New classes

diff --git a/JalviewApplet.jpx b/JalviewApplet.jpx
index 19e5526..0044ab6 100755 (executable)
--- a/JalviewApplet.jpx
+++ b/JalviewApplet.jpx
@@ -54,15 +54,12 @@
   <node name="jalview.jbappletgui" type="Package"/>\r
   <node name="jalview.math" type="Package"/>\r
   <node name="jalview.schemes" type="Package"/>\r
-  <node name="jalview.util" type="Package"/>\r
   <file path="src/jalview/analysis/AAFrequency.java"/>\r
   <file path="src/jalview/io/AlignFile.java"/>\r
   <file path="src/jalview/analysis/AlignmentSorter.java"/>\r
-  <file path="src/jalview/analysis/AlignmentUtil.java"/>\r
   <file path="src/jalview/analysis/AlignSeq.java"/>\r
   <file path="src/jalview/io/BLCFile.java"/>\r
   <file path="src/jalview/io/ClustalFile.java"/>\r
-  <file path="src/jalview/analysis/CompareAlignments.java"/>\r
   <file path="src/jalview/analysis/Conservation.java"/>\r
   <file path="src/jalview/io/FastaFile.java"/>\r
   <file path="src/jalview/io/FileParse.java"/>\r

diff --git a/JalviewX.jpx b/JalviewX.jpx
index 181698e..239991a 100755 (executable)
--- a/JalviewX.jpx
+++ b/JalviewX.jpx
@@ -30,15 +30,18 @@
   <property category="sys" name="ExcludeClassEnabled" value="0"/>\r
   <property category="sys" name="IncludeTestPath" value="1"/>\r
   <property category="sys" name="JDK" value="java version 1.4.2_04-b05"/>\r
-  <property category="sys" name="JvmVersion" value="1.2"/>\r
+  <property category="sys" name="JvmVersion" value="1.4"/>\r
   <property category="sys" name="Libraries" value="all"/>\r
   <property category="sys" name="OutPath" value="classes"/>\r
   <property category="sys" name="SourcePath" value="src;test"/>\r
+  <property category="sys" name="SourceVersion" value="1.4"/>\r
   <property category="sys" name="TestPath" value="test"/>\r
   <property category="sys" name="Title" value=""/>\r
   <property category="sys" name="TitleLabel" value="Title:"/>\r
   <property category="sys" name="Version" value="1.0"/>\r
   <property category="sys" name="VersionLabel" value="@version"/>\r
   <property category="sys" name="WorkingDirectory" value="."/>\r
+  <property category="sys" name="uidesign.size.jalview.jbgui.GPreferences" value="453,333"/>\r
+  <property category="sys" name="uidesign.size.jalview.jbgui.GSequenceLink" value="400,112"/>\r
   <file path="build.xml"/>\r
 </project>\r