempfont = vsmp->font; if (bvp->displayFont != NULL) { vsmp->font = bvp->displayFont; } SelectFont (vsmp->font); vsmp->lineheight = LineHeight(); vsmp->leading = Leading(); vsmp->charw = MaxCharWidth(); seg = VSMEntityDraw (omdp, vsmpp, vsmp); vsmp->font = tempfont; SelectFont (vsmp->font); vsmp->lineheight = LineHeight(); vsmp->leading = Leading(); vsmp->charw = MaxCharWidth(); SelectFont (systemFont); vsmp->extraLevel = oldExtraLevel; bvp->pict = CreatePicture (); LinkSegment (bvp->pict, seg); AttachPicture (bvp->vwr, bvp->pict, vwr_x, vwr_y, vwr_align, 1, 1, NULL); SetViewerProcs (bvp->vwr, ClickDesktop, NULL, ReleaseDesktop, NULL); } } MemFree (vsmpp); InitSelectDesktop (bvp); } ArrowCursor (); } static ParData geneParFmt = {FALSE, FALSE, FALSE, FALSE, TRUE, 0, 0}; typedef struct geneinputdata { GrouP geneGrp; TexT geneText; DoC geneList; Int2 clickedItem; Int2 clickedRow; Int2 selectedItem; Int2 selectedRow; } GeneInputData, PNTR GeneInputDataPtr; typedef struct genechoicedata { FORM_MESSAGE_BLOCK BioseqViewPtr bvp; GeneInputData geneData1; GeneInputData geneData2; Int2 numItems; Int2 geneIdxNum; CharPtr PNTR geneListIdx; } GeneChoiceData, PNTR GeneChoiceDataPtr; static void CopyField (CharPtr str, size_t max, CharPtr source, Int2 col) { Char ch; size_t count; CharPtr ptr; if (str != NULL && max > 0 && source != NULL) { MemSet (str, 0, max); ptr = source; ch = *ptr; while (col > 1 && ch != '\n' && ch != '\0') { while (ch != '\t' && ch != '\n' && ch != '\0') { ptr++; ch = *ptr; } if (ch == '\t') { ptr++; ch = *ptr; } col--; } count = 0; ch = ptr [count]; while (ch != '\t' && ch != '\n' && ch != '\0') { count++; ch = ptr [count]; } max = MIN (max, count); StringNCpy (str, ptr, max); /* remains StringNCpy, not _0 */ } } static void CopyStrFromGeneList (GeneChoiceDataPtr gcp, CharPtr str, size_t max, Int2 row) { CharPtr source; if (gcp != NULL && str != NULL && max > 0) { MemSet (str, 0, max); if (gcp->geneListIdx != NULL && row > 0) { source = gcp->geneListIdx [row - 1]; CopyField (str, max, source, 1); } } } static Int2 FindGeneName (GeneChoiceDataPtr gcp, CharPtr text) { Int2 compare; Int2 left; Int2 mid; Int2 right; Char str [256]; mid = 0; if (gcp != NULL && text != NULL && gcp->geneIdxNum > 0) { left = 1; right = gcp->geneIdxNum; while (left <= right) { mid = (left + right) / 2; CopyStrFromGeneList (gcp, str, sizeof (str) - 2, mid); compare = StringICmp (text, str); if (compare <= 0) { right = mid - 1; } if (compare >= 0) { left = mid + 1; } } if (left <= right + 1) { CopyStrFromGeneList (gcp, str, sizeof (str) - 2, mid); str [StringLen (text)] = '\0'; compare = StringICmp (text, str); if (compare > 0) { mid++; if (mid <= gcp->geneIdxNum) { CopyStrFromGeneList (gcp, str, sizeof (str) - 2, mid); str [StringLen (text)] = '\0'; compare = StringICmp (text, str); if (compare > 0) { mid = 0; } } } } } return mid; } static void AutoScrollGeneName (GeneChoiceDataPtr gcp, TexT t) { GeneInputDataPtr gdp; Boolean goOn; Int2 item; Int2 itm; Int4 line; Int2 num; Int2 numRows; Int2 oldItem; Int2 oldRow; Int2 row; Int4 startsAt; Char str [256]; Char txt [256]; if (gcp != NULL && t != NULL && gcp->geneListIdx != NULL) { if (t == gcp->geneData1.geneText) { gdp = &(gcp->geneData1); } else if (t == gcp->geneData2.geneText) { gdp = &(gcp->geneData2); } else { return; } GetTitle (t, str, sizeof (str) - 2); num = 0; oldItem = gdp->selectedItem; oldRow = gdp->selectedRow; line = FindGeneName (gcp, str); if (line > 0 && line <= gcp->geneIdxNum) { item = 0; row = 0; itm = 1; goOn = TRUE; while (goOn && itm <= gcp->numItems) { GetItemParams4 (gdp->geneList, itm, &startsAt, &numRows, NULL, NULL, NULL); if (line > startsAt + numRows) { itm++; } else { item = itm; row = line - startsAt; goOn = FALSE; } } if (! RowIsVisible (gdp->geneList, item, row, NULL, NULL)) { SetOffset (gdp->geneList, 0, line - 1); } CopyStrFromGeneList (gcp, txt, sizeof (txt) - 2, line); if (StringICmp (txt, str) != 0) { gdp->selectedItem = 0; gdp->selectedRow = 0; InvalDocRows (gdp->geneList, oldItem, oldRow, oldRow); return; } if (oldItem != item || oldRow != row) { gdp->selectedItem = 0; gdp->selectedRow = 0; InvalDocRows (gdp->geneList, oldItem, oldRow, oldRow); gdp->selectedItem = item; gdp->selectedRow = row; InvalDocRows (gdp->geneList, item, row, row); } } } } static void GeneNameText (TexT t) { GeneChoiceDataPtr gcp; gcp = (GeneChoiceDataPtr) GetObjectExtra (t); if (gcp != NULL) { AutoScrollGeneName (gcp, t); } } static ValNodePtr dup_slp_list(ValNodePtr slp_list, Int4 window_size) { ValNodePtr head = NULL; SeqLocPtr slp; SeqLocPtr dup_slp; Int4 start, stop; Int4 offset; SeqIntPtr sint; while(slp_list) { slp = slp_list->data.ptrvalue; if(slp->choice == SEQLOC_INT) { sint = slp->data.ptrvalue; start = MIN(sint->from, sint->to); stop = MAX(sint->from, sint->to); offset = window_size - (stop - start); if(offset > 0) { start -= offset/2; stop += offset/2; if(start < 0) start = 0; } dup_slp = SeqLocIntNew(start, stop, Seq_strand_plus, sint->id); ValNodeAddPointer(&head, 0, dup_slp); } slp_list = slp_list->next; } return head; } static Int4 get_default_window_size(GlobalDrawPtr gdraw_p) { GlobalBspPtr gbp; ValNodePtr curr; Int4 max_len = 0, val; for(curr = gdraw_p->gbp_list; curr != NULL; curr = curr->next) { gbp = (GlobalBspPtr)(curr->data.ptrvalue); max_len = MAX(max_len, gbp->bsp->length); } val = MIN(max_len, 10000); return MAX(max_len/20, val); } static void AcceptGeneName (ButtoN b) { BioseqViewPtr bvp; GeneChoiceDataPtr gcp; GeneDataPtr gdata; ValNodePtr old_g_list = NULL; RecT r; Char str [64]; CharPtr txt; ValNodePtr vnp; WindoW w; Int4 window_size; w = ParentWindow (b); Hide (w); gcp = (GeneChoiceDataPtr) GetObjectExtra (b); if (gcp != NULL && gcp->bvp != NULL) { bvp = gcp->bvp; str [0] = '\0'; txt = GetDocText (gcp->geneData1.geneList, gcp->geneData1.selectedItem, gcp->geneData1.selectedRow, 1); SafeSetTitle (gcp->geneData1.geneText, txt); MemFree (txt); GetTitle (gcp->geneData1.geneText, str, sizeof (str)); bvp->pict = DeletePicture (bvp->pict); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); if (StringHasNoText (str)) { old_g_list = bvp->g_list; bvp->g_list = NULL; } else { vnp = ValNodeNew (NULL); old_g_list = bvp->g_list; if (vnp != NULL) { vnp->data.ptrvalue = StringSave (str); } bvp->g_list = vnp; if (Visible (gcp->geneData2.geneGrp)) { str [0] = '\0'; txt = GetDocText (gcp->geneData2.geneList, gcp->geneData2.selectedItem, gcp->geneData2.selectedRow, 1); SafeSetTitle (gcp->geneData2.geneText, txt); MemFree (txt); GetTitle (gcp->geneData2.geneText, str, sizeof (str)); if (!StringHasNoText (str)) { ValNodeCopyStr (&(bvp->g_list), 0, str); } } } gdata = NULL; if (map_gene_location (bvp->gdraw_p, bvp->g_list, &gdata, NULL, FALSE)) { } PopulateMap (bvp); if (old_g_list != NULL) { ValNodeFreeData (old_g_list); } if (bvp->gdraw_p != NULL) { if (bvp->slp_list != NULL) { free_slp_list (bvp->slp_list); } bvp->slp_list = NULL; window_size = get_default_window_size (bvp->gdraw_p); bvp->slp_list = dup_slp_list (bvp->gdraw_p->slp_list, window_size); } } Remove (w); } static Boolean HighlightGeneName (DoC d, Int2 item, Int2 row, Int2 col) { GeneChoiceDataPtr gcp; GeneInputDataPtr gdp; gcp = (GeneChoiceDataPtr) GetObjectExtra (d); if (gcp != NULL) { if (d == gcp->geneData1.geneList) { gdp = &(gcp->geneData1); } else if (d == gcp->geneData2.geneList) { gdp = &(gcp->geneData2); } else { return FALSE; } return (Boolean) (item == gdp->selectedItem && row == gdp->selectedRow); } else { return FALSE; } } static void ClickGeneName (DoC d, PoinT pt) { GeneChoiceDataPtr gcp; GeneInputDataPtr gdp; Int2 item; Int2 oldItem; Int2 oldRow; Int2 row; gcp = (GeneChoiceDataPtr) GetObjectExtra (d); if (gcp != NULL) { if (d == gcp->geneData1.geneList) { gdp = &(gcp->geneData1); } else if (d == gcp->geneData2.geneList) { gdp = &(gcp->geneData2); } else { return; } MapDocPoint (d, pt, &item, &row, NULL, NULL); if (item > 0 && row > 0) { gdp->clickedItem = item; gdp->clickedRow = row; oldItem = gdp->selectedItem; oldRow = gdp->selectedRow; if (gdp->selectedItem != item || gdp->selectedRow != row) { gdp->selectedItem = 0; gdp->selectedRow = 0; InvalDocRows (d, oldItem, oldRow, oldRow); gdp->selectedItem = item; gdp->selectedRow = row; InvalDocRows (d, item, row, row); } } } } static void ReleaseGeneName (DoC d, PoinT pt) { GeneChoiceDataPtr