X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=163ae25fd3a45a152283f246e93560bfa0eac21d;hb=bc7283e7d80b1f7f5fb7d95c51b96bb3af31593d;hp=809fc026ccb5df09f29307d5a10b8e290f1d8a6e;hpb=006890b02106eb31841e6e84d75f1027434823e0;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 809fc02..163ae25 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,6 +20,29 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+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.Timer;
+import javax.swing.ToolTipManager;
+
 import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.commands.EditCommand;
@@ -53,29 +76,6 @@ import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-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.Timer;
-import javax.swing.ToolTipManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -212,13 +212,21 @@ public class SeqPanel extends JPanel
 
   StringBuffer keyboardNo2;
 
-  java.net.URL linkImageURL;
-
   private final SequenceAnnotationReport seqARep;
 
-  StringBuilder tooltipText = new StringBuilder();
+  /*
+   * the last tooltip on mousing over the alignment (or annotation in wrapped mode)
+   * - the tooltip is not set again if unchanged
+   * - this is the tooltip text _before_ formatting as html
+   */
+  private String lastTooltip;
 
-  String tmpString;
+  /*
+   * the last tooltip on mousing over the alignment (or annotation in wrapped mode)
+   * - used to decide where to place the tooltip in getTooltipLocation() 
+   * - this is the tooltip text _after_ formatting as html
+   */
+  private String lastFormattedTooltip;
 
   EditCommand editCommand;
 
@@ -234,8 +242,7 @@ public class SeqPanel extends JPanel
    */
   public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
   {
-    linkImageURL = getClass().getResource("/images/link.gif");
-    seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+    seqARep = new SequenceAnnotationReport(true);
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -268,6 +275,9 @@ public class SeqPanel extends JPanel
   /**
    * Computes the column and sequence row (and possibly annotation row when in
    * wrapped mode) for the given mouse position
+   * <p>
+   * Mouse position is not set if in wrapped mode with the cursor either between
+   * sequences, or over the left or right vertical scale.
    * 
    * @param evt
    * @return
@@ -335,6 +345,9 @@ public class SeqPanel extends JPanel
   /**
    * Returns the aligned sequence position (base 0) at the mouse position, or
    * the closest visible one
+   * <p>
+   * Returns -1 if in wrapped mode with the mouse over either left or right
+   * vertical scale.
    * 
    * @param evt
    * @return
@@ -822,8 +835,6 @@ public class SeqPanel extends JPanel
 
   String lastMessage;
 
-  private String formattedTooltipText;
-
   @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
@@ -904,11 +915,12 @@ public class SeqPanel extends JPanel
     AlignFrame af = Desktop.getAlignFrameFor(complement);
     FeatureRendererModel fr2 = af.getFeatureRenderer();
 
-    int j = results.getSize();
+    List<SearchResultMatchI> matches = results.getResults();
+    int j = matches.size();
     List<String> infos = new ArrayList<>();
     for (int i = 0; i < j; i++)
     {
-      SearchResultMatchI match = results.getResults().get(i);
+      SearchResultMatchI match = matches.get(i);
       int pos = match.getStart();
       if (pos == match.getEnd())
       {
@@ -984,8 +996,10 @@ public class SeqPanel extends JPanel
       /*
        * just a pixel move without change of 'cell'
        */
+      moveTooltip = false;
       return;
     }
+    moveTooltip = true;
     lastMousePosition = mousePos;
 
     if (mousePos.isOverAnnotation())
@@ -1001,6 +1015,7 @@ public class SeqPanel extends JPanel
       lastMousePosition = null;
       setToolTipText(null);
       lastTooltip = null;
+      lastFormattedTooltip = null;
       ap.alignFrame.setStatus("");
       return;
     }
@@ -1022,7 +1037,7 @@ public class SeqPanel extends JPanel
       mouseOverSequence(sequence, column, pos);
     }
 
-    tooltipText.setLength(6); // "<html>"
+    StringBuilder tooltipText = new StringBuilder(64);
 
     SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
     if (groups != null)
@@ -1056,9 +1071,9 @@ public class SeqPanel extends JPanel
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
-              features,
-              this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+              features, this.ap.getSeqPanel().seqCanvas.fr,
+              MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1076,14 +1091,13 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            unshownFeatures = seqARep.appendFeaturesLengthLimit(
-                    tooltipText, pos, mf, fr2,
-                    MAX_TOOLTIP_LENGTH);
+            unshownFeatures += seqARep.appendFeatures(tooltipText,
+                    pos, mf, fr2, MAX_TOOLTIP_LENGTH);
           }
         }
       }
     }
-    if (tooltipText.length() == 6) // "<html>"
+    if (tooltipText.length() == 0) // nothing added
     {
       setToolTipText(null);
       lastTooltip = null;
@@ -1103,12 +1117,12 @@ public class SeqPanel extends JPanel
                 .append("</i>");
       }
       String textString = tooltipText.toString();
-      if (lastTooltip == null || !lastTooltip.equals(textString))
+      if (!textString.equals(lastTooltip))
       {
-        formattedTooltipText = JvSwingUtils.wrapTooltip(true,
-                textString);
-        setToolTipText(formattedTooltipText);        
         lastTooltip = textString;
+        lastFormattedTooltip = JvSwingUtils.wrapTooltip(true,
+                textString);
+        setToolTipText(lastFormattedTooltip);
       }
     }
   }
@@ -1134,16 +1148,34 @@ public class SeqPanel extends JPanel
 
