AlignPanel RefreshPanels put into paintComponent

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3625e45..c12cf09 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -247,8 +247,7 @@ public class AlignFrame extends GAlignFrame
       viewport.setAlignment( new Alignment(seq) );\r
       updateEditMenuBar();\r
       viewport.updateConsensus();\r
-      alignPanel.RefreshPanels();\r
-      alignPanel.RefreshPanels();\r
+      alignPanel.repaint();\r
   }\r
 \r
   public void moveSelectedSequences(boolean up)\r
@@ -290,7 +289,7 @@ public class AlignFrame extends GAlignFrame
       }\r
     }\r
 \r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
 \r
@@ -365,7 +364,7 @@ public class AlignFrame extends GAlignFrame
         viewport.alignment.getWidth();\r
         viewport.updateConservation();\r
         viewport.updateConsensus();\r
-        alignPanel.RefreshPanels();\r
+        alignPanel.repaint();\r
       }\r
 \r
     }catch(Exception ex){}// could be anything being pasted in here\r
@@ -408,7 +407,7 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){}\r
    viewport.updateConservation();\r
    viewport.updateConsensus();\r
-     alignPanel.RefreshPanels();\r
+     alignPanel.repaint();\r
 \r
   }\r
 \r
@@ -421,8 +420,8 @@ public class AlignFrame extends GAlignFrame
      viewport.setAlignment( new Alignment(seq) );\r
      updateEditMenuBar();\r
      viewport.updateConsensus();\r
-     alignPanel.RefreshPanels();\r
-     alignPanel.RefreshPanels();\r
+     alignPanel.repaint();\r
+     alignPanel.repaint();\r
   }\r
 \r
 \r
@@ -431,7 +430,7 @@ public class AlignFrame extends GAlignFrame
     viewport.alignment.deleteAllGroups();\r
     viewport.setSelectionGroup(null);\r
 \r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
 \r
@@ -489,7 +488,7 @@ public class AlignFrame extends GAlignFrame
           viewport.alignment.deleteGroup(sg);\r
       }\r
 \r
-      alignPanel.RefreshPanels();\r
+      alignPanel.repaint();\r
     }\r
   }\r
 \r
@@ -514,7 +513,7 @@ public class AlignFrame extends GAlignFrame
 \r
 \r
 \r
-      alignPanel.RefreshPanels();\r
+      alignPanel.repaint();\r
     }\r
 \r
   }\r
@@ -525,7 +524,7 @@ public class AlignFrame extends GAlignFrame
     viewport.getAlignment().removeGaps();\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
@@ -547,7 +546,7 @@ public class AlignFrame extends GAlignFrame
     }\r
     viewport.updateConservation();\r
     viewport.updateConsensus();\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
@@ -561,7 +560,7 @@ public class AlignFrame extends GAlignFrame
     }\r
     setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
     viewport.setGapCharacter(thisChar);\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void findMenuItem_actionPerformed(ActionEvent e)\r
@@ -589,13 +588,13 @@ public class AlignFrame extends GAlignFrame
     viewport.setShowFullId( fullSeqId.isSelected() );\r
 \r
     alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
   {\r
       viewport.setColourText( colourTextMenuItem.isSelected() );\r
-      alignPanel.RefreshPanels();\r
+      alignPanel.repaint();\r
   }\r
 \r
   protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
@@ -605,7 +604,7 @@ public class AlignFrame extends GAlignFrame
     scaleAbove.setVisible( wrapMenuItem.isSelected() );\r
     scaleLeft.setVisible( wrapMenuItem.isSelected() );\r
     scaleRight.setVisible( wrapMenuItem.isSelected() );\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   protected void scaleAbove_actionPerformed(ActionEvent e)\r
@@ -631,20 +630,20 @@ public class AlignFrame extends GAlignFrame
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setShowText( viewTextMenuItem.isSelected() );\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
 \r
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
@@ -655,7 +654,7 @@ public class AlignFrame extends GAlignFrame
          AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);\r
          ((Alignment)viewport.alignment).featuresAdded = true;\r
     }\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
@@ -870,7 +869,7 @@ public class AlignFrame extends GAlignFrame
 \r
 \r
 \r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   protected void modifyPID_actionPerformed(ActionEvent e)\r
@@ -952,14 +951,14 @@ public class AlignFrame extends GAlignFrame
   {\r
     addHistoryItem("sort");\r
     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0));\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     addHistoryItem("sort");\r
     AlignmentSorter.sortByID( viewport.getAlignment() );\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
@@ -967,7 +966,7 @@ public class AlignFrame extends GAlignFrame
     addHistoryItem("sort");\r
     AlignmentSorter.sortByGroup(viewport.getAlignment());\r
     AlignmentSorter.sortGroups(viewport.getAlignment());\r
-    alignPanel.RefreshPanels();\r
+    alignPanel.repaint();\r
   }\r
 \r
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
@@ -1078,7 +1077,7 @@ public class AlignFrame extends GAlignFrame
       {\r
         addHistoryItem("sort");\r
         AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
-        alignPanel.RefreshPanels();\r
+        alignPanel.repaint();\r
       }\r
     });\r
 \r