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Added TreeBuilder as parameter to the converter constructor
[jalview.git]
/
src
/
jalview
/
gui
/
CalculationChooser.java
diff --git
a/src/jalview/gui/CalculationChooser.java
b/src/jalview/gui/CalculationChooser.java
index
d0315a6
..
ebb12b9
100644
(file)
--- a/
src/jalview/gui/CalculationChooser.java
+++ b/
src/jalview/gui/CalculationChooser.java
@@
-28,7
+28,7
@@
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.SequenceGroup;
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;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
@@
-108,6
+108,11
@@
public class CalculationChooser extends JPanel
List<String> tips = new ArrayList<>();
List<String> tips = new ArrayList<>();
+ /*
+ * the most recently opened PCA results panel
+ */
+ private PCAPanel pcaPanel;
+
/**
* Constructor
*
/**
* Constructor
*
@@
-478,10
+483,13
@@
public class CalculationChooser extends JPanel
substitutionMatrix, params);
TreeBuilder calculatedTree = treeCalculator
.makeTree(af.getViewport());
substitutionMatrix, params);
TreeBuilder calculatedTree = treeCalculator
.makeTree(af.getViewport());
+
+ ArchaeopteryxInit.createInstance(calculatedTree);
+
TreeModel tree = new TreeModel(calculatedTree);
openTreePanel(tree, treeAlgo, substitutionMatrix);
TreeModel tree = new TreeModel(calculatedTree);
openTreePanel(tree, treeAlgo, substitutionMatrix);
- ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+
}
}
@@
-489,6
+497,9
@@
public class CalculationChooser extends JPanel
// closeFrame();
}
// closeFrame();
}
+
+
+
protected String determineTreeAlgo() // to be modified & expanded
{
String treeAlgorithm = neighbourJoining.isSelected()
protected String determineTreeAlgo() // to be modified & expanded
{
String treeAlgorithm = neighbourJoining.isSelected()
@@
-561,7
+572,7
@@
public class CalculationChooser extends JPanel
JvOptionPane.WARNING_MESSAGE);
return;
}
JvOptionPane.WARNING_MESSAGE);
return;
}
- new PCAPanel(af.alignPanel, modelName, params);
+ pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
}
/**
}
/**
@@
-603,7
+614,6
@@
public class CalculationChooser extends JPanel
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
-
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
}
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
}
@@
-620,4
+630,9
@@
public class CalculationChooser extends JPanel
{
}
}
{
}
}
+
+ public PCAPanel getPcaPanel()
+ {
+ return pcaPanel;
+ }
}
}