X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMSearchThread.java;h=16c7c6843503d41fc7ddde666ba73cc4309bbc27;hb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;hp=8adeb22ad5ba8113022692cd81f06fa2c0add452;hpb=dbdc8807d9059dacf65a087b7bcb8363be53fb8f;p=jalview.git

diff --git a/src/jalview/hmmer/HMMSearchThread.java b/src/jalview/hmmer/HMMSearchThread.java
index 8adeb22..16c7c68 100644
--- a/src/jalview/hmmer/HMMSearchThread.java
+++ b/src/jalview/hmmer/HMMSearchThread.java
@@ -1,6 +1,5 @@
 package jalview.hmmer;
 
-import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -9,7 +8,6 @@ import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StockholmFile;
@@ -29,23 +27,22 @@ import java.util.Scanner;
 
 import javax.swing.JOptionPane;
 
-public class HMMSearchThread implements Runnable
+public class HMMSearchThread extends HmmerCommand implements Runnable
 {
-  /**
+  static final String HMMSEARCH = "hmmsearch";
+
+  /*
    * feature settings from view that job was associated with
    */
   protected FeatureRendererSettings featureSettings = null;
 
-  /**
-   * Object containing frequently used commands.
-   */
-  HMMERCommands cmds = new HMMERCommands();
+  HiddenMarkovModel hmm;
 
-  AlignFrame af;
+  boolean newFrame;
 
-  HiddenMarkovModel hmm;
+  boolean realign = false;
 
-  boolean newFrame, realign = false, trim = false;
+  boolean trim = false;
 
   Integer numberOfSequences = null;
 
@@ -63,11 +60,8 @@ public class HMMSearchThread implements Runnable
 
   File databaseFile = null;
 
-
-
   SequenceI[] seqs;
 
-
   /**
    * Constructor for the HMMSearchThread. If create new frame is set to true, a
    * new frame will be created.
@@ -107,7 +101,6 @@ public class HMMSearchThread implements Runnable
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
             barID);
-    cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
 
     try
     {
@@ -118,7 +111,7 @@ public class HMMSearchThread implements Runnable
     }
     try
     {
-      cmds.exportData(null, null, hmm, hmmTemp.getAbsoluteFile(), null);
+      exportData(null, null, hmm, hmmTemp.getAbsoluteFile(), null);
     } catch (IOException e1)
     {
       e1.printStackTrace();
@@ -145,8 +138,7 @@ public class HMMSearchThread implements Runnable
       e.printStackTrace();
     }
 
-    af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
-            barID);
+    af.setProgressBar("", barID);
 
   }
 
@@ -174,23 +166,18 @@ public class HMMSearchThread implements Runnable
    */
   private boolean runCommand() throws IOException, InterruptedException
   {
-    Boolean dbFound = false;
-    String dbPath = "";
-    File file = new File(cmds.HMMERFOLDER + "/hmmsearch");
-    if (!file.canExecute())
+    String binaryPath = getCommandRoot(HMMSEARCH);
+    if (binaryPath == null)
     {
-      file = new File(cmds.HMMERFOLDER + "/hmmsearch.exe");
-      {
-        if (!file.canExecute())
-        {
-          return false;
-        }
-      }
+      return false;
     }
 
-    String command = cmds.HMMERFOLDER + "/hmmsearch -o "
+    String command = binaryPath + " -o "
             + inputTableTemp.getAbsolutePath() + " -A "
-            + inputAlignmentTemp.getAbsolutePath() + cmds.SPACE;
+            + inputAlignmentTemp.getAbsolutePath() + SPACE;
+
+    boolean dbFound = false;
+    String dbPath = "";
     if (params != null)
     {
       for (ArgumentI arg : params)
@@ -215,16 +202,16 @@ public class HMMSearchThread implements Runnable
           }
           break;
         case "Sequence E-value Cutoff":
-          command += "--incE " + arg.getValue() + cmds.SPACE;
+          command += "--incE " + arg.getValue() + SPACE;
           break;
         case "Sequence Score Threshold":
-          command += "-incT " + arg.getValue() + cmds.SPACE;
+          command += "-incT " + arg.getValue() + SPACE;
           break;
         case "Domain E-value Threshold":
-          command += "--incdomE " + arg.getValue() + cmds.SPACE;
+          command += "--incdomE " + arg.getValue() + SPACE;
           break;
         case "Domain Score Threshold":
-          command += "--incdomT " + arg.getValue() + cmds.SPACE;
+          command += "--incdomT " + arg.getValue() + SPACE;
           break;
         case "Trim Non-Matching Termini":
           trim = true;
@@ -242,7 +229,7 @@ public class HMMSearchThread implements Runnable
       }
     }
 
-    if (dbFound == false || MessageManager.getString("label.this_alignment")
+    if (!dbFound || MessageManager.getString("label.this_alignment")
             .equals(dbPath))
     {
       AlignmentI alignment = af.getViewport().getAlignment();
@@ -258,9 +245,9 @@ public class HMMSearchThread implements Runnable
       writer.close();
     }
 
