/* cn3dmatn.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: cn3dmatn.c * * Author: Yanli Wang * * Version Creation Date: 3/26/98 * * File Description: Functions for cn3d/salsa communication * * Modifications: * $Log: cn3dmatn.c,v $ * Revision 6.93 2000/03/14 16:20:56 lewisg * bug fix: selection on non-aligned residues * * Revision 6.92 2000/02/28 14:47:58 thiessen * fixed "show selected only" in show/hide * * Revision 6.91 2000/01/11 01:16:46 lewisg * fix color selection in Cn3D, other misc. bugs * * Revision 6.90 1999/11/23 16:16:17 vakatov * Fixed a (dangerous!) cast of the callback function Cn3D_FindMMCB() * * Revision 6.89 1999/11/18 00:21:42 lewisg * draw speedups and selection on mouseup * * Revision 6.88 1999/11/15 18:30:08 lewisg * get rid of extra redraws when selecting * * Revision 6.87 1999/11/10 23:19:40 lewisg * rewrite of selection code for ddv * * Revision 6.86 1999/10/29 14:15:28 thiessen * ran all Cn3D source through GNU Indent to prettify * * Revision 6.85 1999/10/05 23:18:20 lewisg * add ddv and udv to cn3d with memory management * * Revision 6.84 1999/09/21 18:09:16 lewisg * binary search added to color manager, various bug fixes, etc. * * Revision 6.83 1999/07/07 15:44:00 ywang * set Cn3D_ObjMgrOpen FALSE as GatherProcLaunch returns OM_MSG_RET_ERROR or OM_MSG_RET_NOPROC * * Revision 6.82 1999/05/27 16:11:21 ywang * initilize all local variables at defined * * Revision 6.81 1999/05/25 22:04:58 ywang * always check mediadata->length before assigning residue information for mediadata to protect memory from corruption upon weird data * * Revision 6.80 1999/05/24 16:55:15 ywang * work around last letter selection problem * * Revision 6.79 1999/05/24 15:16:58 ywang * work around messaging problem on C-terminal dashes selection * * Revision 6.78 1999/05/10 20:24:26 ywang * initialize iRes Cn3DColorSalsaForStrucSeqs * * Revision 6.77 1999/05/04 23:12:47 ywang * fix selection retaining problem on show/hide * * Revision 6.76 1999/04/23 14:25:11 ywang * fix bug for Cn3DObjMgrGetSelected * * Revision 6.75 1999/04/21 21:08:42 ywang * fix small memory leak * * Revision 6.74 1999/04/16 22:21:24 ywang * update residue aligned status on mediadata upon sequence SHOW/HIDE * * Revision 6.73 1999/04/01 17:48:23 ywang * fix bug for coloring salsa for strucseqs data * * Revision 6.72 1999/03/30 22:36:18 ywang * add functions to color salsa for NcbiMimeAsn1_strucseqs & code reorganization * * Revision 6.71 1999/03/22 22:41:14 ywang * remove argument in MediaObjSelect * * Revision 6.70 1999/02/12 15:11:52 ywang * send color message to salsa when user changes highlight color from cn3d * * Revision 6.69 1999/02/11 22:42:39 ywang * explicitly call ObjMgrDeSelect to DeHighlight * * Revision 6.68 1999/02/11 22:40:15 ywang * rename functions * * Revision 6.67 1999/02/11 18:48:15 lewisg * delete color index functions * * Revision 6.66 1999/02/10 23:49:43 lewisg * use RGB values instead of indexed palette * * Revision 6.65 1999/02/10 17:04:21 ywang * work around (Uint1) max number 255 problem for valnode choice number * * Revision 6.64 1999/01/20 22:57:25 ywang * customize