Resolved diffs from 2.8.3

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index bea86b2..ae4ae10 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,11 +20,24 @@
  */
 package jalview.appletgui;
 
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.List;
+import java.util.Vector;
+
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -38,17 +51,6 @@ import jalview.structure.VamsasSource;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Panel;
-import java.awt.Point;
-import java.awt.event.InputEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.Vector;
-
 public class SeqPanel extends Panel implements MouseMotionListener,
         MouseListener, SequenceListener, SelectionListener
 {
@@ -396,41 +398,107 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     return 1;
   }
 
+  /**
+   * Set status message in alignment panel
+   * 
+   * @param sequence
+   *          aligned sequence object
+   * @param res
+   *          alignment column
+   * @param seq
+   *          index of sequence in alignment
+   * @return position of res in sequence
+   */
   void setStatusMessage(SequenceI sequence, int res, int seq)
   {
-    StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
-            + sequence.getName());
+    // TODO remove duplication of identical gui method
+    StringBuilder text = new StringBuilder(32);
+    String seqno = seq == -1 ? "" : " " + (seq + 1);
+    text.append("Sequence" + seqno + " ID: " + sequence.getName());
 
-    Object obj = null;
+    String residue = null;
+    /*
+     * Try to translate the display character to residue name (null for gap).
+     */
+    final String displayChar = String.valueOf(sequence.getCharAt(res));
     if (av.getAlignment().isNucleotide())
     {
-      obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
-              + "");
-      if (obj != null)
+      residue = ResidueProperties.nucleotideName.get(displayChar);
+      if (residue != null)
       {
-        text.append(" Nucleotide: ");
+        text.append(" Nucleotide: ").append(residue);
       }
     }
     else
     {
-      obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
-      if (obj != null)
-      {
-        text.append("  Residue: ");
-      }
-    }
+      residue = "X".equalsIgnoreCase(displayChar) ? "X"
+              : ResidueProperties.aa2Triplet.get(displayChar);
+      if (residue != null)
+      {
+        text.append(" Residue: ").append(residue);
+      }
+    }
+
+    int pos = -1;
+    if (residue != null)
+    {
+      pos = sequence.findPosition(res);
+      text.append(" (").append(Integer.toString(pos)).append(")");
+    }
+    // Object obj = null;
+    // if (av.getAlignment().isNucleotide())
+    // {
+    // obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+    // + "");
+    // if (obj != null)
+    // {
+    // text.append(" Nucleotide: ");
+    // }
+    // }
+    // else
+    // {
+    // obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+    // if (obj != null)
+    // {
+    // text.append("  Residue: ");
+    // }
+    // }
+    //
+    // if (obj != null)
+    // {
+    //
+    // if (obj != "")
+    // {
+    // text.append(obj + " (" + sequence.findPosition(res) + ")");
+    // }
+    // }
 
-    if (obj != null)
-    {
+    ap.alignFrame.statusBar.setText(text.toString());
 
-      if (obj != "")
-      {
-        text.append(obj + " (" + sequence.findPosition(res) + ")");
-      }
-    }
+  }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+  /**
+   * Set the status bar message to highlight the first matched position in
+   * search results.
+   * 
+   * @param results
+   */
+  private void setStatusMessage(SearchResults results)
+  {
+    List<Match> matches = results.getResults();
+    if (!matches.isEmpty())
+    {
+      Match m = matches.get(0);
+      SequenceI seq = m.getSequence();
+      int sequenceIndex = this.av.getAlignment().findIndex(seq);
 
+      /*
+       * Convert position in sequence (base 1) to sequence character array index
+       * (base 0)
+       */
+      int start = m.getStart() - 1;
+      setStatusMessage(seq, start, sequenceIndex);
+    }
   }
 
   public void mousePressed(MouseEvent evt)
@@ -681,6 +749,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         ap.alignFrame.repaint();
       }
     }
+    setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
 
   }
@@ -743,7 +812,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      obj = "X".equalsIgnoreCase(ch) ? "STOP"
+      obj = "X".equalsIgnoreCase(ch) ? "X"
               : ResidueProperties.aa2Triplet.get(ch);
       if (obj != null)
       {
@@ -1393,7 +1462,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
               sequence.findPosition(res));
 
-      Vector links = null;
+      Vector<String> links = null;
       if (allFeatures != null)
       {
         for (int i = 0; i < allFeatures.length; i++)
@@ -1402,7 +1471,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           {
             if (links == null)
             {
-              links = new Vector();
+              links = new Vector<String>();
             }
             for (int j = 0; j < allFeatures[i].links.size(); j++)
             {
@@ -1896,8 +1965,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     av.setColumnSelection(cs);
     av.isColSelChanged(true);
   
-    firePropertyChange("alignment", null, av.getAlignment().getSequences());
-    // PaintRefresher.Refresh(this, av.getSequenceSetId());
+    ap.scalePanelHolder.repaint();
+    ap.repaint();
   
     return true;
   }