JAL-2629 add basic parameter adjustment to hmmsearch/align

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

diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
index 1c2450c..532271b 100644 (file)
--- a/src/jalview/hmmer/HMMAlignThread.java
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -17,6 +17,7 @@ import jalview.io.DataSourceType;
 import jalview.io.StockholmFile;
 import jalview.util.MessageManager;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.ws.params.ArgumentI;
 
 import java.io.File;
 import java.io.IOException;
@@ -25,7 +26,6 @@ import java.util.List;
 import java.util.Map;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 public class HMMAlignThread implements Runnable
 {
@@ -52,6 +52,8 @@ public class HMMAlignThread implements Runnable
 
   HiddenMarkovModel hmm;
 
+  List<ArgumentI> args;
+
   boolean newFrame;
 
   long barID;
@@ -75,7 +77,8 @@ public class HMMAlignThread implements Runnable
    * @param af
    * @param createNewFrame
    */
-  public HMMAlignThread(AlignFrame af, boolean createNewFrame)
+  public HMMAlignThread(AlignFrame af, boolean createNewFrame,
+          List<ArgumentI> args)
   {
     this.af = af;
     alignment = af.getViewport().getAlignment();
@@ -85,6 +88,7 @@ public class HMMAlignThread implements Runnable
     }
     newFrame = createNewFrame;
     featureSettings = af.getFeatureRenderer().getSettings();
+    this.args = args;
   }
 
   /**
@@ -96,71 +100,60 @@ public class HMMAlignThread implements Runnable
   @Override
   public void run()
   {
-    if (af.getSelectedHMM() == null)
-    {
-      JOptionPane.showMessageDialog(af,
-              MessageManager.getString("warn.no_selected_hmm"));
-      return;
-    }
-    else
-    {
-      hmm = af.getSelectedHMM();
-    }
+
+    hmm = af.getSelectedHMM();
+
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
             barID);
     cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
-
-    // if (!alignment.isAligned())
-    // {
-    // alignment.padGaps();
-    // }
-    prepareAlignment();
-    SequenceI[][] subAlignments = msa.getVisibleContigs('-');
-    allOrders = new ArrayList<>();
-    allResults = new SequenceI[subAlignments.length][];
-    int job = 0;
-    for (SequenceI[] seqs : subAlignments)
-    {
-      cmds.uniquifySequences(seqs);
-      try
-      {
-        createTemporaryFiles();
-      } catch (IOException e2)
+      prepareAlignment();
+      SequenceI[][] subAlignments = msa.getVisibleContigs('-');
+      allOrders = new ArrayList<>();
+      allResults = new SequenceI[subAlignments.length][];
+      int job = 0;
+      for (SequenceI[] seqs : subAlignments)
       {
-        e2.printStackTrace();
-      }
-      try
-      {
-        cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
-                hmmTemp.getAbsoluteFile());
-      } catch (IOException e1)
-      {
-        e1.printStackTrace();
-      }
-      try
-      {
-        boolean ran = runCommand();
-        if (!ran)
+        cmds.uniquifySequences(seqs);
+        try
+        {
+          createTemporaryFiles();
+        } catch (IOException e2)
         {
-          JvOptionPane.showInternalMessageDialog(af,
-                  MessageManager.getString("warn.hmmalign_failed"));
-          return;
+          e2.printStackTrace();
         }
-      } catch (IOException | InterruptedException e)
-      {
-        e.printStackTrace();
-      }
-      try
-      {
-        importData(job);
-      } catch (IOException | InterruptedException e)
-      {
-        // TODO Auto-generated catch block
-        e.printStackTrace();
+        try
+        {
+          cmds.exportData(seqs, outTemp.getAbsoluteFile(), hmm,
+                  hmmTemp.getAbsoluteFile());
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+        try
+        {
+          boolean ran = runCommand();
+          if (!ran)
+          {
+            JvOptionPane.showInternalMessageDialog(af,
+                    MessageManager.getString("warn.hmmalign_failed"));
+            return;
+          }
+        } catch (IOException | InterruptedException e)
+        {
+          e.printStackTrace();
+        }
+        try
+        {
+          importData(job);
+        } catch (IOException | InterruptedException e)
+        {
+          // TODO Auto-generated catch block
+          e.printStackTrace();
+        }
+        job++;
       }
-      job++;
-    }
+
 
     displayResults(newFrame);
 
@@ -176,10 +169,16 @@ public class HMMAlignThread implements Runnable
    */
   private void createTemporaryFiles() throws IOException
   {
-    hmmTemp = File.createTempFile("hmm", ".hmm");
-    hmmTemp.deleteOnExit();
-    outTemp = File.createTempFile("output", ".sto");
-    outTemp.deleteOnExit();
+    if (hmmTemp == null)
+    {
+      hmmTemp = File.createTempFile("hmm", ".hmm");
+      hmmTemp.deleteOnExit();
+    }
+    if (outTemp == null)
+    {
+      outTemp = File.createTempFile("output", ".sto");
+      outTemp.deleteOnExit();
+    }
     inputTemp = File.createTempFile("input", ".sto");
     inputTemp.deleteOnExit();
   }
@@ -210,15 +209,17 @@ public class HMMAlignThread implements Runnable
     {
       command += cmds.ALLCOL;
     }
-    boolean trim = true;
-    String bool = Cache.getProperty("TRIM_TERMINI");
-    if ("false".equals(bool))
+    if (args != null)
     {
-      trim = false;
-    }
-    if (trim)
-    {
-      command += cmds.TRIM;
+      for (ArgumentI arg : args)
+      {
+        String name = arg.getName();
+        switch (name)
+        {
+        case "Trim Non-Matching Termini":
+          command += "--trim";
+        }
+      }
     }
     command += " -o " + inputTemp.getAbsolutePath() + cmds.SPACE
             + hmmTemp.getAbsolutePath() + cmds.SPACE
@@ -228,7 +229,7 @@ public class HMMAlignThread implements Runnable
 
   /**
    * Imports the data from the temporary file to which the output of hmmalign is
-   * directed.
+   * directed. this is used for an internal job.
    * 
    * @param index
    *          The index of the 'job' (or region of an alignment).