*/
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;
+ }
+ }
}