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JAL-2805 First try at loading tree through Forester by calling Aptx main
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
9764bb7
..
4e3df8b
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-60,6
+60,8
@@
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.ext.forester.io.SupportedTreeFileFilter;
+import jalview.ext.forester.io.TreeParser;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
@@
-2712,8
+2714,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
- true);
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
if (!copyAnnotation)
{
/*
@@
-3553,7
+3554,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.followSelection = listenToViewSelections.isSelected();
}
viewport.followSelection = listenToViewSelections.isSelected();
}
-
/**
* Constructs a tree panel and adds it to the desktop
*
/**
* Constructs a tree panel and adds it to the desktop
*
@@
-3577,7
+3577,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- for (SequenceI _s : sg.getSequences())
+ for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
{
if (_s.getLength() < sg.getEndRes())
{
{
if (_s.getLength() < sg.getEndRes())
{
@@
-3884,9
+3884,13
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
- MessageManager.getString("label.select_newick_like_tree_file"));
+ MessageManager.getString("label.select_newick_like_tree_file")); // modify
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
+ for (SupportedTreeFileFilter treeFormat : SupportedTreeFileFilter.values())
+ {
+ chooser.setFileFilter(treeFormat.getTreeFilter());
+ }
int value = chooser.showOpenDialog(null);
int value = chooser.showOpenDialog(null);
@@
-3894,9
+3898,15
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
{
String filePath = chooser.getSelectedFile().getPath();
Cache.setProperty("LAST_DIRECTORY", filePath);
+
NewickFile fin = null;
try
{
NewickFile fin = null;
try
{
+ TreeParser treeParser = new TreeParser(filePath);
+ treeParser.loadTree();
+
+
+
fin = new NewickFile(filePath, DataSourceType.FILE);
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
fin = new NewickFile(filePath, DataSourceType.FILE);
viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
} catch (Exception ex)
@@
-4155,7
+4165,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
buildingMenu = false;
}
}
buildingMenu = false;
}
- }).start();
+ }, "BuildWebServiceThread").start();
}
}
@@
-4263,7
+4273,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
final String source)
{
- new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this))
+ new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this),
+ "CrossReferencesThread")
.start();
}
.start();
}
@@
-4542,7
+4553,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
- }).start();
+ }, "DropFileThread").start();
}
}
}
}
@@
-4913,7
+4924,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
});
dbRefFetcher.fetchDBRefs(false);
}
});
dbRefFetcher.fetchDBRefs(false);
}
- }).start();
+ }, "BuildFetchDBMenuThread").start();
}
}