gcp; GeneInputDataPtr gdp; Int2 item; Int2 row; CharPtr str; gcp = (GeneChoiceDataPtr) GetObjectExtra (d); if (gcp != NULL) { if (d == gcp->geneData1.geneList) { gdp = &(gcp->geneData1); } else if (d == gcp->geneData2.geneList) { gdp = &(gcp->geneData2); } else { return; } MapDocPoint (d, pt, &item, &row, NULL, NULL); if (gdp->clickedItem == item && gdp->clickedRow == row && item > 0 && row > 0) { str = GetDocText (d, item, row, 1); SafeSetTitle (gdp->geneText, str); Select (gdp->geneText); MemFree (str); } } } static void ShowSecondGroup (GrouP g) { GeneChoiceDataPtr gcp; gcp = (GeneChoiceDataPtr) GetObjectExtra (g); if (gcp != NULL) { if (GetValue (g) == 2) { SafeShow (gcp->geneData2.geneGrp); } else { SafeHide (gcp->geneData2.geneGrp); } } } static void CleanupGeneChoiceForm (GraphiC g, VoidPtr data) { GeneChoiceDataPtr gcp; gcp = (GeneChoiceDataPtr) data; if (gcp != NULL) { gcp->geneListIdx = MemFree (gcp->geneListIdx); } StdCleanupFormProc (g, data); } static void DisplayGeneChoiceWindow (CharPtr path, BioseqViewPtr bvp) { ButtoN b; GrouP c; Char ch; Pointer dataptr; GrouP g; GeneChoiceDataPtr gcp; CharPtr PNTR geneIdx; ValNodePtr g_list; GrouP h; Boolean hasTwoGenesSelected; Int2 idx; Int2 item; GrouP k; Int2 numItems; Int4 numLines; Int2 numRows; PrompT p; Char str [64]; CharPtr tmp; WindoW w; if (bvp == NULL) return; gcp = (GeneChoiceDataPtr) MemNew (sizeof (GeneChoiceData)); if (gcp == NULL) return; gcp->bvp = bvp; w = MovableModalWindow (-50, -33, -10, -10, "Gene and Product List", NULL); SetObjectExtra (w, gcp, CleanupGeneChoiceForm); k = HiddenGroup (w, 2, 0, ShowSecondGroup); SetObjectExtra (k, gcp, NULL); RadioButton (k, "Find Single Gene"); RadioButton (k, "Enter Gene Range"); SetValue (k, 1); h = HiddenGroup (w, -2, 0, NULL); str [0] = '\0'; if (bvp->g_list != NULL) { g_list = bvp->g_list; StringNCpy_0 (str, (CharPtr) g_list->data.ptrvalue, sizeof (str)); } gcp->geneData1.geneGrp = HiddenGroup (h, -1, 0, NULL); g = HiddenGroup (gcp->geneData1.geneGrp, 4, 0, NULL); p = StaticPrompt (g, "First Symbol", 0, dialogTextHeight, programFont, 'l'); gcp->geneData1.geneText = DialogText (g, str, 10, GeneNameText); SetObjectExtra (gcp->geneData1.geneText, gcp, NULL); gcp->geneData1.geneList = DocumentPanel (gcp->geneData1.geneGrp, 15 * stdCharWidth, 10 * stdLineHeight); SetObjectExtra (gcp->geneData1.geneList, gcp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) gcp->geneData1.geneList, NULL); SetDocProcs (gcp->geneData1.geneList, ClickGeneName, NULL, ReleaseGeneName, NULL); SetDocShade (gcp->geneData1.geneList, NULL, NULL, HighlightGeneName, NULL); DisplayFancy (gcp->geneData1.geneList, path, &geneParFmt, NULL, systemFont, 4); str [0] = '\0'; if (bvp->g_list != NULL) { g_list = bvp->g_list; g_list = g_list->next; if (g_list != NULL) { StringNCpy_0 (str, (CharPtr) g_list->data.ptrvalue, sizeof (str)); } } hasTwoGenesSelected = (Boolean) (str [0] == '\0'); gcp->geneData2.geneGrp = HiddenGroup (h, -1, 0, NULL); g = HiddenGroup (gcp->geneData2.geneGrp, 4, 0, NULL); p = StaticPrompt (g, "Second Symbol", 0, dialogTextHeight, programFont, 'l'); gcp->geneData2.geneText = DialogText (g, str, 10, GeneNameText); SetObjectExtra (gcp->geneData2.geneText, gcp, NULL); gcp->geneData2.geneList = DocumentPanel (gcp->geneData2.geneGrp, 15 * stdCharWidth, 10 * stdLineHeight); SetObjectExtra (gcp->geneData2.geneList, gcp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) gcp->geneData2.geneList, NULL); SetDocProcs (gcp->geneData2.geneList, ClickGeneName, NULL, ReleaseGeneName, NULL); SetDocShade (gcp->geneData2.geneList, NULL, NULL, HighlightGeneName, NULL); DisplayFancy (gcp->geneData2.geneList, path, &geneParFmt, NULL, systemFont, 4); if (hasTwoGenesSelected) { Hide (gcp->geneData2.geneGrp); } else { SetValue (k, 2); } gcp->geneIdxNum = 0; gcp->geneListIdx = NULL; gcp->numItems = 0; c = HiddenGroup (w, 4, 0, NULL); SetGroupSpacing (c, 10, 3); b = DefaultButton (c, "Accept", AcceptGeneName); SetObjectExtra (b, gcp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) k, (HANDLE) h, (HANDLE) c, NULL); GetDocParams4 (gcp->geneData1.geneList, &numItems, &numLines); if (numItems > 0 && numLines > 0 && numLines < 32000) { gcp->numItems = numItems; geneIdx = MemNew (sizeof (CharPtr) * (size_t) (numLines + 3)); gcp->geneListIdx = geneIdx; if (geneIdx != NULL) { gcp->geneIdxNum = numLines; idx = 0; for (item = 1; item <= numItems; item++) { GetItemParams4 (gcp->geneData1.geneList, item, NULL, &numRows, NULL, NULL, &dataptr); if (dataptr != NULL && numRows > 0 && idx < numLines) { tmp = (CharPtr) dataptr; ch = *tmp; geneIdx [idx] = tmp; while (ch != '\0') { if (ch == '\n') { idx++; tmp++; ch = *tmp; geneIdx [idx] = tmp; } else { tmp++; ch = *tmp; } } } } GeneNameText (gcp->geneData1.geneText); } } Show (w); Select (w); Select (gcp->geneData1.geneText); } static int LIBCALLBACK CompareValNodeStrings (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { return StringICmp (str1, str2); } else { return 0; } } else { return 0; } } else { return 0; } } typedef struct getgenesdata { SeqEntryPtr nsep; BioseqPtr segbsp; Boolean dirty; MonitorPtr mon; Int2 count; } GetGenesData, PNTR GetGenesPtr; static Boolean GetGenesOnParts (GatherContextPtr gcp) { BioseqContextPtr bcp; BioseqPtr bsp; Int4 from; GetGenesPtr ggp; GatherRangePtr grp; Int2 i; SeqFeatPtr newsfp; Boolean noLeft; Boolean noRight; Boolean partial5; Boolean partial3; SeqFeatPtr prot; ProtRefPtr prp; SeqIdPtr sip; SeqFeatPtr sfp; Int4 to; SeqFeatXrefPtr xref; if (gcp == NULL) return TRUE; ggp = (GetGenesPtr) gcp->userdata; if (ggp == NULL) return TRUE; switch (gcp->thistype) { case OBJ_BIOSEQ_SEG : (ggp->count)++; MonitorIntValue (ggp->mon, ggp->count); break; case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL) { if (sfp->data.choice == SEQFEAT_GENE || sfp->data.choice == SEQFEAT_CDREGION) { CheckSeqLocForPartial (sfp->location, &noLeft, &noRight); ggp->dirty = TRUE; newsfp = AsnIoMemCopy (sfp, (AsnReadFunc) SeqFeatAsnRead, (AsnWriteFunc) SeqFeatAsnWrite); if (newsfp != NULL) { newsfp->location = SeqLocFree (newsfp->location); for (grp = gcp->rdp, i = 0; grp != NULL && i < gcp->num_interval; grp++, i++) { if (grp->strand == Seq_strand_minus) { from = grp->right; to = grp->left; partial5 = grp->r_trunc; partial3 = grp->l_trunc; } else { from = grp->left; to = grp->right; partial5 = grp->l_trunc; partial3 = grp->r_trunc; } AddSeqFeatInterval (newsfp, ggp->segbsp, from, to, partial5, partial3); } FreeAllFuzz (newsfp->location); SetSeqLocPartial (newsfp->location, noLeft, noRight); newsfp->partial = (newsfp->partial || noLeft || noRight); CreateNewFeature (ggp->nsep, NULL, sfp->data.choice, newsfp); if (sfp->data.choice == SEQFEAT_CDREGION) { sip = SeqLocId (newsfp->product); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { bcp = BioseqContextNew (bsp); prot = BioseqContextGetSeqFeat (bcp, SEQFEAT_PROT, NULL, NULL, 0); BioseqContextFree(bcp); if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; if (prp != NULL) { xref = SeqFeatXrefNew (); if (xref != NULL) { xref->data.choice = SEQFEAT_PROT; xref->data.value.ptrvalue = AsnIoMemCopy (prp, (AsnReadFunc) ProtRefAsnRead, (AsnWriteFunc) ProtRefAsnWrite); xref->next = newsfp->xref; newsfp->xref = xref; } } } } } newsfp->product = SeqLocFree (newsfp->product); } } } } break; default : break; } return TRUE; } static Boolean FetchGenesFromParts (Uint2 entityID, SeqEntryPtr nsep, BioseqPtr segbsp) { GetGenesData ggd; GatherScope gs; Int2 num; ValNode vn; if (nsep == NULL || segbsp == NULL || segbsp->repr != Seq_repr_seg) return FALSE; ggd.nsep = nsep; ggd.segbsp = segbsp; ggd.dirty = FALSE; ggd.count = 0; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 2; gs.nointervals = FALSE; gs.get_feats_location = TRUE; MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof (Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_BIOSEQ_DELTA] = FALSE; gs.ignore[OBJ_BIOSEQ_MAPFEAT] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; vn.choice = SEQLOC_WHOLE; vn.data.ptrvalue = (Pointer) segbsp->id; gs.target = &vn; num = get_seg_num ((SeqLocPtr) (segbsp->seq_ext)); ggd.mon = MonitorIntNew ("Searching components", 0, (Int4) num); GatherEntity (entityID, (Pointer) &ggd, GetGenesOnParts, &gs); MonitorFree (ggd.mon); return ggd.dirty; } extern void ShowGeneList (ButtoN b) { BioseqPtr