- if (seqDetails==null || seqDetails.size()==0)
- {
- // nothing to do
- return;
- }
- // 1. recover correct names and attributes for each sequence in alignment.
- /*
- * TODO: housekeeping w.r.t. recovery of dataset and annotation
- * references for input sequences, and then dataset sequence creation
- * for new sequences retrieved from service // finally, attempt to
- * de-uniquify to recover input sequence identity, and try to map back
- * onto dataset Note: this
- * jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs, true); will
- * NOT WORK - the returned alignment may contain multiple versions of
- * the input sequence, each being a subsequence of the original.
- * deuniquify also removes existing annotation and features added in the
- * previous step... al.setDataset(dataset); // add in new sequences
- * retrieved from sequence search which are not already in dataset. //
- * trigger a 'fetchDBids' to annotate sequences with database ids...
- */
- //jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset, seqDetails, al,true);
-
- jalview.analysis.SeqsetUtils.deuniquify(seqDetails, al.getSequencesArray(),true);
- // 2. Update names of associated nodes in any trees
- for (NewickFile nf:trees)
- {
- // the following works because all trees are already had node/SequenceI associations created.
- jalview.analysis.NJTree njt = new jalview.analysis.NJTree(al.getSequencesArray(), nf);
- // this just updates the displayed leaf name on the tree according to the SequenceIs.
- njt.renameAssociatedNodes();
- }
-