JAL-2629 add sort by evalue and bit score

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4587368..796957e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -69,6 +69,7 @@ import jalview.hmmer.HMMERParamStore;
 import jalview.hmmer.HMMERPreset;
 import jalview.hmmer.HMMSearch;
 import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BackupFiles;
@@ -1111,6 +1112,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new Thread(new HMMSearch(this, args)).start();
     alignPanel.repaint();
   }
+  
+  @Override
+  public void jackhmmer_actionPerformed(boolean withDefaults)
+  {
+    
+    /*
+     * get default parameters, and (if requested) show 
+     * dialog to allow modification
+     */
+    
+    ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new JackHMMER(this, args)).start();
+    alignPanel.repaint();
+    
+  }
 
   /**
    * Checks if the alignment has at least one hidden Markov model, if not shows
@@ -1128,6 +1159,36 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return true;
   }
+  
+  @Override
+  protected void filterByEValue_actionPerformed()
+  {
+    viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+  }
+  
+  @Override
+  protected void filterByScore_actionPerformed()
+  {
+    viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+  }
+  
+  private double inputDouble(String message)
+  {
+    String str = null;
+    Double d = null;
+    while(d == null || d <= 0)
+    {
+      str = JOptionPane.showInputDialog(this.alignPanel, message);
+      try
+      {
+        d = Double.valueOf(str);
+      }
+      catch (NumberFormatException e)
+      {
+      }
+    }
+    return d;
+  }
 
   /**
    * Checks if the alignment contains the required number of sequences.
@@ -1137,13 +1198,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public boolean alignmentIsSufficient(int required)
   {
-    if (getViewport().getAlignment().getSequences().size() < required)
-    {
-      JOptionPane.showMessageDialog(this,
-              MessageManager.getString("label.not_enough_sequences"));
-      return false;
-    }
-    return true;
+      if (getViewport().getSequenceSelection().length < required)
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("label.not_enough_sequences"));
+        return false;
+      }
+      return true;
   }
 
   /**
@@ -3725,6 +3786,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true, false);
   }
 
+  @Override
+  public void sortEValueMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByEValue(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  @Override
+  public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByBitScore(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+  
   /**
    * DOCUMENT ME!
    *