X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=776e9ad6b90787c4d8334e0eff415f6d54f16c15;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=be4f9e63e30f27afc99f8be969a54c2838bc8f5d;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index be4f9e6..776e9ad 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -42,8 +42,8 @@ import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Font;
@@ -54,10 +54,8 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
-import java.util.ListIterator;
 import java.util.Vector;
 
 public class SeqPanel extends Panel implements MouseMotionListener,
@@ -150,13 +148,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   void setCursorRow()
   {
     seqCanvas.cursorY = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorColumn()
   {
     seqCanvas.cursorX = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorRowAndColumn()
@@ -169,7 +167,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       seqCanvas.cursorX = getKeyboardNo1() - 1;
       seqCanvas.cursorY = getKeyboardNo2() - 1;
-      scrollToVisible();
+      scrollToVisible(true);
     }
   }
 
@@ -178,7 +176,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void moveCursor(int dx, int dy)
@@ -204,10 +202,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         seqCanvas.cursorX = original;
       }
     }
-    scrollToVisible();
+    scrollToVisible(false);
   }
 
-  void scrollToVisible()
+  /**
+   * Scroll to make the cursor visible in the viewport.
+   * 
+   * @param jump
+   *          just jump to the location rather than scrolling
+   */
+  void scrollToVisible(boolean jump)
   {
     if (seqCanvas.cursorX < 0)
     {
@@ -228,44 +232,34 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     endEditing();
-    if (av.getWrapAlignment())
+
+    boolean repaintNeeded = true;
+    if (jump)
     {
-      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+      // only need to repaint if the viewport did not move, as otherwise it will
+      // get a repaint
+      repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
+              seqCanvas.cursorY);
     }
     else
     {
-      ViewportRanges ranges = av.getRanges();
-      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      while (seqCanvas.cursorY < ranges.getStartSeq())
-      {
-        ranges.scrollUp(true);
-      }
-      while (seqCanvas.cursorY > ranges.getEndSeq())
+      if (av.getWrapAlignment())
       {
-        ranges.scrollUp(false);
+        av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
       }
-      while (seqCanvas.cursorX < hidden
-              .adjustForHiddenColumns(ranges.getStartRes()))
-      {
-
-        if (!ranges.scrollRight(false))
-        {
-          break;
-        }
-      }
-      while (seqCanvas.cursorX > hidden
-              .adjustForHiddenColumns(ranges.getEndRes()))
+      else
       {
-        if (!ranges.scrollRight(true))
-        {
-          break;
-        }
+        av.getRanges().scrollToVisible(seqCanvas.cursorX,
+                seqCanvas.cursorY);
       }
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
 
-    seqCanvas.repaint();
+    if (repaintNeeded)
+    {
+      seqCanvas.repaint();
+    }
   }
 
   void setSelectionAreaAtCursor(boolean topLeft)
@@ -337,7 +331,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
     }
-    ap.paintAlignment(false);
+    ap.paintAlignment(false, false);
     av.sendSelection();
   }
 
@@ -419,7 +413,6 @@ public class SeqPanel extends Panel implements MouseMotionListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of column in sequence or -1 if at gap
    */
   void setStatusMessage(SequenceI sequence, int column, int seq)
   {
@@ -507,9 +500,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     // For now, ignore the mouseWheel font resizing on Macs
     // As the Button2_mask always seems to be true
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
-            && !av.MAC)
+    if (Platform.isWinMiddleButton(evt))
     {
       mouseWheelPressed = true;
       return;
@@ -530,7 +521,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < 0 || res < 0)
     {
@@ -566,14 +557,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         av.setSelectionGroup(null);
       }
 
-      int column = findRes(evt);
-      boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
-      List<SequenceFeature> features = findFeaturesAtRes(sequence,
-              sequence.findPosition(column));
-      if (isGapped)
-      {
-        removeAdjacentFeatures(features, column + 1, sequence);
-      }
+      int column = findColumn(evt);
+      List<SequenceFeature> features = findFeaturesAtColumn(sequence,
+              column + 1);
 
       if (!features.isEmpty())
       {
@@ -583,8 +569,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         seqCanvas.highlightSearchResults(highlight);
         seqCanvas.getFeatureRenderer().amendFeatures(
                 Collections.singletonList(sequence), features, false, ap);
-
-        seqCanvas.highlightSearchResults(null);
+        av.setSearchResults(null); // clear highlighting
+        seqCanvas.repaint(); // draw new/amended features
       }
     }
   }
@@ -610,7 +596,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   int wrappedBlock = -1;
 
