import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
-import jalview.ext.archaeopteryx.ArchaeopteryxTreeBuilder;
+import jalview.ext.archaeopteryx.AptxInit;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.archaeopteryx.MainFrame;
-import org.forester.phylogeny.Phylogeny;
-
/**
* A dialog where a user can choose and action Tree or PCA calculation options
*/
List<String> tips = new ArrayList<>();
+ /*
+ * the most recently opened PCA results panel
+ */
+ private PCAPanel pcaPanel;
+
/**
* Constructor
*
}
else
{
+ createTree(substitutionMatrix, params);
+
+
+
+
- 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);
-
- ArchaeopteryxTreeBuilder aptxTreeBuilder = new ArchaeopteryxTreeBuilder();
- Phylogeny aptxTree = aptxTreeBuilder.buildAptxTree(calculatedTree);
- MainFrame aptxFrame = Archaeopteryx.createApplication(aptxTree);
-
- int width = 400;
- int height = 550;
- aptxFrame.setMinimumSize(new Dimension(width - 30, height - 50)); // doesn't
- // work
- // as it
- // gets
- // overridden
- // during
- // addInternalFrame?
-
- Desktop.addInternalFrame(aptxFrame, "Archaeopteryx Tree View",
- width, height, true);
}
// closeFrame();
}
+ protected void createTree(String substitutionMatrix,
+ SimilarityParamsI params)
+ {
+ String treeAlgo = determineTreeAlgo();
+ TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
+ substitutionMatrix, params);
+ TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
+
+ AptxInit.createInstance(calculatedTree);
+
+ TreeModel tree = new TreeModel(calculatedTree);
+ openTreePanel(tree, treeAlgo, substitutionMatrix);
+ }
+
+
protected String determineTreeAlgo() // to be modified & expanded
{
String treeAlgorithm = neighbourJoining.isSelected()
JvOptionPane.WARNING_MESSAGE);
return;
}
- new PCAPanel(af.alignPanel, modelName, params);
+ pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
}
/**
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
-
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
}
{
}
}
+
+ public PCAPanel getPcaPanel()
+ {
+ return pcaPanel;
+ }
}