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Start of creating the objects Archaeopteryx needs
[jalview.git]
/
src
/
jalview
/
gui
/
CalculationChooser.java
diff --git
a/src/jalview/gui/CalculationChooser.java
b/src/jalview/gui/CalculationChooser.java
index
f2d65e5
..
bd6c5ee
100644
(file)
--- a/
src/jalview/gui/CalculationChooser.java
+++ b/
src/jalview/gui/CalculationChooser.java
@@
-460,26
+460,26
@@
public class CalculationChooser extends JPanel
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
- String modelName = modelNames.getSelectedItem().toString();
+ String substitutionMatrix = modelNames.getSelectedItem().toString();
SimilarityParamsI params = getSimilarityParameters(doPCA);
if (doPCA)
{
SimilarityParamsI params = getSimilarityParameters(doPCA);
if (doPCA)
{
- openPcaPanel(modelName, params);
+ openPcaPanel(substitutionMatrix, params);
}
else
{
}
else
{
- calculateTree();
- openTreePanel(modelName, params);
+
+ String treeAlgo = determineTreeAlgo();
+ // TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
+ // substitutionMatrix, params);
+
+ openTreePanel(treeAlgo, substitutionMatrix, params);
}
// closeFrame();
}
}
// closeFrame();
}
- protected void calculateTree()
- {
-
- }
protected String determineTreeAlgo() // to be modified & expanded
{
String treeAlgorithm = neighbourJoining.isSelected()
protected String determineTreeAlgo() // to be modified & expanded
{
String treeAlgorithm = neighbourJoining.isSelected()
@@
-509,7
+509,8
@@
public class CalculationChooser extends JPanel
* Open a new Tree panel on the desktop
*
*/
* Open a new Tree panel on the desktop
*
*/
- protected void openTreePanel(String modelName, SimilarityParamsI params)
+ protected void openTreePanel(String treeType, String substitutionMatrix,
+ SimilarityParamsI params)
{
/*
* gui validation shouldn't allow insufficient sequences here, but leave
{
/*
* gui validation shouldn't allow insufficient sequences here, but leave
@@
-517,9
+518,9
@@
public class CalculationChooser extends JPanel
*/
checkEnoughSequences(af.getViewport());
*/
checkEnoughSequences(af.getViewport());
- String treeType = determineTreeAlgo();
- af.newTreePanel(treeType, modelName, params);
+
+ af.newTreePanel(treeType, substitutionMatrix, params);
}
/**
}
/**