-  int findRes(MouseEvent evt)
+  /**
+   * Returns the aligned sequence position (base 0) at the mouse position, or
+   * the closest visible one
+   * 
+   * @param evt
+   * @return
+   */
+  int findColumn(MouseEvent evt)
   {
     int res = 0;
     int x = evt.getX();
@@ -653,7 +646,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     return res;
@@ -714,7 +707,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
 
     int seq = findSeq(evt);
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (seq < av.getAlignment().getHeight()
             && res < av.getAlignment().getSequenceAt(seq).getLength())
@@ -750,7 +743,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   }
 
   @Override
-  public void highlightSequence(SearchResultsI results)
+  public String highlightSequence(SearchResultsI results)
   {
     if (av.isFollowHighlight())
     {
@@ -767,7 +760,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
-
+    return null;
   }
 
   @Override
@@ -786,7 +779,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    final int column = findRes(evt);
+    final int column = findColumn(evt);
     int seq = findSeq(evt);
 
     if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0)
@@ -869,12 +862,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
      */
     if (av.isShowSequenceFeatures())
     {
-      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
-              sequence.findPosition(column));
-      if (isGapped)
-      {
-        removeAdjacentFeatures(allFeatures, column + 1, sequence);
-      }
+      List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence,
+              column + 1);
       for (SequenceFeature sf : allFeatures)
       {
         tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
@@ -907,63 +896,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   }
 
   /**
-   * Removes from the list of features any that start after, or end before, the
-   * given column position. This allows us to retain only those features
-   * adjacent to a gapped position that straddle the position. Contact features
-   * that 'straddle' the position are also removed, since they are not 'at' the
-   * position.
+   * Returns features at the specified aligned column on the given sequence.
+   * Non-positional features are not included. If the column has a gap, then
+   * enclosing features are included (but not contact features).
    * 
-   * @param features
-   * @param column
-   *          alignment column (1..)
    * @param sequence
+   * @param column
+   *          (1..)
+   * @return
    */
-  protected void removeAdjacentFeatures(List<SequenceFeature> features,
-          int column, SequenceI sequence)
+  List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
   {
-    // TODO should this be an AlignViewController method (shared by gui)?
-    ListIterator<SequenceFeature> it = features.listIterator();
-    while (it.hasNext())
-    {
-      SequenceFeature sf = it.next();
-      if (sf.isContactFeature()
-              || sequence.findIndex(sf.getBegin()) > column
-              || sequence.findIndex(sf.getEnd()) < column)
-      {
-        it.remove();
-      }
-    }
-  }
-
-  List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
-  {
-    List<SequenceFeature> result = new ArrayList<>();
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    if (features != null)
-    {
-      for (int i = 0; i < features.length; i++)
-      {
-        if (av.getFeaturesDisplayed() == null || !av.getFeaturesDisplayed()
-                .isVisible(features[i].getType()))
-        {
-          continue;
-        }
-
-        if (features[i].featureGroup != null && !seqCanvas.fr
-                .checkGroupVisibility(features[i].featureGroup, false))
-        {
-          continue;
-        }
-
-        if ((features[i].getBegin() <= res)
-                && (features[i].getEnd() >= res))
-        {
-          result.add(features[i]);
-        }
-      }
-    }
-
-    return result;
+    return seqCanvas.getFeatureRenderer().findFeaturesAtColumn(sequence, column);
   }
 
   Tooltip tooltip;
@@ -1032,7 +976,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       lastMousePress = evt.getPoint();
 
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
       ap.annotationPanel.image = null;
       return;
     }
@@ -1043,7 +987,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    int res = findRes(evt);
+    int res = findColumn(evt);
 
     if (res < 0)
     {
@@ -1178,9 +1122,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       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))
@@ -1225,7 +1169,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         // Find the next gap before the end
         // of the visible region boundary
         boolean blank = false;
-        for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--)
+        for (; fixedRight > lastres; fixedRight--)
         {
           blank = true;
 
@@ -1252,7 +1196,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (sg.getSize() == av.getAlignment().getHeight())
           {
             if ((av.hasHiddenColumns() && startres < av.getAlignment()
-                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
+                    .getHiddenColumns()
+                    .getNextHiddenBoundary(false, startres)))
             {
               endEditing();
               return;
@@ -1451,11 +1396,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (scrollThread != null)
     {
-      scrollThread.running = false;
+      scrollThread.threadRunning = false;
       scrollThread = null;
     }
 
