From fbb18baad3919cbf94fcb5159bbd5269d6af18b4 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 8 Nov 2006 17:37:42 +0000 Subject: [PATCH] currentSeq and set description in dataset --- src/jalview/datamodel/Alignment.java | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 4237db8..288c28a 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -566,22 +566,25 @@ public class Alignment implements AlignmentI // Can only be done once, if dataset is not null // This will not be performed Sequence[] seqs = new Sequence[getHeight()]; + SequenceI currentSeq; for (int i = 0; i < getHeight(); i++) { - if(getSequenceAt(i).getDatasetSequence()!=null) + currentSeq = getSequenceAt(i); + if(currentSeq.getDatasetSequence()!=null) { - seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence(); + seqs[i] = (Sequence)currentSeq.getDatasetSequence(); } else { - seqs[i] = new Sequence(getSequenceAt(i).getName(), + seqs[i] = new Sequence(currentSeq.getName(), AlignSeq.extractGaps( jalview.util.Comparison.GapChars, - getSequenceAt(i).getSequence() + currentSeq.getSequence() ), - getSequenceAt(i).getStart(), - getSequenceAt(i).getEnd()); - seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures(); + currentSeq.getStart(), + currentSeq.getEnd()); + seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures(); + seqs[i].setDescription(currentSeq.getDescription()); getSequenceAt(i).setSequenceFeatures(null); getSequenceAt(i).setDatasetSequence(seqs[i]); } -- 1.7.10.2