JAL-2629 add sort by evalue and bit score

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index a2d5ab8..2c0fbb9 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -60,6 +60,8 @@ action.boxes = Boxes
 action.text = Text
 action.by_pairwise_id = By Pairwise Identity
 action.by_id = By Id
+action.by_evalue = By E-Value
+action.by_bit_score = By Bit Score
 action.by_length = By Length
 action.by_group = By Group
 action.unmark_as_reference = Unmark as Reference 

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 8473904..2d05865 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -86,6 +86,10 @@ public class AlignmentSorter
 
   private static boolean sortLengthAscending;
 
+  private static boolean sortEValueAscending;
+
+  private static boolean sortBitScoreAscending;
+
   /**
    * Sorts sequences in the alignment by Percentage Identity with the given
    * reference sequence, sorting the highest identity to the top
@@ -182,7 +186,7 @@ public class AlignmentSorter
     List<SequenceI> algn;
     synchronized (algn = align.getSequences())
     {
-      List<SequenceI> tmp = new ArrayList<SequenceI>();
+      List<SequenceI> tmp = new ArrayList<>();
 
       for (int i = 0; i < seqs.length; i++)
       {
@@ -268,6 +272,90 @@ public class AlignmentSorter
   }
 
   /**
+   * Sorts by sequence evalue. Currently moves all sequences without an evalue to
+   * the top of the alignment.
+   * 
+   * @param align
+   *                The alignment object to sort
+   */
+  public static void sortByEValue(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
+
+    double[] evalue = new double[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+
+    for (int i = 0; i < nSeq; i++)
+    {
+      seqs[i] = align.getSequenceAt(i);
+      AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
+      if (ann != null)
+      {
+        evalue[i] = ann[0].getEValue();
+      }
+      else
+      {
+        evalue[i] = -1;
+      }
+    }
+
+    QuickSort.sort(evalue, seqs);
+
+    if (sortEValueAscending)
+    {
+      setReverseOrder(align, seqs);
+    }
+    else
+    {
+      setOrder(align, seqs);
+    }
+
+    sortEValueAscending = !sortEValueAscending;
+  }
+
+  /**
+   * Sorts by sequence bit score. Currently moves all sequences without a bit
+   * score to the top of the alignment
+   * 
+   * @param align
+   *                The alignment object to sort
+   */
+  public static void sortByBitScore(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
+
+    double[] score = new double[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+
+    for (int i = 0; i < nSeq; i++)
+    {
+      seqs[i] = align.getSequenceAt(i);
+      AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
+      if (ann != null)
+      {
+        score[i] = ann[0].getEValue();
+      }
+      else
+      {
+        score[i] = -1;
+      }
+    }
+
+    QuickSort.sort(score, seqs);
+
+    if (sortBitScoreAscending)
+    {
+      setReverseOrder(align, seqs);
+    }
+    else
+    {
+      setOrder(align, seqs);
+    }
+
+    sortBitScoreAscending = !sortBitScoreAscending;
+  }
+
+  /**
    * Sorts the alignment by size of group. <br>
    * Maintains the order of sequences in each group by order in given alignment
    * object.
@@ -279,7 +367,7 @@ public class AlignmentSorter
   {
     // MAINTAINS ORIGNAL SEQUENCE ORDER,
     // ORDERS BY GROUP SIZE
-    List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> groups = new ArrayList<>();
 
     if (groups.hashCode() != lastGroupHash)
     {
@@ -315,7 +403,7 @@ public class AlignmentSorter
 
     // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
     // /////////////////////////////////////////////
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
 
     for (int i = 0; i < groups.size(); i++)
     {
@@ -357,7 +445,7 @@ public class AlignmentSorter
     // tmp2 = tmp.retainAll(mask);
     // return tmp2.addAll(mask.removeAll(tmp2))
 
-    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    ArrayList<SequenceI> seqs = new ArrayList<>();
     int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
@@ -436,7 +524,7 @@ public class AlignmentSorter
   {
     int nSeq = align.getHeight();
 
-    List<SequenceI> tmp = new ArrayList<SequenceI>();
+    List<SequenceI> tmp = new ArrayList<>();
 
     tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
 

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0b78527..b32acef 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1324,6 +1324,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       sortGroupMenuItem_actionPerformed();
     }
+    else if (source == sortEValueMenuItem)
+    {
+      sortEValueMenuItem_actionPerformed();
+    }
+    else if (source == sortBitScoreMenuItem)
+    {
+      sortBitScoreMenuItem_actionPerformed();
+    }
     else if (source == removeRedundancyMenuItem)
     {
       removeRedundancyMenuItem_actionPerformed();
@@ -2772,6 +2780,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  public void sortEValueMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByEValue(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  public void sortBitScoreMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByBitScore(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
   public void removeRedundancyMenuItem_actionPerformed()
   {
     new RedundancyPanel(alignPanel);
@@ -3122,6 +3150,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem sortGroupMenuItem = new MenuItem();
 
+  MenuItem sortEValueMenuItem = new MenuItem();
+
+  MenuItem sortBitScoreMenuItem = new MenuItem();
+
   MenuItem removeRedundancyMenuItem = new MenuItem();
 
   MenuItem pairwiseAlignmentMenuItem = new MenuItem();

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a429ece..796957e 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3786,6 +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!
    * 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 62165cd..579da08 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -518,6 +518,26 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
+    JMenuItem sortEValueMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_evalue"));
+    sortEValueMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortEValueMenuItem_actionPerformed(e);
+      }
+    });
+    JMenuItem sortBitScoreMenuItem = new JMenuItem(
+            MessageManager.getString("action.by_bit_score"));
+    sortBitScoreMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sortBitScoreMenuItem_actionPerformed(e);
+      }
+    });
   
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
@@ -1899,6 +1919,8 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortLengthMenuItem);
     sort.add(sortGroupMenuItem);
     sort.add(sortPairwiseMenuItem);
+    sort.add(sortEValueMenuItem);
+    sort.add(sortBitScoreMenuItem);
     sort.add(sortByTreeMenu);
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
@@ -2544,6 +2566,14 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void sortEValueMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  protected void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
   protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
   }