/* $Id: cn3dmodl.c,v 6.92 2001/04/27 20:07:59 juran Exp $ * =========================================================================== * * 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: $Id: cn3dmodl.c,v 6.92 2001/04/27 20:07:59 juran Exp $ * * Author: Yanli Wang * * Version Creation Date: 18/9/1998 * * $Log: cn3dmodl.c,v $ * Revision 6.92 2001/04/27 20:07:59 juran * Heed warnings. * * Revision 6.91 2000/04/08 00:37:31 lewisg * multiple seqentries, NEWSEQ message, etc. * * Revision 6.89 2000/03/23 18:27:25 thiessen * show-by-selected now works for hets/ions/water * * Revision 6.88 2000/03/15 04:43:55 thiessen * various minor fixes * * Revision 6.87 2000/03/14 18:03:13 thiessen * add target row to MMD; remove rowmgr * * Revision 6.86 2000/03/10 18:46:59 lewisg * add show/hide * * Revision 6.85 2000/02/28 14:47:59 thiessen * fixed "show selected only" in show/hide * * Revision 6.84 2000/02/26 00:01:40 thiessen * OpenGL improvements, progress on cleanup of Show/Hide * * Revision 6.83 2000/02/25 02:53:14 thiessen * check AlignMgr rather than bAligned flag to see if a residue is aligned * * Revision 6.82 2000/02/19 21:25:56 thiessen * split of cn3dmodl into cn3dmodl and cn3dstyl * * Revision 6.81 2000/02/14 12:32:31 thiessen * fix solvent identification; progress on seqcons module * * Revision 6.80 2000/02/11 15:52:28 thiessen * transparent solvent if partial occupancy; move alt conf behaviour checkbox to Show/Hide panel * * Revision 6.79 2000/02/10 15:51:59 lewisg * cn3d responds and send correct update messages. many coloring bug fixes * * Revision 6.78 2000/02/07 20:17:37 lewisg * minor bug fixes, use gui font for win32 * * Revision 6.77 1999/12/28 23:06:35 lewisg * udv/cn3d communication * * Revision 6.76 1999/12/28 15:08:43 lewisg * remove remaining mediainfo code * * Revision 6.75 1999/12/27 23:14:11 lewisg * add colormgr show/hide in Cn3D * * Revision 6.74 1999/12/16 15:25:22 thiessen * removed unused buttons/popups from OpenGL version * * Revision 6.73 1999/12/11 01:30:34 lewisg * fix bugs with sharing colors between ddv and cn3d * * Revision 6.72 1999/11/22 14:46:43 thiessen * moved _OPENGL code blocks to only vibrant and ncbicn3d libraries * * Revision 6.71 1999/11/15 18:30:08 lewisg * get rid of extra redraws when selecting * * Revision 6.70 1999/11/10 23:19:41 lewisg * rewrite of selection code for ddv * * Revision 6.69 1999/11/03 16:24:21 lewisg * get rid of non-existing includes * * Revision 6.68 1999/11/02 23:06:07 lewisg * fix cn3d to launch correctly if there is no seqentry associated with bioseq * * Revision 6.67 1999/10/29 14:15:28 thiessen * ran all Cn3D source through GNU Indent to prettify * * Revision 6.66 1999/10/15 20:56:39 lewisg * append DDV_ColorGlobal as userdata. free memory when cn3d terminates. * * Revision 6.65 1999/10/05 23:18:20 lewisg * add ddv and udv to cn3d with memory management * * Revision 6.64 1999/09/21 18:09:15 lewisg * binary search added to color manager, various bug fixes, etc. * * Revision 6.63 1999/09/10 13:49:38 lewisg * eliminate spaces before preprocessor directives * * Revision 6.62 1999/07/27 14:19:09 ywang * fix previous in another way so that not to break any existant code * * Revision 6.61 1999/07/26 21:42:47 vakatov * Fixed a multiple ValNode list deallocation in * ClearSpecialFeature/SpecialFeatureFree * * Revision 6.60 1999/07/15 15:59:41 ywang * improve feature control, call Cn3D_DeHighlightAll after ObjMgrDeSelectAll * * Revision 6.59 1999/07/12 14:15:37 ywang * initialize ButtoN b for internal call Cn3D_ListDomainProc & Cn3D_ListStrucProc * * Revision 6.58 1999/07/07 20:45:35 ywang * clear domaindata, mediadata, special feature before reading in new data in cn3d * * Revision 6.57 1999/07/01 16:01:08 ywang * improve display control panel * * Revision 6.56 1999/06/16 15:13:29 ywang * for feature editing: direct return for 'Cancel' 'Delete' 'Edit' 'Save' if no residues or no feature name selected * * Revision 6.55 1999/06/07 21:25:14 ywang * add iUserDefinedFeatureOld, FeatureOnOld to protect