-    command += hmmTemp.getAbsolutePath() + cmds.SPACE
+    command += hmmTemp.getAbsolutePath() + SPACE
             + databaseFile.getAbsolutePath();
-    return cmds.runCommand(command);
+    return runCommand(command);
   }
 
   /**
@@ -271,55 +258,64 @@ public class HMMSearchThread implements Runnable
   {
     BufferedReader br = new BufferedReader(
             new FileReader(inputAlignmentTemp));
-    if (br.readLine() == null)
+    try
     {
-      JOptionPane.showMessageDialog(af,
-              MessageManager.getString("label.no_sequences_found"));
-      return;
-    }
-    StockholmFile file = new StockholmFile(new FileParse(
-            inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
-    seqs = file.getSeqsAsArray();
+      if (br.readLine() == null)
+      {
+        JOptionPane.showMessageDialog(af,
+                MessageManager.getString("label.no_sequences_found"));
+        return;
+      }
+      StockholmFile file = new StockholmFile(new FileParse(
+              inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
+      seqs = file.getSeqsAsArray();
 
-    readTable();
+      readTable();
 
-    SequenceI[] hmmAndSeqs;
-    if (numberOfSequences != null && numberOfSequences < seqs.length)
-    {
-      hmmAndSeqs = new SequenceI[numberOfSequences + 1];
-    }
-    else
-    {
-      hmmAndSeqs = new SequenceI[seqs.length + 1];
-    }
-    hmmAndSeqs[0] = hmmSeq;
+      SequenceI[] hmmAndSeqs;
+      if (numberOfSequences != null && numberOfSequences < seqs.length)
+      {
+        hmmAndSeqs = new SequenceI[numberOfSequences + 1];
+      }
+      else
+      {
+        hmmAndSeqs = new SequenceI[seqs.length + 1];
+      }
+      hmmAndSeqs[0] = hmmSeq;
 
-    if (numberOfSequences != null && seqs.length > numberOfSequences)
-    {
-      System.arraycopy(seqs, 0, hmmAndSeqs, 1, numberOfSequences);
-    }
-    else
-    {
-      System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqs.length);
-    }
+      if (numberOfSequences != null && seqs.length > numberOfSequences)
+      {
+        System.arraycopy(seqs, 0, hmmAndSeqs, 1, numberOfSequences);
+      }
+      else
+      {
+        System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqs.length);
+      }
 
-    AlignmentI alignment = new Alignment(hmmAndSeqs);
-    AlignFrame frame = new AlignFrame(alignment, 1, 1);
-    frame.setSelectedHMMSequence(hmmSeq);
-    List<ArgumentI> alignArgs = new ArrayList<>();
-    if (trim)
+      AlignmentI alignment = new Alignment(hmmAndSeqs);
+      AlignFrame frame = new AlignFrame(alignment, 1, 1);
+      frame.setSelectedHMMSequence(hmmSeq);
+      List<ArgumentI> alignArgs = new ArrayList<>();
+      if (trim)
+      {
+        alignArgs.add(new BooleanOption(
+                MessageManager.getString("label.trim_termini"),
+                MessageManager.getString("label.trim_termini_desc"), true,
+                true, true, null));
+      }
+      HMMAlignThread hmmalign = new HMMAlignThread(frame, true, alignArgs);
+      hmmalign.hmmalignWaitTillComplete();
+      frame = null;
+      hmmTemp.delete();
+      inputAlignmentTemp.delete();
+      inputTableTemp.delete();
+    } finally
     {
-      alignArgs.add(new BooleanOption(
-              MessageManager.getString("label.trim_termini"),
-              MessageManager.getString("label.trim_termini_desc"), true,
-              true, true, null));
+      if (br != null)
+      {
+        br.close();
+      }
     }
-    HMMAlignThread hmmalign = new HMMAlignThread(frame, true, alignArgs);
-    hmmalign.hmmalignWaitTillComplete();
-    frame = null;
-    hmmTemp.delete();
-    inputAlignmentTemp.delete();
-    inputTableTemp.delete();
   }
 
   /**
@@ -342,7 +338,7 @@ public class HMMSearchThread implements Runnable
 
   }
 
-  public void readTable() throws IOException
+  void readTable() throws IOException
   {
     BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
     String line = "";
@@ -360,26 +356,27 @@ public class HMMSearchThread implements Runnable
             && !"".equals(line))
     {
       Scanner scanner = new Scanner(line);
-    
-      String str = scanner.next();
-      Annotation[] annots = new Annotation[seqs[index].getLength()];
-      for (Annotation an : annots)
+
+      String str = scanner.next(); // full sequence eValue score
+      float eValue = Float.parseFloat(str);
+      int seqLength = seqs[index].getLength();
+      Annotation[] annots = new Annotation[seqLength];
+      for (int j = 0; j < seqLength; j++)
       {
-        an = new Annotation(Float.parseFloat(str));
+        annots[j] = new Annotation(eValue);
       }
       AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
               "Score", annots);
       annot.setScore(Double.parseDouble(str));
       annot.setSequenceRef(seqs[index]);
       seqs[index].addAlignmentAnnotation(annot);
-    
+
       scanner.close();
       line = br.readLine();
       index++;
     }
-    
+
     br.close();
   }
 
-
 }