X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=fb6efe5f4d90102192b1ced6235744bdcc249c64;hb=71b0134718413dd9179768fa51e26170684c2f2c;hp=9a5f6c6808ca3be7332635ac1ed50b493faa52f4;hpb=6716ff86e500acc2800936b3f3c7132927a9246b;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 9a5f6c6..fb6efe5 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -59,7 +59,6 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
@@ -76,12 +75,11 @@ import javax.swing.ToolTipManager;
 public class SeqPanel extends JPanel
         implements MouseListener, MouseMotionListener, MouseWheelListener,
         SequenceListener, SelectionListener
-
 {
-  /** DOCUMENT ME!! */
+  private static final int MAX_TOOLTIP_LENGTH = 300;
+
   public SeqCanvas seqCanvas;
 
-  /** DOCUMENT ME!! */
   public AlignmentPanel ap;
 
   /*
@@ -148,35 +146,33 @@ public class SeqPanel extends JPanel
   SearchResultsI lastSearchResults;
 
   /**
-   * Creates a new SeqPanel object.
+   * Creates a new SeqPanel object
    * 
-   * @param avp
-   *          DOCUMENT ME!
-   * @param p
-   *          DOCUMENT ME!
+   * @param viewport
+   * @param alignPanel
    */
-  public SeqPanel(AlignViewport av, AlignmentPanel ap)
+  public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
     linkImageURL = getClass().getResource("/images/link.gif");
     seqARep = new SequenceAnnotationReport(linkImageURL.toString());
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
-    this.av = av;
+    this.av = viewport;
     setBackground(Color.white);
 
-    seqCanvas = new SeqCanvas(ap);
+    seqCanvas = new SeqCanvas(alignPanel);
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    this.ap = ap;
+    this.ap = alignPanel;
 
-    if (!av.isDataset())
+    if (!viewport.isDataset())
     {
       addMouseMotionListener(this);
       addMouseListener(this);
       addMouseWheelListener(this);
-      ssm = av.getStructureSelectionManager();
+      ssm = viewport.getStructureSelectionManager();
       ssm.addStructureViewerListener(this);
       ssm.addSelectionListener(this);
     }
@@ -363,8 +359,11 @@ public class SeqPanel extends JPanel
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
+      // TODO: once JAL-2759 is ready, change this loop to something more
+      // efficient
       while (!hidden.isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
+              && dx != 0)
       {
         seqCanvas.cursorX += dx;
       }
@@ -419,7 +418,10 @@ public class SeqPanel extends JPanel
     {
       if (av.getWrapAlignment())
       {
-        av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+        // scrollToWrappedVisible expects x-value to have hidden cols subtracted
+        int x = av.getAlignment().getHiddenColumns()
+                .findColumnPosition(seqCanvas.cursorX);
+        av.getRanges().scrollToWrappedVisible(x);
       }
       else
       {
@@ -427,8 +429,12 @@ public class SeqPanel extends JPanel
                 seqCanvas.cursorY);
       }
     }
-    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+
+    if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
+    {
+      setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
+    }
 
     if (repaintNeeded)
     {
@@ -828,7 +834,7 @@ public class SeqPanel extends JPanel
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
       seqARep.appendFeatures(tooltipText, pos, features,
-              this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
+              this.ap.getSeqPanel().seqCanvas.fr);
     }
     if (tooltipText.length() == 6) // <html>
     {
@@ -837,6 +843,11 @@ public class SeqPanel extends JPanel
     }
     else
     {
+      if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
+      {
+        tooltipText.setLength(MAX_TOOLTIP_LENGTH);
+        tooltipText.append("...");
+      }
       String textString = tooltipText.toString();
       if (lastTooltip == null || !lastTooltip.equals(textString))
       {
@@ -1815,21 +1826,10 @@ public class SeqPanel extends JPanel
     final int column = findColumn(evt);
     final int seq = findSeq(evt);
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+    List<SequenceFeature> features = ap.getFeatureRenderer()
             .findFeaturesAtColumn(sequence, column + 1);
-    List<String> links = new ArrayList<>();
-    for (SequenceFeature sf : allFeatures)
-    {
-      if (sf.links != null)
-      {
-        for (String link : sf.links)
-        {
-          links.add(link);
-        }
-      }
-    }
 
-    PopupMenu pop = new PopupMenu(ap, null, links);
+    PopupMenu pop = new PopupMenu(ap, null, features);
     pop.show(this, evt.getX(), evt.getY());
   }