import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
-import jalview.ext.archaeopteryx.ArchaeopteryxTreeBuilder;
+import jalview.ext.archaeopteryx.ArchaeopteryxInit;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
List<String> tips = new ArrayList<>();
+ /*
+ * the most recently opened PCA results panel
+ */
+ private PCAPanel pcaPanel;
+
/**
* Constructor
*
TreeBuilder calculatedTree = treeCalculator
.makeTree(af.getViewport());
TreeModel tree = new TreeModel(calculatedTree);
- openTreePanel(tree, treeAlgo, params);
- ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+ openTreePanel(tree, treeAlgo, substitutionMatrix);
+ ArchaeopteryxInit.createInstance(calculatedTree);
+
}
// closeFrame();
}
+
+
+
protected String determineTreeAlgo() // to be modified & expanded
{
String treeAlgorithm = neighbourJoining.isSelected()
* @param treeAlgo
*/
protected void openTreePanel(TreeModel tree, String treeAlgo,
- SimilarityParamsI params)
+ String substitutionMatrix)
{
/*
* gui validation shouldn't allow insufficient sequences here, but leave
*/
checkEnoughSequences(af.getViewport());
- af.newTreePanel(tree, treeAlgo, params);
+ af.newTreePanel(tree, treeAlgo, substitutionMatrix);
}
/**
JvOptionPane.WARNING_MESSAGE);
return;
}
- new PCAPanel(af.alignPanel, modelName, params);
+ pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
}
/**
{
}
}
+
+ public PCAPanel getPcaPanel()
+ {
+ return pcaPanel;
+ }
}