X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppVarnaBinding.java;h=a738a2c760edda661d8a2ba1be3e7ed055783551;hb=ead72caff9aef9b7103dbb15907aeae777200832;hp=ce0f3df0a773b31b277ed4d66b0e5002e1e52597;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index ce0f3df..a738a2c 100644
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -6,14 +6,16 @@
*
* 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;
@@ -101,17 +103,23 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
private JTextField _seq = new JTextField();
- private JLabel _strLabel = new JLabel(MessageManager.getString("label.str"));
+ private JLabel _strLabel = new JLabel(
+ MessageManager.getString("label.str"));
- private JLabel _seqLabel = new JLabel(MessageManager.getString("label.seq"));
+ private JLabel _seqLabel = new JLabel(
+ MessageManager.getString("label.seq"));
- private JButton _createButton = new JButton(MessageManager.getString("action.create"));
+ private JButton _createButton = new JButton(
+ MessageManager.getString("action.create"));
- private JButton _updateButton = new JButton(MessageManager.getString("action.update"));
+ private JButton _updateButton = new JButton(
+ MessageManager.getString("action.update"));
- private JButton _deleteButton = new JButton(MessageManager.getString("action.delete"));
+ private JButton _deleteButton = new JButton(
+ MessageManager.getString("action.delete"));
- private JButton _duplicateButton = new JButton(MessageManager.getString("action.snapshot"));
+ private JButton _duplicateButton = new JButton(
+ MessageManager.getString("action.snapshot"));
protected JPanel _listPanel = new JPanel();
@@ -143,7 +151,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
{
// super("VARNA in Jalview");
initVarna(seq, struc);
-
+
}
public AppVarnaBinding(ArrayList rnaList)
@@ -155,7 +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();
@@ -188,7 +196,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
try
{
-
+
vp = new VARNAPanel("0", ".");
_RNA1.setRNA(seq, str);
_RNA1.drawRNARadiate(vp.getConfig());
@@ -217,7 +225,7 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
private void initVarnaEdit(ArrayList rnaInList)
{
-
+
DefaultListModel dlm = new DefaultListModel();
int marginTools = 40;
@@ -241,7 +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());
@@ -252,12 +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)
{
@@ -344,7 +352,9 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
ops.add(_deleteButton);
ops.add(_duplicateButton);
- JLabel j = new JLabel(MessageManager.getString("label.structures_manager"), JLabel.CENTER);
+ JLabel j = new JLabel(
+ MessageManager.getString("label.structures_manager"),
+ JLabel.CENTER);
_listPanel.setLayout(new BorderLayout());
// _listPanel.add(ops, BorderLayout.SOUTH);
@@ -807,10 +817,11 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
public void onUINewStructure(VARNAConfig v, RNA r)
{
// patch to fix infinite loop
- // The problem is that onUINewStructure is called when user clicks
+ // 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.
-
+ // 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);
}
@@ -946,14 +957,14 @@ public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
public void onZoomLevelChanged()
{
// TODO Auto-generated method stub
-
+
}
@Override
public void onTranslationChanged()
{
// TODO Auto-generated method stub
-
+
}
}