import jalview.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+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.AlignFrame;
import jalview.gui.AlignViewport;
object.getTree().add(tree);
}
}
+
}
}
}
+ if (!storeDS && av.getCurrentExtTree() != null)
+ {
+ Set<TreeFrameI> externalTreeViews = TreeViewerUtils
+ .getActiveTreeViews()
+ .keySet();
+ for (TreeFrameI treeView : externalTreeViews)
+ {
+ TreeI tree = treeView.getTree();
+ try
+ {
+ tree.outputAsFile(new File("word"));
+ copyFileToJar(jout, "word", "aptx-test","Archeopteryx Tree Session");
+
+
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+
+ }
+
+
/*
* save PCA viewers
if (loadTreesAndStructures)
{
loadTrees(jalviewModel, view, af, av, ap);
+ loadExternalTrees(jprovider, jalviewModel, av);
loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
// and finally return.
return af;
}
+
+ private void loadExternalTrees(jarInputStreamProvider jprovider,
+ JalviewModel jms, AlignViewport av)
+ {
+ // TODO: allow more than one archeopteryx session per project
+ 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 = jm.getTree().get(t);
+ TreeFrameI externalViewer = AptxInit.createInstanceFromNhx(
+ tree.getTitle(), tree.getNewick(),
+ av);
+
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{