import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
-import jalview.ext.archaeopteryx.ArchaeopteryxFrame;
+import jalview.ext.archaeopteryx.AptxInit;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
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);
- ArchaeopteryxFrame.createInstance(calculatedTree);
// 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
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;
+ }
}