diff options
Diffstat (limited to 'sequin/sequin1.c')
| -rw-r--r-- | sequin/sequin1.c | 791 |
1 files changed, 682 insertions, 109 deletions
diff --git a/sequin/sequin1.c b/sequin/sequin1.c index 06cffe29..387f6d33 100644 --- a/sequin/sequin1.c +++ b/sequin/sequin1.c @@ -29,7 +29,7 @@ * * Version Creation Date: 1/22/95 * -* $Revision: 6.622 $ +* $Revision: 6.653 $ * * File Description: * @@ -92,6 +92,7 @@ static char *time_of_compilation = "now"; #include <tax3api.h> #include <validerr.h> #include <algo/blast/api/blast_api.h> +#include <findrepl.h> /* USE_SMARTNET */ #ifdef USE_SMARTNET @@ -130,7 +131,7 @@ static char *time_of_compilation = "now"; #include <Gestalt.h> #endif -#define SEQ_APP_VER "7.70" +#define SEQ_APP_VER "8.03" #ifndef CODECENTER static char* sequin_version_binary = "Sequin Indexer Services Version " SEQ_APP_VER " " __DATE__ " " __TIME__; @@ -147,6 +148,7 @@ extern EnumFieldAssoc biosource_genome_simple_alist []; Boolean useDesktop = FALSE; Boolean useEntrez = FALSE; Boolean useSeqFetch = FALSE; +Boolean useIdLookup = FALSE; Boolean useLocal = FALSE; Boolean useBlast = FALSE; Boolean useMedarch = FALSE; @@ -306,7 +308,7 @@ static Boolean strictLatLonCountry = FALSE; static Int4 SMWriteBioseqObj(VoidPtr bio_data, SMUserDataPtr sm_usr_data, VoidPtr data); static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, - Int4 length, Int4 fd); + Int4 length, void* fd); #define SMART_KEY 1313 #define DUMB_KEY 1314 #endif @@ -391,6 +393,9 @@ static void CheckForCookedBioseqs (SeqEntryPtr sep, Pointer mydata, Int4 index, } } +static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp); + + static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f) { @@ -406,6 +411,9 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f) if (entityID < 1) return FALSE; sep = GetTopSeqEntryForEntityID (entityID); if (sep == NULL) return FALSE; + + if (!FixSpecialCharacters (entityID)) return FALSE; + if (GetSequinAppParam ("PREFERENCES", "ASKBEFOREVALIDATE", NULL, str, sizeof (str))) { if (StringICmp (str, "TRUE") == 0) { if (! (subtoolMode ||smartnetMode || backupMode) ) { @@ -424,15 +432,34 @@ static Boolean OkayToWriteTheEntity (Uint2 entityID, ForM f) } if (indexerVersion) { vsp->alwaysRequireIsoJTA = TRUE; + if (smartnetMode) { + vsp->farFetchCDSproducts = TRUE; + vsp->farFetchMRNAproducts = TRUE; + } } oldErrSev = ErrSetMessageLevel (SEV_MAX); vsp->validateAlignments = TRUE; vsp->alignFindRemoteBsp = TRUE; vsp->doSeqHistAssembly = FALSE; + if (smartnetMode) { + vsp->doSeqHistAssembly = TRUE; + vsp->farIDsInAlignments = TRUE; + if (useEntrez) { + /* + LookupFarSeqIDs (sep, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE); + vsp->inferenceAccnCheck = TRUE; + */ + } + vsp->testLatLonSubregion = testLatLonSubregion; + vsp->strictLatLonCountry = strictLatLonCountry; + } for (j = 0; j < 6; j++) { vsp->errors [j] = 0; } ValidateSeqEntry (sep, vsp); + if (indexerVersion && useEntrez) { + TaxonValidate (sep, vsp); + } ErrSetMessageLevel (oldErrSev); ErrClear (); ErrShow (); @@ -1269,6 +1296,10 @@ static void SmartnetDoneFunc (BaseFormPtr bfp) omudp = ObjMgrGetUserData(bfp->input_entityID, 0, 0, SMART_KEY); if (omudp == NULL) return; + + /* for now set dirty flag to force validation in OkayToWriteTheEntity */ + ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); + omdp = ObjMgrGetData (bfp->input_entityID); sm_usr_data = (SMUserDataPtr) omudp->userdata.ptrvalue; @@ -1558,6 +1589,9 @@ static void ProcessDoneButton (ForM f) vsp->errors [j] = 0; } ValidateSeqEntry (sep, vsp); + if (indexerVersion && useEntrez) { + TaxonValidate (sep, vsp); + } ErrSetMessageLevel (oldErrSev); ErrClear (); ErrShow (); @@ -1603,6 +1637,9 @@ static void ProcessDoneButton (ForM f) } vsp->errfunc = ValidErrCallback; ValidateSeqEntry (sep, vsp); + if (indexerVersion && useEntrez) { + TaxonValidate (sep, vsp); + } ErrSetMessageLevel (oldErrSev); ErrSetHandler (oldErrHook); ErrClear (); @@ -1828,8 +1865,10 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp) { ValNodePtr bad_biop_list, vnp; ObjValNodePtr ovp; + BioSourcePtr biop; + OrgModPtr