bsp; BioseqViewPtr bvp; Uint2 entityID; FILE *fp; ValNodePtr g_list; SeqEntryPtr nsep; Char path [PATH_MAX]; SeqEntryPtr sep; CharPtr str; ValNodePtr vnp; ValNodePtr vnpn; bvp = (BioseqViewPtr) GetObjectExtra (b); if (bvp == NULL) return; WatchCursor (); TmpNam (path); entityID = ObjMgrGetEntityIDForPointer (bvp->bsp); sep = GetTopSeqEntryForEntityID (entityID); nsep = FindNucSeqEntry (sep); if (nsep == NULL) return; bsp = (BioseqPtr) nsep->data.ptrvalue; if (bsp == NULL) return; if (bsp->repr == Seq_repr_seg && (! BioseqHasFeature (bsp))) { if (bvp->hasTargetControl) { if (FetchGenesFromParts (entityID, nsep, bsp)) { ObjMgrSetDirtyFlag (entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0); } } } g_list = BuildGeneList (sep); if (g_list != NULL) { g_list = SortValNode (g_list, CompareValNodeStrings); vnp = g_list; while (vnp != NULL) { vnpn = vnp->next; if (vnpn != NULL) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, (CharPtr) vnpn->data.ptrvalue) == 0) { vnp->next = vnpn->next; vnpn->next = NULL; ValNodeFreeData (vnpn); } else { vnp = vnpn; } } else { vnp = vnpn; } } fp = FileOpen (path, "w"); if (fp != NULL) { vnp = g_list; while (vnp != NULL) { str = (CharPtr) vnp->data.ptrvalue; if (str != NULL && StringLen (str) < 200) { fprintf (fp, "%s\n", str); } vnp = vnp->next; } FileClose (fp); DisplayGeneChoiceWindow (path, bvp); } } ValNodeFreeData (g_list); FileRemove (path); ArrowCursor (); } static void ShowMap (BioseqViewPtr bvp, Boolean show) { if (bvp == NULL) return; if (show) { SafeShow (bvp->vwr); SafeShow (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeShow (bvp->findGeneGrp); SafeHide (bvp->clickMe); } else { SafeHide (bvp->vwr); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeHide (bvp->docTxtControlGrp); SafeHide (bvp->baseCtgControlGrp); SafeHide (bvp->modeControlGrp); SafeHide (bvp->newGphControlGrp); SafeHide (bvp->clickMe); } } static void ShowCompressed (BioseqViewPtr bvp, Boolean show) { if (bvp == NULL) return; if (show) { SafeShow (bvp->vwr); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeShow (bvp->clickMe); } else { SafeHide (bvp->vwr); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeHide (bvp->docTxtControlGrp); SafeHide (bvp->baseCtgControlGrp); SafeHide (bvp->modeControlGrp); SafeHide (bvp->newGphControlGrp); SafeHide (bvp->clickMe); } } static void ShowGraphical (BioseqViewPtr bvp, Boolean show) { if (bvp == NULL) return; if (show) { SafeShow (bvp->vwr); SafeShow (bvp->styleControlGrp); SafeShow (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, TRUE); SafeHide (bvp->findGeneGrp); SafeShow (bvp->clickMe); } else { SafeHide (bvp->vwr); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeHide (bvp->docTxtControlGrp); SafeHide (bvp->baseCtgControlGrp); SafeHide (bvp->modeControlGrp); SafeHide (bvp->newGphControlGrp); SafeHide (bvp->clickMe); } } static void ShowAlignment (BioseqViewPtr bvp, Boolean show) { if (bvp == NULL) return; if (show) { SafeShow (bvp->vwr); SafeShow (bvp->styleControlGrp); SafeShow (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeShow (bvp->clickMe); } else { SafeHide (bvp->vwr); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeHide (bvp->docTxtControlGrp); SafeHide (bvp->baseCtgControlGrp); SafeHide (bvp->modeControlGrp); SafeHide (bvp->newGphControlGrp); SafeHide (bvp->clickMe); } } static void ShowSalsa (BioseqViewPtr bvp, Boolean show) { if (bvp == NULL) return; if (show) { SafeShow (bvp->pnl); SafeShow (bvp->pnlParentGrp); SafeShow (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeShow (bvp->clickMe); } else { SafeHide (bvp->pnlParentGrp); SafeHide (bvp->pnl); Reset (bvp->pnl); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeHide (bvp->docTxtControlGrp); SafeHide (bvp->baseCtgControlGrp); SafeHide (bvp->modeControlGrp); SafeHide (bvp->newGphControlGrp); SafeHide (bvp->clickMe); } } static void ShowDesktop (BioseqViewPtr bvp, Boolean show) { if (bvp == NULL) return; if (show) { SafeShow (bvp->vwr); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeShow (bvp->clickMe); } else { SafeHide (bvp->vwr); Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); SafeHide (bvp->styleControlGrp); SafeHide (bvp->scaleControlGrp); EnableDisableLegendItem (bvp, FALSE); SafeHide (bvp->findGeneGrp); SafeHide (bvp->docTxtControlGrp); SafeHide (bvp->baseCtgControlGrp); SafeHide (bvp->modeControlGrp); SafeHide (bvp->newGphControlGrp); SafeHide (bvp->clickMe); } } typedef struct selectdata { VieweR vwr; SelStructPtr sel; Uint2 entityID; Uint2 itemID; Uint2 itemtype; SeqLocPtr region; } SelectData, PNTR SelectPtr; static Boolean SelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Uint2 entityID; Uint2 itemID; Uint2 itemtype; Int2 parID; SelectPtr sp; sp = (SelectPtr) userdata; parID = SegmentID (ParentSegment (seg)); entityID = segID; itemID = primID; itemtype = (Uint2) parID; if (entityID == sp->entityID && itemID == sp->itemID && itemtype == sp->itemtype) { HighlightPrimitive (sp->vwr, seg, prim, FRAME_PRIMITIVE); } return TRUE; } static Boolean DeselectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Uint2 entityID; Uint2 itemID; Uint2 itemtype; Int2 parID; SelectPtr sp; sp = (SelectPtr) userdata; parID = SegmentID (ParentSegment (seg)); entityID = segID; itemID = primID; itemtype = (Uint2) parID; if (entityID == sp->entityID && itemID == sp->itemID && itemtype == sp->itemtype) { HighlightPrimitive (sp->vwr, seg, prim, PLAIN_PRIMITIVE); } return TRUE; } static void SelectGraphical (BioseqViewPtr bvp, Uint2 selentityID, Uint2 selitemID, Uint2 selitemtype, SeqLocPtr region, Boolean select, Boolean scrollto) { SelectData sd; if (bvp == NULL) return; if (! bvp->highlightSelections) return; /* if (bvp->viewWholeEntity) return; */ sd.vwr = bvp->vwr; sd.sel = ObjMgrGetSelected (); sd.entityID = selentityID; sd.itemID = selitemID; sd.itemtype = selitemtype; sd.region = region; if (select) { ExploreSegment (bvp->pict, (Pointer) &sd, SelectPrim); } else { ExploreSegment (bvp->pict, (Pointer) &sd, DeselectPrim); } } static Boolean InitSelectPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Uint2 entityID; Uint2 itemID; Uint2 itemtype; Int2 parID; SelStructPtr sel; SelectPtr sp; sp = (SelectPtr) userdata; parID = SegmentID (ParentSegment (seg)); entityID = segID; itemID = primID; itemtype = (Uint2) parID; for (sel = sp->sel; sel != NULL; sel = sel->next) { if (entityID == sel->entityID && itemID == sel->itemID && itemtype == sel->itemtype) { HighlightPrimitive (sp->vwr, seg, prim, FRAME_PRIMITIVE); } } return TRUE; } static void InitSelectGraphical (BioseqViewPtr bvp) { SelectData sd; if (bvp == NULL) return; if (! bvp->highlightSelections) return; /* if (bvp->viewWholeEntity) return; */ sd.vwr = bvp->vwr; sd.sel = ObjMgrGetSelected (); sd.entityID = 0; sd.itemID = 0; sd.itemtype = 0; sd.region = NULL; ExploreSegment (bvp->pict, (Pointer) &sd, InitSelectPrim); } static void SelectSalsa (BioseqViewPtr bvp, Uint2 selentityID, Uint2 selitemID, Uint2 selitemtype, SeqLocPtr region, Boolean select, Boolean scrollto) { } static Boolean VSMSelectProc (SegmenT seg, PrimitivE prim, Uint2 segid, Uint2 primID, Uint2 primct, Pointer data) { Uint2 itemID; Uint2 itemtype; SelectPtr sp; sp = (SelectPtr) data; itemID = primID; itemtype = segid; if (itemID == sp->itemID && itemtype == sp->itemtype) { HighlightSegment (sp->vwr, seg, OUTLINE_SEGMENT); } return TRUE; } static Boolean VSMDeselectProc (SegmenT seg, PrimitivE prim, Uint2 segid, Uint2 primID, Uint2 primct, Pointer data) { Uint2 itemID; Uint2 itemtype; SelectPtr sp; sp = (SelectPtr) data; itemID = primID; itemtype = segid; if (itemID == sp->itemID && itemtype == sp->itemtype) { HighlightSegment (sp->vwr, seg, PLAIN_SEGMENT); } return TRUE; } static void SelectDesktop (BioseqViewPtr bvp, Uint2 selentityID, Uint2 selitemID, Uint2 selitemtype, SeqLocPtr region, Boolean select, Boolean scrollto) { SelectData sd; if (bvp == NULL) return; if (! bvp->highlightSelections) return; /* if (bvp->viewWholeEntity) return; */ sd.vwr = bvp->vwr; sd.sel = ObjMgrGetSelected (); sd.entityID = selentityID; sd.itemID = selitemID; sd.itemtype = selitemtype; sd.region = region; if (select) { ExploreSegment (bvp->pict, (Pointer) &sd, VSMSelectProc); } else { ExploreSegment (bvp->pict, (Pointer) &sd, VSMDeselectProc); } } static Boolean VSMInitSelectProc (SegmenT