package jalview.ext.varna;
-import fr.orsay.lri.varna.models.rna.RNA;
-
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
+import fr.orsay.lri.varna.models.rna.RNA;
+
/**
* Data bean wrapping the data items that define one RNA view
*/
public final RNA rna;
- // path to a file holding VARNA session state XML
- public final String varnaSession;
-
public RnaModel(String t, AlignmentAnnotation aa, SequenceI s, RNA r,
- boolean g,
- String sessionFile)
+ boolean g)
{
title = t;
ann = aa;
seq = s;
- gapped = g;
rna = r;
- varnaSession = sessionFile;
+ gapped = g;
}
}
\ No newline at end of file
*/
package jalview.gui;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
+
import java.awt.BorderLayout;
import java.awt.Color;
-import java.lang.reflect.InvocationTargetException;
import java.util.Collection;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.RnaViewerModel;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.RnaModel;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
-
public class AppVarna extends JInternalFrame implements SelectionListener,
SecondaryStructureListener, InterfaceVARNASelectionListener,
VamsasSource
setTitle(theTitle);
String gappedTitle = sname + " (with gaps)";
- RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true,
- null);
+ RnaModel gappedModel = new RnaModel(gappedTitle, aa, seq, null, true);
addModel(gappedModel, gappedTitle);
String trimmedTitle = "trimmed " + sname;
- RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null,
- false, null);
+ RnaModel trimmedModel = new RnaModel(trimmedTitle, aa, seq, null, false);
addModel(trimmedModel, trimmedTitle);
vab.setSelectedIndex(0);
}
+
/**
* Constructor that links the viewer to a parent panel (but has no structures
* yet - use addModel to add them)
if (rnaModel.seq == sequence)
{
int highlightPos = rnaModel.gapped ? index : position - 1;
- // int highlightPos = index;
- // ShiftList shift = offsets.get(rna);
- // if (shift != null)
- // {
- // System.err.print("Orig pos:" + index);
- // highlightPos = shift.shift(index);
- // System.err.println("\nFinal pos:" + index);
- // }
mouseOverHighlighter.highlightRegion(rna, highlightPos, highlightPos);
vab.updateSelectedRNA(rna);
}
}
/*
- * loaded from project file with Varna session data
- */
- if (model.varnaSession != null)
- {
- try
- {
- FullBackup fromSession = vab.vp.loadSession(model.varnaSession);
- vab.addStructure(fromSession.rna, fromSession.config);
- RNA rna = fromSession.rna;
- // copy the model, but now including the RNA object
- RnaModel newModel = new RnaModel(model.title, model.ann, model.seq,
- rna, model.gapped, model.varnaSession);
- if (!model.gapped)
- {
- registerOffset(rna, buildOffset(model.seq));
- }
- models.put(rna, newModel);
- // capture rna selection state when saved
- selectionHighlighter = new VarnaHighlighter(rna);
- return fromSession.rna;
- } catch (ExceptionLoadingFailed e)
- {
- e.printStackTrace();
- return null;
- }
- }
-
- /*
* opened on request in Jalview session
*/
RNA rna = new RNA(modelName);
rna = trimRNA(rna, modelName);
}
models.put(rna, new RnaModel(modelName, model.ann, model.seq, rna,
- model.gapped, null));
+ model.gapped));
vab.addStructure(rna);
return rna;
}
/**
* Set the selected index in the model selection list
*
- * @param selectedR
+ * @param selectedIndex
*/
public void setInitialSelection(final int selectedIndex)
{
+ /*
+ * empirically it needs a second for Varna/AWT to finish loading/drawing
+ * models for this to work; SwingUtilities.invokeLater _not_ a solution;
+ * explanation and/or better solution welcome!
