X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarna.java;h=4fe9ac2139d4a41bf3446fa6e735cd22dd60683e;hb=0155cd99a3b96570ad67dbc992c731ba2ce74bb9;hp=f047199b4f0bafafaa29e3d4b8a3741d4b0c7657;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index f047199..4fe9ac2 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -1,35 +1,51 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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;
@@ -66,12 +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 rnaList = new ArrayList();
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();
@@ -82,6 +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)");
@@ -99,16 +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);
@@ -119,10 +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)
@@ -138,6 +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
{
@@ -400,4 +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
+
+ }
+
}