ensure successive matches to a regex have distinct annotation name (indice suffix...

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 2996c98..33a73d3 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -122,11 +122,8 @@ public class AlignViewport
     this.endSeq = al.getHeight() - 1;
     setFont(font);
 
-    if (System.getProperty("os.name").startsWith("Mac"))
-    {
-      MAC = true;
-    }
-
+    MAC = new jalview.util.Platform().isAMac();
+    
     if (applet != null)
     {
       String param = applet.getParameter("showFullId");
@@ -167,6 +164,7 @@ public class AlignViewport
           upperCasebold = true;
         }
       }
+      
 
     }
 
@@ -276,7 +274,7 @@ public class AlignViewport
           {
             if (ap != null)
             {
-              ap.paintAlignment(true);
+              ap.paintAlignment(false);
             }
             Thread.sleep(200);
           }
@@ -454,7 +452,7 @@ public class AlignViewport
         {
           if (ap != null)
           {
-            ap.paintAlignment(true);
+            ap.paintAlignment(false);
           }
 
           Thread.sleep(200);
@@ -671,6 +669,7 @@ public class AlignViewport
   }
 
   java.awt.Frame nullFrame;
+  protected FeatureSettings featureSettings=null;
   public void setFont(Font f)
   {
     font = f;
@@ -1444,5 +1443,27 @@ public class AlignViewport
       sg.recalcConservation();
     }
   }
+  boolean centreColumnLabels;
+  public boolean getCentreColumnLabels()
+  {
+    return centreColumnLabels;
+  }
+
+  public void updateSequenceIdColours()
+  {
+    Vector groups = alignment.getGroups();
+    for (int ig=0,igSize=groups.size(); ig<igSize; ig++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+      if (sg.idColour!=null)
+      {
+        Vector sqs = sg.getSequences(hiddenRepSequences);
+        for (int s=0,sSize=sqs.size();s<sSize;s++)
+        {
+          this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
+        } 
+      }
+    }
+  }
 
 }