JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

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

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index a5c2e5a..15e269c 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -38,8 +38,8 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
-public class IdPanel extends Panel implements MouseListener,
-        MouseMotionListener
+public class IdPanel extends Panel
+        implements MouseListener, MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
@@ -70,7 +70,7 @@ public class IdPanel extends Panel implements MouseListener,
     // TODO: add in group link parameter
 
     // make a list of label,url pairs
-    HashMap<String, String> urlList = new HashMap<String, String>();
+    HashMap<String, String> urlList = new HashMap<>();
     if (viewport.applet != null)
     {
       for (int i = 1; i < 10; i++)
@@ -169,13 +169,14 @@ public class IdPanel extends Panel implements MouseListener,
     }
     if (tooltip == null)
     {
-      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString(), idCanvas);
+      tooltip = new Tooltip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+              idCanvas);
     }
     else
     {
-      tooltip.setTip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString());
+      tooltip.setTip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
     }
     tooltiptext = null;
   }
@@ -197,7 +198,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   @Override
@@ -278,7 +279,8 @@ public class IdPanel extends Panel implements MouseListener,
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((e.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
       SequenceI sq = av.getAlignment().getSequenceAt(seq);
 
@@ -293,7 +295,7 @@ public class IdPanel extends Panel implements MouseListener,
       }
       else
       {
-        nlinks = new ArrayList<String>();
+        nlinks = new ArrayList<>();
       }
 
       for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
@@ -314,8 +316,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!jalview.util.Platform.isControlDown(e) && !e
-                    .isShiftDown()) && av.getSelectionGroup() != null))
+            || ((!jalview.util.Platform.isControlDown(e)
+                    && !e.isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -331,7 +333,7 @@ public class IdPanel extends Panel implements MouseListener,
       selectSeq(seq);
     }
 
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   void selectSeq(int seq)
@@ -364,8 +366,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
 
   }
@@ -457,7 +459,7 @@ public class IdPanel extends Panel implements MouseListener,
           running = false;
         }
 
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(true, false);
         try
         {
           Thread.sleep(100);