AlignmentI xrefsAlignment = makeCrossReferencesAlignment(dataset,
xrefs);
- final SequenceI[] sequenceSelection = AlignFrame.this.viewport
- .getSequenceSelection();
if (!dna)
{
xrefsAlignment = AlignmentUtils.makeCdsAlignment(
- xrefsAlignment.getSequencesArray(), dataset,
- sequenceSelection);
+ xrefsAlignment.getSequencesArray(), dataset, sel);
xrefsAlignment.alignAs(alignment);
}
boolean copyAlignmentIsAligned = false;
if (dna)
{
- copyAlignment = AlignmentUtils.makeCdsAlignment(
- sequenceSelection, dataset,
+ copyAlignment = AlignmentUtils.makeCdsAlignment(sel, dataset,
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
}
else
{
- copyAlignment = AlignmentUtils.makeCopyAlignment(
- sequenceSelection, xrefs.getSequencesArray(), dataset);
+ copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
+ xrefs.getSequencesArray(), dataset);
}
copyAlignment.setGapCharacter(AlignFrame.this.viewport
.getGapCharacter());
* align cdna to protein - currently only if
* fetching and aligning Ensembl transcripts!
*/
+ // TODO: generalise for other sources of locus/transcript/cds data
if (dna && DBRefSource.ENSEMBL.equalsIgnoreCase(source))
{
copyAlignment.alignAs(xrefsAlignment);
* Makes an alignment containing the given sequences, and adds them to the
* given dataset, which is also set as the dataset for the new alignment
*
+ * TODO: refactor to DatasetI method
+ *
* @param dataset
* @param seqs
* @return