import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.ext.archaeopteryx.AptxInit;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeViewerUtils;
import jalview.ext.varna.RnaModel;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
+import jalview.io.NewickFile;
import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
jms.addTree(tree);
}
}
+
+ }
+ }
+ }
+ if (!storeDS && av.getCurrentExtTree() != null)
+ {
+ Set<TreeFrameI> externalTreeViews = TreeViewerUtils
+ .getActiveTreeViews()
+ .keySet();
+ for (TreeFrameI treeView : externalTreeViews)
+ {
+ TreeI tree = treeView.getTree();
+ try
+ {
+ tree.writeToXml(new File("word"));
+ copyFileToJar(jout, "word", "aptx-test");
+
+
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
+
}
+
}
+
+
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
String varnaStateFile = varna.getStateInfo(model.rna);
jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
- copyFileToJar(jout, varnaStateFile, jarEntryName);
+
rnaSessions.put(model, jarEntryName);
}
SecondaryStructure ss = new SecondaryStructure();
if (loadTreesAndStructures)
{
loadTrees(jms, view, af, av, ap);
+ loadExternalTrees(jprovider, jms, av);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
}
// and finally return.
return af;
}
+
+ private void loadExternalTrees(jarInputStreamProvider jprovider,
+ JalviewModelSequence jms, AlignViewport av)
+ {
+ String treeFile = copyJarEntry(jprovider, "aptx-test", "aptx", null);
+ if (treeFile != null)
+ {
+ try
+ {
+ AptxInit.createInstancesFromFile(treeFile, av);
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ }
+
+
/**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
{
Tree tree = jms.getTree(t);
+ NewickFile newick = new jalview.io.NewickFile(tree.getNewick());
+
+ TreeFrameI externalViewer = AptxInit.createInstanceFromNhx(
+ tree.getTitle(), tree.getNewick(),
+ av);
+
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
+
+
tp = af.showNewickTree(
- new jalview.io.NewickFile(tree.getNewick()),
+ newick,
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
if (tree.getId() != null)
if (this.frefedSequence == null)
{
- frefedSequence = new Vector<SeqFref>();
+ frefedSequence = new Vector<>();
}
viewportsAdded.clear();