import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
-import jalview.ext.archaeopteryx.ArchaeopteryxInit;
+import jalview.ext.archaeopteryx.AptxInit;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.beans.PropertyVetoException;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* Open and calculate the selected tree or PCA on 'OK'
+ *
+ * @throws IOException
*/
protected void calculate_actionPerformed()
{
}
else
{
+ try
+ {
+ createTree(substitutionMatrix, params);
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
- String treeAlgo = determineTreeAlgo();
- TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
- substitutionMatrix, params);
- TreeBuilder calculatedTree = treeCalculator
- .makeTree(af.getViewport());
- TreeModel tree = new TreeModel(calculatedTree);
- openTreePanel(tree, treeAlgo, substitutionMatrix);
- ArchaeopteryxInit.createInstance(calculatedTree);
// closeFrame();
}
-
+ protected void createTree(String substitutionMatrix,
+ SimilarityParamsI params) throws IOException
+ {
+ String treeAlgo = determineTreeAlgo();
+ TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
+ substitutionMatrix, params);
+ TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
+
+ // AptxInit.createInstanceFromCalculation(calculatedTree);
+
+ TreeModel tree = new TreeModel(calculatedTree);
+ jalview.io.NewickFile newick = new jalview.io.NewickFile(
+ tree.getTopNode());
+ String output = newick.print(tree.hasBootstrap(), tree.hasDistances(),
+ tree.hasRootDistance());
+ AptxInit.createInstanceFromNhx(af.getTitle(), output,
+ af.getViewport());
+ // openTreePanel(tree, treeAlgo, substitutionMatrix);
+ }
protected String determineTreeAlgo() // to be modified & expanded
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
-
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
}