X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMAlign.java;h=dd85c7459ccc1dfbe56cb950b86db2f2277ad4be;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=57e35e798cb422ec47a219d03a4f26e4adbdb08b;hpb=57e8b75999c110509906efa4ec8107f23785739f;p=jalview.git

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 57e35e7..dd85c74 100644
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -1,6 +1,7 @@
 package jalview.hmmer;
 
 import jalview.analysis.AlignmentSorter;
+import jalview.analysis.SeqsetUtils.SequenceInfo;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
@@ -24,6 +25,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JInternalFrame;
 
@@ -31,8 +33,6 @@ public class HMMAlign extends HmmerCommand
 {
   static final String HMMALIGN = "hmmalign";
 
-  static final String ARG_TRIM = "--trim";
-
   private final AlignmentI dataset;
 
   /**
@@ -70,6 +70,9 @@ public class HMMAlign extends HmmerCommand
     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
             msgId);
 
+    // ensure alignments are the same length
+    alignment.padGaps();
+
     AlignmentView msa = af.gatherSequencesForAlignment();
     SequenceI[][] subAlignments = msa.getVisibleContigs(alignment.getGapCharacter());
 
@@ -79,7 +82,7 @@ public class HMMAlign extends HmmerCommand
     int job = 0;
     for (SequenceI[] seqs : subAlignments)
     {
-      Hashtable sequencesHash = stashSequences(seqs);
+      Map<String, SequenceInfo> sequencesHash = stashSequences(seqs);
       try
       {
         File modelFile = FileUtils.createTempFile("hmm", ".hmm");