X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=9ba1d3d901cc308303d9b5e565736282c26baadf;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=0bc84cec72da137deb817f3fd1068d78b9920678;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 0bc84ce..9ba1d3d 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -1,22 +1,27 @@
/*
- * 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 2.8.2b1)
+ * 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 .
+ * 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 jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
@@ -37,28 +42,20 @@ import java.awt.event.ComponentEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.io.File;
-import java.text.DateFormat;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Date;
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;
@@ -106,17 +103,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
private JTextField _seq = new JTextField();
- private JLabel _strLabel = new JLabel(" Str:");
+ private JLabel _strLabel = new JLabel(
+ MessageManager.getString("label.str"));
- private JLabel _seqLabel = new JLabel(" Seq:");
+ private JLabel _seqLabel = new JLabel(
+ MessageManager.getString("label.seq"));
- private JButton _createButton = new JButton("Create");
+ private JButton _createButton = new JButton(
+ MessageManager.getString("action.create"));
- private JButton _updateButton = new JButton("Update");
+ private JButton _updateButton = new JButton(
+ MessageManager.getString("action.update"));
- private JButton _deleteButton = new JButton("Delete");
+ private JButton _deleteButton = new JButton(
+ MessageManager.getString("action.delete"));
- private JButton _duplicateButton = new JButton("Snapshot");
+ private JButton _duplicateButton = new JButton(
+ MessageManager.getString("action.snapshot"));
protected JPanel _listPanel = new JPanel();
@@ -148,7 +151,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
{
// super("VARNA in Jalview");
initVarna(seq, struc);
-
+
}
public AppVarnaBinding(ArrayList rnaList)
@@ -160,7 +163,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
private void initVarna(String seq, String str)
{
-
+
DefaultListModel dlm = new DefaultListModel();
DefaultListSelectionModel m = new DefaultListSelectionModel();
@@ -193,7 +196,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
try
{
-
+
vp = new VARNAPanel("0", ".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
@@ -222,7 +225,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
private void initVarnaEdit(ArrayList rnaInList)
{
-
+
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
@@ -246,7 +249,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
FullBackup sel = (FullBackup) _sideList.getSelectedValue();
Mapping map = Mapping.DefaultOutermostMapping(vp.getRNA()
.getSize(), sel.rna.getSize());
- //vp.showRNAInterpolated(sel.rna, sel.config, map);
+ // vp.showRNAInterpolated(sel.rna, sel.config, map);
vp.showRNA(sel.rna, sel.config);
// _seq.setText(sel.rna.getSeq());
_str.setText(sel.rna.getStructDBN());
@@ -257,12 +260,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
try
{
-
+
vp = new VARNAPanel("0", ".");
for (int i = 0; i < rnaInList.size(); i++)
{
rnaInList.get(i).drawRNARadiate(vp.getConfig());
-
+
}
} catch (ExceptionNonEqualLength e)
{
@@ -349,10 +352,12 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
ops.add(_deleteButton);
ops.add(_duplicateButton);
- JLabel j = new JLabel("Structures Manager", JLabel.CENTER);
+ JLabel j = new JLabel(
+ MessageManager.getString("label.structures_manager"),
+ JLabel.CENTER);
_listPanel.setLayout(new BorderLayout());
- //_listPanel.add(ops, BorderLayout.SOUTH);
+ // _listPanel.add(ops, BorderLayout.SOUTH);
_listPanel.add(j, BorderLayout.NORTH);
_listPanel.add(listScroller, BorderLayout.CENTER);
@@ -653,22 +658,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
_rnaList.add(bck.config, bck.rna, bck.name, true);
} catch (ExceptionLoadingFailed e3)
{
- int mn=1;
- Collection mdls=fr.orsay.lri.varna.factories.RNAFactory.loadSecStr(path);
- for (RNA r:mdls)
- {
- r.drawRNA(vp.getConfig());
- String name = r.getName();
- if (name.equals(""))
- {
- name = path.substring(path
- .lastIndexOf(File.separatorChar) + 1);
- }
- if (mdls.size()>1)
+ int mn = 1;
+ Collection mdls = fr.orsay.lri.varna.factories.RNAFactory
+ .loadSecStr(path);
+ for (RNA r : mdls)
{
- name += " (Model "+mn+++")";
- }
- _rnaList.add(vp.getConfig().clone(), r, name, true);
+ r.drawRNA(vp.getConfig());
+ String name = r.getName();
+ if (name.equals(""))
+ {
+ name = path.substring(path
+ .lastIndexOf(File.separatorChar) + 1);
+ }
+ if (mdls.size() > 1)
+ {
+ name += " (Model " + mn++ + ")";
+ }
+ _rnaList.add(vp.getConfig().clone(), r, name, true);
}
}
}
@@ -810,7 +816,13 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
public void onUINewStructure(VARNAConfig v, RNA r)
{
- _rnaList.add(v, r, "", true);
+ // patch to fix infinite loop
+ // The problem is that onUINewStructure is called when user clicks
+ // check with Yann about whether Jalview should do anything with this event.
+ // e.g. if user has used VARNA's menu to import a structure .. Jalview may
+ // need to be told which structure is displayed.
+
+ // _rnaList.add(v, r, "", true);
}
public void onWarningEmitted(String s)
@@ -940,6 +952,20 @@ 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
+
+ }
}
/*
@@ -949,4 +975,4 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
* AppVarnaBinding vab = new AppVarnaBinding(); vab.varnagui.set_seq(str);
* vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
* vab.varnagui.pack(); vab.varnagui.setVisible(true); } }
- */
\ No newline at end of file
+ */