/* salpanel.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: salpanel.c * * Author: Colombe Chappey * * Version Creation Date: 1/27/96 * * $Revision: 6.54 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include #include #include #include #include #include #include #define OBJ_VIRT 254 static Uint1 rectSym [] = { 0xFE, 0x82, 0x82, 0x82, 0x82, 0x82, 0xFE, 0x00 }; static Uint1 diamondSym [] = { 0x10, 0x28, 0x44, 0x82, 0x44, 0x28, 0x10, 0x00 }; static Uint1 ovalSym [] = { 0x38, 0x44, 0x82, 0x82, 0x82, 0x44, 0x38, 0x00 }; static Uint1 leftTriSym [] = { 0x06, 0x1A, 0x62, 0x82, 0x62, 0x1A, 0x06, 0x00 }; static Uint1 rightTriSym [] = { 0xC0, 0xB0, 0x8C, 0x82, 0x8C, 0xB0, 0xC0, 0x00 }; static Uint1 upTriSym [] = { 0x10, 0x28, 0x28, 0x44, 0x44, 0x82, 0xFE, 0x00 }; static Uint1 downTriSym [] = { 0xFE, 0x82, 0x44, 0x44, 0x28, 0x28, 0x10, 0x00 }; static Uint1 rectFillSym [] = { 0xFE, 0xFE, 0xFE, 0xFE, 0xFE, 0xFE, 0xFE, 0x00 }; static Uint1 diamondFillSym [] = { 0x10, 0x38, 0x7C, 0xFE, 0x7C, 0x38, 0x10, 0x00 }; static Uint1 ovalFillSym [] = { 0x38, 0x7C, 0xFE, 0xFE, 0xFE, 0x7C, 0x38, 0x00 }; static Uint1 leftTriFillSym [] = { 0x06, 0x1E, 0x7E, 0xFE, 0x7E, 0x1E, 0x06, 0x00 }; static Uint1 rightTriFillSym [] = { 0xC0, 0xF0, 0xFC, 0xFE, 0xFC, 0xF0, 0xC0, 0x00 }; static Uint1 upTriFillSym [] = { 0x10, 0x38, 0x38, 0x7C, 0x7C, 0xFE, 0xFE, 0x00 }; static Uint1 downTriFillSym [] = { 0xFE, 0xFE, 0x7C, 0x7C, 0x38, 0x38, 0x10, 0x00 }; static Uint1 rightOvalSym [] = { 0x18, 0x14, 0x12, 0x12, 0x12, 0x14, 0x18, 0x00 }; static Uint1 leftOvalSym [] = { 0x38, 0x44, 0x82, 0x82, 0x82, 0x44, 0x38, 0x00 }; static Uint1 rightOvalFillSym [] = { 0x18, 0x1C, 0x1E, 0x1E, 0x1E, 0x1C, 0x18, 0x00 }; static Uint1 leftOvalFillSym [] = { 0x30, 0x50, 0x90, 0x90, 0x90, 0x50, 0x30, 0x00 }; /*###################################################################### # # functions for setting up the color for different object # ######################################################################*/ #define RGB_B(x) (Uint1)((x)&255); #define RGB_G(x) (Uint1)(((x)>>8)&255); #define RGB_R(x) (Uint1)(((x)>>16)&255); static Boolean convert_color(Int4 val, Uint1Ptr color) { if(val<0 || color == NULL) return FALSE; color[0] = RGB_R(val); color[1] = RGB_G(val); color[2] = RGB_B(val); return TRUE; } static Uint4 getcolor_fromstyles (Uint2 itemsubtype) { Int4 c_val; Uint1 color [3]; c_val = GetMuskCParam (itemsubtype, MSM_SEGMENT, MSM_COLOR); if ( convert_color (c_val, color) ) return GetColorRGB (color[0], color[1], color[2]); return GetColorRGB (0, 0, 0); } static Uint4 getcolorforvirtfeat (Uint2 item) { return GetColorRGB ((Uint1)((item % 3) * 40), (Uint1)(255-(item % 3) * 40), (Uint1)((item % 3) * 40)); } /********************************************** *** GetAlignEditData **********************************************/ extern WindoW getwindow_frompanel (PaneL pnl) { /* #ifdef WIN_MAC w = FrontWindow (); #else w = ParentWindow (pnl); #endif */ return ParentWindow (pnl); } extern PaneL GetPanelFromWindow (WindoW w) { SeqEditViewFormPtr wdp; wdp = (SeqEditViewFormPtr) GetObjectExtra (w); if (wdp == NULL) { return NULL; } if ( wdp->pnl == NULL ) { return NULL; } return wdp->pnl; } extern EditAlignDataPtr GetAlignEditData (WindoW w) { PaneL pnl; EditAlignDataPtr adp; pnl = GetPanelFromWindow (w); if (pnl == NULL) return NULL; GetPanelExtra (pnl, &adp); if ( adp == NULL ) return NULL; if ( adp->firstssp == NULL ) return NULL; return adp; } extern EditAlignDataPtr GetAlignDataPanel (PaneL pnl) { EditAlignDataPtr adp; if ( pnl == NULL ) return NULL; GetPanelExtra (pnl, &adp); if ( adp == NULL ) return NULL; if ( adp->firstssp == NULL ) return NULL; return adp; } /********************************************** *** AlignDataSet_Restore *** Inval Rect *** RestorePort **********************************************/ static void get_client_rect (PaneL p, RectPtr prc) { ObjectRect (p, prc); InsetRect (prc, HRZ_BORDER_WIDTH, VER_BORDER_WIDTH); } static void get_client_rectxy (PaneL p, RectPtr prc, Int2 x, Int2 y) { ObjectRect (p, prc); InsetRect (prc, x, y); } /************************************************************** *** *** **************************************************************/ static SelStructPtr get_firstline (SelEdStructPtr sesp1, SelStructPtr buffer) { SelEdStructPtr sesp; SelStructPtr buf; if (buffer == NULL) { ErrPostEx (SEV_ERROR, 0, 0, "fail in get_firstline [25]"); return NULL; } if (sesp1 == NULL) { return buffer; } for (buf=buffer; buf!=NULL; buf=buf->next) { sesp = (SelEdStructPtr) buf->region; if (is_sameId (sesp1->entityID, sesp1->itemID, sesp1->itemtype, 255, sesp->entityID, sesp->itemID, sesp->itemtype, 255) ) break; } if (buf == NULL) { return buffer; } return buf; } /********************************************************************* *** FindNextSegment *********************************************************************/ static SelEdStructPtr FindNextSegment (SelEdStructPtr current) { Uint2 ei, ii; if ( current->next == NULL ) return NULL; ei = current->entityID; ii = current->itemID; current = current->next; while ( current != NULL ) { if (current->entityID == ei && current->itemID == ii) break; current = current->next; } return current; } static CharPtr get_substring (CharPtr str, Int4 drw_start, Int4 drw_width) { Int4 width; Int4 stringlens; CharPtr strp; if (str == NULL ) return NULL; if (str[0]=='\0') return NULL; stringlens = StringLen (str); if ( drw_start >= stringlens ) { return NULL; } strp = str + drw_start; stringlens = StringLen (strp); if (stringlens == 0) return NULL; width = MIN ((Int4) drw_width, (Int4) stringlens); if ( !not_empty_string (strp, width) ) return NULL; return strp; } static SelStructPtr go_to_next_to_draw (EditAlignDataPtr adp, Boolean next, Int4 offset) { TextAlignBufPtr curtdp; SelStructPtr curvnp; SelEdStructPtr curssp = NULL; ValNodePtr vnp = NULL; Int4 from_inbuf; /* alignment coordinates in buffer */ Int4 from_inseq; /* alignment coordinates in buffer */ Int4 drw_width; /* length of drw_str */ Uint2 itemsubtype; CharPtr curstr = NULL; Int4 offsettmp; if (adp->voffset == 0) return adp->buffer; if (offset == 0) return adp->firstssp; from_inseq = adp->hoffset; from_inbuf = adp->hoffset - adp->bufferstart; drw_width = MIN ((Int4) adp->visibleWidth, (Int4) (adp->bufferlength - from_inbuf)); if ( drw_width <= 0 ) { return NULL; } curvnp = adp->buffer; offsettmp = 0; while (offsettmp < offset && from_inseq < adp->length) { curssp = (SelEdStructPtr) curvnp->region; itemsubtype = curvnp->itemtype; if (itemsubtype == EDITDEF_SCA) offsettmp++; else if (itemsubtype == EDITDEF_SCB) offsettmp; else if (curssp->itemtype ==OBJ_BIOSEQ) /*&&itemsubtype==FEATDEF_BAD)*/ { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring(curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) offsettmp++; } if (offsettmp < offset) { if (next) curvnp = curvnp->next; else curvnp = curvnp->prev; } if (offsettmp < offset && curvnp == NULL) { if (next) { curvnp = adp->buffer; adp->hoffset += adp->visibleWidth; from_inbuf += drw_width; from_inseq += drw_width; } else { curvnp = adp->buffertail; adp->hoffset -= adp->visibleWidth; from_inbuf -= drw_width; from_inseq -= drw_width; } if (from_inseq >= adp->length) break; if (from_inseq <= 0 || from_inbuf <= 0 || adp->hoffset<=0) break; drw_width = MIN ((Int4) adp->visibleWidth, (Int4)(adp->bufferlength -(adp->hoffset -adp->bufferstart))); } } if (from_inseq < 0 || from_inbuf < 0 || adp->hoffset<0) { adp->hoffset = adp->bufferstart; return adp->buffer; } if (from_inseq >= adp->length) return NULL; return curvnp; } static SelStructPtr next_to_draw (EditAlignDataPtr adp, Boolean next) { TextAlignBufPtr curtdp; SelStructPtr curvnp; SelStructPtr ssptmp; SelEdStructPtr curssp = NULL; ValNodePtr vnp = NULL; SeqLocPtr curslp; SeqIdPtr sip; CharPtr curstr = NULL; Int4 start, stop; Int4 start2, stop2; Int4 from_inbuf; /* alignment coordinates in buffer */ Int4 from_inseq; /* alignment coordinates in buffer */ Int4 drw_width; /* length of drw_str */ Int4 chklocp; Uint2 itemsubtype; SeqAlignPtr salp = (SeqAlignPtr) adp->sap_align->data; Boolean empty_line; if (next) { if ( adp->firstssp->next == NULL) { adp->hoffset += adp->visibleWidth; return adp->buffer; } else { ssptmp = adp->firstssp->next; } } if (!next) { if ( adp->firstssp->prev == NULL) { if (adp->hoffset == 0) { adp->voffset = 0; return adp->buffer; } adp->hoffset -= adp->visibleWidth; ssptmp = adp->buffertail; } else ssptmp = adp->firstssp->prev; } from_inseq = adp->hoffset; from_inbuf = adp->hoffset - adp->bufferstart; drw_width = MIN ((Int4) adp->visibleWidth, (Int4) (adp->bufferlength - from_inbuf)); if ( drw_width <= 0 ) { return NULL; } empty_line = FALSE; curvnp = ssptmp; while ( from_inseq < adp->length ) { curssp = (SelEdStructPtr) curvnp->region; itemsubtype = curvnp->itemtype; if (itemsubtype == EDITDEF_SCA) return curvnp; if (itemsubtype == EDITDEF_SCB) return curvnp; if (itemsubtype == FEATDEF_TRSL) { if (!empty_line ) { while (curssp!