From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 9 Nov 2011 15:21:10 +0000 (+0000)
Subject: Merge branch 'JAL-986_idwidthprefs' into develop
X-Git-Tag: Jalview_2_9~556
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=63f3c5bdc2ce5540d8f6bfc9ed9af5d454805181;p=jalview.git

Merge branch 'JAL-986_idwidthprefs' into develop

Conflicts:
	.classpath
---

63f3c5bdc2ce5540d8f6bfc9ed9af5d454805181
diff --cc .classpath
index 4e84fb8,01cf242..a1787c4
--- a/.classpath
+++ b/.classpath
@@@ -37,13 -36,10 +37,13 @@@
  	</classpathentry>
  	<classpathentry kind="lib" path="lib/miglayout-4.0-swing.jar"/>
  	<classpathentry kind="lib" path="lib/jswingreader-0.3.jar" sourcepath="/jswingreader"/>
 -	<classpathentry kind="lib" path="lib/min-jaba-client.jar"/>
  	<classpathentry kind="lib" path="lib/commons-codec-1.3.jar"/>
 +	<classpathentry kind="lib" path="lib/min-jaba-client-2.0.jar" sourcepath="/clustengine2"/>
+ 	<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
  	<classpathentry kind="lib" path="appletlib/JmolApplet-12.2.4.jar"/>
  	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
 +<!--	<classpathentry exported="true" kind="var" path="GROOVY_ECLIPSE_HOME/groovy-all-1.0.jar"/> -->
 +	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.java"/>
 +	<classpathentry kind="lib" path="lib/VARNAv3-9.jar"/>
- 	<classpathentry kind="lib" path="lib/Jmol-12.2.4.jar"/>
  	<classpathentry kind="output" path="classes"/>
  </classpath>
diff --cc src/jalview/gui/AlignmentPanel.java
index bfbaf4d,0155a67..474d392
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@@ -955,10 -969,10 +968,10 @@@ public class AlignmentPanel extends GAl
      int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
              + annotationHeight;
  
-     int idWidth = getVisibleIdWidth();
+     int idWidth = getVisibleIdWidth(false);
  
 -    int maxwidth = av.alignment.getWidth();
 -    if (av.hasHiddenColumns)
 +    int maxwidth = av.getAlignment().getWidth();
 +    if (av.hasHiddenColumns())
      {
        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
      }
@@@ -1043,9 -1079,9 +1078,9 @@@
        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
      }
  
 -    int height = ((av.alignment.getHeight() + 1) * av.charHeight)
 +    int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
              + scalePanel.getHeight();
-     int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
+     int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
  
      if (av.getWrapAlignment())
      {