seg, PrimitivE prim, Uint2 segid, Uint2 primID, Uint2 primct, Pointer data) { Uint2 itemID; Uint2 itemtype; SelStructPtr sel; SelectPtr sp; sp = (SelectPtr) data; itemID = primID; itemtype = segid; for (sel = sp->sel; sel != NULL; sel = sel->next) { if (itemID == sel->itemID && itemtype == sel->itemtype) { HighlightSegment (sp->vwr, seg, OUTLINE_SEGMENT); } } return TRUE; } static void InitSelectDesktop (BioseqViewPtr bvp) { SelectData sd; if (bvp == NULL) return; if (! bvp->highlightSelections) return; /* if (bvp->viewWholeEntity) return; */ sd.vwr = bvp->vwr; sd.sel = ObjMgrGetSelected (); sd.entityID = 0; sd.itemID = 0; sd.itemtype = 0; sd.region = NULL; ExploreSegment (bvp->pict, (Pointer) &sd, VSMInitSelectProc); } static void SelectRegion (VieweR viewer, SegmenT segment, PrimitivE primitive, SeqLocPtr region, Uint2 entityID) { BioseqPtr bsp; RecT d; ViewPData extra; RecT r; RecT s; SegPPtr seg; WindoW tempPort; BoxInfo pLimits; if (viewer == NULL || segment == NULL || primitive == NULL || region == NULL) return; seg = (SegPPtr) segment; if (seg->base.code != SEGMENT && seg->base.code != PICTURE) return; if (! seg->seg.visible) return; if (Visible (viewer) && AllParentsVisible (viewer)) { GetPanelExtra ((PaneL) viewer, &extra); TryGetPrimitiveLimits ((BasePPtr) primitive, extra.scale.scaleX, extra.scale.scaleY, &pLimits); bsp = GetBioseqGivenSeqLoc (region, entityID); if (bsp == NULL) return; if (ABS (pLimits.left - pLimits.right) < bsp->length) return; pLimits.left = SeqLocStart (region); pLimits.right = SeqLocStop (region); if (! BoxInViewport (&r, &(pLimits), &(extra.scale))) return; InsetRect (&r, 0, -3); if (ABS (r.left - r.right) < 2) { InsetRect (&r, -1, 0); } ObjectRect (viewer, &s); InsetRect (&s, 2, 2); SectRect (&r, &s, &d); tempPort = SavePort (viewer); Select (viewer); Dotted (); FrameRect (&d); Solid (); RestorePort (tempPort); } } static Boolean DrawSelectionPrim (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { Uint2 entityID; Uint2 itemID; Uint2 itemtype; Int2 parID; SelStructPtr sel; SelectPtr sp; parID = SegmentID (ParentSegment (seg)); itemtype = (Uint2) parID; if (itemtype != OBJ_BIOSEQ) return TRUE; sp = (SelectPtr) userdata; entityID = segID; itemID = primID; for (sel = sp->sel; sel != NULL; sel = sel->next) { if (entityID == sel->entityID && itemID == sel->itemID && itemtype == sel->itemtype && sel->region != NULL) { SelectRegion (sp->vwr, seg, prim, sel->region, entityID); } } return TRUE; } static void DrawSelectionRange (VieweR viewer, SegmenT segment) { Boolean okay; SelectData sd; SelStructPtr sel; sd.vwr = viewer; sd.sel = ObjMgrGetSelected (); sd.entityID = 0; sd.itemID = 0; sd.itemtype = 0; sd.region = NULL; okay = FALSE; for (sel = sd.sel; sel != NULL; sel = sel->next) { if (sel->itemtype == OBJ_BIOSEQ && sel->region != NULL) { okay = TRUE; } } if (okay) { ExploreSegment (segment, (Pointer) &sd, DrawSelectionPrim); } } static void CopyGraphicalToClipboard (BioseqViewPtr bvp) { if (bvp == NULL || bvp->vwr == NULL) return; CopyViewer (bvp->vwr); } #ifdef WIN_MOTIF extern CharPtr Nlm_XrmGetResource (const Char PNTR _resource); #endif static void PrintGraphical (BioseqViewPtr bvp) { MsgAnswer ans; if (bvp == NULL || bvp->vwr == NULL) return; #ifdef WIN_MOTIF Message (MSG_OK, "Printing of graphics under MOTIF is not supported at this time."); #else ans = Message (MSG_YN, "Do you want to print just the visible area?"); if (ans == ANS_YES) { PrintViewer (bvp->vwr); } else { PrintAllViewer (bvp->vwr); } #endif } typedef struct expboundstruc { FILE *file; ViewPData extra; RecT vwrct; } ExpBound, PNTR ExpBoundPtr; static Boolean ExpBoundCallback (SegmenT seg, PrimitivE prim, Uint2 segID, Uint2 primID, Uint2 primCt, VoidPtr userdata) { ExpBoundPtr ebp; Uint2 entityID; Uint2 itemID; Uint2 itemType; BoxInfo pLimits; SegmenT pseg; RecT r; if (seg == NULL || prim == NULL || segID == 0 || primID == 0 || userdata == NULL) return TRUE; ebp = (ExpBoundPtr) userdata; pseg = ParentSegment (seg); if (pseg == NULL) return TRUE; entityID = segID; itemID = primID; itemType = SegmentID (pseg); if (itemType == 0) return TRUE; if (TryGetPrimitiveLimits ((BasePPtr) prim, ebp->extra.scale.scaleX, ebp->extra.scale.scaleY, &pLimits)) { if (BoxInViewport (&r, &(pLimits), &(ebp->extra.scale))) { OffsetRect (&r, -ebp->vwrct.left, -ebp->vwrct.top); if (ebp->file != NULL) { fprintf (ebp->file, "%d %d %d %d %d %d %d\n", (int) entityID, (int) itemID, (int) itemType, (int) r.left, (int) r.top, (int) r.right, (int) r.bottom); } } } return TRUE; } static void ExploreToGetBoundaries (VieweR vwr, SegmenT seg, CharPtr filename) { ExpBound exp; if (vwr == NULL || seg == NULL || filename == NULL || *filename == '\0') return; GetPanelExtra ((PaneL) vwr, &(exp.extra)); ObjectRect (vwr, &(exp.vwrct)); InsetRect (&(exp.vwrct), 4, 4); exp.file = FileOpen (filename, "w"); if (exp.file != NULL) { ExploreSegment (seg, &exp, ExpBoundCallback); } FileClose (exp.file); } static void GifGraphical (BioseqViewPtr bvp, CharPtr filename, CharPtr dfault) { if (bvp == NULL || bvp->vwr == NULL) return; ExploreToGetBoundaries (bvp->vwr, bvp->pict, filename); } static void ExportSalsa (BioseqViewPtr bvp, CharPtr filename, CharPtr dfault) { SaveSalsaPanel (bvp->pnl); } #define MIN_HEIGHT 100 static void ResizeMap (BioseqViewPtr bvp) { Int2 height; Int2 oldstyle; RecT r; Int2 style; if (bvp == NULL) return; if (bvp->vwr != NULL) { if (Visible (bvp->vwr) && AllParentsVisible (bvp->vwr)) { ObjectRect (ParentWindow (bvp->vwr), &r); height = r.bottom - r.top; if (height >= MIN_HEIGHT) { WatchCursor (); oldstyle = GetMuskCurrentSt (); style = GetValue (bvp->style) - 1; SetMuskCurrentSt (GetMuskStyleName (style)); ObjectRect (bvp->vwr, &r); InsetRect (&r, 4, 4); bvp->pict = DeletePicture (bvp->pict); bvp->pict = GlobalPictureUpdate (bvp->gdraw_p, bvp->g_list, r.right - r.left, r.bottom - r.top); if (bvp->gdraw_p->is_circle) { AttachPicture (bvp->vwr, bvp->pict, 0, 0, UPPER_LEFT, 1, 1, NULL); } else { AttachPicture (bvp->vwr, bvp->pict, INT4_MIN, 0, UPPER_LEFT, 1, 1, NULL); } SetViewerProcs (bvp->vwr, ClickMap, DragMap, ReleaseMap, NULL); SetMuskCurrentSt (GetMuskStyleName (oldstyle)); ArrowCursor (); } } } } static void ResizeCompressed (BioseqViewPtr bvp) { BioseqPtr bsp; ErrSev oldErrSev; if (bvp == NULL) return; if (bvp->vwr != NULL) { if (Visible (bvp->vwr) && AllParentsVisible (bvp->vwr)) { Reset (bvp->vwr); bvp->pict = DeletePicture (bvp->pict); bsp = bvp->bsp; oldErrSev = ErrSetMessageLevel (SEV_FATAL); BioseqLock (bsp); PopulateCompressed (bvp); BioseqUnlock (bsp); ErrSetMessageLevel (oldErrSev); } } } static void ResizeGraphical (BioseqViewPtr bvp) { if (bvp == NULL) return; if (bvp->vwr != NULL) { if (Visible (bvp->vwr) && AllParentsVisible (bvp->vwr)) { ViewerWasResized (bvp->vwr); } } } static void ResizeSalsa (BioseqViewPtr bvp) { if (bvp == NULL) return; if (bvp->pnl != NULL) { if (Visible (bvp->pnl) && AllParentsVisible (bvp->pnl)) { SalsaPanelHasResized (bvp->pnl); } } } static void ResizeDesktop (BioseqViewPtr bvp) { if (bvp == NULL) return; if (bvp->vwr != NULL) { if (Visible (bvp->vwr) && AllParentsVisible (bvp->vwr)) { ViewerWasResized (bvp->vwr); } } } BioseqPageData mapPageData = { "Map", FALSE, FALSE, TRUE, FALSE, -1, PopulateMap, ShowMap, SelectGraphical, CopyGraphicalToClipboard, PrintGraphical, NULL, NULL, ResizeMap, NULL }; BioseqPageData sumPageData = { "Summary", TRUE, FALSE, FALSE, FALSE, -1, PopulateCompressed, ShowCompressed, SelectGraphical, CopyGraphicalToClipboard, PrintGraphical, NULL, NULL, ResizeCompressed, NULL }; BioseqPageData gphPageData = { "Graphic", TRUE, TRUE, TRUE, FALSE, -1, PopulateGraphic, ShowGraphical, SelectGraphical, CopyGraphicalToClipboard, PrintGraphical, NULL, GifGraphical, ResizeGraphical, NULL }; BioseqPageData alnPageData = { "Alignment", TRUE, TRUE, TRUE, TRUE, -1, PopulateAlignment, ShowAlignment, SelectGraphical, CopyGraphicalToClipboard, PrintGraphical, NULL, NULL, ResizeGraphical, NULL }; BioseqPageData seqPageData = { "Sequence", TRUE, TRUE, FALSE, FALSE, -1, PopulateSalsa, ShowSalsa, SelectSalsa, NULL, NULL, ExportSalsa, NULL, ResizeSalsa, NULL }; BioseqPageData dskPageData = { "Desktop", TRUE, TRUE, TRUE, FALSE, -1, PopulateDesktop, ShowDesktop, SelectDesktop, CopyGraphicalToClipboard, PrintGraphical, NULL, NULL, ResizeDesktop, NULL };