X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=55f06fce3e56ad2b7c606c8dd797eaad68262c7b;hb=a9b20fb4f95f8a4435b09d513959443c266c719c;hp=809fc026ccb5df09f29307d5a10b8e290f1d8a6e;hpb=006890b02106eb31841e6e84d75f1027434823e0;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 809fc02..55f06fc 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,8 +20,31 @@
  */
 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.bin.Console;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -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;
 
@@ -234,13 +242,11 @@ 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);
-    
-    
+
     this.av = viewport;
     setBackground(Color.white);
 
@@ -268,6 +274,9 @@ 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
@@ -332,9 +341,13 @@ public class SeqPanel extends JPanel
 
     return new MousePos(col, seqIndex, annIndex);
   }
+
   /**
    * 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
@@ -470,45 +483,85 @@ public class SeqPanel extends JPanel
 
   void moveCursor(int dx, int dy)
   {
-    seqCanvas.cursorX += dx;
-    seqCanvas.cursorY += dy;
+    moveCursor(dx, dy, false);
+  }
 
+  void moveCursor(int dx, int dy, boolean nextWord)
+  {
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
-    if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+    if (nextWord)
     {
-      int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
-
-      if (!hidden.isVisible(seqCanvas.cursorX))
-      {
-        int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
-        int[] region = hidden.getRegionWithEdgeAtRes(visx);
-
-        if (region != null) // just in case
+      int maxHeight = av.getAlignment().getHeight();
+      SequenceI seqAtRow = av.getAlignment()
+              .getSequenceAt(seqCanvas.cursorY);
+      // look for next gap or residue
+      boolean isGap = Comparison
+              .isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+      int p = seqCanvas.cursorX, lastP, r = seqCanvas.cursorY, lastR;
+      do
+      {
+        lastP = p;
+        lastR = r;
+        if (dy != 0)
         {
-          if (dx == 1)
+          r += dy;
+          if (r < 0)
           {
-            // moving right
-            seqCanvas.cursorX = region[1] + 1;
+            r = 0;
           }
-          else if (dx == -1)
+          if (r >= maxHeight)
           {
-            // moving left
-            seqCanvas.cursorX = region[0] - 1;
+            r = maxHeight - 1;
           }
+          seqAtRow = av.getAlignment().getSequenceAt(r);
         }
-        seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
-      }
+        p = nextVisible(hidden, maxWidth, p, dx);
+      } while ((dx != 0 ? p != lastP : r != lastR)
+              && isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
+      seqCanvas.cursorX = p;
+      seqCanvas.cursorY = r;
+    }
+    else
+    {
+      int maxWidth = av.getAlignment().getWidth();
+      seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX,
+              dx);
+      seqCanvas.cursorY += dy;
+    }
+    scrollToVisible(false);
+  }
+
+  private int nextVisible(HiddenColumns hidden, int maxWidth, int original,
+          int dx)
+  {
+    int newCursorX = original + dx;
+    if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
+    {
+      int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
+      int[] region = hidden.getRegionWithEdgeAtRes(visx);
 
-      if (seqCanvas.cursorX >= maxWidth
-              || !hidden.isVisible(seqCanvas.cursorX))
+      if (region != null) // just in case
       {
-        seqCanvas.cursorX = original;
+        if (dx == 1)
+        {
+          // moving right
+          newCursorX = region[1] + 1;
+        }
+        else if (dx == -1)
+        {
+          // moving left
+          newCursorX = region[0] - 1;
+        }
       }
     }
-
-    scrollToVisible(false);
+    newCursorX = (newCursorX < 0) ? 0 : newCursorX;
+    if (newCursorX >= maxWidth || !hidden.isVisible(newCursorX))
+    {
+      newCursorX = original;
+    }
+    return newCursorX;
   }
 
   /**
@@ -566,7 +619,7 @@ public class SeqPanel extends JPanel
     if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
     {
       setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
-            seqCanvas.cursorX, seqCanvas.cursorY);
+              seqCanvas.cursorX, seqCanvas.cursorY);
     }
 
     if (repaintNeeded)
@@ -575,7 +628,6 @@ public class SeqPanel extends JPanel
     }
   }
 
-
   void setSelectionAreaAtCursor(boolean topLeft)
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
@@ -822,8 +874,6 @@ public class SeqPanel extends JPanel
 
   String lastMessage;
 
