X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=de65dc59ca50e65de1306be12f1ebfb2391d572c;hb=d253d66e8bf5bb3567194bc709c068fc2aed278d;hp=ab6dd9a8f8ffe14f1f6d930026a4ffa21824bd50;hpb=b94e9d2b3e667c6925e3e40bac63de219fc717a7;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index ab6dd9a..de65dc5 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -54,6 +54,7 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
 
@@ -528,7 +529,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < 0 || res < 0)
     {
@@ -564,8 +565,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         av.setSelectionGroup(null);
       }
 
-      List<SequenceFeature> features = findFeaturesAtRes(sequence,
-              sequence.findPosition(findRes(evt)));
+      int column = findColumn(evt);
+      List<SequenceFeature> features = findFeaturesAtColumn(sequence,
+              column + 1);
 
       if (!features.isEmpty())
       {
@@ -573,12 +575,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         highlight.addResult(sequence, features.get(0).getBegin(), features
                 .get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight);
-        SequenceFeature[] featuresArray = features
-                .toArray(new SequenceFeature[features.size()]);
         seqCanvas.getFeatureRenderer().amendFeatures(
-                new SequenceI[] { sequence }, featuresArray, false, ap);
-
-        seqCanvas.highlightSearchResults(null);
+                Collections.singletonList(sequence), features, false, ap);
+        av.setSearchResults(null); // clear highlighting
+        seqCanvas.repaint(); // draw new/amended features
       }
     }
   }
@@ -604,7 +604,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   int wrappedBlock = -1;
 
-  int findRes(MouseEvent evt)
+  /**
+   * Returns the aligned sequence position (base 0) at the mouse position, or
+   * the closest visible one
+   * 
+   * @param evt
+   * @return
+   */
+  int findColumn(MouseEvent evt)
   {
     int res = 0;
     int x = evt.getX();
@@ -707,7 +714,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < av.getAlignment().getHeight()
             && res < av.getAlignment().getSequenceAt(seq).getLength())
@@ -779,7 +786,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    final int column = findRes(evt);
+    final int column = findColumn(evt);
     int seq = findSeq(evt);
 
     if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
@@ -802,9 +809,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     final char ch = sequence.getCharAt(column);
-    int respos = Comparison.isGap(ch) ? -1 : sequence.findPosition(column);
+    boolean isGapped = Comparison.isGap(ch);
+    // find residue at column (or nearest if at a gap)
+    int respos = sequence.findPosition(column);
 
-    if (ssm != null && respos != -1)
+    if (ssm != null && !isGapped)
     {
       mouseOverSequence(sequence, column, respos);
     }
@@ -813,30 +822,21 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     text.append("Sequence ").append(Integer.toString(seq + 1))
             .append(" ID: ").append(sequence.getName());
 
-    String obj = null;
-    if (respos != -1)
+    if (!isGapped)
     {
       if (av.getAlignment().isNucleotide())
       {
-        obj = ResidueProperties.nucleotideName.get(ch);
-        if (obj != null)
-        {
-          text.append(" Nucleotide: ").append(obj);
-        }
+        String base = ResidueProperties.nucleotideName.get(ch);
+        text.append(" Nucleotide: ").append(base == null ? ch : base);
       }
       else
       {
-        obj = (ch == 'x' || ch == 'X') ? "X" : ResidueProperties.aa2Triplet
+        String residue = (ch == 'x' || ch == 'X') ? "X"
+                : ResidueProperties.aa2Triplet
                 .get(String.valueOf(ch));
-        if (obj != null)
-        {
-          text.append(" Residue: ").append(obj);
-        }
-      }
-      if (obj != null)
-      {
-        text.append(" (").append(Integer.toString(respos)).append(")");
+        text.append(" Residue: ").append(residue == null ? ch : residue);
       }
+      text.append(" (").append(Integer.toString(respos)).append(")");
     }
 
     ap.alignFrame.statusBar.setText(text.toString());
@@ -864,12 +864,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     /*
-     * add feature details to tooltip if over one or more features
+     * add feature details to tooltip, including any that straddle
+     * a gapped position
      */
-    if (respos != -1)
+    if (av.isShowSequenceFeatures())
     {
-      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
-              respos);
+      List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence,
+              column + 1);
       for (SequenceFeature sf : allFeatures)
       {
         tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
@@ -901,9 +902,19 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
   }
 
-  List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
+  /**
+   * Returns features at the specified aligned column on the given sequence.
+   * Non-positional features are not included. If the column has a gap, then
+   * enclosing features are included (but not contact features).
+   * 
+   * @param sequence
+   * @param column
+   *          (1..)
+   * @return
+   */
+  List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
   {
-    return seqCanvas.getFeatureRenderer().findFeaturesAtRes(sequence, res);
+    return seqCanvas.getFeatureRenderer().findFeaturesAtColumn(sequence, column);
   }
 
   Tooltip tooltip;
@@ -983,7 +994,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (res < 0)
     {
@@ -1165,7 +1176,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         // Find the next gap before the end
         // of the visible region boundary
         boolean blank = false;
-        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
+        for (; fixedRight > lastres; fixedRight--)
         {
           blank = true;
 
@@ -1396,7 +1407,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       scrollThread = null;
     }
 
-    int res = findRes(evt);
+    int column = findColumn(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
     startWrapBlock = wrappedBlock;
@@ -1408,16 +1419,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if (sequence == null || res > sequence.getLength())
+    if (sequence == null || column > sequence.getLength())
     {
       return;
     }
 
     stretchGroup = av.getSelectionGroup();
 
-    if (stretchGroup == null || !stretchGroup.contains(sequence, res))
+    if (stretchGroup == null || !stretchGroup.contains(sequence, column))
     {
-      stretchGroup = av.getAlignment().findGroup(sequence, res);
+      stretchGroup = av.getAlignment().findGroup(sequence, column);
       if (stretchGroup != null)
       {
         // only update the current selection if the popup menu has a group to
@@ -1429,13 +1440,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     // DETECT RIGHT MOUSE BUTTON IN AWT
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
-              sequence.findPosition(res));
+      List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence,
+              sequence.findPosition(column + 1));
 
       Vector<String> links = null;
-      for (int i = 0; i < allFeatures.size(); i++)
+      for (SequenceFeature sf : allFeatures)
       {
-        SequenceFeature sf = allFeatures.get(i);
         if (sf.links != null)
         {
           if (links == null)
@@ -1453,7 +1463,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (av.cursorMode)
     {
-      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorX = findColumn(evt);
       seqCanvas.cursorY = findSeq(evt);
       seqCanvas.repaint();
       return;
@@ -1465,8 +1475,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       // define a new group here
       SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
+      sg.setStartRes(column);
+      sg.setEndRes(column);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
       stretchGroup = sg;
@@ -1524,7 +1534,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = findRes(evt);
+    int res = findColumn(evt);
     int y = findSeq(evt);
 
     if (wrappedBlock != startWrapBlock)
@@ -1862,8 +1872,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getAlignment()
-                    .getHiddenColumns().getHiddenRegions() == null))
+            && (av.getColumnSelection() == null))
     {
       System.err.println("Bad things");
     }