saved features being overwritten by temporary feature * * Revision 6.54 1999/06/07 20:26:11 ywang * change prompt for featue editing * * Revision 6.53 1999/06/07 19:39:50 ywang * remove obsolete user defined features, an obsolete feature means a feature whose region has been completely overwirtten by a later defined feature * * Revision 6.52 1999/06/03 20:29:24 ywang * fix bug in aligned domain display when they are from same structure * * Revision 6.51 1999/05/27 16:11:22 ywang * initilize all local variables at defined * * Revision 6.50 1999/05/03 16:54:23 ywang * fix bug for recording and matching mol-id for user defined features * * Revision 6.49 1999/04/22 21:10:44 ywang * check NULL pointer on domain counting * * Revision 6.48 1999/04/21 21:15:09 ywang * replace Cn3D_DeHighlightAll with ObjMgrDeSelectAll * * Revision 6.46 1999/04/16 22:21:23 ywang * update residue aligned status on mediadata upon sequence SHOW/HIDE * * Revision 6.45 1999/04/15 21:37:35 ywang * add AssignDomainAlignedStatusForStrucSeqs * * Revision 6.44 1999/04/14 17:43:26 ywang * synchronize object show/hide upon action 'Show Selected Only' action * * Revision 6.43 1999/04/14 17:19:15 ywang * synchronize object show/hide upon action 'Show Selected Only' action * * Revision 6.42 1999/04/13 23:06:14 ywang * fix bug for coloring strucseqs data * * Revision 6.41 1999/04/06 20:11:02 lewisg * more opengl * * Revision 6.40 1999/04/02 20:51:57 ywang * fix warnings * * Revision 6.39 1999/03/22 22:41:52 ywang * redesign feature page, fix bugs * * Revision 6.38 1999/03/18 23:13:03 ywang * modify feature window * * Revision 6.37 1999/03/18 22:28:56 ywang * add functions for saveout+readin+index user defined features * * Revision 6.36 1999/03/08 21:16:21 ywang * initialize variables * * Revision 6.35 1999/03/08 19:34:35 ywang * redesign Feature page * * Revision 6.34 1999/03/03 23:17:21 lewisg * one master struct at a time, list slaves in structure info, bug fixes * * Revision 6.33 1999/03/01 20:21:30 ywang * put in options for residue on/off control * * Revision 6.32 1999/02/24 23:00:02 ywang * minor name change for user defined feature at MGD nodecn3dmodl.c * * Revision 6.31 1999/02/12 15:42:56 ywang * change void static to static void for ClearSpecialFeaturewithMGD(void) * * Revision 6.30 1999/02/11 22:38:51 ywang * fix bug on display highlight residues only--if no res are highlighted, cn3d sets that button status as FALSE and draw whole structurescn3dwin.c * * Revision 6.29 1999/02/08 18:42:25 ywang * improve feature editing * * Revision 6.28 1999/02/04 16:14:44 ywang * support delete added features * * Revision 6.27 1999/02/03 23:09:24 ywang * add functions to allow editing 'added feature' in Model menu * * Revision 6.26 1999/02/02 22:25:27 ywang * improve feature edit function * * Revision 6.25 1999/02/01 21:10:09 ywang * correct mistake * * Revision 6.24 1999/02/01 20:43:25 ywang * improve 'Model' menu * * Revision 6.23 1999/01/27 21:51:51 ywang * add label to 'Model' menu * * Revision 6.22 1999/01/27 16:21:55 ywang * redesign 'Model' menu * * Revision 6.21 1999/01/26 17:14:35 ywang * redesign Display menu and add 'display highlight residues only' function * * Revision 6.20 1999/01/20 18:21:19 ywang * include salmedia.h due to the move around of MediaInfo from cn3dmsg.h to the new created salmedia.h * * Revision 6.19 1998/12/16 22:49:37 ywang * fix compiling warnings on Win32 * * Revision 6.17 1998/11/09 22:03:31 ywang * fix bugs for modeling * * Revision 6.16 1998/11/06 23:01:05 ywang * fix bugs for modeling * * Revision 6.15 1998/11/04 13:03:30 kans * fixed variable name * * Revision 6.14 1998/11/04 00:06:19 ywang * add function for modeling: change render/color for special residue(s) * * Revision 6.13 1998/10/21 15:48:23 ywang * rearrange View Control menu * * Revision 6.12 1998/10/20 17:50:37 ywang * fix MMDB/VAST domain number inconsistency problem * * Revision 6.11 1998/10/20 16:54:39 ywang * fix bug in AssignDomainAlignedStatus * * Revision 6.10 1998/10/13 14:44:17 ywang * fix bugs for single struc case in AssignDomainAlignedStatus * * Revision 6.9 1998/10/08 21:39:15 ywang * fix bug for assign domain aligned status * * Revision 6.8 1998/10/08 00:07:19 ywang * fix domain aligned status bug * * Revision 6.6 1998/10/02 18:25:15 kans * some functions did not have void as a return, which the Mac compiler detected * * Revision 6.5 1998/10/01 21:55:39 ywang * put function for object display control * * Revision 6.4 1998/09/30 22:10:46 ywang * control display on three levels: structure, chain, domain * * Revision 6.3 1998/09/23 22:04:02 ywang * synchronize show/hide between cn3d and salsa when display complexity is changed * * Revision 6.2 1998/09/23 18:38:48 ywang * add functions to control display on domain level * * Revision 6.1 1998/09/22 18:02:54 ywang * panels and functions for display control * */ #include #ifdef _OPENGL #include #else #include #endif #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include static ButtoN Cn3D_bDisplayHighlight; static Boolean Cn3D_NoSingleHL = FALSE; static ButtoN Cn3D_bAlignOn, Cn3D_bUnalignOn; static ButtoN Cn3D_bDisplayAlignedDomain; static LisT Cn3D_lStruc; static LisT Cn3D_lFeature; static DomainInfo **domaindata; static Int4 iDomainCount = 0; Boolean Cn3D_fAlignOn, Cn3D_fUnalignOn; /* globals for above buttons */ static ButtoN Cn3D_altConfIdOverlay; Nlm_Boolean allowAltConfIdOverlay(void) { return GetStatus(Cn3D_altConfIdOverlay); } static ButtoN Cn3D_bDisplayApply; /*-------------------------------------------------------------------*/ void LIBCALLBACK Cn3DCheckNoSingleHighlight(PFB pfbThis, Int4 iModel, Int4 iIndex, Pointer ptr) { PMGD pmgdThis = NULL; PDNMG pdnmgThis = NULL; pmgdThis = (PMGD) pfbThis; if (pmgdThis->bHighlighted == 1) Cn3D_NoSingleHL = FALSE; } /*-----------------------------------------------*/ void Cn3DCheckHighlighted(void) { PDNMS pdnmsMaster = NULL, pdnmsSlave = NULL; PMSD pmsdMaster = NULL, pmsdSlave = NULL; /* replace old function which depends on ObjMgr */ /* by doing so, highlight for non ObjMgr registered residues will */ /* also be picked up when do Cn3D_Redraw */ Cn3D_NoSingleHL = TRUE; pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster != NULL) { pmsdMaster = pdnmsMaster->data.ptrvalue; TraverseGraphs(pdnmsMaster, 0, 0, NULL, Cn3DCheckNoSingleHighlight); pdnmsSlave = pmsdMaster->pdnmsSlaves; while (pdnmsSlave && Cn3D_NoSingleHL) { TraverseGraphs(pdnmsSlave, 0, 0, NULL, Cn3DCheckNoSingleHighlight); pdnmsSlave = pdnmsSlave->next; } } } /*---------------------------------------------------------*/ static void Cn3D_SelectDomainProc(LisT l) { SetStatus(Cn3D_bDisplayAlignedDomain, FALSE); } /*---------------------------------------------------------*/ /* fill out domain list */ NLM_EXTERN void Cn3D_ListDomainProc(void) { Char MolName[20]; Int4 iCount = 0, iCountActive = 0; Reset(Cn3D_lFeature); for (iCount = 0; iCount < iDomainCount; iCount++) { domaindata[iCount]->bVisibleParent = GetItemStatus(Cn3D_lStruc, domaindata[iCount]->iStrucIndex + 1); } for (iCount = 0; iCount < iDomainCount; iCount++) { if (domaindata[iCount]->iDomain == 0) sprintf(MolName, "%4s %2s", domaindata[iCount]->pcPDBName, domaindata[iCount]->pcMolName); else sprintf(MolName, "%4s %2s %2d", domaindata[iCount]->pcPDBName, domaindata[iCount]->pcMolName, domaindata[iCount]->iDomain); if (domaindata[iCount]->bVisibleParent) { ListItem(Cn3D_lFeature, (CharPtr) MolName); iCountActive++; if (!GetStatus(Cn3D_bDisplayAlignedDomain)) SetItemStatus(Cn3D_lFeature, iCountActive, domaindata[iCount]->bVisible); else { if (domaindata[iCount]->bAligned) { SetItemStatus(Cn3D_lFeature, iCountActive, TRUE); domaindata[iCount]->bVisible = TRUE; } else if (!domaindata[iCount]->bAligned) { SetItemStatus(Cn3D_lFeature, iCountActive, FALSE); domaindata[iCount]->bVisible = FALSE; } } } } return; } /*---------------------------------------------------------*/ static void Cn3D_ListAlignedDomainProc(ButtoN b) { Cn3D_ListDomainProc(); } /*---------------------------------------------------------*/ static void FillFeatureListProc(LisT l) { Cn3D_ListDomainProc(); } /*---------------------------------------------------------*/ static void SetDomainParentStatus(Int4 Index, Byte bVisible) { Int4 iCount = 0; for (iCount = 0; iCount < iDomainCount; iCount++) { if (domaindata[iCount]->iStrucIndex == Index) domaindata[iCount]->bVisibleParent = bVisible; } } /*---------------------------------------------------------*/ static void Cn3D_ReSetModVisibleStatus(PVNMO pvnmoThis, Byte bVisible) { PMOD pmodThis = NULL; while (pvnmoThis) { pmodThis = (PMOD) pvnmoThis->data.ptrvalue; pmodThis->bVisible = bVisible; pvnmoThis = pvnmoThis->next; } } /*---------------------------------------------------------*/ static void Cn3D_ReSetMmVisibleStatus(PDNMM pdnmmHead, Byte bVisible) { PMMD pmmdThis = NULL; PDNMG pdnmg = NULL; PMGD pmgd = NULL; for (; pdnmmHead; pdnmmHead = pdnmmHead->next) { pmmdThis = pdnmmHead->data.ptrvalue; if (pmmdThis) { if (pmmdThis->bWhat != (Byte) AM_PROT && pmmdThis->bWhat != (Byte) AM_RNA && pmmdThis->bWhat != (Byte) AM_DNA) continue; Cn3D_SetVisible(Cn3D_ColorData.pDDVColorGlobal, pmmdThis, bVisible); for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; pmgd->bVisible = bVisible; } } } } /*---------------------------------------------------------*/ static void Cn3D_ReSetVisibleStatus(void) { PDNMS pdnmsMaster = NULL, pdnmsSlave = NULL; PMSD pmsdMaster = NULL, pmsdSlave = NULL; PDNMM pdnmmHead = NULL; PMMD pmmdThis = NULL; PDNMG pdnmg = NULL; PMGD pmgd = NULL; PVNMO pvnmoThis = NULL; pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster != NULL) { pmsdMaster = (PMSD) pdnmsMaster->data.ptrvalue; pmsdMaster->bVisible = 1; pvnmoThis = pmsdMaster->pvnmoHead; Cn3D_ReSetModVisibleStatus(pvnmoThis, 1); pdnmmHead = pmsdMaster->pdnmmHead; Cn3D_ReSetMmVisibleStatus(pdnmmHead, 1); pdnmsSlave = pmsdMaster->pdnmsSlaves; while (pdnmsSlave) { pmsdSlave = (PMSD) pdnmsSlave->data.ptrvalue; pmsdSlave->bVisible = 1; pvnmoThis = pmsdSlave->pvnmoHead; Cn3D_ReSetModVisibleStatus(pvnmoThis, 1); pdnmmHead = pmsdSlave->pdnmmHead; Cn3D_ReSetMmVisibleStatus(pdnmmHead, 1); pdnmsSlave = pdnmsSlave->next; } } } /* sets values in the show/hide list for structures */ NLM_EXTERN void Cn3D_SetStrucList(void) { PDNMS pdnmsMaster, pdnmsSlave; PMSD pmsdMaster, pmsdSlave; Int4 iCount = 0; Reset(Cn3D_lStruc); pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster != NULL) { pmsdMaster = (PMSD) pdnmsMaster->data.ptrvalue; ListItem(Cn3D_lStruc, pmsdMaster->pcPDBName); SetItemStatus(Cn3D_lStruc, iCount + 1, pmsdMaster->bVisible); iCount++; pdnmsSlave = pmsdMaster->pdnmsSlaves; while (pdnmsSlave) { pmsdSlave = (PMSD) pdnmsSlave->data.ptrvalue; ListItem(Cn3D_lStruc, pmsdSlave->pcPDBName); SetItemStatus(Cn3D_lStruc, iCount + 1, pmsdSlave->bVisible); iCount++; pdnmsSlave = pdnmsSlave->next; } } } /*---------------------------------------------------------*/ void AssignDomainAlignedStatusForStrucSeqs(void) { PDNMS pdnmsMaster = NULL; PMSD pmsdMaster = NULL; PDNMM pdnmmHead = NULL, pdnmmHead_temp = NULL; PMMD pmmdThis = NULL; PDNMG pdnmg = NULL; PMGD pmgd = NULL; Int4 iCount = 0, iCountChain = 0; pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster == NULL) return; pmsdMaster = (PMSD) pdnmsMaster->data.ptrvalue; pdnmmHead = pmsdMaster->pdnmmHead; for (iCount = 0; iCount < iDomainCount; iCount++) { domaindata[iCount]->bAligned = FALSE; pdnmmHead_temp = pdnmmHead; iCountChain = 0; while (pdnmmHead_temp) { pmmdThis = pdnmmHead_temp->data.ptrvalue; if (pmmdThis == NULL) break; if (pmmdThis->bWhat != (Byte) AM_PROT && pmmdThis->bWhat != (Byte) AM_RNA && pmmdThis->bWhat != (Byte) AM_DNA) goto setout1; if (domaindata[iCount]->iChainIndex == iCountChain) { for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; if (pmgd->iDomain == domaindata[iCount]->iDomain && pmgd->bReserved) { domaindata[iCount]->bAligned = TRUE; goto setout2; } } } setout1: pdnmmHead_temp = pdnmmHead_temp->next; iCountChain++; } setout2: continue; } } /*---------------------------------------------------------*/ void AssignDomainAlignedStatus(void) { Int4 iCount = 0, iCountStruc = 0; PDNMS pdnmsMaster = NULL; PMSD pmsdMaster = NULL; BiostrucAnnotSetPtr pbsaThis = NULL; BiostrucFeatureSetPtr pbsfsThis = NULL; BiostrucFeaturePtr pbsfThis = NULL; Int2 iDomainMaster = 0, iDomainSlave = 0; pdnmsMaster = GetSelectedModelstruc(); if (!pdnmsMaster) return; else pmsdMaster = pdnmsMaster->data.ptrvalue; pbsaThis = pmsdMaster->psaStrucAlignment; if (pbsaThis == NULL) return; pbsfsThis = pbsaThis->features; iDomainMaster = (Int2) (pbsfsThis->id % 100); for (iCount = 0; iCount < iDomainCount; iCount++) { pbsfThis = pbsfsThis->features; iCountStruc = 0; while (pbsfThis) { iDomainSlave = (Int2) (((pbsfThis->id - pbsfThis->id % 10) / 10) % 100); iCountStruc++; if (domaindata[iCount]->iStrucIndex == 0) { if ( (StringNCmp (pbsfThis->name, domaindata[iCount]->pcPDBName, 4) == 0) && (pbsfThis->name[4] == domaindata[iCount]->pcMolName[0])) { /* if((Char) pbsfThis->name[5] == '0'){ */ if (iDomainMaster == 0) { domaindata[iCount]->bAligned = TRUE; } else if (iDomainMaster == domaindata[iCount]->iDomain) { domaindata[iCount]->bAligned = TRUE; } } } else if (domaindata[iCount]->iStrucIndex == iCountStruc) { if ( (StringNCmp (pbsfThis->name + 7, domaindata[iCount]->pcPDBName, 4) == 0) && (pbsfThis->name[11] == domaindata[iCount]->pcMolName[0])) { if (iDomainSlave == 0) { domaindata[iCount]->bAligned = TRUE; } else if (iDomainSlave == domaindata[iCount]->iDomain) { domaindata[iCount]->bAligned = TRUE; } } } pbsfThis = pbsfThis->next; } } } /*---------------------------------------------------------*/ void LIBCALL Cn3D_CountDomainProc(void) { Int4 iCount = 0; Int4 idom = 0; Int4 iCountStruc = 0, iCountChain = 0; PDNMS pdnmsMaster = NULL, pdnmsSlave = NULL; PMSD pmsdMaster = NULL, pmsdSlave = NULL; PDNMM pdnmmHead = NULL; PMMD pmmdThis = NULL; PDNMG pdnmg = NULL; PMGD pmgd = NULL; Boolean EncounterZeroDomain = FALSE; pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster == NULL) return; if (pdnmsMaster != NULL) { pmsdMaster = (PMSD) pdnmsMaster->data.ptrvalue; pdnmmHead = pmsdMaster->pdnmmHead; while (pdnmmHead) { pmmdThis = pdnmmHead->data.ptrvalue; if (pmmdThis) { if (pmmdThis->bWhat != (Byte) AM_PROT && pmmdThis->bWhat != (Byte) AM_RNA && pmmdThis->bWhat != (Byte) AM_DNA) goto pre_setout1; idom = 0; EncounterZeroDomain = FALSE; for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; if (!EncounterZeroDomain) { if (pmgd->iDomain == 0) { iCount++; EncounterZeroDomain = TRUE; } } if (pmgd->iDomain > idom) { idom = (Int4) pmgd->iDomain; iCount++; } } } pre_setout1: pdnmmHead = pdnmmHead->next; } pdnmsSlave = pmsdMaster->pdnmsSlaves; while (pdnmsSlave) { pmsdSlave = (PMSD) pdnmsSlave->data.ptrvalue; pdnmmHead = pmsdSlave->pdnmmHead; while (pdnmmHead) { pmmdThis = pdnmmHead->data.ptrvalue; if (pmmdThis) { if (pmmdThis->bWhat != (Byte) AM_PROT && pmmdThis->bWhat != (Byte) AM_RNA && pmmdThis->bWhat != (Byte) AM_DNA) goto pre_setout2; idom = 0; EncounterZeroDomain = FALSE; for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; if (!EncounterZeroDomain) { if (pmgd->iDomain == 0) { iCount++; EncounterZeroDomain = TRUE; } } pmgd = (PMGD) pdnmg->data.ptrvalue; if (pmgd->iDomain > idom) { idom = (Int4) pmgd->iDomain; iCount++; } } } pre_setout2: pdnmmHead = pdnmmHead->next; } pdnmsSlave = pdnmsSlave->next; } } iDomainCount = iCount; /* to allocate memory for domaindata */ domaindata = (Pointer) MemNew((size_t) (iDomainCount * sizeof(Pointer))); for (iCount = 0; iCount < iDomainCount; iCount++) { domaindata[iCount] = (DomainInfoPtr) MemNew(sizeof(DomainInfo)); } /* to load pdbname, chain id, domain id into domaindata */ iCount = 0; iCountStruc = 0; iCountChain = 0; pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster != NULL) { pmsdMaster = (PMSD) pdnmsMaster->data.ptrvalue; pdnmmHead = pmsdMaster->pdnmmHead; while (pdnmmHead) { pmmdThis = pdnmmHead->data.ptrvalue; if (pmmdThis) { if (pmmdThis->bWhat != (Byte) AM_PROT && pmmdThis->bWhat != (Byte) AM_RNA && pmmdThis->bWhat != (Byte) AM_DNA) goto setout1; Cn3D_SetVisible(Cn3D_ColorData.pDDVColorGlobal, pmmdThis, TRUE); idom = 0; EncounterZeroDomain = FALSE; for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; if (!EncounterZeroDomain) { if (pmgd->iDomain == 0) { StringCpy(domaindata[iCount]->pcPDBName, pmsdMaster->pcPDBName); StringCpy(domaindata[iCount]->pcMolName, pmmdThis->pcMolName); domaindata[iCount]->iDomain = 0; domaindata[iCount]->iStrucIndex = iCountStruc; domaindata[iCount]->iChainIndex = iCountChain; domaindata[iCount]->bVisible = TRUE; domaindata[iCount]->bVisibleParent = TRUE; iCount++; EncounterZeroDomain = TRUE; } } if (pmgd->iDomain > idom) { idom = (Int4) pmgd->iDomain; StringCpy(domaindata[iCount]->pcPDBName, pmsdMaster->pcPDBName); StringCpy(domaindata[iCount]->pcMolName, pmmdThis->pcMolName); domaindata[iCount]->iDomain = pmgd->iDomain; domaindata[iCount]->iStrucIndex = iCountStruc; domaindata[iCount]->iChainIndex = iCountChain; domaindata[iCount]->bVisible = TRUE; domaindata[iCount]->bVisibleParent = TRUE; iCount++; } } iCountChain++; } setout1: pdnmmHead = pdnmmHead->next; } iCountStruc++; pdnmsSlave = pmsdMaster->pdnmsSlaves; while (pdnmsSlave) { pmsdSlave = (PMSD) pdnmsSlave->data.ptrvalue; pdnmmHead = pmsdSlave->pdnmmHead; while (pdnmmHead) { pmmdThis = pdnmmHead->data.ptrvalue; if (pmmdThis) { if (pmmdThis->bWhat != (Byte) AM_PROT && pmmdThis->bWhat != (Byte) AM_RNA && pmmdThis->bWhat != (Byte) AM_DNA) goto setout2; idom = 0; EncounterZeroDomain = FALSE; for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; if (!EncounterZeroDomain) { if (pmgd->iDomain == 0) { StringCpy(domaindata[iCount]->pcPDBName, pmsdSlave->pcPDBName); StringCpy(domaindata[iCount]->pcMolName, pmmdThis->pcMolName); domaindata[iCount]->iDomain = 0; domaindata[iCount]->iStrucIndex = iCountStruc; domaindata[iCount]->iChainIndex = iCountChain; domaindata[iCount]->bVisible = TRUE; domaindata[iCount]->bVisibleParent = TRUE; iCount++; EncounterZeroDomain = TRUE; } } if (pmgd->iDomain > idom) { idom = (Int4) pmgd->iDomain; StringCpy(domaindata[iCount]->pcPDBName, pmsdSlave->pcPDBName); StringCpy(domaindata[iCount]->pcMolName, pmmdThis->pcMolName); domaindata[iCount]->iDomain = pmgd->iDomain; domaindata[iCount]->iStrucIndex = iCountStruc; domaindata[iCount]->iChainIndex = iCountChain; domaindata[iCount]->bVisible = TRUE; domaindata[iCount]->bVisibleParent = TRUE; iCount++; } /* if(pmgd->bReserved && !domaindata[iCount - 1]->bAligned) domaindata[iCount - 1]->bAligned = TRUE; */ } iCountChain++; } setout2: pdnmmHead = pdnmmHead->next; } iCountStruc++; pdnmsSlave = pdnmsSlave->next; } } if (pmsdMaster->iMimeType == NcbiMimeAsn1_strucseqs) { AssignDomainAlignedStatusForStrucSeqs(); } else AssignDomainAlignedStatus(); } /*---------------------------------------------------------*/ static void SetDomainDataItemStatus(LisT l) { Int4 iCount = 0, iCountActive = 0; for (iCount = 0; iCount < iDomainCount; iCount++) { if (domaindata[iCount]->bVisibleParent) { domaindata[iCount]->bVisible = GetItemStatus(Cn3D_lFeature, iCountActive + 1); iCountActive++; } } return; } /*---------------------------------------------------------*/ Int4 iCountItemGet(PMSD pmsdThis, PMMD pmmdThis, PMGD pmgdThis, Int4 iCountStruc) { Int4 iCount = 0, iCountLive = 0; Int2 iDomain = 0; if (pmgdThis == NULL) iDomain = 0; else iDomain = pmgdThis->iDomain; for (iCount = 0; iCount < iDomainCount; iCount++) { if (!domaindata[iCount]->bVisibleParent) continue; if (StringCmp(pmsdThis->pcPDBName, domaindata[iCount]->pcPDBName) == 0 && StringCmp(pmmdThis->pcMolName, domaindata[iCount]->pcMolName) == 0 && iDomain == domaindata[iCount]->iDomain && iCountStruc == domaindata[iCount]->iStrucIndex) return (iCountLive + 1); iCountLive++; } return 0; } /*---------------------------------------------------------*/ NLM_EXTERN void fnAlignList(LisT l) /* set the values of the alignment pane */ { Int4 iCount = 0; PDNMS pdnmsMaster = NULL, pdnmsSlave = NULL; PMSD pmsdMaster = NULL, pmsdSlave = NULL; BiostrucFeaturePtr pbsfThis = NULL; PDNMM pdnmmHead = NULL; PMMD pmmdThis = NULL; Byte bVisible = 0; SeqIdPtr sipThis = NULL; Uint2 entityID = 0, itemID = 0, itemtype = 0; #ifndef _OPENGL Cn3D_SaveActiveCam(); #endif iCount = 0; pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster != NULL) { pmsdMaster = (PMSD) pdnmsMaster->data.ptrvalue; bVisible = pmsdMaster->bVisible; pmsdMaster->bVisible = GetItemStatus(Cn3D_lStruc, iCount + 1); SetDomainParentStatus(iCount, pmsdMaster->bVisible); pdnmmHead = pmsdMaster->pdnmmHead; Cn3D_ReSetMmVisibleStatus(pdnmmHead, pmsdMaster->bVisible); if (pmsdMaster->iMimeType != NcbiMimeAsn1_strucseqs) { TraverseGraphs(pdnmsMaster, 0, 0, NULL, fnClearMarkedResidues); pmsdMaster->bAligned = 0; } pdnmsSlave = pmsdMaster->pdnmsSlaves; if (pmsdMaster->psaStrucAlignment != NULL) { pbsfThis = pmsdMaster->psaStrucAlignment->features->features; iCount++; while (pdnmsSlave) { pmsdSlave = (PMSD) pdnmsSlave->data.ptrvalue; bVisible = pmsdSlave->bVisible; TraverseGraphs(pdnmsSlave, 0, 0, NULL, fnClearMarkedResidues); pmsdSlave->bVisible = GetItemStatus(Cn3D_lStruc, iCount + 1); SetDomainParentStatus(iCount, pmsdSlave->bVisible); if (pmsdMaster->bVisible && pmsdSlave->bVisible) { fnMarkAlignedResidues(pdnmsMaster, pdnmsSlave, pbsfThis); pmsdMaster->bAligned++; } pbsfThis = pbsfThis->next; if (bVisible != pmsdSlave->bVisible) { pdnmmHead = pmsdSlave->pdnmmHead; Cn3D_ReSetMmVisibleStatus(pdnmmHead, pmsdSlave->bVisible); } iCount++; pdnmsSlave = pdnmsSlave->next; } } } #ifndef _OPENGL Cn3D_v3d->is_zoomed = TRUE; /* keep the proteins from moving */ #endif } /*---------------------------------------------------------*/ static void SynchronizeModVisibleStatus(PFB pfbThis) { PMSD pmsdThis = NULL; PMMD pmmdThis = NULL; PDNMG pdnmg = NULL; PMGD pmgdThis = NULL; PVNMO pvnmoThis = NULL; PMOD pmodThis = NULL; ValNodePtr pvnThis = NULL; pmsdThis = ToMSDParent(pfbThis); pvnmoThis = pmsdThis->pvnmoHead; if (pfbThis->bMe == AM_MGD) { while (pvnmoThis) { pmodThis = pvnmoThis->data.ptrvalue; pmodThis->bVisible = 0; pvnThis = pmodThis->pvnContains; while (pvnThis) { pmgdThis = (PMGD) pvnThis->data.ptrvalue; if (GetStatus(Cn3D_bDisplayHighlight)) pmodThis->bVisible = (pmgdThis->bVisible && pmgdThis->bHighlighted); else pmodThis->bVisible = pmgdThis->bVisible; if (pmodThis->bVisible == 1) break; pvnThis = pvnThis->next; } pvnmoThis = pvnmoThis->next; } } /* not currently used... else if (pfbThis->bMe == AM_MMD) { pmmdThis = (PMMD) pfbThis; while (pvnmoThis) { pmodThis = pvnmoThis->data.ptrvalue; if (IsGraphNode((PFB) pmodThis->pvnContains->data.ptrvalue)) { if (pmmdThis == GetParentMol((PFB) pmodThis->pvnContains->data.ptrvalue)) { pmodThis->bVisible = Cn3D_IsVisible(Cn3D_ColorData.pDDVColorGlobal, pmmdThis); } } pvnmoThis = pvnmoThis->next; } } */ } /*---------------------------------------------------------*/ void LIBCALL ResetDisplayCtrls(void) /* set the values of the alignment pane */ { Cn3D_ReSetVisibleStatus(); Cn3D_SetStrucList(); Cn3D_ListDomainProc(); SetStatus(Cn3D_bAlignOn, Cn3D_fAlignOn); SetStatus(Cn3D_bUnalignOn, Cn3D_fUnalignOn); return; } /*---------------------------------------------------------*/ GrouP LIBCALL DisplayControls(Nlm_GrouP prnt) { GrouP g, h; PrompT ppt1, /*ppt2,*/ ppt3, ppt4; g = HiddenGroup(prnt, -1, 0, NULL); if (!g) return NULL; SetGroupSpacing(g, 3, 9); #ifdef WIN_MOTIF SetGroupMargins(g, 4, 1); SetGroupSpacing(g, 2, 1); #else SetGroupMargins(g, 1, 1); SetGroupSpacing(g, 0, 0); #endif StaticPrompt(g, "", 0, stdLineHeight, systemFont, 'l'); StaticPrompt(g, "", 0, stdLineHeight, systemFont, 'l'); h = HiddenGroup(g, 0, -4, NULL); SetGroupSpacing(h, 30, 10); ppt1 = StaticPrompt(h, "Molecule", 0, stdLineHeight + 5, systemFont, 'c'); Cn3D_lStruc = MultiList(h, 6, 10, FillFeatureListProc); StaticPrompt(h, "", 0, stdLineHeight, systemFont, 'l'); StaticPrompt(h, "", 0, stdLineHeight, systemFont, 'l'); AlignObjects(ALIGN_LEFT, (HANDLE) ppt1, (HANDLE) Cn3D_lStruc, NULL); ppt3 = StaticPrompt(h, "Domain", 0, stdLineHeight + 5, systemFont, 'c'); Cn3D_bDisplayAlignedDomain = CheckBox(h, "Aligned Domain