=NULL) { if (curssp->region !=NULL) { curslp = (SeqLocPtr) curssp->region; sip = SeqLocId (curslp); start2=SeqLocStart(curslp); chklocp =chkloc(sip, start2, adp->sqloc_list, &start2); start= SeqCoordToAlignCoord(start2, sip, salp, 0, chklocp); stop2=SeqLocStop(curslp); chklocp =chkloc(sip, stop2, adp->sqloc_list, &stop2); stop = SeqCoordToAlignCoord(stop2, sip, salp, 0, chklocp); if (start<=stop && startfrom_inseq) return curvnp; } curssp = FindNextSegment (curssp); } } } else if (itemsubtype>=EDITDEF_RF1 && itemsubtype<=EDITDEF_RF6) { if (curssp->region !=NULL && !empty_line) { curslp = (SeqLocPtr) curssp->region; if ( SeqLocStop (curslp) > from_inseq && curssp->data != NULL) return curvnp; } } else if (curssp->itemtype ==OBJ_BIOSEQ) /*&&itemsubtype==FEATDEF_BAD)*/ { if (curssp->data !=NULL) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring(curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) if (adp->draw_emptyline || (!adp->draw_emptyline && !stringhasnochar(curstr, 0, drw_width) )) { empty_line = FALSE; return curvnp; } else empty_line = TRUE; } } else if (curssp->itemtype==OBJ_SEQFEAT && itemsubtype==FEATDEF_PROT) { if (curssp->data !=NULL && !empty_line) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring(curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) return curvnp; } } else if (curssp->itemtype ==OBJ_SEQFEAT) { if ( !empty_line ) { while (curssp!=NULL) { if (curssp->region !=NULL) { curslp = (SeqLocPtr) curssp->region; sip = SeqLocId (curslp); start2=SeqLocStart(curslp); chklocp =chkloc(sip, start2, adp->sqloc_list, &start2); start= SeqCoordToAlignCoord(start2, sip, salp, 0, chklocp); stop2=SeqLocStop(curslp); chklocp =chkloc(sip, stop2, adp->sqloc_list, &stop2); stop = SeqCoordToAlignCoord(stop2, sip, salp, 0, chklocp); if (start<=stop && start=from_inseq) return curvnp; } curssp = FindNextSegment (curssp); } } } else if (itemsubtype == EDITDEF_CPL) { if (curssp->data !=NULL && !empty_line) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring (curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) return curvnp; } } else if( itemsubtype==SEQFEAT_GENE || itemsubtype==SEQFEAT_RNA || itemsubtype==SEQFEAT_CDREGION) { if ( !empty_line ) { while (curssp!=NULL) { if (curssp->region !=NULL) { curslp = (SeqLocPtr) curssp->region; sip = SeqLocId (curslp); start2=SeqLocStart(curslp); chklocp =chkloc(sip, start2, adp->sqloc_list, &start2); start= SeqCoordToAlignCoord(start2, sip, salp, 0, chklocp); stop2=SeqLocStop(curslp); chklocp =chkloc(sip, stop2, adp->sqloc_list, &stop2); stop = SeqCoordToAlignCoord(stop2, sip, salp, 0, chklocp); if (start<=stop && startfrom_inseq) return curvnp; } curssp = FindNextSegment (curssp); } } } else { /** ErrPostEx (SEV_ERROR, 0, 0, "fail in next_to_draw [46] subtype %ld type %ld", (long) itemsubtype, (long) curssp->itemtype); **/ return NULL; } if (next) curvnp = curvnp->next; else curvnp = curvnp->prev; if (curvnp == NULL) { if (next) { curvnp = adp->buffer; adp->hoffset += adp->visibleWidth; from_inbuf += drw_width; from_inseq += drw_width; } else { curvnp = adp->buffertail; adp->hoffset -= adp->visibleWidth; from_inbuf -= drw_width; from_inseq -= drw_width; } if (from_inseq >= adp->length) break; drw_width = MIN ((Int4) adp->visibleWidth, (Int4)(adp->bufferlength -(adp->hoffset -adp->bufferstart))); } } return NULL; } /******************************************************** *** SetupScrollBar *** *** *********************************************************/ extern BaR SeqEdGetSlateScrollBar (PaneL pnl) { EditAlignDataPtr adp; if (pnl) { adp=GetAlignDataPanel (pnl); if(adp!=NULL) { if (adp->vscrollbar_mode) { return GetSlateVScrollBar ((SlatE)pnl); } return GetSlateHScrollBar ((SlatE)pnl); } } return NULL; } extern Int4 SeqEdGetValueScrollBar (PaneL pnl) { return GetValue(SeqEdGetSlateScrollBar(pnl)); } extern void SeqEdSetValueScrollBar (PaneL pnl, Int4 value) { SetValue(SeqEdGetSlateScrollBar(pnl), value); } extern void SeqEdCorrectBarPage (PaneL pnl, Int4 page1, Int4 page2) { BaR sb; sb = SeqEdGetSlateScrollBar (pnl); CorrectBarPage (sb, page1, page2); } extern void SeqEdCorrectBarValue (PaneL pnl, Int4 value) { BaR sb; sb = SeqEdGetSlateScrollBar (pnl); CorrectBarValue (sb, value); } extern void SeqEdCorrectBarMax (PaneL pnl, Int4 value) { BaR sb; sb = SeqEdGetSlateScrollBar (pnl); CorrectBarMax (sb, value); } extern void SeqEdSetCorrectBarMax (PaneL pnl, EditAlignDataPtr adp, float hratio) { BaR sb; Int4 cbm = 0; if (adp->nlines < 11) { adp->voffset = 0; adp->hoffset = 0; adp->firstssp = get_firstline (NULL, adp->buffer); } else { adp->hoffset = (Int4)(hratio * (float)adp->length); adp->voffset = hoffset2voffset (adp, adp->anp_list, adp->visibleWidth, 0, adp->length-1, adp->hoffset); } if (adp->nlines < 0) cbm = 0; else cbm = MAX ((Int4) 0, (Int4) (adp->nlines -1)); sb = SeqEdGetSlateScrollBar (pnl); CorrectBarMax (sb, cbm); SetValue (sb, (Int4)(adp->voffset)); } static void count_feature_buf_line (ValNodePtr fnp_list, Int4 g_left, Int4 g_right, ValNodePtr PNTR feature_line) { FeatNodePtr fnp; Int4 c_left, c_right; ValNodePtr vnp; Boolean found; if(fnp_list == NULL) return; while(fnp_list) { fnp = (FeatNodePtr)fnp_list->data.ptrvalue; c_left = fnp->extremes.left; c_right = fnp->extremes.right; if(!(c_left > g_right || c_right < g_left)) { found = FALSE; for(vnp = *feature_line; vnp != NULL && !found; vnp = vnp->next) { if(vnp->data.intvalue == (Int4)(fnp->itemID)) found = TRUE; } if(!found) ValNodeAddInt(feature_line, 0, (Int4)(fnp->itemID)); } fnp_list = fnp_list->next; } } static Int4 CountTextAlignNodeNum(AlignNodePtr anp, Int4 m_left, Int4 m_right) { Int4 num_line = 0; Int4 g_left, g_right; AlignSegPtr asp; ValNodePtr feature_line, curr; /*the number of lines for a feature*/ g_left = anp->extremes.left; g_right = anp->extremes.right; if(m_left > g_right || m_right < g_left) return 0; num_line = 1; feature_line = NULL; /*process the GAPs and the DIAGs segs*/ for(asp = anp->segs; asp !=NULL; asp = asp->next) { g_left = asp->gr.left; g_right = asp->gr.right; if(!(g_left > m_right || g_right < m_left)) { switch(asp->type) { case GAP_SEG: break; case REG_SEG: case DIAG_SEG: g_left = MAX(m_left, g_left); g_right = MIN(m_right, g_right); count_feature_buf_line (asp->cnp, g_left, g_right, &feature_line); break; default: break; } } if(g_left > m_right) break; } if(feature_line != NULL) { for(curr = feature_line; curr != NULL; curr = curr->next) ++num_line; ValNodeFree(feature_line); } return num_line; } static Int4 addline_perblock (EditAlignDataPtr adp, Int4 diffs) { Int4 line = 0; ValNodePtr vnp; SeqParamPtr prm; Int1 j; if (adp->draw_scale) line += (Int4) diffs; if (adp->draw_bars) line += (Int4) diffs; for (vnp = adp->params; vnp != NULL; vnp = vnp->next) { prm = (SeqParamPtr) vnp->data.ptrvalue; if ( prm->complement ) line += (Int4) diffs; for (j=0; j<=6; j++) if (prm->rf[j]) line += (Int4) diffs; } return line; } static Int4 feat_linenum (Int4 slp_start, Int4 slp_stop, Int4 line_len, Int4 left, Int4 right) { Int4 modstart; Int4 modstop; slp_start = MAX (slp_start, left); modstart = slp_start % line_len; if ( modstart > 0) slp_start -= modstart; slp_stop = MIN (slp_stop, right); modstop = slp_stop % line_len; if ( modstop > 0) slp_stop += line_len; return (Int4)((slp_stop - slp_start) / line_len); } static Int4 CountFeatNum (ValNodePtr adpfeat, Int4 line_len, Int4 left, Int4 right){ ValNodePtr vnp; SelEdStructPtr sesp; SeqLocPtr slp; Int4 line = 0; for (vnp = adpfeat; vnp != NULL; vnp = vnp->next) { sesp = (SelEdStructPtr) vnp->data.ptrvalue; for (; sesp != NULL; sesp = sesp->next) { if (vnp->choice ==FEATDEF_CDS && sesp->regiontype ==OM_REGION_SEQLOC && sesp->region !=NULL) { slp = (SeqLocPtr) sesp->region;; if (SeqLocStart(slp) > right || SeqLocStop(slp) < left) line+=0; else { line+= feat_linenum (SeqLocStart(slp), SeqLocStop(slp), line_len, left, right); } } } } return line; } static Int4 count_nline (EditAlignDataPtr adp, ValNodePtr anp_list, Int4 line_len, Int4 left, Int4 right, Int4 voffset) { AlignNodePtr anp; Int4 c_start, c_stop; Int4 line_num = 0; Int4 h_block = 0; ValNodePtr curr; if(anp_list == NULL) return h_block; if(voffset == 0) return h_block; anp = (AlignNodePtr)anp_list->data.ptrvalue; if(left == -1) left = anp->extremes.left; if(right == -1) right = anp->extremes.right; if(left > anp->extremes.right || right < anp->extremes.left) return h_block; left = MAX(left, anp->extremes.left); right = MIN(right, anp->extremes.right); if (left >= right) return h_block; c_start = left; while(line_num < voffset) { c_stop = MIN(right, (c_start+line_len-1)); for(curr = anp_list; curr != NULL; curr = curr->next) { anp = (AlignNodePtr)curr->data.ptrvalue; line_num += CountTextAlignNodeNum(anp, c_start, c_stop); } line_num += (Int4) addline_perblock (adp, 1); line_num += (Int4) CountFeatNum (adp->feat, line_len, c_start, c_stop); line_num += (Int4) CountFeatNum (adp->seqfeat, line_len, c_start, c_stop); if (line_num > voffset) break; ++h_block; c_start = c_stop+1; } return c_start; } extern Int4 hoffset2voffset (EditAlignDataPtr adp, ValNodePtr anp_list, Int4 line_len, Int4 left, Int4 right, Int4 hoffset) { AlignNodePtr anp; Int4 c_start, c_stop; Int4 line_num = 0; Int4 preline; Int4 h_block = 0; ValNodePtr curr; if(anp_list == NULL) return h_block; if(hoffset == 0) return h_block; anp = (AlignNodePtr)anp_list->data.ptrvalue; if(left == -1) left = anp->extremes.left; if(right == -1) right = anp->extremes.right; if(left > anp->extremes.right || right < anp->extremes.left) return h_block; left = MAX(left, anp->extremes.left); right = MIN(right, anp->extremes.right); if (left >= right) return h_block; c_start = left; while(c_startnext) { anp = (AlignNodePtr)curr->data.ptrvalue; line_num += CountTextAlignNodeNum(anp, c_start, c_stop); } line_num += (Int4) addline_perblock (adp, 1); line_num += (Int4) CountFeatNum (adp->feat, line_len, c_start, c_stop); line_num += (Int4) CountFeatNum (adp->seqfeat, line_len, c_start, c_stop); ++h_block; c_start = c_stop+1; } preline = line_num; return preline; } /******************************************* *** Scrolling functions *** *** function test whether in/out buffer: *** not used *** ********************************************/ extern void VscrlProc (BaR sb, SlatE s, Int4 newval, Int4 oldval) { EditAlignDataPtr adp; RecT r; Int4 pixels; WindoW tempPort; Int4 temp; Int4 x; Int4 oldhoffset; if ( s == NULL ) { return; } if ( (adp = GetAlignDataPanel ((PaneL) s)) == NULL ) return; if ( adp->seqnumber == 0 ) return; tempPort = SavePort ((PaneL) s); Select ((PaneL) s); ObjectRect ((PaneL) s, &r); if ((newval > oldval && newval - oldval <= adp->vPage ) || (newval < oldval && oldval - newval <= adp->vPage )) { InsetRect (&r, HRZ_BORDER_WIDTH, VER_BORDER_WIDTH); pixels = (oldval - newval) * adp->lineheight; r.bottom = r.top + adp->pnlLine * adp->lineheight +1; r.top = r.top + 1; ScrollRect (&r, 0, pixels); } adp->voffset = GetValue (sb); if (abs(newval - oldval) == 1) { oldhoffset = adp->hoffset; temp = oldhoffset + adp->visibleWidth + adp->visibleLength; temp = MIN (temp, adp->bufferstart + adp->bufferlength); if ((oldhoffset + adp->visibleWidth > adp->bufferstart && temp < adp->bufferstart + adp->bufferlength) || temp == adp->length) { adp->firstssp = next_to_draw (adp, (Boolean)((newval-oldval)>0)); } else { data_collect_arrange (adp, TRUE); if (temp < adp->length) InvalRect (&r); } if (adp->hoffset == 0 && adp->firstssp->prev == NULL && adp->voffset != 0) { adp->voffset = 0; CorrectBarValue (sb, (Int4) 0); } if (adp->hoffset+adp->visibleWidth>adp->length && adp->voffsetnlines) { adp->voffset = adp->nlines; CorrectBarValue (sb, (Int4) adp->nlines); } } else { x = adp->seqnumber; if (adp->draw_scale) x++; if (adp->draw_bars) x++; adp->hoffset = count_nline (adp, adp->anp_list, adp->visibleWidth, 0, adp->length-1, (Int4)((FloatLo)adp->voffset)); if (adp->hoffset > adp->bufferstart && adp->hoffset+adp->visibleLength+ adp->visibleWidth < adp->bufferstart +adp->bufferlength) { data_collect_arrange (adp, FALSE); } else { data_collect_arrange (adp, TRUE); } if (x == 0) { adp->firstssp=go_to_next_to_draw(adp, TRUE, (Int4)0); } else { adp->firstssp=go_to_next_to_draw(adp, TRUE, (Int4)(adp->voffset%x)); } InvalRect (&r); } RestorePort(tempPort); Update (); } extern void HscrlProc (BaR sb, SlatE s, Int4 newval, Int4 oldval) { EditAlignDataPtr adp; RecT r; Int4 pixels; WindoW tempPort; if ( s == NULL ) { return; } if ( (adp = GetAlignDataPanel ((PaneL) s)) == NULL ) return; if ( adp->seqnumber == 0 ) return; tempPort = SavePort ((PaneL) s); Select ((PaneL) s); ObjectRect ((PaneL) s, &r); if ((newval > oldval && newval - oldval <= adp->hPage ) || (newval < oldval && oldval - newval <= adp->hPage )) { InsetRect (&r, HRZ_BORDER_WIDTH, VER_BORDER_WIDTH); pixels = (oldval - newval) * adp->charw +1; ScrollRect (&r, pixels, 0); } else { InvalRect (&r); } adp->hoffset = GetValue (sb); RestorePort(tempPort); Update (); } /******************************************************************* *** *** do_resize *** *******************************************************************/ extern void do_resize_panel (PaneL pnl, EditAlignDataPtr adp, Int4 width, Int4 height, Boolean rearrange) { Int4 old_voffset; Int4 new_buffer; Int4 j; Int4 lg; Int4 old_visibleWidth; Int4 x, y; float hratio; x = (width - adp->margin.right) / adp->charw; if (x < 0) x = 0; hratio = (float)adp->hoffset / (float)adp->length; adp->pnlWidth = x; if (adp->pnlWidth < adp->marginleft + 10) { adp->firstssp = NULL; return; } x = (height - adp->margin.bottom) / adp->lineheight; if (x < 0) x = 0; adp->pnlLine = x; if (adp->pnlLine < 3) { adp->firstssp = NULL; return; } y = 0; x = 0; if (adp->columnpcell > 0) { y = (Int4) (adp->pnlWidth -adp->marginleft) / (Int4) adp->columnpcell; x = (Int4) (adp->pnlWidth -adp->marginleft -y) % (Int4)(adp->columnpcell); if (x == 9) x = -1; } old_visibleWidth = adp->visibleWidth; adp->visibleWidth = (Int4) (adp->pnlWidth -adp->marginleft -y -x); if (adp->visibleWidth < 10) { adp->firstssp = NULL; return; } if ( adp->seqnumber == 0 ) return; if (old_visibleWidth != adp->visibleWidth) { old_voffset = adp->voffset; adp->voffset = (Int4)(((float)old_visibleWidth/(float)adp->visibleWidth) * (float)old_voffset); } new_buffer = adp->pnlLine * adp->visibleWidth; if (new_buffer * 3 > adp->minbufferlength) { adp->minbufferlength = new_buffer * 3; if ( adp->colonne != NULL ) MemFree (adp->colonne); adp->colonne = NULL; lg = adp->minbufferlength + adp->editbuffer + 4; adp->colonne = (Int4Ptr) MemNew ((size_t) (lg * sizeof(Int4))); for (j=0; jminbufferlength +adp->editbuffer; j++) adp->colonne[j] = -1; rearrange = TRUE; } adp->vPage = adp->pnlLine - 1; adp->hPage = adp->visibleWidth - 1; data_collect_arrange (adp, rearrange); SeqEdSetCorrectBarMax (pnl, adp, hratio); SeqEdCorrectBarPage (pnl, adp->vPage, adp->vPage); SeqEdCorrectBarValue (pnl, SeqEdGetValueScrollBar (pnl)); } extern void do_resize_window (PaneL pnl, EditAlignDataPtr adp, Boolean rearrange) { SeqEditViewFormPtr wdp; WindoW w; RecT rw; /* window rect */ RecT rp; /* panel rect */ RecT rb; /* buttons rect */ RecT rct; /* new rect for panel */ Int4 buttonwidth, buttonheight; Int4 x, y; w = getwindow_frompanel (pnl); wdp = (SeqEditViewFormPtr) GetObjectExtra (w); if (wdp == NULL) return; ObjectRect (w, &rw); get_client_rect (pnl, &rp); GetPosition (pnl, &rp); x = adp->xoff; y = rw.bottom - rw.top; LoadRect ( &rct, x, adp->yoff, (Int4)(rw.right - rw.left - adp->x), (Int4)(y - adp->y)); SetPosition (pnl, &rct ); AdjustPrnt (pnl, &rct, FALSE); ObjectRect (pnl, &rp ); GetPosition ((GrouP) wdp->btngp, &rb); buttonwidth = rb.right - rb.left; buttonheight = rb.bottom - rb.top; LoadRect (&rb, x, (Int4)(y -buttonheight - adp->ybutt - 1), (Int4)(x+ buttonwidth), (Int4)(y-adp->ybutt-1)); SetPosition(wdp->btngp, &rb); AdjustPrnt (wdp->btngp, &rb, FALSE); ResetClip (); Update (); InsetRect (&rp, 4, 4); do_resize_panel (pnl, adp, (Int4)(rp.right - rp.left), (Int4)(rp.bottom - rp.top), rearrange); return; } /***********************************************************************/ /***********************************************************************/ /***********************************************************************/ /***********************************************************************/ /***********************************************************************/ /***********************************************************************/ /*********************************************************************** *** Draw Scale *** draw_scale *** draw_bars *** ***********************************************************************/ static void draw_scale (EditAlignDataPtr adp, Int4 hoffset, Int4 scalelength, PoinT *ptlh) { Char str[128]; Int4 scal; Int4 ptx, pty; Int4 j; Int4 marqueediff; if ( !adp->draw_scale ) return; SetColor (adp->colorRefs[COLOR_SCALE]); ptx = ptlh->x + adp->margin.left + (Int4)(adp->charw * 0.5) - 2; pty = ptlh->y + adp->ascent; marqueediff = (Int4)( 2.00 / 6.00 * adp->lineheight); for ( j = hoffset; j < hoffset + scalelength; j++) { if ( adp->colonne[j] > -1) { scal = (Int4)(adp->gr.left + 1 + adp->colonne[j]); if (scal % 10 == 0) { sprintf (str, "%d", (int)scal); MoveTo ((Int4)(ptx - StringWidth(str) + (adp->charw/2) +1), (Int4)(pty + marqueediff)); PaintString (str); } } if (adp->columnpcell > 0 && j > hoffset) if ((Int4) j % (Int4) adp->columnpcell == 0) ptx += adp->charw; ptx += adp->charw; } Black(); return ; } static void draw_bars (EditAlignDataPtr adp, Int4 hoffset, Int4 scalelength, PoinT *ptlh) { Int4 scal; Int4 ptx; Int4 y; Int4 j; Int4 marqueelong, marqueeshort, marqueediff; if ( !adp->draw_bars ) return; SetColor (adp->colorRefs[COLOR_SCALE]); ptx = ptlh->x + adp->margin.left + (Int4)(adp->charw * 0.5) - 1; y = ptlh->y + (Int4) (2.00 / 6.00 * adp->lineheight); marqueelong = (Int4) (4.00 / 6.00 * adp->lineheight); marqueeshort= (Int4) (2.00 / 6.00 * adp->lineheight); marqueediff = (Int4) (2.00 / 6.00 * adp->lineheight); for ( j = hoffset; j < hoffset + scalelength; j++) { if ( adp->colonne[j] > -1) { scal = (Int4)(adp->gr.left + 1 + adp->colonne[j]); if (scal % 10 == 0) { MoveTo (ptx , y ); LineTo (ptx , (Int4)(y + marqueelong)); } else if (scal % 5 == 0) { MoveTo (ptx , (Int4)(y + marqueediff)); LineTo (ptx , (Int4)(y + marqueediff + marqueeshort)); } } if (adp->columnpcell > 0 && j > hoffset) if ((Int4) j % (Int4) adp->columnpcell == 0) ptx += adp->charw; ptx += adp->charw; } Black(); return ; } /*********************************************************************** *** draw_id ************************************************************************/ static void draw_id (EditAlignDataPtr adp, PoinT *pt, Int4 index, CharPtr strid, Uint1 strand, Int4 pos, Uint2 itemtype, Boolean idselected, Boolean is_master, Int4 group) { Char str[128], str1[128]; RecT rct; CharPtr tmp; Int4 stringlens; Int4 j; Int4 total = 0; Int4 posspace; /*!!!!!!!!!!!!!!!!!!!!!!!!!!*/ idselected = FALSE; if (adp->length < 1000) { posspace = 4; } else if (adp->length < 10000) { posspace = 5; } else if (adp->length < 100000) { posspace = 6; } else if (adp->length < 1000000) { posspace = 7; } else { posspace = 8; } if (adp->marginwithindex) total += 3; if (adp->marginwithgroup) total += 4; if (adp->marginwithpos) total += posspace; total += 2; str[0] = '\0'; tmp = str; if (adp->marginwithindex && index > 0) { sprintf (str1, "%3d ",(int) index); } else { sprintf (str1, " "); } tmp = StringMove (tmp, str1); tmp[0] = '\0'; adp->marginwithgroup = FALSE; if (adp->marginwithgroup) { if (group >= 0) sprintf (str1, "%4d ",(int) group); else sprintf (str1, " "); tmp = StringMove (tmp, str1); tmp[0] = '\0'; } if (strid != NULL && strid[0]!='\0') { stringlens = (Int4)(StringLen (strid)); /******!!!!!!!!!!!!!!! if (stringlens > 4) { if (strid[0] == 'l' && strid[1] == 'c' && strid[2] == 'l') { strid += 4; stringlens -= 4; } } !!!!!!!!!!!!!!!!!*********/ for (j=0; jsize_labels) { for (j=stringlens; jsize_labels; j++) str1 [j] = ' '; str1 [j] = '\0'; stringlens = (Int4)(StringLen (str1)); } stringlens = MIN (adp->marginleft - total, stringlens); str1 [stringlens] = '\0'; tmp = StringMove (tmp, str1); } else if (adp->marginleft > 20) { sprintf (str1, " "); tmp = StringMove (tmp, str1); } /* symbol[0] = ' '; if (strand == Seq_strand_minus) symbol[1] = '<'; else symbol[1] = '>'; symbol[2] = '\0'; tmp = StringMove (tmp, symbol); */ if (adp->marginwithpos) { if (posspace <= 4) { if (pos > 0) sprintf (str1, "%4ld ", (long) pos); else sprintf (str1, " "); } else if (posspace == 5) { if (pos > 0) sprintf (str1, "%5ld ", (long) pos); else sprintf (str1, " "); } else if (posspace == 6) { if (pos > 0) sprintf (str1, "%6ld ", (long) pos); else sprintf (str1, " "); } else { if (pos > 0) sprintf (str1, "%7ld ", (long) pos); else sprintf (str1, " "); } tmp = StringMove (tmp, str1); } *tmp = '\0'; stringlens = (Int4)(StringLen(str)); if (stringlens < adp->marginleft -1) for (j = stringlens; j < adp->marginleft; j++, tmp++) *tmp = ' '; str [adp->marginleft -1] = ' '; str [adp->marginleft] = '\0'; if ( itemtype != OBJ_BIOSEQ && adp->displaytype ) SelectColor (162, 163, 82); else if (is_master && !adp->all_sequences) SetColor (adp->colorRefs[COLOR_ID_MASTER]); else SetColor (adp->colorRefs[COLOR_ID]); if ( !idselected ) { Black(); MoveTo (pt->x, (Int4)(pt->y + adp->ascent)); PaintString (str); } else { InvertColors (); LoadRect(&rct, pt->x, pt->y, (Int4)(pt->x +stringlens *adp->charw -2), (Int4)(pt->y + adp->lineheight)); EraseRect (&rct); MoveTo (pt->x, (Int4)(pt->y +adp->ascent)); PaintString (str); InvertColors(); } Black(); return; } /****************************************************************** *** paint_caret, draw caret : draws caret *** *** Now caret is a T between basis of letters *** Before it was a bar between letters: pt1.x = pt.x + ( column + marginleft ) * charw -1; pt1.y = pt.y; pt2.x = pt1.x; pt2.y = pt1.y + lineheight -2; *** *******************************************************************/ static void paint_caret (PoinT pt, Int4 column, Int4 charw, Int4 lineheight, Int4 marginleft) { PoinT pt1, pt2; Int4 lenv = 3; Int4 lenh = 2; Int4 row; Red (); WidePen (2); row = pt.x + ( column + marginleft ) * charw -1; pt1.x = row; pt1.y = pt.y + lineheight -1; pt2.x = row; pt2.y = pt1.y -lenv; DrawLine (pt1, pt2); pt2.x = row +lenh; pt2.y = pt1.y; DrawLine (pt1, pt2); pt2.x = row -lenh; pt2.y = pt1.y; DrawLine (pt1, pt2); WidePen (1); Black (); } static void draw_caret (EditAlignDataPtr adp, SelEdStructPtr sesp, PoinT pt, Int4 line) { SeqLocPtr slp; Int4 column; if (!adp->display_panel) { if ( is_samess_ses (&(adp->caret), sesp)) { slp = (SeqLocPtr) adp->caret.region; if(SeqPosInLineColumn (SeqLocStart(slp), adp->alignline[line], &column, adp->hoffset, adp) ) { paint_caret (pt, column, adp->charw, adp->lineheight, adp->marginleft); } } } } /********************************************************************* *** PaintSubseq : paint visible sequence **********************************************************************/ /*browse a structure to find out the colour number idx (zero-based) seq_color is a field in MediaInfo structure; see cn3dmsg.h*/ static ResidueColorCellPtr GiveClrFromIdx(Int4 idx,ValNodePtr seq_color) { Int4 i; i=0; while(seq_color){ if (i==idx) { return((ResidueColorCellPtr)seq_color->data.ptrvalue); } seq_color=seq_color->next; i++; } return NULL; } static void PaintSubseq (Int4 k, Int4 lg, Int4 from, PoinT *pt, CharPtr vstr, Boolean invert, EditAlignDataPtr adp, Boolean draw_diff, CharPtr *masterstr, Boolean cmplt, ValNodePtr seq_color,SeqIdPtr sip) { CharPtr strPtr; Char str[512]; Uint4 curColor; Int4 to = k + lg; Int4 caret_color = 0; CharPtr masterstrptr = NULL; RecT rct; Uint4 blackColor = GetColorRGB(0,0,0), whiteColor = GetColorRGB(255, 255, 255), newColor; Boolean pretty = (Boolean) (seq_color!=NULL); ResidueColorCellPtr rgb; Int4 from2; dashedstring ((CharPtr) str, 512); strPtr = str; if (pretty) { from2=AlignCoordToSeqCoord (from, sip, (SeqAlignPtr)adp->sap_align->data, adp->sqloc_list, 0); if (from2!=GAP_RESIDUE) rgb=GiveClrFromIdx(from2,seq_color); else rgb=NULL; if(rgb != NULL ){ curColor = GetColorRGB (rgb->rgb[0], rgb->rgb[1],rgb->rgb[2]); } else curColor =blackColor; } else { curColor = adp->colorRefs[(Uint1)(vstr[k] - '*')]; } if (curColor == (Uint4)172) curColor = blackColor; if (masterstr != NULL) { if (*masterstr != NULL) masterstrptr = *masterstr; } while ( k < to ) { if (pretty) { from2=AlignCoordToSeqCoord (k+from, sip, (SeqAlignPtr)adp->sap_align->data, adp->sqloc_list, 0); if (from2!=GAP_RESIDUE) rgb=GiveClrFromIdx(from2,seq_color); else rgb=NULL; if(rgb != NULL ){ newColor= GetColorRGB (rgb->rgb[0], rgb->rgb[1],rgb->rgb[2]); } else newColor=blackColor ; if (vstr[k] == '-') newColor=blackColor ; } else { newColor = adp->colorRefs[(Uint1)(vstr[k] - '*')]; } /* if (newColor == (Uint4)172) newColor = blackColor; */ /* yanli comment it out so that residues */ /* with magenta color can be seen in salsa */ if (newColor == whiteColor) newColor = blackColor; /* yanli added this so that residues colored with white */ /* in Cn3D(with color by Domain) are drawn as black in salsa to be visible */ if ( adp->colonne [from +k -adp->bufferstart] < 0 ) { *strPtr = 0; strPtr = str; if (cmplt) strPtr = complement_string (strPtr); MoveTo ((Int4)(pt->x +adp->margin.left), (Int4)(pt->y + adp->ascent)); PaintString (strPtr); pt->x += caret_color * adp->charw; caret_color = 1; strPtr = str; Black(); if ((from +k -adp->bufferstart) > adp->length) return; pt->x += adp->intersalpwidth * adp->charw; k += adp->intersalpwidth; SetColor (curColor); } else if (curColor != newColor) { *strPtr = 0; strPtr = str; if (cmplt) strPtr = complement_string (strPtr); MoveTo ((Int4)(pt->x +adp->margin.left), (Int4)(pt->y +adp->ascent)); if (invert) { SetColor (adp->colorRefs[COLOR_SELECT]); InvertColors (); LoadRect (&rct, (Int4)(pt->x+adp->margin.left), pt->y, (Int4)(pt->x +adp->margin.left+ caret_color*adp->charw), (Int4)(pt->y +adp->lineheight -1)); EraseRect (&rct); InvertColors (); if (adp->colorRefs[COLOR_SELECT]==blackColor) White(); else { Black (); } } else { SetColor (curColor); } PaintString (strPtr); pt->x += caret_color *adp->charw; caret_color = 1; strPtr = str; if ( draw_diff && masterstrptr != NULL ) { if (vstr[k] !='-') { if (ISA_na(adp->mol_type)) { if ((*masterstrptr == vstr[k]) && (vstr[k]<65 || vstr[k]>91)) *strPtr = '.'; else *strPtr = vstr[k]; } else { if (TO_LOWER(*masterstrptr) == TO_LOWER(vstr[k])) { *strPtr = '.'; } else { *strPtr = vstr[k]; } } } else *strPtr = vstr[k]; masterstrptr++; } else *strPtr = vstr[k]; strPtr++; if (adp->columnpcell > 0) { if ((Int4) (k+1) % (Int4) adp->columnpcell == 0) { *strPtr = ' '; strPtr++; caret_color++; } } curColor = newColor; k++; } else { if ( draw_diff && masterstrptr != NULL ) { if (vstr[k] !='-') { if (ISA_na(adp->mol_type)) { if ((*masterstrptr == vstr[k]) && (vstr[k]<65 || vstr[k]>91)) *strPtr = '.'; else *strPtr = vstr[k]; } else { if (TO_LOWER(*masterstrptr) == TO_LOWER(vstr[k])) { *strPtr = '.'; } else { *strPtr = vstr[k]; } } } else *strPtr = vstr[k]; masterstrptr++; } else *strPtr = vstr[k]; strPtr++; caret_color++; if (adp->columnpcell > 0) { if ((Int4) (k+1) % (Int4) adp->columnpcell == 0) { *strPtr = ' '; strPtr++; caret_color++; } } k++; } } *strPtr = 0; strPtr = str; if (cmplt) strPtr = complement_string (strPtr); MoveTo ((Int4)(pt->x +adp->margin.left), (Int4)(pt->y +adp->ascent)); if (invert) { SetColor (adp->colorRefs[COLOR_SELECT]); InvertColors (); LoadRect (&rct, (Int4)(pt->x+adp->margin.left), pt->y, (Int4)(pt->x +adp->margin.left+ caret_color*adp->charw), (Int4)(pt->y +adp->lineheight -1)); EraseRect (&rct); InvertColors (); if(adp->colorRefs[COLOR_SELECT]==blackColor) White(); else { Black (); } } else { SetColor (curColor); } PaintString (strPtr); Black (); pt->x += caret_color *adp->charw; *masterstr = masterstrptr; return; } /***************************************************************** *** draw_seq ******************************************************************/ static ValNodePtr deleteseqloc (ValNodePtr head, ValNodePtr delp) { ValNodePtr next = NULL, pre = NULL, tmp = NULL; tmp = head; while (tmp!=NULL) { next = tmp->next; if (tmp == delp) { if (pre==NULL) { head = next; } else { pre->next = next; } tmp->next = NULL; SeqLocFree ((SeqLocPtr)tmp->data.ptrvalue); tmp->data.ptrvalue = NULL; ValNodeFree (tmp); } else pre = tmp; tmp = next; } return head; } static ValNodePtr simplifySeqLocList (ValNodePtr valnode) { ValNodePtr vnpa = NULL, vnpb = NULL; SeqLocPtr slpa, slpb; SeqIntPtr sint; Boolean check = TRUE, loopin = TRUE; while (check) { check = FALSE; loopin = TRUE; vnpa = valnode; while (vnpa != NULL && loopin) { for (vnpb = vnpa->next; vnpb != NULL; vnpb = vnpb->next) { slpa = (SeqLocPtr)vnpa->data.ptrvalue; slpb = (SeqLocPtr)vnpb->data.ptrvalue; if (SeqLocCompare (slpa, slpb) == SLC_A_IN_B) { valnode = deleteseqloc (valnode, vnpa); check = TRUE; loopin = FALSE; break; } else if (SeqLocCompare (slpa, slpb) == SLC_B_IN_A) { valnode = deleteseqloc (valnode, vnpb); check = TRUE; loopin = FALSE; break; } else if (SeqLocCompare (slpa, slpb) == SLC_A_EQ_B) { valnode = deleteseqloc (valnode, vnpb); check = TRUE; loopin = FALSE; break; } else if (SeqLocCompare (slpa, slpb) == SLC_A_OVERLAP_B) { sint = (SeqIntPtr) slpa->data.ptrvalue; if (SeqLocStart(slpa) < SeqLocStart(slpb)) { sint->to = SeqLocStop(slpb); } else { sint = (SeqIntPtr) slpa->data.ptrvalue; sint->from = SeqLocStart(slpb); } valnode = deleteseqloc (valnode, vnpb); check = TRUE; loopin = FALSE; break; } else if (SeqLocStop(slpa) == SeqLocStart(slpb)-1) { sint = (SeqIntPtr) slpa->data.ptrvalue; sint->to = SeqLocStop(slpb); valnode = deleteseqloc (valnode, vnpb); check = TRUE; loopin = FALSE; break; } else if (SeqLocStart(slpa) == SeqLocStop(slpb)+1) { sint = (SeqIntPtr) slpa->data.ptrvalue; sint->from = SeqLocStart(slpb); valnode = deleteseqloc (valnode, vnpb); check = TRUE; loopin = FALSE; break; } } if (loopin && vnpa != NULL) vnpa = vnpa->next; } } return valnode; } static Int4 getnextpos (ValNodePtr vnp, Int4 *stop) { ValNodePtr tmp; SeqLocPtr slp; SeqIntPtr sint; Int4 valmin = (Int4)(INT4_MAX-2), val = (Int4)-1, val2 = (Int4)-1; for (tmp=vnp; tmp!=NULL; tmp=tmp->next) { slp = (SeqLocPtr) tmp->data.ptrvalue; if (SeqLocStart(slp) < valmin) { valmin = SeqLocStart(slp); } } if (valmin < (Int4)(INT4_MAX-2)) { for (tmp=vnp; tmp!