}
public String formatSequences(String format, SequenceI[] seqs,
- String[] omitHiddenColumns)
+ String[] omitHiddenColumns, int[] exportRange)
{
- return formatSequences(format, replaceStrings(seqs, omitHiddenColumns));
+ return formatSequences(format,
+ replaceStrings(seqs, omitHiddenColumns, exportRange));
}
/**
* @return new sequences
*/
public SequenceI[] replaceStrings(SequenceI[] seqs,
- String[] omitHiddenColumns)
+ String[] omitHiddenColumns, int[] startEnd)
{
if (omitHiddenColumns != null)
{
SequenceI[] tmp = new SequenceI[seqs.length];
+
+ int startRes;
+ int endRes;
+ int startIndex;
+ int endIndex;
for (int i = 0; i < seqs.length; i++)
{
+ startRes = seqs[i].getStart();
+ endRes = seqs[i].getEnd();
+
+ startIndex = startEnd[0];
+ endIndex = startEnd[1];
+
+ if (startEnd != null)
+ {
+ // get first non-gaped residue start position
+ while (jalview.util.Comparison.isGap(seqs[i]
+ .getCharAt(startIndex)) && startIndex < endIndex)
+ {
+ startIndex++;
+ }
+
+ // get last non-gaped residue end position
+ while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex))
+ && endIndex > startIndex)
+ {
+ endIndex--;
+ }
+
+ startRes = seqs[i].findPosition(startIndex);
+ startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
+ : startRes;
+ endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ }
+
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
- seqs[i].getStart(), seqs[i].getEnd());
+ startRes, endRes);
tmp[i].setDescription(seqs[i].getDescription());
}
seqs = tmp;
}
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, ColumnSelection colSel)
+ String[] omitHidden, int[] exportRange, ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden,
+ return formatSequences(format, alignment, omitHidden, exportRange,
getCacheSuffixDefault(format), colSel, null);
}
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, ColumnSelection colSel, SequenceGroup sgp)
+ String[] omitHidden, int[] exportRange, ColumnSelection colSel,
+ SequenceGroup sgp)
{
- return formatSequences(format, alignment, omitHidden,
+ return formatSequences(format, alignment, omitHidden, exportRange,
getCacheSuffixDefault(format), colSel, sgp);
}
* @return string representation of the alignment formatted as format
*/
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, boolean suffix, ColumnSelection colSel)
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ ColumnSelection colSel)
{
- return formatSequences(format, alignment, omitHidden, suffix, colSel,
+ return formatSequences(format, alignment, omitHidden, exportRange,
+ suffix, colSel,
null);
}
public String formatSequences(String format, AlignmentI alignment,
- String[] omitHidden, boolean suffix, ColumnSelection colSel,
+ String[] omitHidden, int[] exportRange, boolean suffix,
+ ColumnSelection colSel,
jalview.datamodel.SequenceGroup selgp)
{
if (omitHidden != null)
// TODO: JAL-1486 - set start and end for output correctly. basically,
// AlignmentView.getVisibleContigs does this.
Alignment alv = new Alignment(replaceStrings(
- alignment.getSequencesArray(), omitHidden));
+ alignment.getSequencesArray(), omitHidden, exportRange));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
if (ala != null)
{