From 59183747dbffe3ab6b141c5440d2f70799ae360b Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:38:42 +0000
Subject: [PATCH] Applet reads in annotation files

---
 src/jalview/appletgui/AlignFrame.java     |    3 +++
 src/jalview/appletgui/AlignViewport.java  |    6 +++---
 src/jalview/appletgui/AlignmentPanel.java |    3 ++-
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dfd58b2..496a8bb 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -992,6 +992,8 @@ public void itemStateChanged(ItemEvent evt)
     resetAllColourSchemes();
     if(alignPanel.overviewPanel!=null)
       alignPanel.overviewPanel.updateOverviewImage();
+
+    viewport.alignment.adjustSequenceAnnotations();
     alignPanel.repaint();
   }
 
@@ -1872,6 +1874,7 @@ public void itemStateChanged(ItemEvent evt)
         font.addActionListener(this);
         scaleAbove.setLabel("Scale Above");
         scaleAbove.setState(true);
+        scaleAbove.setEnabled(false);
         scaleAbove.addItemListener(this);
         scaleLeft.setEnabled(false);
         scaleLeft.setState(true);
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e9078dd..50a90fe 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -221,7 +221,7 @@ public class AlignViewport
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
-                                             AlignmentAnnotation.LINE_GRAPH);
+                                             AlignmentAnnotation.BAR_GRAPH);
       if (showConservation)
       {
         alignment.addAnnotation(conservation);
@@ -231,7 +231,7 @@ public class AlignViewport
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
-                                        AlignmentAnnotation.LINE_GRAPH);
+                                        AlignmentAnnotation.BAR_GRAPH);
       if (showQuality)
       {
         alignment.addAnnotation(quality);
@@ -294,7 +294,7 @@ public class AlignViewport
     if (consensus == null)
     {
       consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.LINE_GRAPH);
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index d7411fa..0e9a0d8 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -113,10 +113,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener
     scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
     idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
 
-    annotationPanel.adjustPanelHeight();
+    int ap = annotationPanel.adjustPanelHeight();
     annotationPanel.repaint();
     Dimension d = calculateIdWidth();
     d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
+    alabels.setSize(d.width+4, ap );
     idPanel.idCanvas.setSize(d);
     hscrollFillerPanel.setSize(d);
 
-- 
1.7.10.2