JAL-2811 release note

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 531eca6..e11af48 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -215,8 +215,8 @@ public class SeqPanel extends JPanel
               + hgap + seqCanvas.getAnnotationHeight();
 
       int y = evt.getY();
-      y -= hgap;
-      x = Math.max(0, x - seqCanvas.labelWidthWest);
+      y = Math.max(0, y - hgap);
+      x = Math.max(0, x - seqCanvas.getLabelWidthWest());
 
       int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
       if (cwidth < 1)
@@ -320,13 +320,13 @@ public class SeqPanel extends JPanel
   void setCursorRow()
   {
     seqCanvas.cursorY = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorColumn()
   {
     seqCanvas.cursorX = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorRowAndColumn()
@@ -339,7 +339,7 @@ public class SeqPanel extends JPanel
     {
       seqCanvas.cursorX = getKeyboardNo1() - 1;
       seqCanvas.cursorY = getKeyboardNo2() - 1;
-      scrollToVisible();
+      scrollToVisible(true);
     }
   }
 
@@ -348,7 +348,7 @@ public class SeqPanel extends JPanel
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void moveCursor(int dx, int dy)
@@ -376,10 +376,16 @@ public class SeqPanel extends JPanel
       }
     }
 
-    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)
     {
@@ -400,20 +406,41 @@ public class SeqPanel extends JPanel
     }
 
     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
     {
-      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
+      if (av.getWrapAlignment())
+      {
+        av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+      }
+      else
+      {
+        av.getRanges().scrollToVisible(seqCanvas.cursorX,
+                seqCanvas.cursorY);
+      }
     }
-    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+
+    if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
+    {
+      setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
+    }
 
-    seqCanvas.repaint();
+    if (repaintNeeded)
+    {
+      seqCanvas.repaint();
+    }
   }
 
+
   void setSelectionAreaAtCursor(boolean topLeft)
   {
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
@@ -719,10 +746,12 @@ public class SeqPanel extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on mouse movement is to update the status bar to show the current
+   * sequence position, and (if features are shown) to show any features at the
+   * position in a tooltip. Does nothing if the mouse move does not change
+   * residue position.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent evt)
@@ -735,7 +764,8 @@ public class SeqPanel extends JPanel
     }
 
     final int column = findColumn(evt);
-    int seq = findSeq(evt);
+    final int seq = findSeq(evt);
+
     if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
     {
       lastMouseSeq = -1;
@@ -852,11 +882,12 @@ public class SeqPanel extends JPanel
 
   /**
    * set when the current UI interaction has resulted in a change that requires
-   * overview shading to be recalculated. this could be changed to something
-   * more expressive that indicates what actually has changed, so selective
-   * redraws can be applied
+   * shading in overviews and structures to be recalculated. this could be
+   * changed to a something more expressive that indicates what actually has
+   * changed, so selective redraws can be applied (ie. only structures, only
+   * overview, etc)
    */
-  private boolean needOverviewUpdate = 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
@@ -1626,7 +1657,7 @@ public class SeqPanel extends JPanel
         av.getRanges().scrollRight(true);
 
       }
-      else if (!av.getWrapAlignment())
+      else
       {
         av.getRanges().scrollUp(false);
       }
@@ -1637,12 +1668,18 @@ public class SeqPanel extends JPanel
       {
         av.getRanges().scrollRight(false);
       }
-      else if (!av.getWrapAlignment())
+      else
       {
         av.getRanges().scrollUp(true);
       }
     }
-    // TODO Update tooltip for new position.
+
+    /*
+     * update status bar and tooltip for new position
+     * (need to synthesize a mouse movement to refresh tooltip)
+     */
+    mouseMoved(e);
+    ToolTipManager.sharedInstance().mouseMoved(e);
   }
 
   /**
@@ -1656,7 +1693,7 @@ public class SeqPanel extends JPanel
     final int res = findColumn(evt);
     final int seq = findSeq(evt);
     oldSeq = seq;
-    needOverviewUpdate = false;
+    updateOverviewAndStructs = false;
 
     startWrapBlock = wrappedBlock;
 
@@ -1821,7 +1858,7 @@ public class SeqPanel extends JPanel
     // 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()
+    updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
             && afterDrag;
     if (stretchGroup.cs != null)
     {
@@ -1843,8 +1880,8 @@ public class SeqPanel extends JPanel
     PaintRefresher.Refresh(this, av.getSequenceSetId());
     // TODO: structure colours only need updating if stretchGroup used to or now
     // does contain sequences with structure views
-    ap.paintAlignment(needOverviewUpdate, needOverviewUpdate);
-    needOverviewUpdate = false;
+    ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+    updateOverviewAndStructs = false;
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -1898,7 +1935,7 @@ public class SeqPanel extends JPanel
       if (res > (stretchGroup.getStartRes() - 1))
       {
         stretchGroup.setEndRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
     else if (changeStartRes)
@@ -1906,7 +1943,7 @@ public class SeqPanel extends JPanel
       if (res < (stretchGroup.getEndRes() + 1))
       {
         stretchGroup.setStartRes(res);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }
 
@@ -1940,7 +1977,7 @@ public class SeqPanel extends JPanel
       if (stretchGroup.getSequences(null).contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
       else
       {
@@ -1950,7 +1987,7 @@ public class SeqPanel extends JPanel
         }
 
         stretchGroup.addSequence(nextSeq, false);
-        needOverviewUpdate |= av.isSelectionDefinedGroup();
+        updateOverviewAndStructs |= av.isSelectionDefinedGroup();
       }
     }