-    int res = findRes(evt);
+    int column = findColumn(evt);
     int seq = findSeq(evt);
     oldSeq = seq;
     startWrapBlock = wrappedBlock;
@@ -1467,16 +1412,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    if (sequence == null || res > sequence.getLength())
+    if (sequence == null || column > sequence.getLength())
     {
       return;
     }
 
     stretchGroup = av.getSelectionGroup();
 
-    if (stretchGroup == null || !stretchGroup.contains(sequence, res))
+    if (stretchGroup == null || !stretchGroup.contains(sequence, column))
     {
-      stretchGroup = av.getAlignment().findGroup(sequence, res);
+      stretchGroup = av.getAlignment().findGroup(sequence, column);
       if (stretchGroup != null)
       {
         // only update the current selection if the popup menu has a group to
@@ -1486,11 +1431,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
-      List<SequenceFeature> allFeatures = findFeaturesAtRes(sequence,
-              sequence.findPosition(res));
+      List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence,
+              sequence.findPosition(column + 1));
 
       Vector<String> links = null;
       for (SequenceFeature sf : allFeatures)
@@ -1501,10 +1446,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           {
             links = new Vector<>();
           }
-          for (int j = 0; j < sf.links.size(); j++)
-          {
-            links.addElement(sf.links.elementAt(j));
-          }
+          links.addAll(sf.links);
         }
       }
       APopupMenu popup = new APopupMenu(ap, null, links);
@@ -1515,7 +1457,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (av.cursorMode)
     {
-      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorX = findColumn(evt);
       seqCanvas.cursorY = findSeq(evt);
       seqCanvas.repaint();
       return;
@@ -1527,8 +1469,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       // define a new group here
       SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
+      sg.setStartRes(column);
+      sg.setEndRes(column);
       sg.addSequence(sequence, false);
       av.setSelectionGroup(sg);
       stretchGroup = sg;
@@ -1576,7 +1518,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
     PaintRefresher.Refresh(ap, av.getSequenceSetId());
-    ap.paintAlignment(needOverviewUpdate);
+    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
     needOverviewUpdate = false;
     changeEndRes = false;
     changeStartRes = false;
@@ -1586,7 +1528,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   public void doMouseDraggedDefineMode(MouseEvent evt)
   {
-    int res = findRes(evt);
+    int res = findColumn(evt);
     int y = findSeq(evt);
 
     if (wrappedBlock != startWrapBlock)
@@ -1701,7 +1643,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       mouseExited(evt);
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
       scrollThread.setEvent(evt);
     }
@@ -1717,9 +1659,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = 0;
     }
 
-    if (scrollThread != null)
+    if ((scrollThread != null) && (scrollThread.isRunning()))
     {
-      scrollThread.running = false;
+      scrollThread.stopScrolling();
       scrollThread = null;
     }
   }
@@ -1742,9 +1684,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     if (evt == null)
     {
-      if (scrollThread != null)
+      if ((scrollThread != null) && (scrollThread.isRunning()))
       {
-        scrollThread.running = false;
+        scrollThread.stopScrolling();
         scrollThread = null;
       }
       mouseDragging = false;
@@ -1767,7 +1709,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     MouseEvent evt;
 
-    boolean running = false;
+    private volatile boolean threadRunning = true;
 
     public ScrollThread()
     {
@@ -1781,14 +1723,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     public void stopScrolling()
     {
-      running = false;
+      threadRunning = false;
+    }
+
+    public boolean isRunning()
+    {
+      return threadRunning;
     }
 
     @Override
     public void run()
     {
-      running = true;
-      while (running)
+      while (threadRunning)
       {
 
         if (evt != null)
@@ -1797,23 +1743,23 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (mouseDragging && evt.getY() < 0
                   && av.getRanges().getStartSeq() > 0)
           {
-            running = av.getRanges().scrollUp(true);
+            av.getRanges().scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height && av
                   .getAlignment().getHeight() > av.getRanges().getEndSeq())
           {
-            running = av.getRanges().scrollUp(false);
+            av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && evt.getX() < 0)
           {
-            running = av.getRanges().scrollRight(false);
+            av.getRanges().scrollRight(false);
           }
 
           else if (mouseDragging && evt.getX() >= getSize().width)
           {
-            running = av.getRanges().scrollRight(true);
+            av.getRanges().scrollRight(true);
           }
         }