JAL-1620 version bump and release notes

[jalview.git] / src / jalview / gui / AppVarna.java

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index efa9a8a..014e6eb 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,34 +1,51 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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.MessageManager;
 import jalview.util.ShiftList;
+
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
@@ -65,12 +82,23 @@ public class AppVarna extends JInternalFrame implements
   public AppVarna(String sname, SequenceI seq, String strucseq,
           String struc, String name, AlignmentPanel ap)
   {
+
+    // System.out.println("1:"+sname);
+    // System.out.println("2:"+seq);
+    // System.out.println("3:"+strucseq);
+    // System.out.println("4:"+struc);
+    // System.out.println("5:"+name);
+    // System.out.println("6:"+ap);
     this.ap = ap;
     ArrayList<RNA> rnaList = new ArrayList<RNA>();
     RNA rna1 = new RNA(name);
     try
     {
+
       rna1.setRNA(strucseq, replaceOddGaps(struc));
+      // System.out.println("The sequence is :"+rna1.getSeq());
+      // System.out.println("The sequence is:"+struc);
+      // System.out.println("The sequence is:"+replaceOddGaps(struc).toString());
     } catch (ExceptionUnmatchedClosingParentheses e2)
     {
       e2.printStackTrace();
@@ -81,6 +109,7 @@ public class AppVarna extends JInternalFrame implements
     RNA trim = trimRNA(rna1, "trimmed " + sname);
     rnaList.add(trim);
     rnaList.add(rna1);
+
     rnas.put(seq, rna1);
     rnas.put(seq, trim);
     rna1.setName(sname + " (with gaps)");
@@ -98,16 +127,18 @@ public class AppVarna extends JInternalFrame implements
     }
     vab = new AppVarnaBinding(rnaList);
     // vab = new AppVarnaBinding(seq,struc);
-    // System.out.println("Hallo: "+name);
     this.name = sname + " trimmed to " + name;
     initVarna();
+
     ssm = ap.getStructureSelectionManager();
+    // System.out.println(ssm.toString());
     ssm.addStructureViewerListener(this);
     ssm.addSelectionListener(this);
   }
 
   public void initVarna()
   {
+
     // vab.setFinishedInit(false);
     varnaPanel = vab.get_varnaPanel();
     setBackground(Color.white);
@@ -118,10 +149,12 @@ public class AppVarna extends JInternalFrame implements
     // getContentPane().add(vab.getTools(), BorderLayout.NORTH);
     varnaPanel.addVARNAListener(this);
     varnaPanel.addSelectionListener(this);
-    jalview.gui.Desktop.addInternalFrame(this, MessageManager.formatMessage("label.varna_params", new String[]{name}),
-            getBounds().width, getBounds().height);
+    jalview.gui.Desktop.addInternalFrame(this,
+            MessageManager.formatMessage("label.varna_params", new String[]
+            { name }), getBounds().width, getBounds().height);
     this.pack();
     showPanel(true);
+
   }
 
   public String replaceOddGaps(String oldStr)
@@ -137,6 +170,7 @@ public class AppVarna extends JInternalFrame implements
   public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
+
     RNA rnaTrim = new RNA(name);
     try
     {
@@ -399,4 +433,18 @@ public class AppVarna extends JInternalFrame implements
 
   }
 
+  @Override
+  public void onTranslationChanged()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void onZoomLevelChanged()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }