JAL-2491 Renamed comp scrolling flag for consistency; small tweaks

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 13332d3..f17703a 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -438,9 +438,9 @@ public class AlignViewport extends AlignmentViewport implements
     int seqOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
-      complementPanel.setFollowingComplementScroll(false);
+      complementPanel.setToScrollComplementPanel(false);
       complementPanel.scrollToCentre(sr, seqOffset);
-      complementPanel.setFollowingComplementScroll(true);
+      complementPanel.setToScrollComplementPanel(true);
     }
   }
 

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 4ecf05f..c3458f9 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -779,7 +779,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
     vpRanges.setViewportStartAndWidth(x, width);
 
-    if (av.getWrapAlignment() || !fastPaint || av.MAC)
+    if (av.getWrapAlignment() || !fastPaint)
     {
       repaint();
     }
@@ -823,7 +823,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       }
       vpRanges.setViewportStartAndHeight(offy, height);
     }
-    if (av.getWrapAlignment() || !fastPaint || av.MAC)
+    if (av.getWrapAlignment() || !fastPaint)
     {
       repaint();
     }
@@ -1022,9 +1022,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
-   * true, suppresses invoking the same method recursively.
+   * false, suppresses invoking the same method recursively.
    */
-  private boolean followingComplementScroll = true;
+  private boolean scrollComplementaryPanel = true;
 
   private void jbInit() throws Exception
   {
@@ -1133,14 +1133,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
    * 
    * @param b
    */
-  protected void setFollowingComplementScroll(boolean b)
+  protected void setToScrollComplementPanel(boolean b)
   {
-    this.followingComplementScroll = b;
+    this.scrollComplementaryPanel = b;
   }
 
-  protected boolean isFollowingComplementScroll()
+  protected boolean isSetToScrollComplementPanel()
   {
-    return this.followingComplementScroll;
+    return this.scrollComplementaryPanel;
   }
 
   @Override
@@ -1157,11 +1157,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     // now update any complementary alignment (its viewport ranges object
     // is different so does not get automatically updated)
-    if (isFollowingComplementScroll())
+    if (isSetToScrollComplementPanel())
     {
-      setFollowingComplementScroll(false);
+      setToScrollComplementPanel(false);
       av.scrollComplementaryAlignment(getComplementPanel());
-      setFollowingComplementScroll(true);
+      setToScrollComplementPanel(true);
     }
 
   }

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 786e9c2..0f37544 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -151,7 +151,7 @@ public class OverviewPanel extends Panel implements Runnable,
     od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av
             .getRanges());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+    // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 347cceb..76f1275 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -744,12 +744,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       // 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.setFollowingComplementScroll(false);
+      ap.setToScrollComplementPanel(false);
       if (ap.scrollToPosition(results, true))
       {
         ap.alignFrame.repaint();
       }
-      ap.setFollowingComplementScroll(true);
+      ap.setToScrollComplementPanel(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5653340..e2cff80 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1047,9 +1047,9 @@ public class AlignViewport extends AlignmentViewport implements
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
               .getAlignPanel();
-      complementPanel.setDontScrollComplement(true);
+      complementPanel.setToScrollComplementPanel(false);
       complementPanel.scrollToCentre(sr, verticalOffset);
-      complementPanel.setDontScrollComplement(false);
+      complementPanel.setToScrollComplementPanel(true);
     }
   }
 

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 673c008..769dc86 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -104,9 +104,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
-   * true, suppresses invoking the same method recursively.
+   * false, suppresses invoking the same method recursively.
    */
-  private boolean dontScrollComplement = false;
+  private boolean scrollComplementaryPanel = true;
 
   private PropertyChangeListener propertyChangeListener;
 
@@ -769,7 +769,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
           @Override
           public void run()
         {
-            setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+            // When updating scrolling to use ViewportChange events, this code
+            // could not be validated and it is not clear if it is now being
+            // called. Log warning here in case it is called and unforeseen
+            // problems occur
+            Cache.log
+                    .warn("Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+            // scroll to start of panel
+            vpRanges.setStartRes(0);
+            vpRanges.setStartSeq(0);
           }
         });
       }
@@ -1827,14 +1836,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @param b
    */
-  protected void setDontScrollComplement(boolean b)
+  protected void setToScrollComplementPanel(boolean b)
   {
-    this.dontScrollComplement = b;
+    this.scrollComplementaryPanel = b;
   }
 
-  protected boolean isDontScrollComplement()
+  protected boolean isSetToScrollComplementPanel()
   {
-    return this.dontScrollComplement;
+    return this.scrollComplementaryPanel;
   }
 
   /**
@@ -1873,11 +1882,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     // now update any complementary alignment (its viewport ranges object
     // is different so does not get automatically updated)
-    if (!isDontScrollComplement())
+    if (isSetToScrollComplementPanel())
     {
-      setDontScrollComplement(true);
+      setToScrollComplementPanel(false);
       av.scrollComplementaryAlignment();
-      setDontScrollComplement(false);
+      setToScrollComplementPanel(true);
     }
   }
 }

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index da2cdbb..1b047a3 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -124,7 +124,7 @@ public class OverviewPanel extends JPanel implements Runnable,
                   .getColumnSelection(), av.getRanges());
           // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
           // merged
-          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+          // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -141,7 +141,8 @@ public class OverviewPanel extends JPanel implements Runnable,
                   .getColumnSelection(), av.getRanges());
           // TODO set via ViewportRanges in overview dimensions once JAL-2388 is
           // merged
-          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
+
+          // ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index cd69bdc..26f8e9e 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -982,7 +982,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   @Override
   public void propertyChange(PropertyChangeEvent evt)
   {
-    if (av.getWrapAlignment())
+    if (!av.getWrapAlignment())
     {
       if (evt.getPropertyName().equals("startres")
               || evt.getPropertyName().equals("endres"))

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ef2f782..ca79342 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -668,12 +668,12 @@ public class SeqPanel extends JPanel implements MouseListener,
       // 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.setDontScrollComplement(true);
+      ap.setToScrollComplementPanel(false);
       if (ap.scrollToPosition(results, false))
       {
         seqCanvas.revalidate();
       }
-      ap.setDontScrollComplement(false);
+      ap.setToScrollComplementPanel(true);
     }
     setStatusMessage(results);
     seqCanvas.highlightSearchResults(results);

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 56060ab..e4c24e1 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -217,9 +217,11 @@ public class OverviewDimensions
     }
 
     // update scroll values
-    scrollCol = visXAsRes;
-    scrollRow = visYAsRes;
+    // scrollCol = visXAsRes;
+    // scrollRow = visYAsRes;
+    ranges.setStartRes(visXAsRes);
 
+    ranges.setStartSeq(visYAsRes);
   }
 
   /**
@@ -274,7 +276,7 @@ public class OverviewDimensions
     g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
   }
 
-  public int getScrollCol()
+  /*public int getScrollCol()
   {
     return scrollCol;
   }
@@ -282,7 +284,7 @@ public class OverviewDimensions
   public int getScrollRow()
   {
     return scrollRow;
-  }
+  }*/
 
   // TODO should be removed, when unit test has mock Graphics object available
   // to check boxX/boxY