Merge branch 'JAL-986_idwidthprefs' into develop

Conflicts:
	.classpath

diff --cc .classpath
index 4e84fb8,01cf242..a1787c4
--- 1/.classpath
--- 2/.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 help/html/features/preferences.html
Simple merge

diff --cc src/jalview/bin/Cache.java
Simple merge

diff --cc src/jalview/gui/AlignmentPanel.java
index bfbaf4d,0155a67..474d392
--- 1/src/jalview/gui/AlignmentPanel.java
--- 2/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())
      {

diff --cc src/jalview/gui/Preferences.java
Simple merge

diff --cc src/jalview/jbgui/GPreferences.java
Simple merge