+ */
+ synchronized (this)
+ {
+ try
+ {
+ wait(1000);
+ } catch (InterruptedException e)
+ {
+ // meh
+ }
+ }
vab.setSelectedIndex(selectedIndex);
}
+
+
+ /**
+ * Add a model with associated Varna session file
+ *
+ * @param rna
+ * @param modelName
+ */
+ public RNA addModelSession(RnaModel model, String modelName,
+ String sessionFile)
+ {
+ if (!model.ann.isValidStruc())
+ {
+ throw new IllegalArgumentException("Invalid RNA structure annotation");
+ }
+
+ try
+ {
+ FullBackup fromSession = vab.vp.loadSession(sessionFile);
+ vab.addStructure(fromSession.rna, fromSession.config);
+ RNA rna = fromSession.rna;
+ // copy the model, but now including the RNA object
+ RnaModel newModel = new RnaModel(model.title, model.ann, model.seq,
+ rna, model.gapped);
+ if (!model.gapped)
+ {
+ registerOffset(rna, buildOffset(model.seq));
+ }
+ models.put(rna, newModel);
+ // capture rna selection state when saved
+ selectionHighlighter = new VarnaHighlighter(rna);
+ return fromSession.rna;
+ } catch (ExceptionLoadingFailed e)
+ {
+ System.err
+ .println("Error restoring Varna session: " + e.getMessage());
+ return null;
+ }
+ }
}
*/
package jalview.gui;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.JalviewVarnaBinding;
+import jalview.structure.AtomSpec;
+import jalview.util.MessageManager;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import fr.orsay.lri.varna.models.VARNAConfig;
import fr.orsay.lri.varna.models.rna.RNA;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.JalviewVarnaBinding;
-import jalview.structure.AtomSpec;
-import jalview.util.MessageManager;
-
public class AppVarnaBinding extends JalviewVarnaBinding
{
public VARNAPanel vp;
- // remove unused (commented out) fields?
- // protected JPanel _tools = new JPanel();
- //
- // private JPanel _input = new JPanel();
- //
- // private JPanel _strPanel = new JPanel();
- //
- // private JTextField _str = new JTextField();
- //
- // private JTextField _seq = new JTextField();
- //
- // private JLabel _strLabel = new JLabel(
- // MessageManager.getString("label.str"));
- //
- // private JButton _updateButton = new JButton(
- // MessageManager.getString("action.update"));
- //
- // private JButton _deleteButton = new JButton(
- // MessageManager.getString("action.delete"));
- //
- // private JButton _duplicateButton = new JButton(
- // MessageManager.getString("action.snapshot"));
- //
protected JPanel _listPanel = new JPanel();
private ReorderableJList _sideList = null;
vp.setBackground(_backgroundColor);
- // MC commented out stuff not added to panel - remove?
- // Font textFieldsFont = Font.decode("MonoSpaced-PLAIN-12");
- //
- // _seq.setFont(textFieldsFont);
- // if (!rnaList.isEmpty())
- // {
- // _seq.setText(rnaList.get(0).getSeq());
- // }
-
- // _updateButton.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // FullBackup sel = (FullBackup) _sideList.getSelectedValue();
- // sel.rna.setSequence("A");
- // }
- // });
- //
- // _strLabel.setPreferredSize(new Dimension(marginTools, 15));
- // _strLabel.setHorizontalTextPosition(JLabel.LEFT);
- // _str.setFont(textFieldsFont);
- // _strPanel.setLayout(new BorderLayout());
- // _strPanel.add(_strLabel, BorderLayout.WEST);
- // _strPanel.add(_str, BorderLayout.CENTER);
- //
- // _input.setLayout(new GridLayout(1, 0));
- // _input.add(_strPanel);
- //
- // JPanel goPanel = new JPanel();
- // goPanel.setLayout(new BorderLayout());
- //
- // _tools.setLayout(new BorderLayout());
- // _tools.add(_input, BorderLayout.CENTER);
- // _tools.add(goPanel, BorderLayout.EAST);
- //
- // goPanel.add(_updateButton, BorderLayout.CENTER);
- //
- // JPanel ops = new JPanel();
- // ops.setLayout(new GridLayout(1, 2));
- // ops.add(_deleteButton);
- // ops.add(_duplicateButton);
-
JLabel j = new JLabel(
MessageManager.getString("label.structures_manager"),
JLabel.CENTER);
*/
package jalview.gui;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.ws.params.AutoCalcSetting;
import jalview.ws.params.WsParamSetI;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
"varna");
- RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped,
- tempStateFile);
- appVarna.addModel(rna, rnaTitle);
+ RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
+ appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
appVarna.setInitialSelection(viewer.getSelectedRna());
}
git://source.jalview.org / jalview.git / commitdiff