X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMAlign.java;h=d66ec337e561a4e1e8071c54b5f4e3e3c0e1daf5;hb=6642847b7a5154da9d39ee568036f85576b9f171;hp=163e85bffed429737c65f8e99b838ef01c49a6f8;hpb=37f0332f53a8564ba7a9d55b993f8bfd2f368c80;p=jalview.git

diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
index 163e85b..d66ec33 100644
--- a/src/jalview/hmmer/HMMAlign.java
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -31,8 +31,6 @@ public class HMMAlign extends HmmerCommand
 {
   static final String HMMALIGN = "hmmalign";
 
-  static final String ARG_TRIM = "--trim";
-
   private final AlignmentI dataset;
 
   /**
@@ -64,17 +62,15 @@ public class HMMAlign extends HmmerCommand
   @Override
   public void run()
   {
-    HiddenMarkovModel hmm = af.getSelectedHMM();
-    if (hmm == null)
-    {
-      System.err.println("Can't run hmmalign as no HMM profile selected");
-      return;
-    }
+    HiddenMarkovModel hmm = getHmmProfile();
 
     long msgId = System.currentTimeMillis();
     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());
 
@@ -97,8 +93,8 @@ public class HMMAlign extends HmmerCommand
         boolean ran = runCommand(modelFile, alignmentFile, resultFile);
         if (!ran)
         {
-          JvOptionPane.showInternalMessageDialog(af,
-                  MessageManager.getString("warn.hmmalign_failed"));
+          JvOptionPane.showInternalMessageDialog(af, MessageManager
+                  .formatMessage("warn.command_failed", "hmmalign"));
           return;
         }
 
@@ -157,9 +153,9 @@ public class HMMAlign extends HmmerCommand
       }
     }
     args.add("-o");
-    args.add(resultFile.getAbsolutePath());
-    args.add(modelFile.getAbsolutePath());
-    args.add(alignmentFile.getAbsolutePath());
+    args.add(getFilePath(resultFile, true));
+    args.add(getFilePath(modelFile, true));
+    args.add(getFilePath(alignmentFile, true));
     
     return runCommand(args);
   }
@@ -177,7 +173,7 @@ public class HMMAlign extends HmmerCommand
   private SequenceI[] importData(File resultFile,
           List<AlignmentOrder> allOrders) throws IOException
   {
-    StockholmFile file = new StockholmFile(resultFile.getAbsolutePath(),
+    StockholmFile file = new StockholmFile(getFilePath(resultFile, false),
             DataSourceType.FILE);
     SequenceI[] result = file.getSeqsAsArray();
     AlignmentOrder msaorder = new AlignmentOrder(result);
@@ -212,14 +208,6 @@ public class HMMAlign extends HmmerCommand
       al.setDataset(dataset);
     }
 
-    /*
-     * hack to ensure hmm set on alignment
-     */
-    if (al.getSequenceAt(0).hasHMMProfile())
-    {
-      al.setHmmConsensus(al.getSequenceAt(0));
-    }
-
     displayInNewFrame(al, allOrders, hidden, title);
   }