diff options
Diffstat (limited to 'biostruc/cdd/cddserver.c')
| -rw-r--r-- | biostruc/cdd/cddserver.c | 53 |
1 files changed, 40 insertions, 13 deletions
diff --git a/biostruc/cdd/cddserver.c b/biostruc/cdd/cddserver.c index 2766e6de..aab6d293 100644 --- a/biostruc/cdd/cddserver.c +++ b/biostruc/cdd/cddserver.c @@ -1,4 +1,4 @@ -/* $Id: cddserver.c,v 1.44 2004/04/01 13:43:05 lavr Exp $ +/* $Id: cddserver.c,v 1.45 2004/05/10 20:55:57 bauer Exp $ *=========================================================================== * * PUBLIC DOMAIN NOTICE @@ -29,7 +29,7 @@ * * Initial Version Creation Date: 2/10/2000 * -* $Revision: 1.44 $ +* $Revision: 1.45 $ * * File Description: * CD WWW-Server, Cd summary pages and alignments directly from the @@ -38,6 +38,9 @@ * Modifications: * -------------------------------------------------------------------------- * $Log: cddserver.c,v $ +* Revision 1.45 2004/05/10 20:55:57 bauer +* fixed problem with CAV +* * Revision 1.44 2004/04/01 13:43:05 lavr * Spell "occurred", "occurrence", and "occurring" * @@ -1688,6 +1691,7 @@ static void CDDSrvInfoBlk(CddPtr pcdd, FILE *table, CharPtr dbversion, fprintf(table,"</td>\n"); dtp = CddGetCreateDate(pcdd); utp = CddGetUpdateDate(pcdd); + if (NULL == dtp && NULL!= utp) dtp = utp; fprintf(table," <td align=\"RIGHT\" class=\"medium1\" NOWRAP><strong>Created:</strong></td>\n"); if (utp) { fprintf(table," <td align=\"LEFT\" class=\"medium1\" NOWRAP>%2d-%3s-%4d</td>\n",(int)dtp->data[3],NCBI_months[dtp->data[2]-1],(int)dtp->data[1]+1900); @@ -2122,19 +2126,22 @@ static Boolean CddUseThisMMDBid(ValNodePtr location, CddSumPtr pcds) /* use Paul's function to output HTML or Text-formatted alignments */ /*---------------------------------------------------------------------------*/ /*---------------------------------------------------------------------------*/ -Boolean CddInvokeAlignView(NcbiMimeAsn1Ptr pvnNcbi, CharPtr CDDalign, Int2 iPDB, +Boolean CddInvokeAlignView(NcbiMimeAsn1Ptr pvnNcbi, Int2 iPDB, CharPtr QuerySeq, CharPtr QueryAlign, CharPtr dbversion, CddPtr pcdd, Boolean bHasPdb, FloatHi tbit, Uint2 pwidth, Int4 iQueryGi, CharPtr QueryName, Int4 iFeatNum, CddSumPtr pcds, Int4 alen, Int4 nTaxIds, Int4Ptr iTaxids, ValNodePtr txids, CdTreeNodePtr pcdtree) { - Uint4 size = 2 * FileLength(CDDalign); + Uint4 size; Uint4 uCAVoptions = 0; BytePtr buf; + Nlm_ByteStorePtr bsp = NULL; + AsnIoBSPtr aibp = NULL; BiostrucAnnotSetPtr basp; BiostrucFeatureSetPtr bfsp; AsnIoMemPtr aimp; + AsnIoPtr aip; /* debugging */ CddDescrPtr pCddesc; CharPtr cCurrDesc; Char source[PATH_MAX]; @@ -2160,12 +2167,6 @@ Boolean CddInvokeAlignView(NcbiMimeAsn1Ptr pvnNcbi, CharPtr CDDalign, Int2 iPDB, piSize = (Int4Ptr) GetAlignmentSize(salp); size = (Uint4) (piSize[0] * (8000 + piSize[1] * 400)); } - buf = MemNew(size); - aimp = (AsnIoMemPtr) AsnIoMemOpen("wb",buf,size); - if (NULL == aimp) return(FALSE); - if (!NcbiMimeAsn1AsnWrite(pvnNcbi,aimp->aip,NULL)) return(FALSE); - AsnIoFlush(aimp->aip); - AsnIoMemClose(aimp); if (CddHasAnnotation(pcdd)) { aap = pcdd->alignannot; @@ -2216,6 +2217,32 @@ Boolean CddInvokeAlignView(NcbiMimeAsn1Ptr pvnNcbi, CharPtr CDDalign, Int2 iPDB, printf(" <td width=\"100%%\"> \n"); printf("<PRE>\n"); } + bsp = Nlm_BSNew(1024); + aibp = AsnIoBSOpen((char *)"wb",bsp); + NcbiMimeAsn1AsnWrite(pvnNcbi,aibp->aip,NULL); + AsnIoFlush(aibp->aip); + AsnIoBSClose(aibp); aibp = NULL; + size = Nlm_BSLen(bsp); + + buf = (BytePtr)MemNew(size); + Nlm_BSSeek(bsp,0,0); + if (Nlm_BSRead(bsp,buf,size) != size) { + CddHtmlError("Error creating buffer for Alignment viewer!"); + } + Nlm_BSFree(bsp); bsp = NULL; + +/* old code, with 'static' buf size + aimp = (AsnIoMemPtr) AsnIoMemOpen("wb",buf,size); + if (NULL == aimp) return(FALSE); + if (!NcbiMimeAsn1AsnWrite(pvnNcbi,aimp->aip,NULL)) return(FALSE); + AsnIoFlush(aimp->aip); + AsnIoMemClose(aimp); +*/ +/* debugging code + aip = AsnIoOpen("CAV_debug_data","w"); + NcbiMimeAsn1AsnWrite(pvnNcbi,aip,NULL); + AsnIoClose(aip); +*/ CAV_DisplayMultiple(buf, uCAVoptions, pwidth, tbit, NULL, nFeatures, pafeat); MemFree(buf); if (iPDB != 2 && iPDB != 8) printf("</PRE>\n"); @@ -2746,7 +2773,7 @@ Int2 Main() SeqAlignPtr salpCopy, salpFlat; SeqAlignPtr salpQuery = NULL; SeqAnnotPtr psaCAlignHead = NULL; - SeqAnnotPtr sap; + SeqAnnotPtr sap, sapTemp = NULL; SeqEntryPtr sep, sequences = NULL; SeqEntryPtr sepQuery = NULL; SeqIdPtr sip, sipNew, sipQuery, sipRet; @@ -3051,7 +3078,7 @@ Int2 Main() CddHtmlError("Error setting environment variable BLASTDB"); } www_arg = WWWGetValueByIndex(www_info,indx); - Qstatus = (Int2) QBlastGetResults(www_arg,&salpTemp,&bspQuery,&blast_program,&blast_database,&other_returns, &error_returns); + Qstatus = (Int2) QBlastGetResults(www_arg,&sapTemp,&bspQuery,&blast_program,&blast_database,&other_returns, &error_returns); if (Qstatus != 0) CddHtmlError("Could not retrieve query sequence from BLAST queue!"); sipQuery = bspQuery->id; oidp = ObjectIdNew(); @@ -3984,7 +4011,7 @@ Int2 Main() /*---------------------------------------------------------------------------*/ if (iSeqStrMode == CDDSEQUONLY) { CddFixSequenceFormat(pbsaSeq->sequences); - if (!CddInvokeAlignView(pvnNcbi,CDDalign,iPDB,QuerySeq,QueryAlign,dbversion, + if (!CddInvokeAlignView(pvnNcbi,iPDB,QuerySeq,QueryAlign,dbversion, pcdd,bHasPdb,tbit,pwidth,iQueryGi,QueryName,iFeatNum, pcds,alen,nTaxIds,iTaxids,txids,pcdtree)) CddHtmlError("Could not display alignment"); 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