[Biojava-dev] [Bug 2234] Error during "rich" conversion of genbank to EMBL format

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2234





------- Comment #4 from holland at ebi.ac.uk  2007-03-15 06:11 EST -------
I've identified the problem areas in the EMBLFormat code. I will fix them
tomorrow.

Note to self:

if (format.equals(EMBL_FORMAT)) {
                // accession; SV version; circular/linear; moltype; dataclass;
division; length BP.
                locusLine.append(rs.getAccession());
                locusLine.append("; ");
--- INSERT "SV versionLine;" here
                locusLine.append(rs.getCircular()?"circular; ":"linear; ");
                locusLine.append(moltype);

        // version line
--- WRAP in test - only execute if EMBL_PRE87_FORMAT
        if (versionLine!=null) StringTools.writeKeyValueLine(VERSION_TAG,
versionLine, 5, this.getLineWidth(), null, VERSION_TAG, this.getPrintStream());
        else StringTools.writeKeyValueLine(VERSION_TAG,
accession+"."+rs.getVersion(), 5, this.getLineWidth(), null, VERSION_TAG,
this.getPrintStream());
        this.getPrintStream().println(DELIMITER_TAG+"   ");


        // date line
-- INSERT commaa before space before Created
        StringTools.writeKeyValueLine(DATE_TAG, (cdat==null?udat:cdat)+" (Rel.
"+(crel==null?"0":crel)+" Created)", 5, this.getLineWidth(), null, DATE_TAG,
this.getPrintStream());

--- CHECK that leading space chomped first - does this record start in space
then "? It ends in "; on last line but does not start on same line
if (key.equals(TITLE_TAG)) {
                        if (val.length()>1) {
                            if (val.endsWith(";")) val =
val.substring(0,val.length()-1); // chomp semicolon
                            if (val.endsWith("\"")) val =
val.substring(1,val.length()-2); // chomp quotes
                            title = val;
                        } else title=null; // single semi-colon indicates no
title
                    }

            // add-in other dbxrefs where present
            for (Iterator j = f.getRankedCrossRefs().iterator(); j.hasNext(); )
{
                RankedCrossRef rcr = (RankedCrossRef)j.next();
                CrossRef cr = rcr.getCrossRef();
--- REMOVE taxon: prefix - shouldn't be there...
                StringTools.writeKeyValueLine(FEATURE_TAG,
"/db_xref=\"taxon:"+cr.getDbname()+":"+cr.getAccession()+"\"", 21,
this.getLineWidth(), null, FEATURE_TAG, this.getPrintStream());
            }




-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.