From 401d9943c5fddb0327391f6b7682c19249007691 Mon Sep 17 00:00:00 2001 From: TZVanaalten Date: Tue, 15 Aug 2017 10:55:35 +0100 Subject: [PATCH] JAL-2629 fix uniquified sequence names appearing when running hmmbuild --- src/jalview/hmmer/HMMBuildThread.java | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java index 48796e4..63236ea 100644 --- a/src/jalview/hmmer/HMMBuildThread.java +++ b/src/jalview/hmmer/HMMBuildThread.java @@ -2,6 +2,7 @@ package jalview.hmmer; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; @@ -89,8 +90,15 @@ public class HMMBuildThread implements Runnable } array = alignment.getSequencesArray(); } - cmds.uniquifySequences(array); - cmds.exportData(array, stoTemp, null, null); + SequenceI[] newArr = new SequenceI[array.length]; + int index = 0; + for (SequenceI seq : array) + { + newArr[index] = new Sequence(seq); + index++; + } + cmds.uniquifySequences(newArr); + cmds.exportData(newArr, stoTemp, null, null); jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array); } catch (FileNotFoundException e) -- 1.7.10.2