     String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
             anns);
-    setToolTipText(tooltip);
-    lastTooltip = tooltip;
+    if (!tooltip.equals(lastTooltip))
+    {
+      lastTooltip = tooltip;
+      lastFormattedTooltip = tooltip == null ? null
+              : JvSwingUtils.wrapTooltip(true, tooltip);
+      setToolTipText(lastFormattedTooltip);
+    }
 
     String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
             anns[rowIndex]);
     ap.alignFrame.setStatus(msg);
   }
 
-  private Point lastp = null;
+  /*
+   * if Shift key is held down while moving the mouse, 
+   * the tooltip location is not changed once shown
+   */
+  private Point lastTooltipLocation = null;
+
+  /*
+   * this flag is false for pixel moves within a residue,
+   * to reduce tooltip flicker
+   */
+  private boolean moveTooltip = true;
 
+  /*
+   * a dummy tooltip used to estimate where to position tooltips
+   */
   private JToolTip tempTip = new JLabel().createToolTip();
 
   /*
@@ -1156,33 +1188,30 @@ public class SeqPanel extends JPanel
   {
     // BH 2018
 
-    if (tooltipText == null || tooltipText.length() <= 6)
+    if (lastTooltip == null || !moveTooltip)
     {
       return null;
     }
 
-    if (lastp != null && event.isShiftDown())
+    if (lastTooltipLocation != null && event.isShiftDown())
     {
-      return lastp;
+      return lastTooltipLocation;
     }
 
-    Point p = lastp;
     int x = event.getX();
     int y = event.getY();
     int w = getWidth();
 
-    tempTip.setTipText(formattedTooltipText);
+    tempTip.setTipText(lastFormattedTooltip);
     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?
+    Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20?
 
-    return lastp = p;
+    return lastTooltipLocation = p;
   }
 
-  String lastTooltip;
-
   /**
    * set when the current UI interaction has resulted in a change that requires
    * shading in overviews and structures to be recalculated. this could be
@@ -1219,7 +1248,7 @@ public class SeqPanel extends JPanel
   {
     char sequenceChar = sequence.getCharAt(column);
     int pos = sequence.findPosition(column);
-    setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+    setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
 
     return pos;
   }
@@ -1235,7 +1264,7 @@ public class SeqPanel extends JPanel
    * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
    * </pre>
    * 
-   * @param sequence
+   * @param seqName
    * @param seqIndex
    *          sequence position in the alignment (1..)
    * @param sequenceChar
@@ -1243,7 +1272,7 @@ public class SeqPanel extends JPanel
    * @param residuePos
    *          the sequence residue position (if not over a gap)
    */
-  protected void setStatusMessage(SequenceI sequence, int seqIndex,
+  protected void setStatusMessage(String seqName, int seqIndex,
           char sequenceChar, int residuePos)
   {
     StringBuilder text = new StringBuilder(32);
@@ -1253,7 +1282,7 @@ public class SeqPanel extends JPanel
      */
     String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
     text.append("Sequence").append(seqno).append(" ID: ")
-            .append(sequence.getName());
+            .append(seqName);
 
     String residue = null;
 
@@ -1298,7 +1327,8 @@ public class SeqPanel extends JPanel
     {
       return;
     }
-    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+    SequenceI ds = alignedSeq.getDatasetSequence();
     for (SearchResultMatchI m : results.getResults())
     {
       SequenceI seq = m.getSequence();
@@ -1310,8 +1340,8 @@ public class SeqPanel extends JPanel
       if (seq == ds)
       {
         int start = m.getStart();
-        setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
-                start);
+        setStatusMessage(alignedSeq.getName(), sequenceIndex,
+                seq.getCharAt(start - 1), start);
         return;
       }
     }
@@ -2076,7 +2106,7 @@ public class SeqPanel extends JPanel
       return;
     }
 
-    if (evt.getClickCount() > 1)
+    if (evt.getClickCount() > 1 && av.isShowSequenceFeatures())
     {
       sg = av.getSelectionGroup();
       if (sg != null && sg.getSize() == 1