Only", Cn3D_ListAlignedDomainProc); Cn3D_lFeature = MultiList(h, 6, 8, Cn3D_SelectDomainProc); StaticPrompt(h, "", 0, stdLineHeight, systemFont, 'l'); AlignObjects(ALIGN_LEFT, (HANDLE) ppt3, (HANDLE) Cn3D_lFeature, NULL); ppt4 = StaticPrompt(h, "Residue", 0, stdLineHeight + 5, systemFont, 'c'); Cn3D_bAlignOn = CheckBox(h, "Aligned", NULL); Cn3D_bUnalignOn = CheckBox(h, "Unaligned", NULL); Cn3D_bDisplayHighlight = CheckBox(h, "Show Selected Only", NULL); AlignObjects(ALIGN_LEFT, (HANDLE) ppt4, (HANDLE) Cn3D_bDisplayHighlight, NULL); SetStatus(Cn3D_bDisplayHighlight, FALSE); SetStatus(Cn3D_bAlignOn, Cn3D_fAlignOn); SetStatus(Cn3D_bUnalignOn, Cn3D_fUnalignOn); Cn3D_altConfIdOverlay = CheckBox(g, "Overlay uncorrelated conformer ensembles", NULL); AlignObjects(ALIGN_CENTER, (HANDLE) Cn3D_altConfIdOverlay, (HANDLE) g, NULL); SetStatus(Cn3D_altConfIdOverlay, TRUE); StaticPrompt(g, "", 0, stdLineHeight + 5, systemFont, 'c'); Cn3D_bDisplayApply = PushButton(g, "Apply!", Cn3D_DisplayProc); AlignObjects(ALIGN_CENTER, (HANDLE) Cn3D_bDisplayApply, (HANDLE) h, NULL); ResetDisplayCtrls(); return g; } static void SetResidueVisibilities(PDNMS pdnmsThis, Int4 iCountStruc, SeqAlignPtr salp) { PMSD pmsdThis; PDNMM pdnmmHead; PMMD pmmdThis = NULL; PDNMG pdnmg = NULL; PMGD pmgd = NULL; PVNMO pvnmoThis = NULL; Int4 currentRow = -1, currentAlignLoc = -2; Boolean bIsPorNA; pmsdThis = (PMSD) pdnmsThis->data.ptrvalue; pdnmmHead = pmsdThis->pdnmmHead; while (pdnmmHead) { pmmdThis = pdnmmHead->data.ptrvalue; if (pmmdThis) { bIsPorNA = (pmmdThis->bWhat == (Byte) AM_PROT || pmmdThis->bWhat == (Byte) AM_RNA || pmmdThis->bWhat == (Byte) AM_DNA); if (bIsPorNA) Cn3D_SetVisible(Cn3D_ColorData.pDDVColorGlobal, pmmdThis, TRUE); else pmmdThis->bVisible = TRUE; if (bIsPorNA && salp && pmmdThis->pSeqId) currentRow = ViewMgr_TRow2VRow(salp, pmmdThis->iTargetRow); else currentRow = -1; for (pdnmg = pmmdThis->pdnmgHead; pdnmg != NULL; pdnmg = pdnmg->next) { pmgd = (PMGD) pdnmg->data.ptrvalue; /* first check to see if whole structure is visible */ if (bIsPorNA) pmgd->bVisible = GetItemStatus(Cn3D_lFeature, iCountItemGet(pmsdThis, pmmdThis, pmgd, iCountStruc)); else pmgd->bVisible = TRUE; if (pmgd->bVisible && GetStatus(Cn3D_bDisplayHighlight)) pmgd->bVisible = pmgd->bHighlighted; if (bIsPorNA) { if (salp && currentRow > 0) currentAlignLoc = AlnMgrMapBioseqToSeqAlign(salp, pdnmg->choice - 1, currentRow, NULL); if ((currentAlignLoc >= 0 && !Cn3D_fAlignOn) || (currentAlignLoc < 0 && !Cn3D_fUnalignOn)) pmgd->bVisible = 0; } } } SynchronizeModVisibleStatus((PFB) pmgd); pdnmmHead = pdnmmHead->next; } } /*---------------------------------------------------------*/ NLM_EXTERN void Cn3D_DisplayProc(ButtoN b) { LisT l = NULL; SeqAlignPtr salp = NULL; SeqAnnotPtr sanp; PDNMS pdnmsMaster = NULL, pdnmsSlave = NULL; Int4 iCountStruc = 0; Cn3D_fAlignOn = GetStatus(Cn3D_bAlignOn); Cn3D_fUnalignOn = GetStatus(Cn3D_bUnalignOn); fnAlignList(l); SetDomainDataItemStatus(l); if (GetStatus(Cn3D_bDisplayHighlight)) { Cn3DCheckHighlighted(); if (Cn3D_NoSingleHL) SetStatus(Cn3D_bDisplayHighlight, FALSE); } /* get pointer to current SeqAlign */ for (sanp = Cn3D_ColorData.sap; sanp != NULL; sanp = sanp->next) { if (sanp->data != NULL) { salp = sanp->data; break; } } pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster) { SetResidueVisibilities(pdnmsMaster, iCountStruc, salp); iCountStruc++; pdnmsSlave = ((PMSD) pdnmsMaster->data.ptrvalue)->pdnmsSlaves; while (pdnmsSlave) { SetResidueVisibilities(pdnmsSlave, iCountStruc, salp); iCountStruc++; pdnmsSlave = pdnmsSlave->next; } } #ifndef _OPENGL Cn3D_v3d->is_zoomed = TRUE; /* keep the proteins from moving */ #endif Cn3dObjMgrGetSelected(); fnCn3D_RedrawWrapper(FALSE); return; } /*-------------------------------------------*/ void ClearDomainData(void) { Int4 iCount = 0; for (iCount = 0; iCount < iDomainCount; iCount++) { MemFree(domaindata[iCount]); } if (domaindata) MemFree(domaindata); domaindata = NULL; iDomainCount = 0; SetStatus(Cn3D_bDisplayHighlight, FALSE); Cn3D_NoSingleHL = FALSE; return; }