Merge branch 'bug/JAL-2034contextchange' into develop

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 7dfac5e..0878cbb 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -389,38 +389,12 @@ public class SeqPanel extends JPanel implements MouseListener,
     endEditing();
     if (av.getWrapAlignment())
     {
-      ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
     }
     else
     {
-      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
-      {
-        ap.scrollUp(true);
-      }
-      while (seqCanvas.cursorY > av.getRanges().getEndSeq())
-      {
-        ap.scrollUp(false);
-      }
-      if (!av.getWrapAlignment())
-      {
-        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        while (seqCanvas.cursorX < hidden.adjustForHiddenColumns(av
-                .getRanges().getStartRes()))
-        {
-          if (!ap.scrollRight(false))
-          {
-            break;
-          }
-        }
-        while (seqCanvas.cursorX > hidden.adjustForHiddenColumns(av
-                .getRanges().getEndRes()))
-        {
-          if (!ap.scrollRight(true))
-          {
-            break;
-          }
-        }
-      }
+      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
+              av);
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
@@ -590,6 +564,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    boolean didDrag = mouseDragging; // did we come here after a drag
     mouseDragging = false;
     mouseWheelPressed = false;
 
@@ -602,7 +577,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (!editingSeqs)
     {
-      doMouseReleasedDefineMode(evt);
+      doMouseReleasedDefineMode(evt, didDrag);
       return;
     }
 
@@ -696,17 +671,16 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.isFollowHighlight())
     {
-      /*
-       * if scrollToPosition requires a scroll adjustment, this flag prevents
-       * another scroll event being propagated back to the originator
-       * 
-       * @see AlignmentPanel#adjustmentValueChanged
-       */
-      ap.setDontScrollComplement(true);
+      // don't allow highlight of protein/cDNA to also scroll a complementary
+      // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+      // over residue to change abruptly, causing highlighted residue in panel 2
+      // to change, causing a scroll in panel 1 etc)
+      ap.setToScrollComplementPanel(false);
       if (ap.scrollToPosition(results, false))
       {
         seqCanvas.revalidate();
       }
+      ap.setToScrollComplementPanel(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);
@@ -788,7 +762,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    if (av.isShowSequenceFeatures())
+    if (av.isShowSequenceFeatures() && pos != -1)
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
@@ -861,7 +835,8 @@ public class SeqPanel extends JPanel implements MouseListener,
   /**
    * Sets the status message in alignment panel, showing the sequence number
    * (index) and id, residue and residue position for the given sequence and
-   * column position. Returns the calculated residue position in the sequence.
+   * column position. Returns the calculated residue position in the sequence,
+   * or -1 for a gapped column position.
    * 
    * @param sequence
    *          aligned sequence object
@@ -869,7 +844,7 @@ public class SeqPanel extends JPanel implements MouseListener,
    *          alignment column
    * @param seq
    *          index of sequence in alignment
-   * @return position of res in sequence
+   * @return position of column in sequence or -1 if at a gap
    */
   int setStatusMessage(SequenceI sequence, final int column, int seq)
   {
@@ -907,9 +882,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     int pos = -1;
-    pos = sequence.findPosition(column);
     if (residue != null)
     {
+      pos = sequence.findPosition(column);
       text.append(" (").append(Integer.toString(pos)).append(")");
     }
     ap.alignFrame.statusBar.setText(text.toString());
@@ -1586,23 +1561,23 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (e.isShiftDown())
       {
-        ap.scrollRight(true);
+        av.getRanges().scrollRight(true);
 
       }
       else
       {
-        ap.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
     else
     {
       if (e.isShiftDown())
       {
-        ap.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
       else
       {
-        ap.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
     // TODO Update tooltip for new position.
@@ -1737,7 +1712,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
             .findFeaturesAtRes(sequence.getDatasetSequence(),
                     sequence.findPosition(res));
-    List<String> links = new ArrayList<String>();
+    List<String> links = new ArrayList<>();
     for (SequenceFeature sf : allFeatures)
     {
       if (sf.links != null)
@@ -1754,12 +1729,15 @@ public class SeqPanel extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Update the display after mouse up on a selection or group
    * 
    * @param evt
-   *          DOCUMENT ME!
+   *          mouse released event details
+   * @param afterDrag
+   *          true if this event is happening after a mouse drag (rather than a
+   *          mouse down)
    */
-  public void doMouseReleasedDefineMode(MouseEvent evt)
+  public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
   {
     if (stretchGroup == null)
     {
@@ -1768,7 +1746,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
     boolean vischange = stretchGroup.recalcConservation(true);
-    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup();
+    needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
+            && afterDrag;
     if (stretchGroup.cs != null)
     {
       stretchGroup.cs.alignmentChanged(stretchGroup,
@@ -1970,23 +1949,23 @@ public class SeqPanel extends JPanel implements MouseListener,
           if (mouseDragging && (evt.getY() < 0)
                   && (av.getRanges().getStartSeq() > 0))
           {
-            running = ap.scrollUp(true);
+            running = av.getRanges().scrollUp(true);
           }
 
           if (mouseDragging && (evt.getY() >= getHeight())
                   && (av.getAlignment().getHeight() > av.getRanges()
                           .getEndSeq()))
           {
-            running = ap.scrollUp(false);
+            running = av.getRanges().scrollUp(false);
           }
 
           if (mouseDragging && (evt.getX() < 0))
           {
-            running = ap.scrollRight(false);
+            running = av.getRanges().scrollRight(false);
           }
           else if (mouseDragging && (evt.getX() >= getWidth()))
           {
-            running = ap.scrollRight(true);
+            running = av.getRanges().scrollRight(true);
           }
         }
 
@@ -2022,11 +2001,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         ap.getCalculationDialog().validateCalcTypes();
       }
 
-      // process further ?
-      if (!av.followSelection)
-      {
-        return;
-      }
+      return;
+    }
+
+    // process further ?
+    if (!av.followSelection)
+    {
+      return;
     }
 
     /*