Merge branch 'develop' into features/mchmmer

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e11af48..ce6bcbd 100644 (file)
--- 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);
     }
@@ -250,7 +246,7 @@ public class SeqPanel extends JPanel
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     return res;
@@ -363,10 +359,25 @@ public class SeqPanel extends JPanel
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      while (!hidden.isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+      if (!hidden.isVisible(seqCanvas.cursorX))
       {
-        seqCanvas.cursorX += dx;
+        int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
+        int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+        if (region != null) // just in case
+        {
+          if (dx == 1)
+          {
+            // moving right
+            seqCanvas.cursorX = region[1] + 1;
+          }
+          else if (dx == -1)
+          {
+            // moving left
+            seqCanvas.cursorX = region[0] - 1;
+          }
+        }
+        seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
       }
 
       if (seqCanvas.cursorX >= maxWidth
@@ -419,7 +430,10 @@ 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()
+                .absoluteToVisibleColumn(seqCanvas.cursorX);
+        av.getRanges().scrollToWrappedVisible(x);
       }
       else
       {
@@ -832,7 +846,7 @@ 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>
     {
@@ -841,6 +855,11 @@ 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))
       {
@@ -1253,9 +1272,9 @@ public class SeqPanel extends JPanel
     {
       fixedColumns = true;
       int y1 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryLeft(startres);
+              .getNextHiddenBoundary(true, startres);
       int y2 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryRight(startres);
+              .getNextHiddenBoundary(false, startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1331,7 +1350,8 @@ public class SeqPanel extends JPanel
           if (sg.getSize() == av.getAlignment().getHeight())
           {
             if ((av.hasHiddenColumns() && startres < av.getAlignment()
-                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
+                    .getHiddenColumns()
+                    .getNextHiddenBoundary(false, startres)))
             {
               endEditing();
               return;
@@ -1650,7 +1670,8 @@ public class SeqPanel extends JPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    if (e.getWheelRotation() > 0)
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
     {
       if (e.isShiftDown())
       {
@@ -1662,7 +1683,7 @@ public class SeqPanel extends JPanel
         av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
@@ -1819,21 +1840,10 @@ 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());
   }
 
@@ -1857,7 +1867,7 @@ public class SeqPanel extends JPanel
 
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
-    boolean vischange = stretchGroup.recalcConservation(true);
+    boolean vischange = stretchGroup.recalcAnnotations(true);
     updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
             && afterDrag;
     if (stretchGroup.cs != null)
@@ -2282,4 +2292,13 @@ public class SeqPanel extends JPanel
 
     return true;
   }
+
+  /**
+   * 
+   * @return null or last search results handled by this panel
+   */
+  public SearchResultsI getLastSearchResults()
+  {
+    return lastSearchResults;
+  }
 }