C++ (Cpp) embBtreeGenBankTX Beispiele

Beispiel #1

Datei: dbxflat.c Projekt: dalehamel/birch-native-sources

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;
}

Beispiel #2

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;
}