JAL-1216 switch to official release of VARNA 3.9

diff --git a/.classpath b/.classpath
index 5e80147..0633302 100644 (file)
--- a/.classpath
+++ b/.classpath
@@ -45,8 +45,8 @@
        <classpathentry kind="lib" path="lib/jdas-1.0.4.jar"/>
        <classpathentry kind="lib" path="lib/spring-core-3.0.5.RELEASE.jar"/>
        <classpathentry kind="lib" path="lib/spring-web-3.0.5.RELEASE.jar"/>
+       <classpathentry kind="lib" path="lib/VARNAv3-9.jar" sourcepath="/Users/jimp/Documents/Jalview/VARNA/VARNAv3-9-src.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
        <classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
-       <classpathentry kind="lib" path="lib/VARNAv3-9-dev.jar" sourcepath="/VARNA3-1"/>
        <classpathentry kind="output" path="classes"/>
 </classpath>

diff --git a/lib/VARNAv3-9-dev.jar b/lib/VARNAv3-9-dev.jar
deleted file mode 100644 (file)
index 865de94..0000000
Binary files a/lib/VARNAv3-9-dev.jar and /dev/null differ

diff --git a/lib/VARNAv3-9.jar b/lib/VARNAv3-9.jar
new file mode 100644 (file)
index 0000000..86ac411
Binary files /dev/null and b/lib/VARNAv3-9.jar differ

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index dd570c0..70e68ee 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -17,17 +17,28 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.bin.Cache;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.ShiftList;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
-import java.awt.*;
 
-import javax.swing.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
 
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.util.ShiftList;
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
@@ -415,4 +426,18 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
 }

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 1b95afb..61c44c2 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -43,20 +43,14 @@ import java.util.List;
 
 import javax.swing.DefaultListModel;
 import javax.swing.DefaultListSelectionModel;
-import javax.swing.Icon;
 import javax.swing.JButton;
-import javax.swing.JFrame;
 import javax.swing.JLabel;
 import javax.swing.JList;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
 import javax.swing.JTextField;
 import javax.swing.ListModel;
 import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
-import javax.swing.UnsupportedLookAndFeelException;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 
@@ -944,6 +938,20 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
     // TODO Auto-generated method stub
 
   }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }
 
 /*