JAL-2629 exported HMMs are now named correctly

[jalview.git] / src / jalview / hmmer / HMMBuildThread.java

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index fb904f9..853b5f1 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -2,9 +2,11 @@ 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;
+import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -22,9 +24,9 @@ public class HMMBuildThread implements Runnable
   HMMERCommands cmds = new HMMERCommands();
   AlignFrame af;
   AlignmentI alignment;
-
   SequenceGroup group;
 
+  boolean forGroup = false;
   boolean canRun = true;
 
   File hmmTemp = null;
@@ -39,6 +41,7 @@ public class HMMBuildThread implements Runnable
     if (af.getViewport().getSelectionGroup() != null)
     {
       group = af.getViewport().getSelectionGroup();
+      forGroup = true;
     }
     alignment = af.getViewport().getAlignment();
 
@@ -72,14 +75,13 @@ public class HMMBuildThread implements Runnable
     {
     try
     {
+        SequenceI[] array;
         List<SequenceI> seqs = alignment
                 .getHMMConsensusSequences(true);
         cmds.setHmmSeqs(seqs);
-        if (group != null)
+        if (forGroup)
         {
-          SequenceI[] array = group.getSelectionAsNewSequences(alignment);
-
-          cmds.exportData(array, stoTemp, null, null);
+          array = group.getSelectionAsNewSequences(alignment);
         }
         else
         {
@@ -87,9 +89,21 @@ public class HMMBuildThread implements Runnable
           {
             alignment.padGaps();
           }
-          cmds.exportData(alignment.getSequencesArray(), stoTemp, null,
-                  null);
+          array = alignment.getSequencesArray();
+        }
+
+        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)
     {
       // TODO Auto-generated catch block
@@ -98,7 +112,13 @@ public class HMMBuildThread implements Runnable
     }
     try
     {
-      runCommand();
+        boolean ran = runCommand();
+        if (!ran)
+        {
+          JvOptionPane.showInternalMessageDialog(af,
+                  MessageManager.getString("warn.hmmbuild_failed"));
+          return;
+        }
     } catch (IOException | InterruptedException e)
     {
       // TODO Auto-generated catch block
@@ -126,12 +146,40 @@ public class HMMBuildThread implements Runnable
   
 
   
-  private void runCommand() throws IOException, InterruptedException
+  private boolean runCommand() throws IOException, InterruptedException
   {
-    final String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
-            + af.getName() + cmds.SPACE + hmmTemp.getAbsolutePath()
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
+    if (!file.canExecute())
+    {
+      return false;
+    }
+    String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME;
+    if (forGroup)
+    {
+      command += group.getName();
+    }
+    else
+    {
+      String name = af.getName();
+      if (name == null)
+      {
+        name = "Alignment";
+      }
+      command += name;
+    }
+    command += cmds.SPACE;
+    if (!alignment.isNucleotide())
+    {
+      command += cmds.FORCEAMINO; // TODO check for rna
+    }
+    else
+    {
+      command += cmds.FORCEDNA;
+    }
+
+    command += hmmTemp.getAbsolutePath()
             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
-    cmds.runCommand(command);
+    return cmds.runCommand(command);
   }
   
   private void importData() throws IOException, InterruptedException