color for secondary structure & rearrange Option menu * * Revision 6.63 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 6.62 1999/01/19 23:42:49 ywang * fix bugs over improving color msg * * Revision 6.61 1999/01/19 18:25:26 kans * send default rgb to ObjMgrSetColor * * Revision 6.60 1999/01/19 17:51:06 ywang * fix bug in Cn3DSendColorMsg on NULL sip * * Revision 6.59 1999/01/19 17:31:51 ywang * switch color message from many to once * * Revision 6.58 1998/12/16 22:49:39 ywang * fix compiling warnings on Win32 * * Revision 6.57 1998/12/16 19:32:20 ywang * improve highlight residues function when rerendering * * Revision 6.56 1998/10/27 15:55:51 ywang * add functions for testing color by sequence conservation * * Revision 6.55 1998/10/21 15:51:26 ywang * reset residue color for salsa before cn3d redraws so that residues shown in salsa will become black if they are not shown in cn3d window * * Revision 6.54 1998/10/19 20:16:06 ywang * add function FillSeqinfoForSeqEditViewProcs so that salsa can get color array * * Revision 6.53 1998/10/19 17:43:02 kans * prototype needed for Cn3DSendColorMsg * * Revision 6.52 1998/10/16 22:06:09 ywang * make global color array for sequence display * * Revision 6.51 1998/10/07 21:19:50 kans * ObjMgrAlsoSelect changes (CC) * * Revision 6.50 1998/09/23 22:07:32 ywang * fix file name error * * =========================================================================== */ #include #include #include #include /* for sequence load funcs */ #include #include #include #include #include /* the MMDB-API header */ #include #include #include #include #include #include #include #include #include /* udv */ #include /* ddv */ extern Int1 bColorAlignments[]; static void LIBCALLBACK Cn3D_FindMMCB(PFB pfbThis, Nlm_Int4 iModel, Nlm_Int4 iIndex, Pointer ptr) { PDNMM* ModelList = (PDNMM*) ptr; PMMD pmmdThis = NULL; if (pfbThis == NULL) return; if (pfbThis->bMe == (Byte) AM_MMD) { /* is this molecular model data? */ pmmdThis = (PMMD) pfbThis; if (pmmdThis->pSeqId) DValNodeAddPointer (ModelList, 0, pmmdThis); } } PDNMM FindMM(void) /* find coordinates of the bounding box of a structure */ { PDNMM ModelList = NULL; PDNMS pdnmsThis = NULL, pdnmsThisSlave = NULL; PMSD pmsdThis = NULL; pdnmsThis = GetSelectedModelstruc(); if(pdnmsThis == NULL) return NULL; TraverseModels(pdnmsThis, TRAVERSE_MOLECULE, 0, &ModelList, Cn3D_FindMMCB); pmsdThis = pdnmsThis->data.ptrvalue; if(pmsdThis == NULL) return ModelList; for(pdnmsThis = pmsdThis->pdnmsSlaves; pdnmsThis != NULL; pdnmsThis = pdnmsThis->next) { TraverseModels(pdnmsThis, TRAVERSE_MOLECULE, 0, &ModelList, Cn3D_FindMMCB); } return ModelList; } /*----------------------------------------------*/ void DoMediaHL(PMMD pmmdThis, Int4 from, Int4 to, Boolean highlight) { PDNMG pdnmgThis = NULL; PMGD pmgdThis = NULL; PVNMA pvnmaThis = NULL; PMAD pmadThis = NULL; PVNAL pvnalThis = NULL; PALD paldThis = NULL; Byte MainAtom = 0; pdnmgThis = pmmdThis->pdnmgHead; if (pdnmgThis == NULL) return; pmgdThis = pdnmgThis->data.ptrvalue; if ((pmgdThis->bWhat & (Byte) RES_RNA) || (pmgdThis->bWhat & (Byte) RES_DNA)) MainAtom = AM_PALPHA; if (pmgdThis->bWhat & (Byte) RES_AA) MainAtom = AM_CALPHA; while (pdnmgThis) { if (pdnmgThis->choice <= to && pdnmgThis->choice >= from) { pmgdThis = pdnmgThis->data.ptrvalue; if (pmgdThis == NULL) goto setout; fnPreCHLresidue(pdnmgThis, highlight); } setout: pdnmgThis = pdnmgThis->next; } } /*----------------------------------------------*/ void MediaHL(SelStructPtr sel, Boolean highlight) { /* media action -- highlight... */ SeqLocPtr slp = NULL; SeqIntPtr sintp = NULL; SeqIdPtr sip = NULL; Int4 from = 0, to = 0; PDNMM ModelList,iList; PMMD pmmdThis; Bioseq *bsp; slp = sel->region; if (slp == NULL) return; sintp = slp->data.ptrvalue; if(sintp == NULL) return; sip = sintp->id; from = SeqLocStart(slp); to = SeqLocStop(slp); if(to == LAST_RESIDUE || to == APPEND_RESIDUE ) { bsp = BioseqLockById(sip); if (bsp) { to = bsp->length-1; BioseqUnlock(bsp); } } /* residue starts with number 1 in structure, but with number 0 in sequence */ from++; to++; ModelList = FindMM(); for(iList = ModelList; iList != NULL; iList = iList->next) { pmmdThis = iList->data.ptrvalue; if(pmmdThis == NULL) continue; if (SeqIdForSameBioseq(sip, pmmdThis->pSeqId)) DoMediaHL(pmmdThis, from, to, highlight); } DValNodeFree(ModelList); } /* selection originating from Cn3D */ void MediaObjSelect(PDNMG pdnmgThis, Boolean highlight) { PMGD pmgdThis = NULL; PMMD pmmdThis = NULL; SeqLocPtr slp = NULL; Uint2 entityID, itemID; Int4 from, to; pmgdThis = pdnmgThis->data.ptrvalue; pmmdThis = GetParentMol((PFB) pmgdThis); if (pmmdThis == NULL)return; entityID = BioseqFindEntity(pmmdThis->pSeqId, &itemID); if(pmmdThis->pSeqId && entityID != 0) { from = pdnmgThis->choice - 1; to = pdnmgThis->choice - 1; slp = SeqLocIntNew(from, to, 0, pmmdThis->pSeqId); if (highlight) ObjMgrAlsoSelect(entityID, itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC, slp); /* now explicitly use ObjMgrDeSelect */ else ObjMgrDeSelect(entityID, itemID, OBJ_BIOSEQ, OM_REGION_SEQLOC, slp); ObjMgrSendMsg(OM_MSG_MOUSEUP, entityID, itemID, OBJ_BIOSEQ); } else { fnPreCHLresidue(pdnmgThis, highlight); #ifdef _OPENGL Cn3D_Redraw(FALSE); #else RedrawViewer3D(Cn3D_v3d); #endif } } /*-----------------------------------------------*/ void LIBCALLBACK Cn3DCheckAndDoHighlight(PFB pfbThis, Int4 iModel, Int4 iIndex, Pointer ptr) { PMGD pmgdThis = NULL; PDNMG pdnmgThis = NULL; PMMD pmmdThis = NULL; PMSD pmsdThis = NULL; pmgdThis = (PMGD) pfbThis; if (pmgdThis && pmgdThis->bHighlighted == 1) { pdnmgThis = pmgdThis->pdnmgLink; fnPreCHLresidue(pdnmgThis, TRUE); } } /*-----------------------------------------------*/ void Cn3dObjMgrGetSelected(void) { #ifndef _OPENGL 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 */ pdnmsMaster = GetSelectedModelstruc(); if (pdnmsMaster != NULL) { pmsdMaster = pdnmsMaster->data.ptrvalue; if (pmsdMaster->bVisible == 1) { TraverseGraphs(pdnmsMaster, 0, 0, NULL, Cn3DCheckAndDoHighlight); } pdnmsSlave = pmsdMaster->pdnmsSlaves; while (pdnmsSlave) { pmsdSlave = pdnmsSlave->data.ptrvalue; if (pmsdSlave->bVisible == 1) { TraverseGraphs(pdnmsSlave, 0, 0, NULL, Cn3DCheckAndDoHighlight); } pdnmsSlave = pdnmsSlave->next; } } #endif }