mod; - bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE); + bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE, FALSE); for (vnp = bad_biop_list; vnp != NULL; vnp = vnp->next) { @@ -1837,6 +1876,8 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp) vsp->descr = NULL; vsp->bsp = NULL; vsp->bssp = NULL; + biop = NULL; + mod = NULL; if (vnp->choice == OBJ_SEQFEAT) { @@ -1852,6 +1893,7 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp) { vsp->bssp = vsp->sfp->idx.parentptr; } + biop = (BioSourcePtr) vsp->sfp->data.value.ptrvalue; } else if (vnp->choice == OBJ_SEQDESC) { @@ -1872,13 +1914,27 @@ static void ReportBadSpecificHostValues (SeqEntryPtr sep, ValidStructPtr vsp) vsp->bssp = ovp->idx.parentptr; } } + biop = vsp->descr->data.ptrvalue; } - ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_TaxonomyLookupProblem, "Invalid value for specific host"); + if (biop != NULL && biop->org != NULL && biop->org->orgname != NULL) + { + mod = biop->org->orgname->mod; + while (mod != NULL && mod->subtype != ORGMOD_nat_host) + { + mod = mod->next; + } + if (mod != NULL) + { + ValidErr (vsp, SEV_WARNING, ERR_SEQ_DESCR_BadSpecificHost, "Invalid value for specific host: %s", mod->subname); + } + } } bad_biop_list = ValNodeFree (bad_biop_list); } +static Boolean log_tax_asn = FALSE; +static Boolean log_tax_set = FALSE; static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp) @@ -1930,11 +1986,29 @@ static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp) last = vnp2; } +#ifdef OS_UNIX + if (! log_tax_set) { + str = (CharPtr) getenv ("LOG_TAX_ASN"); + if (StringDoesHaveText (str)) { + if (StringICmp (str, "TRUE") == 0) { + log_tax_asn = TRUE; + } + } + log_tax_set = TRUE; + } +#endif + sev = ErrSetMessageLevel (SEV_WARNING); + if (log_tax_asn) { + LaunchAsnTextViewer ((Pointer) t3rq, (AsnWriteFunc) Taxon3RequestAsnWrite, "tax3 request"); + } t3ry = Tax3SynchronousQuery (t3rq); ErrSetMessageLevel (sev); Taxon3RequestFree (t3rq); if (t3ry == NULL) return; + if (log_tax_asn) { + LaunchAsnTextViewer ((Pointer) t3ry, (AsnWriteFunc) Taxon3ReplyAsnWrite, "tax3 result"); + } for (trp = t3ry->reply, vnp = srclist.head; trp != NULL && vnp != NULL; @@ -2038,7 +2112,7 @@ static void TaxonValidate (SeqEntryPtr sep, ValidStructPtr vsp) ReportBadSpecificHostValues (sep, vsp); } -static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit) +static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit, Boolean inferenceAccnCheck) { Boolean allRawOrSeg = TRUE; @@ -2102,7 +2176,7 @@ static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit) } } } - if (useEntrez) { + if (useEntrez && inferenceAccnCheck) { LookupFarSeqIDs (sep, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE); vsp->inferenceAccnCheck = TRUE; } @@ -2142,16 +2216,61 @@ static void ValSeqEntryFormEx (ForM f, Boolean doAligns, Int2 limit) } } +static void CountInfAccnVer (SeqFeatPtr sfp, Pointer userdata) + +{ + Int4Ptr countP; + GBQualPtr gbq; + + if (sfp == NULL || userdata == NULL) return; + countP = (Int4Ptr) userdata; + + for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { + if (StringICmp (gbq->qual, "inference") == 0) { + (*countP)++; + } + } +} + +static Boolean SmallInferenceAccnVer (ForM f) + +{ + BaseFormPtr bfp; + Int4 count = 0; + SeqEntryPtr sep; + + bfp = (BaseFormPtr) GetObjectExtra (f); + if (bfp == NULL) return FALSE; + + sep = GetTopSeqEntryForEntityID (bfp->input_entityID); + if (sep == NULL) return FALSE; + + VisitFeaturesInSep (sep, (Pointer) &count, CountInfAccnVer); + + if (count < 100) return TRUE; + + if (indexerVersion) { + Message (MSG_POST, "Validation skipping %ld inference accession.version tests", + (long) count); + } + + return FALSE; +} + extern void ValSeqEntryForm (ForM f) { - ValSeqEntryFormEx (f, TRUE, VALIDATE_ALL); + Boolean inferenceAccnCheck; + + inferenceAccnCheck = SmallInferenceAccnVer (f); + ValSeqEntryFormEx (f, TRUE, VALIDATE_ALL, inferenceAccnCheck); } static void ValSeqEntryProc (IteM i) { BaseFormPtr bfp; + Boolean inferenceAccnCheck; #ifdef WIN_MAC bfp = (BaseFormPtr) currentFormDataPtr; @@ -2159,7 +2278,8 @@ static void ValSeqEntryProc (IteM i) bfp = (BaseFormPtr) GetObjectExtra (i); #endif if (bfp != NULL) { - ValSeqEntryForm (bfp->form); + inferenceAccnCheck = SmallInferenceAccnVer (bfp->form); + ValSeqEntryFormEx (bfp->form, TRUE, VALIDATE_ALL, inferenceAccnCheck); } } @@ -2174,7 +2294,22 @@ static void ValSeqEntryProcNoAln (IteM i) bfp = (BaseFormPtr) GetObjectExtra (i); #endif if (bfp != NULL) { - ValSeqEntryFormEx (bfp->form, FALSE, VALIDATE_ALL); + ValSeqEntryFormEx (bfp->form, FALSE, VALIDATE_ALL, FALSE); + } +} + +static void ValSeqEntryProcInfAccn (IteM i) + +{ + BaseFormPtr bfp; + +#ifdef WIN_MAC + bfp = (BaseFormPtr) currentFormDataPtr; +#else + bfp = (BaseFormPtr) GetObjectExtra (i); +#endif + if (bfp != NULL) { + ValSeqEntryFormEx (bfp->form, FALSE, VALIDATE_ALL, TRUE); } } @@ -2189,7 +2324,7 @@ static void ValSeqEntryProcSpec (IteM i, Int2 limit) bfp = (BaseFormPtr) GetObjectExtra (i); #endif if (bfp != NULL) { - ValSeqEntryFormEx (bfp->form, FALSE, limit); + ValSeqEntryFormEx (bfp->form, FALSE, limit, FALSE); } } @@ -4021,7 +4156,7 @@ replaced by the actual characters from the first sequence."; const char *nucleotide_alphabet = "ABCDGHKMRSTUVWYabcdghkmrstuvwy"; const char *protein_alphabet = "ABCDEFGHIKLMPQRSTUVWXYZabcdefghiklmpqrstuvwxyz"; -extern TSequenceInfoPtr GetDefaultSequenceInfo () +extern TSequenceInfoPtr GetDefaultSequenceInfo (void) { TSequenceInfoPtr sequence_info = SequenceInfoNew(); @@ -5661,76 +5796,13 @@ static void DuplicateViewProc (IteM i) } } -extern SeqEntryPtr RestoreFromFile (CharPtr path); -extern SeqEntryPtr RestoreFromFile (CharPtr path) - -{ - BioseqPtr bsp; - BioseqSetPtr bssp; - Pointer dataptr; - Uint2 datatype; - Uint2 entityID; - SeqEntryPtr rsult; - SeqEntryPtr sep; - - rsult = NULL; - if (path != NULL && path [0] != '\0') { - dataptr = ObjMgrGenericAsnTextFileRead (path, &datatype, &entityID); - if (dataptr != NULL && entityID > 0) { - if (datatype == OBJ_SEQSUB || datatype == OBJ_SEQENTRY || - datatype == OBJ_BIOSEQ || datatype == OBJ_BIOSEQSET) { - WatchCursor (); - sep = GetTopSeqEntryForEntityID (entityID); - if (sep == NULL) { - sep = SeqEntryNew (); - if (sep != NULL) { - if (datatype == OBJ_BIOSEQ) { - bsp = (BioseqPtr) dataptr; - sep->choice = 1; - sep->data.ptrvalue = bsp; - SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep); - } else if (datatype == OBJ_BIOSEQSET) { - bssp = (BioseqSetPtr) dataptr; - sep->choice = 2; - sep->data.ptrvalue = bssp; - SeqMgrSeqEntry (SM_BIOSEQSET, (Pointer) bssp, sep); - } else { - sep = SeqEntryFree (sep); - } - } - sep = GetTopSeqEntryForEntityID (entityID); - } - if (sep != NULL) { - rsult = SeqEntryNew (); - if (rsult != NULL) { - rsult->choice = sep->choice; - rsult->data.ptrvalue = sep->data.ptrvalue; - sep->data.ptrvalue = NULL; - if (datatype == OBJ_SEQSUB) { - SeqSubmitFree ((SeqSubmitPtr) dataptr); - } else { - SeqEntryFree (sep); - } - /*Message (MSG_OK, "Call new object manager free function");*/ - } - } - ArrowCursor (); - } - /* - ObjMgrDelete (entityID); - */ - } - } - return rsult; -} static void RestoreSeqEntryProc (IteM i) { - SeqEntryPtr currsep; BaseFormPtr bfp; - SeqEntryPtr oldsep; Char path [PATH_MAX]; + Uint2 new_entityID; #ifdef WIN_MAC bfp = currentFormDataPtr; @@ -5739,14 +5811,12 @@ static void RestoreSeqEntryProc (IteM i) #endif if (bfp != NULL && bfp->input_itemtype == OBJ_BIOSEQ) { if (GetInputFileName (path, sizeof (path), "", "TEXT")) { - SeqEntrySetScope (NULL); - oldsep = RestoreFromFile (path); - currsep = GetTopSeqEntryForEntityID (bfp->input_entityID); - ReplaceSeqEntryWithSeqEntry (currsep, oldsep, TRUE); - SeqEntrySetScope (NULL); - bfp->input_entityID = ObjMgrGetEntityIDForChoice (currsep); - ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); - ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); + new_entityID = RestoreEntityIDFromFile (path, bfp->input_entityID); + if (new_entityID != 0) { + bfp->input_entityID = new_entityID; + ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); + ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); + } } } } @@ -6686,6 +6756,8 @@ static void BioseqViewFormMenus (WindoW w) SetObjectExtra (i, bfp, NULL); i = CommandItem (sub, "Validate no Alignments/ A", ValSeqEntryProcNoAln); SetObjectExtra (i, bfp, NULL); + i = CommandItem (sub, "Validate check Inference", ValSeqEntryProcInfAccn); + SetObjectExtra (i, bfp, NULL); SeparatorItem (sub); i = CommandItem (sub, "Validate Inst", ValSeqEntryProcInst); SetObjectExtra (i, bfp, NULL); @@ -7378,10 +7450,16 @@ static void SequinSeqViewFormMessage (ForM f, Int2 mssg) if (bfp != NULL) { switch (mssg) { case VIB_MSG_SAVE : - SaveSeqSubmitProc (bfp, FALSE); + if (FixSpecialCharacters (bfp->input_entityID)) + { + SaveSeqSubmitProc (bfp, FALSE); + } break; case VIB_MSG_SAVE_AS : - SaveSeqSubmitProc (bfp, TRUE); + if (FixSpecialCharacters (bfp->input_entityID)) + { + SaveSeqSubmitProc (bfp, TRUE); + } break; case VIB_MSG_CLOSE : CloseProc (bfp); @@ -9077,6 +9155,7 @@ static void SetupMacMenus (void) validateMenu = SubMenu (m, "Validate"); CommandItem (validateMenu, "Validate Record/ V", ValSeqEntryProc); CommandItem (validateMenu, "Validate no Alignments", ValSeqEntryProcNoAln); + CommandItem (validateMenu, "Validate check Inference", ValSeqEntryProcInfAccn); SeparatorItem (validateMenu); CommandItem (validateMenu, "Validate Inst", ValSeqEntryProcInst); CommandItem (validateMenu, "Validate Hist", ValSeqEntryProcHist); @@ -9804,6 +9883,7 @@ static void ReadSettings (void) useDesktop = FALSE; useEntrez = FALSE; useLocal = FALSE; + useIdLookup = FALSE; useBlast = FALSE; useMedarch = FALSE; newMedarch = FALSE; @@ -9820,6 +9900,7 @@ static void ReadSettings (void) useDesktop = TRUE; useEntrez = TRUE; useLocal = TRUE; + useIdLookup = TRUE; useBlast = TRUE; useMedarch = TRUE; newMedarch = TRUE; @@ -9833,6 +9914,7 @@ static void ReadSettings (void) useDesktop = TRUE; useEntrez = TRUE; useLocal = TRUE; + useIdLookup = TRUE; useBlast = TRUE; useMedarch = TRUE; newMedarch = TRUE; @@ -9845,6 +9927,7 @@ static void ReadSettings (void) useDesktop = TRUE; useEntrez = TRUE; useLocal = TRUE; + useIdLookup = TRUE; useBlast = TRUE; useMedarch = TRUE; newMedarch = TRUE; @@ -9856,6 +9939,7 @@ static void ReadSettings (void) useDesktop = TRUE; useEntrez = TRUE; useLocal = TRUE; + useIdLookup = TRUE; useBlast = TRUE; useMedarch = TRUE; newMedarch = TRUE; @@ -9939,6 +10023,22 @@ static void ReadSettings (void) if (StringICmp (str, "TRUE") == 0) { allowDownload = FALSE; useEntrez = FALSE; + useMedarch = FALSE; + useTaxon = FALSE; + } + } + + useSeqFetch = useEntrez; + + if (GetSequinAppParam ("SETTINGS", "SUPPRESSSEQFETCH", NULL, str, sizeof (str))) { + if (StringICmp (str, "TRUE") == 0) { + useSeqFetch = FALSE; + } + } + + if (GetSequinAppParam ("SETTINGS", "SUPPRESSIDLOOKUP", NULL, str, sizeof (str))) { + if (StringICmp (str, "TRUE") == 0) { + useIdLookup = FALSE; } } @@ -9953,6 +10053,12 @@ static void ReadSettings (void) } } + if (GetSequinAppParam ("SETTINGS", "SUPPRESSLOCAL", NULL, str, sizeof (str))) { + if (StringICmp (str, "TRUE") == 0) { + useLocal = FALSE; + } + } + if (GetSequinAppParam ("SETTINGS", "GENOMETAG", NULL, str, sizeof (str))) { TrimSpacesAroundString (str); if (! StringHasNoText (str)) { @@ -10140,7 +10246,7 @@ extern Pointer ReadFromDirSub (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityI #endif #ifdef OS_MSWIN sprintf (cmmd, "%s %s -o %s", dirsubfetchcmd, accn, path); - system (cmmd); + RunSilent (cmmd); #endif fp = FileOpen (path, "r"); @@ -10197,7 +10303,7 @@ static Int2 LIBCALLBACK DirSubBioseqFetchFunc (Pointer data) #endif #ifdef OS_MSWIN sprintf (cmmd, "%s %s -o %s", dirsubfetchcmd, tsip->accession, path); - system (cmmd); + RunSilent (cmmd); #endif fp = FileOpen (path, "r"); @@ -10265,7 +10371,7 @@ extern Pointer ReadFromSmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID #endif #ifdef OS_MSWIN sprintf (cmmd, "%s %s -o %s", smartfetchcmd, accn, path); - system (cmmd); + RunSilent (cmmd); #endif fp = FileOpen (path, "r"); @@ -10323,7 +10429,7 @@ static Int2 LIBCALLBACK SmartBioseqFetchFunc (Pointer data) #endif #ifdef OS_MSWIN sprintf (cmmd, "%s %s -o %s", smartfetchcmd, tsip->accession, path); - system (cmmd); + RunSilent (cmmd); #endif fp = FileOpen (path, "r"); @@ -10358,6 +10464,136 @@ static Boolean SmartFetchEnable (void) return TRUE; } +static CharPtr hupfetchproc = "HUPBioseqFetch"; + +static CharPtr hupfetchcmd = NULL; + +extern Pointer ReadFromHUP (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID); +extern Pointer ReadFromHUP (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entityID) + +{ + Char cmmd [256]; + Pointer dataptr; + FILE* fp; + Char path [PATH_MAX]; + + if (datatype != NULL) { + *datatype = 0; + } + if (entityID != NULL) { + *entityID = 0; + } + if (! dirsubMode) return NULL; + if (StringHasNoText (accn)) return NULL; + + if (hupfetchcmd == NULL) { + if (GetAppParam ("SEQUIN", "HUP", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) { + hupfetchcmd = StringSaveNoNull (cmmd); + } + } + if (hupfetchcmd == NULL) return NULL; + + TmpNam (path); + +#ifdef OS_UNIX + sprintf (cmmd, "csh %s %s > %s", hupfetchcmd, accn, path); + system (cmmd); +#endif +#ifdef OS_MSWIN + sprintf (cmmd, "%s %s -o %s", hupfetchcmd, accn, path); + RunSilent (cmmd); +#endif + + fp = FileOpen (path, "r"); + if (fp == NULL) { + FileRemove (path); + return NULL; + } + dataptr = ReadAsnFastaOrFlatFile (fp, datatype, entityID, FALSE, FALSE, TRUE, FALSE); + FileClose (fp); + FileRemove (path); + return dataptr; +} + + +static Int2 LIBCALLBACK HUPBioseqFetchFunc (Pointer data) + +{ + BioseqPtr bsp; + Char cmmd [256]; + Pointer dataptr; + Uint2 datatype; + Uint2 entityID; + FILE* fp; + OMProcControlPtr ompcp; + ObjMgrProcPtr ompp; + Char path [PATH_MAX]; + SeqEntryPtr sep = NULL; + SeqIdPtr sip; + TextSeqIdPtr tsip; + OMUserDataPtr omudp; + + ompcp = (OMProcControlPtr) data; + if (ompcp == NULL) return OM_MSG_RET_ERROR; + ompp = ompcp->proc; + if (ompp == NULL) return OM_MSG_RET_ERROR; + sip = (SeqIdPtr) ompcp->input_data; + if (sip == NULL) return OM_MSG_RET_ERROR; + + if (sip->choice != SEQID_GENBANK) return OM_MSG_RET_ERROR; + tsip = (TextSeqIdPtr) sip->data.ptrvalue; + if (tsip == NULL || StringHasNoText (tsip->accession)) return OM_MSG_RET_ERROR; + + if (hupfetchcmd == NULL) { + if (GetAppParam ("SEQUIN", "HUP", "FETCHSCRIPT", NULL, cmmd, sizeof (cmmd))) { + hupfetchcmd = StringSaveNoNull (cmmd); + } + } + if (hupfetchcmd == NULL) return OM_MSG_RET_ERROR; + + TmpNam (path); + +#ifdef OS_UNIX + sprintf (cmmd, "csh %s %s > %s", hupfetchcmd, tsip->accession, path); + system (cmmd); +#endif +#ifdef OS_MSWIN + sprintf (cmmd, "%s %s -o %s", hupfetchcmd, tsip->accession, path); + RunSilent (cmmd); +#endif + + fp = FileOpen (path, "r"); + if (fp == NULL) { + FileRemove (path); + return OM_MSG_RET_ERROR; + } + dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, &entityID, FALSE, FALSE, TRUE, FALSE); + FileClose (fp); + FileRemove (path); + + if (dataptr == NULL) return OM_MSG_RET_OK; + + sep = GetTopSeqEntryForEntityID (entityID); + if (sep == NULL) return OM_MSG_RET_ERROR; + bsp = BioseqFindInSeqEntry (sip, sep); + ompcp->output_data = (Pointer) bsp; + ompcp->output_entityID = ObjMgrGetEntityIDForChoice (sep); + + omudp = ObjMgrAddUserData(ompcp->output_entityID, ompp->procid, OMPROC_FETCH, 0); + + + return OM_MSG_RET_DONE; +} + +static Boolean HUPFetchEnable (void) + +{ + ObjMgrProcLoad (OMPROC_FETCH, hupfetchproc, hupfetchproc, + OBJ_SEQID, 0, OBJ_BIOSEQ, 0, NULL, + HUPBioseqFetchFunc, PROC_PRIORITY_DEFAULT); + return TRUE; +} + static CharPtr tpasmartfetchproc = "TPASmartBioseqFetch"; static CharPtr tpasmartfetchcmd = NULL; @@ -10395,7 +10631,7 @@ extern Pointer ReadFromTPASmart (CharPtr accn, Uint2Ptr datatype, Uint2Ptr entit #endif #ifdef OS_MSWIN sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, accn, path); - system (cmmd); + RunSilent (cmmd); #endif fp = FileOpen (path, "r"); @@ -10452,7 +10688,7 @@ static Int2 LIBCALLBACK TPASmartBioseqFetchFunc (Pointer data) #endif #ifdef OS_MSWIN sprintf (cmmd, "%s %s -o %s", tpasmartfetchcmd, tsip->accession, path); - system (cmmd); + RunSilent (cmmd); #endif fp = FileOpen (path, "r"); @@ -10547,7 +10783,7 @@ static void CountBioSources (BioSourcePtr biop, Pointer userdata) (*count)++; } -static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, Int4 