static AjBool dbxflat_ParseGenbank(EmbPBtreeEntry entry, AjPFile inf) { AjPStr line = NULL; ajlong pos = 0L; AjBool ret = ajTrue; AjPStr sumline = NULL; line = ajStrNewC(""); sumline = ajStrNew(); while(!ajStrPrefixC(line,"//") && ret) { if(ajStrPrefixC(line,"LOCUS")) { entry->fpos = pos; ajFmtScanS(line,"%*S%S",&entry->id); } if(svfield) if(ajStrPrefixC(line,"VERSION")) embBtreeGenBankAC(line,svfield->data); if(accfield) if(ajStrPrefixC(line,"ACCESSION")) embBtreeGenBankAC(line,accfield->data); if(keyfield) if(ajStrPrefixC(line,"KEYWORDS")) { ajStrAssignS(&sumline,line); ret = ajReadlineTrim(inf,&line); while(ret && *MAJSTRGETPTR(line)==' ') { ajStrAppendS(&sumline,line); ret = ajReadlineTrim(inf,&line); } ajStrRemoveWhiteExcess(&sumline); embBtreeGenBankKW(sumline,keyfield->data,keyfield->len); continue; } if(desfield) if(ajStrPrefixC(line,"DEFINITION")) { ajStrAssignS(&sumline,line); ret = ajReadlineTrim(inf,&line); while(ret && *MAJSTRGETPTR(line)==' ') { ajStrAppendS(&sumline,line); ret = ajReadlineTrim(inf,&line); } ajStrRemoveWhiteExcess(&sumline); embBtreeGenBankDE(sumline,desfield->data,desfield->len); continue; } if(orgfield) if(ajStrPrefixC(line,"SOURCE")) { ret = ajReadlineTrim(inf,&line); ajStrAppendC(&line,";"); while(ret && *MAJSTRGETPTR(line)==' ') { ajStrAppendS(&sumline,line); ret = ajReadlineTrim(inf,&line); } ajStrRemoveWhiteExcess(&sumline); embBtreeGenBankTX(sumline,orgfield->data,orgfield->len); continue; } pos = ajFileResetPos(inf); if(!ajReadlineTrim(inf,&line)) ret = ajFalse; } ajStrDel(&line); ajStrDel(&sumline); return ret; }
static AjBool dbxflat_ParseGenbank(EmbPBtreeEntry entry, AjPFile inf) { AjPStr line = NULL; ajlong pos = 0L; AjBool ret = ajTrue; AjPStr sumline = NULL; line = ajStrNewC(""); sumline = ajStrNew(); while(!ajStrPrefixC(line,"//") && ret) { if(ajStrPrefixC(line,"LOCUS")) { entry->fpos = pos; ajFmtScanS(line,"%*S%S",&entry->id); } if(entry->do_sv) if(ajStrPrefixC(line,"VERSION")) embBtreeGenBankAC(line,entry->sv); if(entry->do_accession) if(ajStrPrefixC(line,"ACCESSION")) embBtreeGenBankAC(line,entry->ac); if(entry->do_keyword) if(ajStrPrefixC(line,"KEYWORDS")) { ajStrAssignS(&sumline,line); ret = ajReadlineTrim(inf,&line); while(ret && *MAJSTRGETPTR(line)==' ') { ajStrAppendS(&sumline,line); ret = ajReadlineTrim(inf,&line); } ajStrRemoveWhiteExcess(&sumline); embBtreeGenBankKW(sumline,entry->kw,entry->kwlen); continue; } if(entry->do_description) if(ajStrPrefixC(line,"DEFINITION")) { ajStrAssignS(&sumline,line); ret = ajReadlineTrim(inf,&line); while(ret && *MAJSTRGETPTR(line)==' ') { ajStrAppendS(&sumline,line); ret = ajReadlineTrim(inf,&line); } ajStrRemoveWhiteExcess(&sumline); embBtreeGenBankDE(sumline,entry->de,entry->delen); continue; } if(entry->do_taxonomy) if(ajStrPrefixC(line,"SOURCE")) { ret = ajReadlineTrim(inf,&line); ajStrAppendC(&line,";"); while(ret && *MAJSTRGETPTR(line)==' ') { ajStrAppendS(&sumline,line); ret = ajReadlineTrim(inf,&line); } ajStrRemoveWhiteExcess(&sumline); embBtreeGenBankTX(sumline,entry->tx,entry->txlen); continue; } pos = ajFileResetPos(inf); if(!ajReadlineTrim(inf,&line)) ret = ajFalse; } ajStrDel(&line); ajStrDel(&sumline); return ret; }