/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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
*
* 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.
- *
+ *
* 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
*/
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.event.*;
-import java.awt.event.*;
-import java.io.*;
+import javax.swing.JInternalFrame;
+import javax.swing.JSplitPane;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.ShiftList;
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
import fr.orsay.lri.varna.models.VARNAConfig;
import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
import fr.orsay.lri.varna.models.rna.RNA;
public class AppVarna extends JInternalFrame implements
AlignmentPanel ap;
- public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
- String name, AlignmentPanel ap)
+ public AppVarna(String sname, SequenceI seq, String strucseq,
+ String struc, String name, AlignmentPanel ap)
{
System.out.println("je suis là (AppVarna!!");
System.out.println("1:"+sname);
{
e3.printStackTrace();
}
-
- RNA trim = trimRNA(rna1, "trimmed "+sname);
+ 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)");
+ rna1.setName(sname + " (with gaps)");
{
seqs.put(trim, seq);
vab = new AppVarnaBinding(rnaList);
// vab = new AppVarnaBinding(seq,struc);
// System.out.println("Hallo: "+name);
- this.name = sname+" trimmed to "+name;
+ this.name = sname + " trimmed to " + name;
initVarna();
ssm = ap.getStructureSelectionManager();
ShiftList shift = offsets.get(rna);
if (shift != null)
{
- // System.err.print("Orig pos:"+index);
- index = shift.shift(index);
- // System.err.println("\nFinal pos:"+index);
+ // System.err.print("Orig pos:"+index);
+ index = shift.shift(index);
+ // System.err.println("\nFinal pos:"+index);
}
mouseOverHighlighter.highlightRegion(rna, index, index);
vab.updateSelectedRNA(rna);
if (shift != null)
{
int i = shift.shift(arg1.getIndex());
- // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+ // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
ssm.mouseOverVamsasSequence(seq, i, this);
}
else
}
+ @Override
+ public void onTranslationChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void onZoomLevelChanged()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
}