fd) +static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, void* fd) { AsnIoMemPtr aimp; BaseFormPtr bfp; @@ -10668,7 +10904,7 @@ static Int4 SMReadBioseqObj(VoidPtr data, CharPtr buffer, Int4 length, Int4 fd) } sm_user_data = MemNew(sizeof(SMUserData)); - sm_user_data->fd = fd; + sm_user_data->fd = (void*) fd; sm_user_data->header = header; if(bio_data == NULL) { @@ -11038,8 +11274,6 @@ Int2 Main (void) subtoolEntityID = 0; leaveAsOldAsn = FALSE; - useSeqFetch = useEntrez; - #if defined(OS_UNIX) || defined(WIN_MOTIF) {{ Nlm_Int4 argc = GetArgc(); @@ -11090,6 +11324,10 @@ Int2 Main (void) backupMode = TRUE; } else if (StringCmp (argv[i], "-noseqfetch") == 0) { useSeqFetch = FALSE; + } else if (StringCmp (argv[i], "-nolocalfetch") == 0) { + useLocal = FALSE; + } else if (StringCmp (argv[i], "-noseqidlookup") == 0) { + useIdLookup = FALSE; } #ifdef USE_SMARTNET else if (StringCmp (argv[i], "-ds") == 0) { @@ -11127,6 +11365,10 @@ Int2 Main (void) nohelpMode = TRUE; else if (StringCmp (argv[i], "-noseqfetch") == 0) useSeqFetch = FALSE; + else if (StringCmp (argv[i], "-nolocalfetch") == 0) + useLocal = FALSE; + else if (StringCmp (argv[i], "-noseqidlookup") == 0) + useIdLookup = FALSE; #ifdef USE_SMARTNET else if (StringNCmp (argv[i], "-z", 2) == 0) { smartnetMode = TRUE; @@ -11253,33 +11495,64 @@ Int2 Main (void) VSeqMgrInit (FALSE); WatchCursor (); -#ifdef USE_SMARTNET - if (dirsubMode) { - DirSubFetchEnable (); - SmartFetchEnable (); - TPASmartFetchEnable (); - } -#endif + /* register fetch functions */ -/*#ifdef USE_ENTREZ*/ if (useEntrez) { /* EntrezBioseqFetchEnable ("Sequin", FALSE); */ if (useSeqFetch) { /* ID1BioseqFetchEnable ("Sequin", FALSE); */ PubSeqFetchEnable (); PubMedFetchEnable (); - } else { + } else if (useIdLookup) { PubSeqFetchEnableEx (FALSE, TRUE, TRUE, TRUE, TRUE); PubMedFetchEnable (); } } -/*#endif*/ -/*#ifdef USE_LOCAL*/ +#ifdef USE_SMARTNET + if (dirsubMode) { + if (useSeqFetch) { + /* DirSubFetchEnable (); */ + TPASmartFetchEnable (); + SmartFetchEnable (); + HUPFetchEnable (); + } + } +#endif + if (useLocal) { LocalSeqFetchInit (FALSE); } -/*#endif*/ + +/* +#ifdef USE_SMARTNET + if (dirsubMode) { + if (only_use_smart) { + SmartFetchEnable (); + } else { + DirSubFetchEnable (); + SmartFetchEnable (); + TPASmartFetchEnable (); + } + } +#endif + + if (! only_use_smart) { + if (useEntrez) { + if (useSeqFetch) { + PubSeqFetchEnable (); + PubMedFetchEnable (); + } else { + PubSeqFetchEnableEx (FALSE, TRUE, TRUE, TRUE, TRUE); + PubMedFetchEnable (); + } + } + + if (useLocal) { + LocalSeqFetchInit (FALSE); + } + } +*/ #ifdef WIN_MAC SetDeactivate (NULL, MacDeactProc); @@ -11639,6 +11912,9 @@ Int2 Main (void) Remove (initSubmitForm); Remove (formatForm); Remove (helpForm); + + FreeSqnTempFiles (); + ArrowCursor (); Update (); @@ -11732,7 +12008,7 @@ extern void MakeBadSpecificHostValueTable (IteM i) sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; - bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE); + bad_biop_list = Taxon3CheckSpecificHostInSeqEntry (sep, TRUE, FALSE); if (bad_biop_list == NULL) { @@ -11747,3 +12023,300 @@ extern void MakeBadSpecificHostValueTable (IteM i) CloseLog (lip); lip = FreeLog (lip); } + + +typedef struct updatefeaturesform { + FORM_MESSAGE_BLOCK + DialoG new_features; + ValNodePtr feat_list; + SeqAnnotPtr sap; +} UpdateFeaturesFormData, PNTR UpdateFeaturesFormPtr; + + +static void CleanupUpdateFeaturesForm (GraphiC g, VoidPtr data) +{ + UpdateFeaturesFormPtr f; + + f = (UpdateFeaturesFormPtr) data; + if (f != NULL) { + f->feat_list = FreeClickableList (f->feat_list); + f->sap = SeqAnnotFree (f->sap); + } + StdCleanupFormProc (g, data); +} + + + +static CharPtr GetNewItemDescription (SeqFeatPtr sfp) +{ + CharPtr location, label, row_text; + Char buf[129]; + + location = SeqLocPrintUseBestID (sfp->location); + label = (CharPtr) FeatDefTypeLabel(sfp); + + FeatDefLabel (sfp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT); + + row_text = (CharPtr) MemNew (sizeof (Char) * + (StringLen (label) + + StringLen (buf) + + StringLen (location) + + 6)); + sprintf (row_text, "%s:%s:%s\n", label, buf, location); + location = MemFree (location); + return row_text; +} + + +static ClickableItemPtr PutFeaturesInOldItem (ValNodePtr item_list) +{ + ClickableItemPtr cip_olditems, cip; + ValNodePtr vnp; + + cip_olditems = (ClickableItemPtr) MemNew (sizeof (ClickableItemData)); + if (item_list == NULL) { + cip_olditems->description = StringSave ("No old features found"); + cip_olditems->chosen = FALSE; + } else { + for (vnp = item_list; vnp != NULL; vnp = vnp->next) { + cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData)); + cip->description = GetNewItemDescription (vnp->data.ptrvalue); + cip->chosen = TRUE; + ValNodeAddPointer (&(cip->item_list), OBJ_SEQFEAT, vnp->data.ptrvalue); + ValNodeAddPointer (&(cip_olditems->subcategories), 0, cip); + } + cip_olditems->description = StringSave ("Old Features (check to delete)"); + cip_olditems->chosen = TRUE; + } + return cip_olditems; +} + + +static void MarkChosenFeatures (ValNodePtr item_list, Boolean delete_marked) +{ + ClickableItemPtr cip; + ValNodePtr vnp; + SeqFeatPtr sfp; + + while (item_list != NULL) { + cip = (ClickableItemPtr) item_list->data.ptrvalue; + if (cip != NULL) { + for (vnp = cip->item_list; vnp != NULL; vnp = vnp->next) { + if (vnp->choice == OBJ_SEQFEAT) { + sfp = (SeqFeatPtr) vnp->data.ptrvalue; + if ((cip->chosen && delete_marked) || (!cip->chosen && !delete_marked)) { + sfp->idx.deleteme = TRUE; + } + } + } + } + item_list = item_list->next; + } +} + + +static void MarkChosenFeaturesForBioseqs (ValNodePtr feat_list) +{ + ClickableItemPtr cip, cip_new, cip_old; + + if (feat_list == NULL) return; + cip = (ClickableItemPtr) feat_list->data.ptrvalue; + if (cip->item_list != NULL && cip->item_list->choice == OBJ_BIOSEQ) { + if (cip->subcategories != NULL) { + cip_new = (ClickableItemPtr) cip->subcategories->data.ptrvalue; + MarkChosenFeatures (cip_new->subcategories, FALSE); + if (cip->subcategories->next != NULL) { + cip_old = (ClickableItemPtr) cip->subcategories->next->data.ptrvalue; + MarkChosenFeatures (cip_old->subcategories, TRUE); + } + } + MarkChosenFeaturesForBioseqs (feat_list->next); + } else if (feat_list->next != NULL && feat_list->next->next == NULL && cip->item_list == NULL) { + cip_new = (ClickableItemPtr) feat_list->data.ptrvalue; + cip_old = (ClickableItemPtr) feat_list->next->data.ptrvalue; + MarkChosenFeatures (cip_new->subcategories, FALSE); + MarkChosenFeatures (cip_old->subcategories, TRUE); + } +} + + +static void DoUpdateFeatures (ButtoN b) +{ + UpdateFeaturesFormPtr f; + + f = (UpdateFeaturesFormPtr) GetObjectExtra (b); + if (f == NULL) return; + + MarkChosenFeaturesForBioseqs (f->feat_list); + + SmartAttachSeqAnnotToSeqEntry (f->input_entityID, f->sap, NULL); + f->sap = NULL; + + DeleteMarkedObjects (f->input_entityID, 0, NULL); + ObjMgrSetDirtyFlag (f->input_entityID, TRUE); + ObjMgrSendMsg (OM_MSG_UPDATE, f->input_entityID, 0, 0); + + Remove (f->form); +} + + +extern void UpdateFeatures (IteM i) +{ + BaseFormPtr bfp; + SeqEntryPtr sep; + Pointer dataptr; + Uint2 datatype; + FILE *fp; + Char path [PATH_MAX]; + SeqAnnotPtr sap; + SeqFeatPtr sfp; + ValNodePtr new_feat_list = NULL, no_bsp_list = NULL, old_item_list; + Int4 leftmost = -1, rightmost = -1, new_left, new_right, tmp; + BioseqPtr bsp, last_bsp = NULL; + ClickableItemPtr cip = NULL, cip_newitems = NULL, cip_olditems, cip_newfeat; + SeqLocPtr slp; + WindoW w; + GrouP h, g, c; + ButtoN b; + UpdateFeaturesFormPtr f; + Char id [42]; + +#ifdef WIN_MAC + bfp = currentFormDataPtr; +#else + bfp = GetObjectExtra (i); +#endif + if (bfp == NULL) return; + sep = GetTopSeqEntryForEntityID (bfp->input_entityID); + if (sep == NULL) return; + + path [0] = '\0'; + if (!GetInputFileName (path, sizeof (path), "", "TEXT")) { + return; + } + + fp = FileOpen (path, "r"); + if (fp == NULL) { + Message (MSG_ERROR, "Unable to open file!"); + return; + } + dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, FALSE, FALSE, + TRUE, TRUE); + FileClose (fp); + if (dataptr == NULL || datatype != OBJ_SEQANNOT) { + Message (MSG_ERROR, "File does not contain feature table!"); + return; + } + + sap = (SeqAnnotPtr) dataptr; + if (sap->type != 1) { + Message (MSG_ERROR, "File does not contain feature table!"); + sap = SeqAnnotFree (sap); + return; + } + + // list features for each bioseq + for (sfp = sap->data; sfp != NULL; sfp = sfp->next) { + bsp = BioseqFindFromSeqLoc (sfp->location); + if (bsp == NULL) { + ValNodeAddPointer (&no_bsp_list, OBJ_SEQFEAT, sfp); + } else { + if (bsp != last_bsp) { + if (last_bsp != NULL) { + slp = SeqLocIntNew (leftmost, rightmost, Seq_strand_plus, SeqIdDup (SeqIdFindWorst (bsp->id))); + old_item_list = ListFeaturesOverlappingLocation (last_bsp, slp, 0, 0); + slp = SeqLocFree (slp); + cip_olditems = PutFeaturesInOldItem (old_item_list); + old_item_list = ValNodeFree (old_item_list); + ValNodeAddPointer (&(cip->subcategories), 0, cip_olditems); + } + cip = (ClickableItemPtr) MemNew (sizeof (ClickableItemData)); + ValNodeAddPointer (&(cip->item_list), OBJ_BIOSEQ, bsp); + + SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id, PRINTID_FASTA_LONG, sizeof (id) - 1); + cip->description = StringSave (id); + cip_newitems = (ClickableItemPtr) MemNew (sizeof (ClickableItemData)); + cip_newitems->description = StringSave ("New Features (check to import)"); + cip_newitems->chosen = TRUE; + ValNodeAddPointer (&(cip->subcategories), 0, cip_newitems); + last_bsp = bsp; + ValNodeAddPointer (&new_feat_list, 0, cip); + leftmost = -1; + rightmost = -1; + } + cip_newfeat = (ClickableItemPtr) MemNew (sizeof (ClickableItemData)); + cip_newfeat->description = GetNewItemDescription (sfp); + cip_newfeat->chosen = TRUE; + ValNodeAddPointer (&(cip_newfeat->item_list), OBJ_SEQFEAT, sfp); + ValNodeAddPointer (&(cip_newitems->subcategories), 0, cip_newfeat); + new_left = SeqLocStart (sfp->location); + new_right = SeqLocStop (sfp->location); + if (new_left > new_right) { + tmp = new_left; + new_left = new_right; + new_right = tmp; + } + if (leftmost == -1 || new_left < leftmost) { + leftmost = new_left; + } + if (rightmost == -1 || new_right > rightmost) { + rightmost = new_right; + } + } + } + if (last_bsp != NULL) { + slp = SeqLocIntNew (leftmost, rightmost, Seq_strand_plus, SeqIdDup (SeqIdFindWorst (bsp->id))); + old_item_list = ListFeaturesOverlappingLocation (last_bsp, slp, 0, 0); + slp = SeqLocFree (slp); + cip_olditems = PutFeaturesInOldItem (old_item_list); + old_item_list = ValNodeFree (old_item_list); + ValNodeAddPointer (&(cip->subcategories), 0, cip_olditems); + } + + if (no_bsp_list != NULL) { + Message (MSG_ERROR, "%d features in table are not found on a Bioseq in this record!", ValNodeLen (no_bsp_list)); + no_bsp_list = ValNodeFree (no_bsp_list); + } + + if (new_feat_list == NULL) { + Message (MSG_ERROR, "No features found!"); + sap = SeqAnnotFree (sap); + return; + } + if (new_feat_list->next == NULL) { + no_bsp_list = new_feat_list; + cip = (ClickableItemPtr) new_feat_list->data.ptrvalue; + new_feat_list = cip->subcategories; + cip->subcategories = NULL; + no_bsp_list = FreeClickableList (no_bsp_list); + } + + + /* Now create dialog to allow user to select new features to import and existing features to delete */ + f = (UpdateFeaturesFormPtr) MemNew (sizeof (UpdateFeaturesFormData)); + w = FixedWindow (-50, -33, -10, -10, "Update Features", StdCloseWindowProc); + SetObjectExtra (w, f, CleanupUpdateFeaturesForm); + f->form = (ForM) w; + f->input_entityID = bfp->input_entityID; + f->feat_list = new_feat_list; + f->sap = sap; + h = HiddenGroup (w, -1, 0, NULL); + SetGroupSpacing (h, 10, 10); + g = HiddenGroup (h, 2, 0, NULL); + f->new_features = CreateClickableListDialog (g, "New Features (check to import)", "label1", NULL, NULL, NULL, GetDiscrepancyItemText); + PointerToDialog (f->new_features, new_feat_list); +/* f->old_features = CreateClickableListDialog (g, "Old Features", "label1", + ScrollToDiscrepancyItem, EditDiscrepancyItem, bfp, + GetDiscrepancyItemText); */ + c = HiddenGroup (h, 4, 0, NULL); + b = PushButton (c, "Accept", DoUpdateFeatures); + SetObjectExtra (b, f, NULL); + PushButton (c, "Cancel", StdCancelButtonProc); + + AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); + Show (w); + Select (w); + + +} + |