=NULL; tmp=tmp->next) { slp = (SeqLocPtr) tmp->data.ptrvalue; if (SeqLocStart(slp) == valmin) { val = SeqLocStart(slp); val2 = SeqLocStop (slp); sint = (SeqIntPtr) slp->data.ptrvalue; sint->from = INT4_MAX; sint->to = INT4_MAX; break; } } } *stop = val2; return val; } static void draw_seq (EditAlignDataPtr adp, SelEdStructPtr sesp, Int4 from, Int4 drw_width, PoinT ptlh, CharPtr drw_str, Boolean draw_diff, CharPtr masterstr, Boolean cplmt, Uint2 itemtype, Boolean check_selection) { SelStructPtr ssptmp; SeqIdPtr sip; Int4 start, stop; Int4 left, right; Int4 seg_lg; Int4 k, k1; Int4 chklocp; Int4 iCount = 0; SeqLocPtr slp; ValNodePtr startp = NULL; SeqIdPtr sesp_sip= NULL; SeqIntPtr sinp = NULL; SeqEditViewProcsPtr svpp; ValNodePtr vnp_seqinfo; ValNodePtr vnp_color = NULL; SeqIdPtr vnpcn3d_sip = NULL; MediaInfoPtr MIPtr; adp->start_select = -1; start = stop = -1; ssptmp = NULL; if (check_selection) { ssptmp = ObjMgrGetSelected (); for (; ssptmp != NULL; ssptmp = ssptmp->next) { if ( checkssp_for_editor (ssptmp) && is_samess_ses (ssptmp, sesp) ) { sip = SeqLocId ((SeqLocPtr) ssptmp->region); start = SeqLocStart ((SeqLocPtr) ssptmp->region); adp->start_select = start; chklocp =chkloc(sip, start, adp->sqloc_list, &start); start = SeqCoordToAlignCoord (start, sip, (SeqAlignPtr) adp->sap_align->data, 0, chklocp); stop = SeqLocStop ((SeqLocPtr) ssptmp->region); chklocp =chkloc(sip, stop, adp->sqloc_list, &stop); stop = SeqCoordToAlignCoord (stop, sip, (SeqAlignPtr) adp->sap_align->data, 0, chklocp); /****** if (start<=stop && (start < from + drw_width && (stop + 1) > from)) ******/ if ((start < from + drw_width && (stop + 1) > from)) { if(start<=stop) slp = SeqLocIntNew (start, stop, Seq_strand_plus, sip); else slp = SeqLocIntNew (stop, start, Seq_strand_plus, sip); ValNodeAddPointer (&startp, 0, (Pointer)slp); iCount ++; } } } } svpp = (SeqEditViewProcsPtr) GetAppProperty ("SeqEditDisplayForm"); if(sesp->regiontype == 1){ slp = (SeqLocPtr)sesp->region; sinp = (SeqIntPtr)slp->data.ptrvalue; sesp_sip = sinp->id; } if (svpp) { if (svpp->Cn3D_On && sesp_sip) { vnp_seqinfo = svpp->seqinfo; while(vnp_seqinfo){ MIPtr=(MediaInfoPtr)vnp_seqinfo->data.ptrvalue; /* if (MIPtr->entityID==sesp->entityID && MIPtr->itemID==sesp->itemID){ vnp_color=MIPtr->seq_color; vnpcn3d_sip = MIPtr->sip; break; } */ /* yanli comment it out, instead doing the following */ if(SeqIdForSameBioseq(sesp_sip, MIPtr->sip)){ vnp_color=MIPtr->seq_color; vnpcn3d_sip = MIPtr->sip; /* do not break so as to get the latest one */ } vnp_seqinfo=vnp_seqinfo->next; } } } if (iCount > 0) { k = 0; k1 = from; startp = simplifySeqLocList (startp); start = getnextpos (startp, &stop); while ( k < drw_width && start >= 0) { if ( k + from < start ) { left = (Int4) k1; right= start; seg_lg = MIN (right - left, drw_width); PaintSubseq (k, seg_lg, from, &ptlh, drw_str, FALSE, adp, draw_diff, &masterstr, cplmt, vnp_color,vnpcn3d_sip); k += seg_lg; } else if ( k +from >= start && k +from < stop + 1) { left = (Int4) MAX (k1, start); right= (Int4) MIN (from + drw_width, stop + 1); seg_lg = MIN (right - left, drw_width); PaintSubseq (k, seg_lg, from, &ptlh, drw_str, TRUE, adp, draw_diff, &masterstr, cplmt, vnp_color,vnpcn3d_sip); k += seg_lg; k1 = stop + 1; start = getnextpos (startp, &stop); } } if ( k < drw_width) { left = (Int4) k1; right= (Int4) from + drw_width; seg_lg = MIN (right - left, drw_width); PaintSubseq (k, seg_lg, from, &ptlh, drw_str, FALSE, adp, draw_diff, &masterstr, cplmt, vnp_color,vnpcn3d_sip); } } else { PaintSubseq (0, drw_width, from, &ptlh, drw_str, FALSE, adp, draw_diff, &masterstr, cplmt, vnp_color,vnpcn3d_sip); } if (startp != NULL) ValNodeFree (startp); return; } /***************************************************************** *** draw_line ******************************************************************/ static void draw_line (EditAlignDataPtr adp, Int4 start, Int4 stop, Uint1 strand, PoinT *pt, Int4 from, Int4 drw_width, Int4 line, Int4 alignline, Uint4 color, Uint2 wideline, Boolean selected, Boolean partialstart, Boolean partialstop, BoolPtr gapline) { PoinT pt1, pt2, pttmp; PoinT oldpt1, oldpt2; FloatLo hgt = (FloatLo)(2.5 / 4.0); RecT leftrct, rightrct; Int4 left, right; Int4 yline; Int4 column; Int4 above, below; Int4 j, k; Int4 col1; Uint1 startin, stopin; BoolPtr gap; left = (Int4) MAX ((Int4) from, (Int4) start); SeqPosInLineColumn (left, alignline, &column, adp->hoffset, adp); yline = pt->y + (Int4) (hgt * adp->ascent); pt1.x = pt->x + (column + adp->marginleft) * adp->charw; pt1.y = yline; if (adp->columnpcell > 0) { col1 = column - (column-1)/adp->columnpcell; } right = (Int4) MIN ((Int4)from+drw_width-1, (Int4)stop); SeqPosInLineColumn (right, alignline, &column, adp->hoffset, adp); pt2.x = pt->x + (column + adp->marginleft + 1) * adp->charw; pt2.y = yline; startin = stopin = 0; if ( start >= from ) { if (strand == Seq_strand_minus) startin = 1; else startin = 2; } if (stop < from+drw_width && stop != start) { if (strand == Seq_strand_minus) stopin = 1; else stopin = 2; } oldpt1.x = pt1.x; oldpt1.y = pt1.y; oldpt2.x = pt2.x; oldpt2.y = pt2.y; if (starthoffset, adp); if (k==right && stopin == 0) { column++; } pttmp.x = pt->x + (column + adp->marginleft) * adp->charw; DrawLine (pt1, pttmp); Solid (); pt1.x = pttmp.x; j = k; } } } if (selected) { #ifdef WIN_MAC above = 2; below = 4; #endif #ifdef WIN_MSWIN above = 3; below = 3; #endif #ifdef WIN_MOTIF above = 3; below = 3; #endif WidePen (1); Black (); pt1.y = pt2.y = yline + below; DrawLine (pt1, pt2); pt1.y = pt2.y = yline - above; DrawLine (pt1, pt2); White (); pt1.y = pt2.y = yline + below - 1; DrawLine (pt1, pt2); pt1.y = pt2.y = yline - above + 1; DrawLine (pt1, pt2); } WidePen (1); SetColor (color); pt1.x = oldpt1.x; pt1.y = oldpt1.y; pt2.x = oldpt2.x; pt2.y = oldpt2.y; if (startin == 1) { #ifdef WIN_MAC LoadRect(&leftrct, pt1.x , (Int2)(pt1.y -3), (Int2)(pt1.x +7), (Int4)(pt1.y +4) ); OffsetRect (&leftrct, 0, 1); #endif #ifdef WIN_MSWIN LoadRect(&leftrct, pt1.x , (Int2)(pt1.y -3), (Int2)(pt1.x +7), (Int2)(pt1.y +4) ); #endif #ifdef WIN_MOTIF LoadRect(&leftrct, pt1.x , (Int2)(pt1.y -3), (Int2)(pt1.x +7), (Int2) (pt1.y +4) ); #endif if (partialstart) CopyBits (&leftrct, leftTriSym); else CopyBits (&leftrct, leftTriFillSym); } else if (startin == 2) { #ifdef WIN_MAC LoadRect(&leftrct, pt1.x , (Int2)(pt1.y -3), (Int2)(pt1.x +7), (Int2)(pt1.y +4)); OffsetRect (&leftrct, 0, 1); #endif #ifdef WIN_MSWIN LoadRect(&leftrct, pt1.x , (Int2)(pt1.y -3), (Int2)(pt1.x +7), (Int2)(pt1.y +4)); #endif #ifdef WIN_MOTIF LoadRect(&leftrct, pt1.x , (Int2)(pt1.y -3), (Int2)(pt1.x +7), (Int2)(pt1.y +4)); #endif if (partialstart) CopyBits (&leftrct, rectSym); else CopyBits (&leftrct, rectFillSym); } if (stopin == 1) { #ifdef WIN_MAC LoadRect(&rightrct, (Int2)(pt2.x -7), (Int2)(pt2.y -3), pt2.x, (Int2)(pt2.y +4)); OffsetRect (&rightrct, 0, 1); #endif #ifdef WIN_MSWIN LoadRect(&rightrct, (Int2)(pt2.x -7), (Int2)(pt2.y -3), pt2.x, (Int2)(pt2.y +4)); #endif #ifdef WIN_MOTIF LoadRect(&rightrct, (Int2)(pt2.x -7), (Int2)(pt2.y -3), pt2.x, (Int2)(pt2.y +4)); #endif if (partialstop) CopyBits (&leftrct, rectSym); else CopyBits (&rightrct, rectFillSym); } else if (stopin == 2) { #ifdef WIN_MAC LoadRect (&rightrct, (Int2)(pt2.x -7), (Int2)(pt2.y -3), pt2.x, (Int2)(pt2.y +4)); OffsetRect (&rightrct, 0, 1); #endif #ifdef WIN_MSWIN LoadRect (&rightrct, (Int2)(pt2.x -7), (Int2)(pt2.y -3), pt2.x, (Int2)(pt2.y +4)); #endif #ifdef WIN_MOTIF LoadRect (&rightrct, (Int2)(pt2.x -7), (Int2)(pt2.y -3), pt2.x, (Int2)(pt2.y +4)); #endif if (partialstop) CopyBits (&rightrct,rightTriSym); else CopyBits (&rightrct,rightTriFillSym); } Black (); WidePen (1); } /********************************************************************* *** draw_cds *********************************************************************/ static void draw_trans (EditAlignDataPtr adp, SelEdStructPtr cds, CharPtr trans, PoinT *pt, Int4 from, Int4 drw_width, Uint2 offset) { SeqLocPtr slp; CharPtr transtr; CharPtr strPtr, transPtr; Int4 left, right; Int2 k; if ( trans == NULL || cds == NULL ) return; slp = (SeqLocPtr) cds->region; if (slp == NULL) return; left = (Int4) MAX ((Int4) from, (Int4) SeqLocStart(slp)); right = (Int4) MIN ((Int4) from+drw_width, (Int4) SeqLocStop(slp)+1); if (right < left) { ErrPostEx (SEV_ERROR, 0, 0, "fail in draw_trans: left %ld right %ld", (long) left, (long) right); } transtr = (CharPtr)MemNew ((size_t)(512 * (sizeof (Char)))); emptystring (transtr, 512); transtr[0] = ' '; transtr[511] = '\0'; strPtr = transtr; strPtr += (Int2) (left - from); transPtr = trans; transPtr += cds->offset; /*!!!!!!!!!!!!! += cds->codonstart ?? */ if (SeqLocStart(slp) < from) transPtr += (Int2)(from - SeqLocStart(slp)); if (adp->prot_mode == MPROTAA) { for (k =0; k < (right - left); k++, strPtr++, transPtr++) { if ( *transPtr=='M' || *transPtr=='*') *strPtr = *transPtr; } } else { for (k =0; k < (right - left); k++, strPtr++, transPtr++) { *strPtr = *transPtr; } } strPtr++; *strPtr= '\0'; draw_seq (adp, cds, from, drw_width, *pt, transtr, FALSE, NULL, TRUE, OBJ_SEQFEAT, FALSE); transtr = (CharPtr)MemFree (transtr); return; } /********************************************************************* *** draw_pept *********************************************************************/ static void draw_pept (EditAlignDataPtr adp, SelEdStructPtr cds, PoinT *pt, Int4 from, Int4 drw_width, Int2 line, Uint2 offset) { ValNodePtr pept; if (cds!=NULL) { pept = cds->data; if (pept != NULL) { if (pept->data.ptrvalue != NULL) { draw_trans (adp, cds, (CharPtr) pept->data.ptrvalue, pt, from, drw_width, offset); } } } } /********************************************************************* *** draw_feat *********************************************************************/ static void draw_feat (EditAlignDataPtr adp, Uint2 eid, Uint2 iid, Uint2 it, Uint2 choice, Int4 start, Int4 stop, Uint1 strand, CharPtr label, PoinT *pt, Int4 from, Int4 drw_width, Int2 line, Int4 alignline, Uint4 color, Boolean partialstart, Boolean partialstop, BoolPtr gapline) { Char str[128]; Uint2 wideline; Boolean featselect; if ( start > stop || start >= from + drw_width || stop < from ) return; if (it == OBJ_VIRT) { wideline = 5; if (choice == SEQFEAT_CDREGION ) sprintf (str, "CDS %d", (int) iid); else if (choice == SEQFEAT_GENE) sprintf (str, "gene %d", (int) iid); else if (choice == SEQFEAT_RNA) sprintf (str, "mRNA %d", (int) iid); str[15] = '\0'; draw_id (adp, pt, -1, str, strand, 0, 3, FALSE, FALSE, -1); } else { wideline = 3; draw_id (adp, pt, -1, label, strand, 0, 3, FALSE, FALSE, -1); } featselect = (Boolean) (is_selectedbyID (eid, iid, it) != NULL); draw_line (adp, start, stop, strand, pt, from, drw_width, line, alignline, color, wideline, featselect, partialstart, partialstop, gapline); } static void what_inline (EditAlignDataPtr adp, Int4 line, Uint2 ei, Uint2 ii, Uint2 it, Uint2 ist, Uint2 al) { adp->seqEntity_id [line] = ei; adp->item_id [line] = ii; adp->itemtype[line] = it; adp->itemsubtype[line] = ist; adp->alignline [line]= al; } static Boolean id_is_invalid (EditAlignDataPtr adp, PoinT ptlh) { RecT rect; LoadRect(&rect, ptlh.x, ptlh.y, (Int2)(ptlh.x + adp->marginleft * adp->charw), (Int2)(ptlh.y + adp->lineheight)); return RectInRgn (&rect, updateRgn); } static Boolean row_is_invalid (EditAlignDataPtr adp, PoinT ptlh) { RecT rect; LoadRect (&rect, (Int2)(ptlh.x + adp->margin.left - adp->charw), ptlh.y, (Int2)(ptlh.x + adp->pnlWidth * adp->charw + 1), (Int2)(ptlh.y + adp->lineheight)); return RectInRgn (&rect, updateRgn); } static Int2 rang (Uint2 format, SelEdStructPtr ssp) { if (format == OBJ_BIOSEQ) return ssp->entityID; if (format == OBJ_SEQALIGN) return ssp->itemID; return 0; } static Int2 getparam (ValNodePtr vnprm, Uint2 eID, Uint2 iID, Uint1 choice) { ValNodePtr vnp; SeqParamPtr prm; for (vnp = vnprm; vnp != NULL; vnp = vnp->next) { prm = (SeqParamPtr) vnp->data.ptrvalue; if (prm->entityID == eID && prm->itemID == iID) { if (choice == 1) return prm->group; } } return -1; } static CharPtr seqid_tolabel (SeqIdPtr sip, Uint2 choice) { BioseqPtr bsp; SeqIdPtr tmp = NULL; Char str[120]; CharPtr strp; Uint4 val; str[0] = '\0'; if (choice && choice <= PRINTID_GIcc) { bsp = BioseqLockById(sip); if (bsp!=NULL) { if (choice==PRINTID_GIcc) tmp = SeqIdFindBest (bsp->id, 0); else tmp = bsp->id; if (tmp) { SeqIdWrite (tmp, str, PRINTID_TEXTID_ACCESSION, 120); val=WHICH_db_accession(str); if (val==0) choice = PRINTID_FASTA_SHORT; SeqIdWrite (tmp, str, choice, 120); BioseqUnlock(bsp); strp = StringSave (str); return strp; } BioseqUnlock(bsp); } } if (choice!=0 && sip) { SeqIdWrite (sip, str, choice, 120); strp = StringSave (str); return strp; } strp = StringSave (str); return strp; } /***************************************************************** *** *** Draw Alignment in Panel p *** ******************************************************************/ static Char strcmpl[] = "complement"; extern void on_draw (PaneL p) { PoinT ptlh; /* PoinT at the top of lineheight */ RecT rp; /* Panel Rect */ EditAlignDataPtr adp; TextAlignBufPtr curtdp; SelStructPtr curvnp; SelEdStructPtr curssp = NULL; ValNodePtr vnp = NULL; SeqLocPtr curslp; SeqLocPtr sip; SeqAlignPtr salp; Int4 from_inbuf; /* alignment coordinates in buffer */ Int4 from_inseq; /* alignment coordinates in buffer */ Int4 stringlens; Int4 start, stop; Int4 start2, stop2; Int4 line; /* current line */ Int4 curalgline; Int4 drw_width; /* length of drw_str */ Int4 group; Int4 chklocp, chklocp2; Uint2 itemsubtype; Uint4 offset; CharPtr stridp; CharPtr curstr = NULL; CharPtr masterbuf =NULL, masterstr =NULL; Int2 oldstyle; Boolean invalid_id; Boolean invalid_row; Boolean is_master, draw_diff; Boolean first = TRUE; Boolean line_drawn; Boolean empty_line; Int1 gapinline; BoolPtr gapline, gaplinep; if ( (adp = GetAlignDataPanel (p)) == NULL ) return; if ( adp->seqnumber == 0 ) return; salp = (SeqAlignPtr) adp->sap_align->data; if ( adp->firstssp == NULL ) { adp->firstssp = get_firstline (NULL, adp->buffer); } if ( adp->firstssp == NULL ) return; if ( adp->firstssp->region == NULL ) return; from_inseq = adp->hoffset; from_inbuf = adp->hoffset - adp->bufferstart; drw_width = MIN ((Int4) adp->visibleWidth, (Int4) (adp->bufferlength - from_inbuf)); if ( drw_width <= 0 || adp->bufferstart < 0 ) { return; } oldstyle = GetMuskCurrentSt (); SetMuskCurrentSt (GetMuskStyleName (adp->styleNum)); line = (drw_width +2) * sizeof(Boolean); gapline = (BoolPtr) MemNew ((size_t)(line)); MemSet ((Pointer)gapline, (int)(FALSE), (size_t)(line)); gaplinep = NULL; gapinline = LINE_NOGAP; empty_line = FALSE; curssp = (SelEdStructPtr) adp->firstssp->region; if (curssp->itemtype ==OBJ_SEQFEAT) { for (curvnp=adp->firstssp; curvnp!=NULL; curvnp=curvnp->prev) { curssp = (SelEdStructPtr) curvnp->region; if (curssp->itemtype==OBJ_BIOSEQ) /*&&curvnp->itemtype==FEATDEF_BAD)*/ { if (curssp->data !=NULL) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring(curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) { gapinline=getgapsfromstring(curstr, 0, drw_width, &gapline); empty_line =(Boolean)(gapinline == LINE_ONLYGAP); if (gapinline == LINE_NOGAP) gaplinep = NULL; else gaplinep = gapline; } } break; } } } get_client_rect (p, &rp); SelectFont ((FonT)(adp->font)); ptlh.x = rp.left; ptlh.y = rp.top; line = 0; curalgline = 0; adp->visibleLength = drw_width; masterbuf = get_master (adp->linebuff, adp->master.entityID, adp->master.itemID, adp->master.itemtype); curvnp = adp->firstssp; while ( line < adp->pnlLine ) { curssp = (SelEdStructPtr) curvnp->region; if (curssp !