-  private String formattedTooltipText;
-
   @Override
   public void mouseOverSequence(SequenceI sequence, int index, int pos)
   {
@@ -904,19 +954,19 @@ 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())
       {
         SequenceI seq = match.getSequence();
         SequenceI ds = seq.getDatasetSequence() == null ? seq
                 : seq.getDatasetSequence();
-        MappedFeatures mf = fr2
-                .findComplementFeaturesAtResidue(ds, pos);
+        MappedFeatures mf = fr2.findComplementFeaturesAtResidue(ds, pos);
         if (mf != null)
         {
           for (SequenceFeature sf : mf.features)
@@ -984,8 +1034,10 @@ 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 +1053,7 @@ public class SeqPanel extends JPanel
       lastMousePosition = null;
       setToolTipText(null);
       lastTooltip = null;
+      lastFormattedTooltip = null;
       ap.alignFrame.setStatus("");
       return;
     }
@@ -1022,7 +1075,7 @@ 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)
@@ -1056,8 +1109,7 @@ public class SeqPanel extends JPanel
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
-              features,
+      unshownFeatures = seqARep.appendFeatures(tooltipText, pos, features,
               this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
 
       /*
@@ -1076,14 +1128,13 @@ 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 +1154,11 @@ 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);
       }
     }
   }
@@ -1125,6 +1175,7 @@ public class SeqPanel extends JPanel
     final int column = pos.column;
     final int rowIndex = pos.annotationIndex;
 
+    // TODO - get yOffset for annotation, too
     if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation()
             || rowIndex < 0)
     {
@@ -1133,17 +1184,36 @@ public class SeqPanel extends JPanel
     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 
     String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
-            anns);
-    setToolTipText(tooltip);
-    lastTooltip = tooltip;
+            anns, 0, av, ap);
+    if (tooltip == null ? tooltip != lastTooltip
+            : !tooltip.equals(lastTooltip))
+    {
+      lastTooltip = tooltip;
+      lastFormattedTooltip = tooltip == null ? null
+              : JvSwingUtils.wrapTooltip(true, tooltip);
+      setToolTipText(lastFormattedTooltip);
+    }
 
     String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
-            anns[rowIndex]);
+            anns[rowIndex], 0, av);
     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 +1226,30 @@ 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;
+
+    // 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
@@ -1190,7 +1257,8 @@ public class SeqPanel extends JPanel
    * changed, so selective redraws can be applied (ie. only structures, only
    * overview, etc)
    */
-  private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
+  private boolean updateOverviewAndStructs = false; // TODO: refactor to
+                                                    // avcontroller
 
   /**
    * set if av.getSelectionGroup() refers to a group that is defined on the
@@ -1219,7 +1287,7 @@ 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 +1303,7 @@ 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 +1311,7 @@ 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);
@@ -1252,8 +1320,7 @@ public class SeqPanel extends JPanel
      * Sequence number (if known), and sequence name.
      */
     String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
-    text.append("Sequence").append(seqno).append(" ID: ")
-            .append(sequence.getName());
+    text.append("Sequence").append(seqno).append(" ID: ").append(seqName);
 
     String residue = null;
 
@@ -1298,7 +1365,8 @@ 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 +1378,8 @@ 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;
       }
     }
@@ -1511,12 +1579,12 @@ public class SeqPanel extends JPanel
     String label = null;
     if (groupEditing)
     {
-        message.append("Edit group:");
+      message.append("Edit group:");
       label = MessageManager.getString("action.edit_group");
     }
     else
     {
-        message.append("Edit sequence: " + seq.getName());
+      message.append("Edit sequence: " + seq.getName());
       label = seq.getName();
       if (label.length() > 10)
       {
@@ -1708,8 +1776,7 @@ public class SeqPanel extends JPanel
           {
             for (int j = 0; j < startres - editLastRes; j++)
             {
-              if (!Comparison
-                      .isGap(groupSeqs[g].getCharAt(fixedRight - j)))
+              if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
               {
                 blank = false;
                 break;
@@ -2076,7 +2143,7 @@ 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
@@ -2101,8 +2168,8 @@ public class SeqPanel extends JPanel
          * highlight the first feature at the position on the alignment
          */
         SearchResultsI highlight = new SearchResults();
-        highlight.addResult(sequence, features.get(0).getBegin(), features
-                .get(0).getEnd());
+        highlight.addResult(sequence, features.get(0).getBegin(),
+                features.get(0).getEnd());
         seqCanvas.highlightSearchResults(highlight, true);
 
         /*
@@ -2366,7 +2433,7 @@ public class SeqPanel extends JPanel
       return;
     }
 
-    res = Math.min(res, av.getAlignment().getWidth()-1);
+    res = Math.min(res, av.getAlignment().getWidth() - 1);
 
     if (stretchGroup.getEndRes() == res)
     {
@@ -2739,7 +2806,7 @@ public class SeqPanel extends JPanel
     {
       if (av.getAlignment() == null)
       {
-        Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+        Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
                 + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;
@@ -2864,6 +2931,8 @@ public class SeqPanel extends JPanel
      * if hidden column selection has changed
      */
     ap.paintAlignment(hiddenChanged, hiddenChanged);
+    // propagate any selection changes
+    PaintRefresher.Refresh(ap, av.getSequenceSetId());
 
     return true;
   }