From: janengelhardt <engelhardt87@googlemail.com>
Date: Sun, 28 Aug 2011 04:32:18 +0000 (+0200)
Subject: Including of VARNAv-3.9;
X-Git-Tag: Jalview_2_9~576^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ab1c8821340f7c198c03d6209609e3b1bbb38113;p=jalview.git

Including of VARNAv-3.9;

Change-Id: Ib55f047ae763999c7db2b601105b6655132ee171
---

diff --git a/.classpath b/.classpath
index 3324c5f..86aa215 100644
--- a/.classpath
+++ b/.classpath
@@ -41,6 +41,6 @@
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.java"/>
-	<classpathentry kind="lib" path="lib/VARNAv3-8b.jar"/>
+	<classpathentry kind="lib" path="lib/VARNAv3-9.jar"/>
 	<classpathentry kind="output" path="classes"/>
 </classpath>
diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html
index 5f989a5..8455f47 100755
--- a/help/html/calculations/structureconsensus.html
+++ b/help/html/calculations/structureconsensus.html
@@ -37,8 +37,8 @@ similar to a sequence logo but counts the numbers of base pairs. There
 are two residues per column, the actual column and the interacting
 base. The opening bracket is always the one on the left side.<br>
 Like sequence logos the relative amount of a specific base pair can be
-estimated by it's size in the logo. The tooltip of a column gives the
-exact numbers for all occuring valid base pairs.
+estimated by it's size in the logo. The tool tip of a column gives the
+exact numbers for all occurring valid base pairs.
 </p>
 </body>
 </html>
diff --git a/help/html/features/varna.html b/help/html/features/varna.html
index f044a44..12d9207 100644
--- a/help/html/features/varna.html
+++ b/help/html/features/varna.html
@@ -39,7 +39,7 @@ associated with the alignment are available.
     Structures associated with the alignment are marked by having &quot;consensus&quot; attached to their name. VARNA contains two different entries for consensus structures.
     <ul>
       <li>Consensus structure: the individual sequence folded into the consensus structure</li>
-      <li>Trimed consensus structure: the individual sequence
+      <li>Trimmed consensus structure: the individual sequence
 	folded into the the gap-free consensus structure. That means all
 	columns that contained gaps in the individual sequence were
 	removed. If this breaks a base-pair the pairing is removed also.
@@ -60,13 +60,13 @@ associated with the alignment are available.
 <li>Highlighting bases - Move mouse over columns in the Jalview alignment panel</li>
 </ul>
 
-<p><strong>Functionality provided by Jmol</strong></p>
+<p><strong>Functionality provided by VARNA</strong></p>
 <p>VARNA's own functions are accessed by right-clicking in the
 structure display area. That will open the VARNA pop-up menu,
 which provides access to a number of features like different draw algorithm, color highlighting or annotations. 
 </p>
 <p><strong>More Information</strong></p>
-<p>VARNA is a very powerful RNA viewer on it's own. Only the
+<p>VARNA is a very powerful RNA viewer on its own. Only the
 essentials have been described here - the interested reader is
 referred to <a href="http://varna.lri.fr/usermanual.html">VARNA's own
 comprehensive online documentation</a>.</p>
diff --git a/lib/VARNAv3-9.jar b/lib/VARNAv3-9.jar
new file mode 100644
index 0000000..b1db0a0
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 35e9d35..ecc6cb6 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -43,7 +43,6 @@ import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
 import fr.orsay.lri.varna.models.VARNAConfig;
 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
-import fr.orsay.lri.varna.models.rna.ModeleStyleBP;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 
@@ -179,12 +178,6 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,S
   }
 
 @Override
-public void onLayoutChanged() {
-	// TODO Auto-generated method stub
-	
-}
-
-@Override
 public void onUINewStructure(VARNAConfig v, RNA r) {
 	// TODO Auto-generated method stub
 	
@@ -221,4 +214,12 @@ public void mouseOverStructure(int atomIndex, String strInfo) {
 	
 }
 
+@Override
+public void onStructureRedrawn()
+{
+  // TODO Auto-generated method stub
+  
+}
+
+
 }
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 51819fa..88cc288 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -861,6 +861,13 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding imple
 		// TODO Auto-generated method stub
 		
 	}
+
+  @Override
+  public void onStructureRedrawn()
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }