Use paintAlignment

[jalview.git] / src / jalview / appletgui / AlignmentPanel.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index db3cb8c..2b9e4e6 100755 (executable)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -28,7 +28,7 @@ public class AlignmentPanel
     extends Panel implements AdjustmentListener\r
 {\r
 \r
-  AlignViewport av;\r
+  public AlignViewport av;\r
   OverviewPanel overviewPanel;\r
   SeqPanel seqPanel;\r
   IdPanel idPanel;\r
@@ -115,6 +115,16 @@ public class AlignmentPanel
 \r
   }\r
 \r
+  public SequenceRenderer getSequenceRenderer()\r
+  {\r
+    return seqPanel.seqCanvas.sr;\r
+  }\r
+\r
+  public FeatureRenderer getFeatureRenderer()\r
+  {\r
+    return seqPanel.seqCanvas.fr;\r
+  }\r
+\r
   public void alignmentChanged()\r
   {\r
     av.alignmentChanged(this);\r
@@ -502,6 +512,22 @@ public class AlignmentPanel
 \r
   }\r
 \r
+  public void paintAlignment(boolean updateOverview)\r
+  {\r
+    repaint();\r
+\r
+    if(updateOverview)\r
+    {\r
+      jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
+          .sequenceColoursChanged(this);\r
+\r
+      if (overviewPanel != null)\r
+      {\r
+        overviewPanel.updateOverviewImage();\r
+      }\r
+    }\r
+  }\r
+\r
   public void update(Graphics g)\r
   {\r
     paint(g);\r
@@ -548,15 +574,6 @@ public class AlignmentPanel
     scalePanel.repaint();\r
     annotationPanel.repaint();\r
     idPanel.idCanvas.repaint();\r
-\r
-    if (getBounds() == g.getClipBounds())\r
-    {\r
-      if (overviewPanel != null)\r
-      {\r
-        overviewPanel.updateOverviewImage();\r
-      }\r
-    }\r
-\r
   }\r
 \r
   protected Panel sequenceHolderPanel = new Panel();\r