X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=56efe53acf2c44a2525d6449723bd309176d7f8f;hb=6081884ff7c5a50b2a9f6615f7a864bdc5699bf2;hp=241e0a3776c94e9d497663f8512bb32f5856ec50;hpb=15c3c0e89d9157187e1ccc6962b115cb255dd04a;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 241e0a3..56efe53 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -515,8 +515,10 @@ public class AnnotationLabels extends JPanel
           public void actionPerformed(ActionEvent e)
           {
             sel_row.setShowGroupsForContactMatrix(chitem.getState());
-            ap.getAnnotationPanel()
-                    .paint(ap.getAnnotationPanel().getGraphics());
+            // so any annotation colour changes are propagated - though they
+            // probably won't be unless the annotation row colours are removed
+            // too!
+            ap.alignmentChanged();
           }
         });
         pop.add(chitem);
@@ -562,7 +564,10 @@ public class AnnotationLabels extends JPanel
                                 "action.clustering_matrix_for",
                                 cm.getAnnotDescr(), 5f),
                         progBar = System.currentTimeMillis());
-                cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
+                cm.setGroupSet(GroupSet.makeGroups(cm, true));
+                cm.randomlyReColourGroups();
+                cm.transferGroupColorsTo(alignmentAnnotation);
+                ap.alignmentChanged();
                 ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
                 ap.alignFrame.setProgressBar(null, progBar);
               }
@@ -1213,7 +1218,13 @@ public class AnnotationLabels extends JPanel
         {
           // If no manual adjustment to ID column with has been made then adjust
           // width match widest of alignment or annotation id widths
+          boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH",
+                  false);
           width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
+          if (clip && width < givenWidth && !allowShrink)
+          {
+            width = givenWidth;
+          }
         }
         else if (newAnnotationIdWidth != annotationIdWidth
                 && newAnnotationIdWidth > givenWidth
@@ -1233,10 +1244,7 @@ public class AnnotationLabels extends JPanel
     }
     else
     {
-      Graphics2D g2d = (Graphics2D) g;
-      Graphics dummy = g2d.create();
-      int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
-              null);
+      int newAnnotationIdWidth = drawLabels(g, clip, width, false, null);
       width = Math.max(newAnnotationIdWidth, givenWidth);
     }
     drawLabels(g, clip, width, true, null);
@@ -1260,9 +1268,28 @@ public class AnnotationLabels extends JPanel
    * @param fmetrics
    *          FontMetrics if Graphics object g is null
    */
-  public int drawLabels(Graphics g, boolean clip, int width,
+  public int drawLabels(Graphics g0, boolean clip, int width,
           boolean actuallyDraw, FontMetrics fmetrics)
   {
+    if (clip)
+    {
+      clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS",
+              true);
+    }
+    Graphics g = null;
+    // create a dummy Graphics object if not drawing and one is supplied
+    if (g0 != null)
+    {
+      if (!actuallyDraw)
+      {
+        Graphics2D g2d = (Graphics2D) g0;
+        g = g2d.create();
+      }
+      else
+      {
+        g = g0;
+      }
+    }
     int actualWidth = 0;
     if (g != null)
     {