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 868404b..853b5f1 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -1,31 +1,50 @@
 package jalview.hmmer;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenMarkovModel;
+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;
 import jalview.util.MessageManager;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.util.Map;
+import java.util.List;
+
+import javax.swing.JOptionPane;
 
 public class HMMBuildThread implements Runnable
 {
-
+  HMMERCommands cmds = new HMMERCommands();
   AlignFrame af;
   AlignmentI alignment;
+  SequenceGroup group;
 
-  long barID;
+  boolean forGroup = false;
+  boolean canRun = true;
+
+  File hmmTemp = null;
+
+  File stoTemp = null;
 
-  Map<Integer, SequenceI> hmmSeqs;
+  long barID;
   
   public HMMBuildThread(AlignFrame af)
   {
     this.af = af;
+    if (af.getViewport().getSelectionGroup() != null)
+    {
+      group = af.getViewport().getSelectionGroup();
+      forGroup = true;
+    }
     alignment = af.getViewport().getAlignment();
+
   }
 
   @Override
@@ -34,12 +53,57 @@ public class HMMBuildThread implements Runnable
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             barID);
+    cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+    if (alignment == null && group == null)
+    {
+      JOptionPane.showMessageDialog(af,
+              MessageManager.getString("label.no_sequence_data"));
+      return;
+    }
+    try
+    {
+      hmmTemp = File.createTempFile("hmm", ".hmm");
+      hmmTemp.deleteOnExit();
+      stoTemp = File.createTempFile("output", ".sto");
+      stoTemp.deleteOnExit();
+    } catch (IOException e1)
+    {
+      e1.printStackTrace();
+    }
 
     try
     {
     try
     {
-      exportAlignment();
+        SequenceI[] array;
+        List<SequenceI> seqs = alignment
+                .getHMMConsensusSequences(true);
+        cmds.setHmmSeqs(seqs);
+        if (forGroup)
+        {
+          array = group.getSelectionAsNewSequences(alignment);
+        }
+        else
+        {
+          if (!alignment.isAligned())
+          {
+            alignment.padGaps();
+          }
+          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
@@ -48,7 +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
@@ -56,6 +126,7 @@ public class HMMBuildThread implements Runnable
     }
     try
     {
+
       importData();
     } catch (IOException | InterruptedException e)
     {
@@ -64,7 +135,7 @@ public class HMMBuildThread implements Runnable
     }
     } catch (Exception e)
     {
-
+      e.printStackTrace();
     } finally
     {
       af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
@@ -73,39 +144,57 @@ public class HMMBuildThread implements Runnable
   }
 
   
-  private void exportAlignment() throws IOException
+
+  
+  private boolean runCommand() throws IOException, InterruptedException
   {
-    hmmSeqs = alignment.getHMMConsensusSequences(true);
-    if (!alignment.isAligned())
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
+    if (!file.canExecute())
     {
-      alignment.padGaps();
+      return false;
     }
-    HMMERCommands.exportData(alignment, true, false,
-            new HiddenMarkovModel());
-  }
-  
-  private void runCommand() throws IOException, InterruptedException
-  {
-    final String command = HMMERCommands.HMMBUILD + HMMERCommands.NAME
-            + af.getName() + HMMERCommands.SPACE
-            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
-            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
-    HMMERCommands.runCommand(command);
+    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;
+    return cmds.runCommand(command);
   }
   
   private void importData() throws IOException, InterruptedException
   {
-    af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
+    cmds.addHMMConsensusSequences(af);
+    af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
             FileFormat.HMMER3, null);
-    for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
-    {
-      SequenceI seq = entry.getValue();
-      Integer pos = entry.getKey();
-      HMMERCommands.addHMMConsensusSequence(af, seq, pos);
-    }
-    af.alignPanel.alignmentChanged();
+    hmmTemp.delete();
+    stoTemp.delete();
   }
   
+  public boolean canRun()
+  {
+    return canRun;
+  }