X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=875743b4bbada221eedff69e9741b703ef900af4;hb=f13c8f13408308b89e271ee9f4f11bd0493c1973;hp=9359569c86fb15aa85a80b6e4b1c5acef959fd00;hpb=0e5e2bec7c3518eab6df87070b23164b135af828;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 9359569..875743b 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -59,11 +59,12 @@ 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;
 
+import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JToolTip;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
@@ -76,12 +77,11 @@ 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 +148,35 @@ 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);
     }
@@ -434,7 +434,10 @@ 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
       {
@@ -695,6 +698,8 @@ public class SeqPanel extends JPanel
 
   String lastMessage;
 
+  private String formattedTooltipText;
+
   @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
@@ -740,8 +745,8 @@ public class SeqPanel extends JPanel
       ap.setToScrollComplementPanel(true);
     }
 
-    boolean noFastPaint = wasScrolled && av.getWrapAlignment();
-    if (seqCanvas.highlightSearchResults(results, noFastPaint))
+    boolean fastPaint = !(wasScrolled && av.getWrapAlignment());
+    if (seqCanvas.highlightSearchResults(results, fastPaint))
     {
       setStatusMessage(results);
     }
@@ -847,7 +852,7 @@ 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>
     {
@@ -856,19 +861,28 @@ 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))
       {
-        String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+        formattedTooltipText = JvSwingUtils.wrapTooltip(true,
                 textString);
         setToolTipText(formattedTooltipText);
+        
         lastTooltip = textString;
       }
     }
   }
 
+  
   private Point lastp = null;
 
+  private JToolTip tempTip = new JLabel().createToolTip();
+
   /*
    * (non-Javadoc)
    * 
@@ -877,19 +891,31 @@ public class SeqPanel extends JPanel
   @Override
   public Point getToolTipLocation(MouseEvent event)
   {
-    int x = event.getX(), w = getWidth();
-    int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
-    // close to edge
+    // BH 2018
+
+    if (tooltipText == null || tooltipText.length() == 6)
+      return null;
+
+    if (lastp != null && event.isShiftDown())
+      return lastp;
+
     Point p = lastp;
-    if (!event.isShiftDown() || p == null)
-    {
-      p = (tooltipText != null && tooltipText.length() > 6)
-              ? new Point(event.getX() + wdth, event.getY() - 20)
-              : null;
-    }
+    int x = event.getX();
+    int y = event.getY();
+    int w = getWidth();
+
+    tempTip.setTipText(formattedTooltipText);
+    int tipWidth = (int) tempTip.getPreferredSize().getWidth();
+    
+    // was      x += (w - x < 200) ? -(w / 2) : 5;
+    x = (x + tipWidth < w ? x + 10 : w - tipWidth);
+    p = new Point(x, y + 20); // BH 2018 was - 20?
     /*
      * TODO: try to modify position region is not obcured by tooltip
+     * 
+     * Done? 
      */
+
     return lastp = p;
   }
 
@@ -1647,17 +1673,13 @@ public class SeqPanel extends JPanel
         SearchResultsI highlight = new SearchResults();
         highlight.addResult(sequence, features.get(0).getBegin(), features
                 .get(0).getEnd());
-        seqCanvas.highlightSearchResults(highlight, false);
+        seqCanvas.highlightSearchResults(highlight, true);
 
         /*
-         * open the Amend Features dialog; clear highlighting afterwards,
-         * whether changes were made or not
+         * open the Amend Features dialog
          */
-        List<SequenceI> seqs = Collections.singletonList(sequence);
-        seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
-                ap);
-        av.setSearchResults(null); // clear highlighting
-        seqCanvas.repaint(); // draw new/amended features
+        new FeatureEditor(ap, Collections.singletonList(sequence), features,
+                false).showDialog();
       }
     }
   }
@@ -1666,7 +1688,8 @@ 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())
       {
@@ -1678,7 +1701,7 @@ public class SeqPanel extends JPanel
         av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
@@ -1835,21 +1858,10 @@ 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());
   }
 
@@ -2298,4 +2310,13 @@ public class SeqPanel extends JPanel
 
     return true;
   }
+
+  /**
+   * 
+   * @return null or last search results handled by this panel
+   */
+  public SearchResultsI getLastSearchResults()
+  {
+    return lastSearchResults;
+  }
 }