HiddenSequences now array, not hashtable

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8bed8e2..dbc1c92 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -314,7 +314,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }\r
 \r
 \r
-        if (SwingUtilities.isRightMouseButton(evt))\r
+        if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1)\r
         {\r
             if (av.getColumnSelection() == null)\r
             {\r
@@ -418,8 +418,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(graphStretch>-1)\r
       {\r
         av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
-        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)\r
-          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;\r
+        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0)\r
+          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;\r
         graphStretchY = evt.getY();\r
         adjustPanelHeight();\r
         ap.repaint();\r
@@ -667,6 +667,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             return;\r
         }\r
 \r
+\r
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 \r
         int x = 0, y = 0;\r
@@ -689,6 +690,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;\r
             }\r
 \r
+\r
             lastSS = ' ';\r
             lastSSX = 0;\r
 \r
@@ -706,6 +708,28 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }\r
             }\r
 \r
+            if (av.updatingConsensus && aa[i].label.equals("Consensus"))\r
+            {\r
+              g.setColor(Color.darkGray);\r
+              g.drawString("Recalculating Consensus....", 20, y - 5);\r
+              y += av.charHeight;\r
+              continue;\r
+            }\r
+            else if (av.updatingConservation && aa[i].label.equals("Conservation"))\r
+            {\r
+              g.setColor(Color.darkGray);\r
+              g.drawString("Recalculating Conservation.....", 20, y - 5);\r
+              y += av.charHeight;\r
+              continue;\r
+            }\r
+            else if (av.updatingConservation && aa[i].label.equals("Quality"))\r
+            {\r
+              g.setColor(Color.darkGray);\r
+              g.drawString("Recalculating Quality....", 20, y - 5);\r
+              continue;\r
+            }\r
+\r
+\r
             if (row.hasText)\r
             {\r
                 iconOffset = av.charHeight / 2 + 4;\r
@@ -952,7 +976,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
               }\r
           }\r
 \r
-            if (row.graph>0)\r
+            if (row.graph>0 && row.graphHeight>0)\r
             {\r
                 if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
                 {\r