=NULL) { adp->lastses = curssp; itemsubtype = curvnp->itemtype; invalid_row = row_is_invalid(adp, ptlh); invalid_id = id_is_invalid (adp, ptlh); if (itemsubtype == EDITDEF_SCA) { what_inline(adp, line, LINE0, LINE0, LINE0, LINE0, curalgline); if ( invalid_row ) { draw_scale (adp, from_inbuf, adp->visibleWidth, &ptlh); } line++; ptlh.y += adp->lineheight; } else if (itemsubtype == EDITDEF_SCB) { what_inline(adp, line, LINE0, LINE0, LINE0, LINE0, curalgline); if ( invalid_row ) { draw_bars (adp, from_inbuf, adp->visibleWidth, &ptlh); } line++; ptlh.y += adp->lineheight; } else if (itemsubtype>=EDITDEF_RF1 && itemsubtype<=EDITDEF_RF6) { if (curssp->data !=NULL && !empty_line) { curslp = (SeqLocPtr) curssp->region; vnp = (ValNodePtr) curssp->data; if ( SeqLocStop (curslp) > from_inseq && vnp != NULL) { what_inline (adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); curstr = (CharPtr) vnp->data.ptrvalue; offset = (Uint2)(itemsubtype - EDITDEF_RF1) % (Uint2)3; if (itemsubtype>=EDITDEF_RF1 && itemsubtypeinput_format, curssp), NULL, Seq_strand_plus, 0, curssp->itemtype, FALSE, FALSE, -1); else draw_id (adp, &ptlh, rang(adp->input_format, curssp), NULL, Seq_strand_minus, 0, curssp->itemtype, FALSE, FALSE, -1); if ( invalid_row ) { draw_trans (adp, curssp, curstr, &ptlh, from_inseq, drw_width, offset); } } line++; ptlh.y += adp->lineheight; } } else if ( itemsubtype == FEATDEF_TRSL ) { if (!empty_line) { first = TRUE; line_drawn = FALSE; while ( curssp != NULL && curssp->data != NULL) { curslp = (SeqLocPtr) curssp->region; sip = SeqLocId (curslp); start2 = SeqLocStart(curslp); chklocp =chkloc(sip, start2, adp->sqloc_list, &start2); start= SeqCoordToAlignCoord (start2, sip, salp, 0, chklocp); stop2 = SeqLocStop(curslp); chklocp =chkloc(sip, stop2, adp->sqloc_list, &stop2); stop = SeqCoordToAlignCoord (stop2, sip, salp, 0, chklocp); if (start < from_inseq + drw_width && stop >= from_inseq) { if ( invalid_row ) { draw_pept (adp, curssp, &ptlh, from_inseq, drw_width, line, 0); } if (first) { what_inline (adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); line_drawn = TRUE; first = FALSE; } } curssp = FindNextSegment (curssp); } if (line_drawn) { line++; ptlh.y += adp->lineheight; } } } else if ( itemsubtype == EDITDEF_CPL ) { if (curssp->data !=NULL && !empty_line) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring (curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) /* !!!!!!! */ { what_inline (adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); if ( invalid_id && (( !adp->displaytype && curssp->itemtype != OBJ_BIOSEQ) || adp->displaytype)) draw_id (adp, &ptlh, -1, strcmpl, 255, 0, curssp->itemtype, FALSE, FALSE, -1); if ( invalid_row && (( !adp->displaytype && curssp->itemtype != OBJ_BIOSEQ) || adp->displaytype) ) { draw_seq (adp, curssp, from_inseq, drw_width, ptlh, curstr, draw_diff, masterstr, TRUE, itemsubtype, FALSE); } line++; ptlh.y += adp->lineheight; } } } else if (curssp->itemtype == OBJ_BIOSEQ) { if (curssp->data !=NULL) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring(curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) { gapinline=getgapsfromstring(curstr, 0, drw_width, &gapline); empty_line =(Boolean)(gapinline == LINE_ONLYGAP); if (gapinline == LINE_NOGAP) gaplinep = NULL; else gaplinep = gapline; if (adp->draw_emptyline || (!adp->draw_emptyline && !empty_line)) { what_inline (adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); is_master = is_samess_ses (&(adp->master), curssp); draw_diff=!(!adp->charmode || (adp->charmode && is_master)); masterstr = NULL; if ( draw_diff ) { stringlens = StringLen (masterbuf); if ( from_inbuf < stringlens ) masterstr = masterbuf + from_inbuf; } if ( invalid_id ) { if (adp->displaytype) { if (adp->marginwithgroup) group=getparam(adp->params,curssp->entityID, curssp->itemID, 1); else group = -1; sip = SeqLocId((SeqLocPtr) curssp->region); start=AlignCoordToSeqCoord(from_inseq, sip,salp, adp->sqloc_list, 0) +1; stridp = seqid_tolabel (sip, adp->printid); draw_id (adp, &ptlh, rang(adp->input_format, curssp), stridp, curtdp->strand, start, curssp->itemtype, FALSE, is_master, group); } } if ( invalid_row && adp->displaytype ) { draw_seq (adp, curssp, from_inseq, drw_width, ptlh, curstr, draw_diff, masterstr, FALSE, curssp->itemtype, TRUE); draw_caret (adp, curssp, ptlh, line); } line++; ptlh.y += adp->lineheight; } } } } else if (curssp->itemtype==OBJ_SEQFEAT && itemsubtype==FEATDEF_PROT) { if (curssp->data !=NULL && !empty_line) { vnp = (ValNodePtr) curssp->data; curtdp = (TextAlignBufPtr) vnp->data.ptrvalue; curstr = get_substring(curtdp->buf, from_inbuf, drw_width); if ( curstr != NULL ) { what_inline (adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); draw_id (adp, &ptlh, -1, curtdp->label, curtdp->strand, 0, curssp->itemtype, FALSE, FALSE, -1); if ( invalid_row ) { draw_seq (adp, curssp, from_inseq, drw_width, ptlh, curstr, draw_diff, masterstr, FALSE, curssp->itemtype, FALSE); } line++; ptlh.y += adp->lineheight; } } } else if ( curssp->itemtype ==OBJ_SEQFEAT ) { if (!empty_line) { first = TRUE; line_drawn = FALSE; while (curssp!=NULL) { curslp = (SeqLocPtr) curssp->region; sip = SeqLocId (curslp); start2 = SeqLocStart(curslp); chklocp = chkloc(sip, start2, adp->sqloc_list, &start2); start= SeqCoordToAlignCoord (start2, sip, salp, 0, chklocp); stop2 = SeqLocStop(curslp); chklocp2 = chkloc(sip, stop2, adp->sqloc_list, &stop2); stop = SeqCoordToAlignCoord (stop2, sip, salp, 0, chklocp2); if (start <= stop && start < from_inseq + drw_width && stop >= from_inseq) { if ( invalid_row ) { draw_feat (adp, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, start, stop, SeqLocStrand(curslp), curssp->label, &ptlh, from_inseq, drw_width, line, curalgline, (Uint4) getcolor_fromstyles(itemsubtype), (Boolean)(chklocp==-1), (Boolean)(chklocp2==APPEND_RESIDUE), gaplinep); } if (first) { what_inline(adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); line_drawn = TRUE; first = FALSE; } } curssp = FindNextSegment (curssp); } if (line_drawn) { line++; ptlh.y += adp->lineheight; } } } else if( itemsubtype==SEQFEAT_GENE || itemsubtype==SEQFEAT_RNA || itemsubtype==SEQFEAT_CDREGION) { if (!empty_line) { first = TRUE; line_drawn = FALSE; while (curssp!=NULL) { curslp = (SeqLocPtr) curssp->region; sip = SeqLocId (curslp); start2 = SeqLocStart(curslp); chklocp =chkloc(sip, start2, adp->sqloc_list, &start2); start= SeqCoordToAlignCoord (start2, sip, salp, 0, chklocp); stop2 = SeqLocStop(curslp); chklocp2 =chkloc(sip, stop2, adp->sqloc_list, &stop2); stop = SeqCoordToAlignCoord (stop2, sip, salp, 0, chklocp); if (start <= from_inseq + drw_width && stop >= from_inseq) { if ( invalid_row ) { draw_feat (adp, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, start, stop, SeqLocStrand(curslp), curssp->label, &ptlh, from_inseq, drw_width, line, curalgline, (Uint4) getcolorforvirtfeat(curssp->itemID), (Boolean)(chklocp==-1), (Boolean)(chklocp2==APPEND_RESIDUE), gaplinep); } if (first) { what_inline (adp, line, curssp->entityID, curssp->itemID, curssp->itemtype, itemsubtype, curalgline); line_drawn = TRUE; first = FALSE; } } curssp = FindNextSegment (curssp); } if (line_drawn) { line++; ptlh.y += adp->lineheight; } } } else { /** ErrPostEx (SEV_ERROR, 0, 0, "fail in on_draw [46] subtype %ld type %ld", (long) itemsubtype, (long) curssp->itemtype); **/ return; } if (line == adp->pnlLine) break; curvnp = curvnp->next; if (curvnp == NULL) { if (adp->rowpcell > 0 && ((Int4)(curalgline+1) % (Int4)adp->rowpcell) == 0) { what_inline(adp,line,LINE0,LINE0, LINE0, LINE0, curalgline); ptlh.y += adp->lineheight; line++; } curvnp = adp->buffer; curalgline++; /***************** *******************/ if (curalgline>500) break; /***************** *******************/ from_inbuf += drw_width; from_inseq += drw_width; if (from_inseq >= adp->length) break; drw_width = MIN ((Int4) adp->visibleWidth, (Int4)(adp->bufferlength - (adp->hoffset -adp->bufferstart) - adp->visibleLength)); adp->visibleLength += drw_width; } } } MemFree (gapline); SetMuskCurrentSt (GetMuskStyleName (oldstyle)); return; }