annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
true);
localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
- true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
- true);
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
}
else
{
{
startRes = seqs[i].getStart();
endRes = seqs[i].getEnd();
-
-
if (startEnd != null)
{
startIndex = startEnd[0];
}
startRes = seqs[i].findPosition(startIndex);
- startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
- : startRes;
- endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ endRes = seqs[i].findPosition(endIndex);
}
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
- suffix, colSel,
- null);
+ suffix, colSel, null);
}
public String formatSequences(String format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
- ColumnSelection colSel,
- jalview.datamodel.SequenceGroup selgp)
+ ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
{
if (omitHidden != null)
{
return this.formatSequences(format, alignment, suffix);
}
- public AlignmentI readFile(String inFile, String type, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFile(inFile, type, format);
- return al;
- }
-
- public AlignmentI readFromFile(FileParse source, String format)
- throws java.io.IOException
- {
- AlignmentI al = super.readFromFile(source, format);
- return al;
- }
-
/**
* validate format is valid for IO in Application. This is basically the
* AppletFormatAdapter.isValidFormat call with additional checks for
selectedOnly);
}
-
}