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JAL-2884 old Newick trees are now loaded in as Aptx as well
author
kjvdheide
<kjvanderheide@dundee.ac.uk>
Thu, 11 Jan 2018 14:11:44 +0000
(14:11 +0000)
committer
kjvdheide
<kjvanderheide@dundee.ac.uk>
Thu, 11 Jan 2018 14:11:44 +0000
(14:11 +0000)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
4a15024
..
7c10544
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-37,10
+37,15
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
import jalview.datamodel.StructureViewerModel.StructureData;
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.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;
import jalview.renderer.ResidueShaderI;
import jalview.schemabinding.version2.AlcodMap;
import jalview.schemabinding.version2.AlcodonFrame;
@@
-1095,9
+1100,24
@@
public class Jalview2XML
jms.addTree(tree);
}
}
jms.addTree(tree);
}
}
+
}
}
}
}
}
}
+ if (!storeDS && av.getCurrentExtTree() != null)
+ {
+ Set<TreeFrameI> externalTreeViews = TreeViewerUtils
+ .getActiveTreeViews()
+ .keySet();
+ for (TreeFrameI treeView : externalTreeViews)
+ {
+ TreeI tree = treeView.getTree();
+ // tree.writeToJalviewProject(outputFile);
+
+ }
+
+ }
+
// SAVE ANNOTATIONS
/**
// SAVE ANNOTATIONS
/**
@@
-3653,12
+3673,20
@@
public class Jalview2XML
{
Tree tree = jms.getTree(t);
{
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)
{
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
+
+
tp = af.showNewickTree(
tp = af.showNewickTree(
- new jalview.io.NewickFile(tree.getNewick()),
+ newick,
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
if (tree.getId() != null)
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
if (tree.getId() != null)
@@
-5333,7
+5361,7
@@
public class Jalview2XML
if (this.frefedSequence == null)
{
if (this.frefedSequence == null)
{
- frefedSequence = new Vector<SeqFref>();
+ frefedSequence = new Vector<>();
}
viewportsAdded.clear();
}
viewportsAdded.clear();