final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
/**
* Constructor
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ final JComboBox<String> scoreModelsCombo = new JComboBox<>();
scoreModelsCombo.setRenderer(renderer);
/*
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
/*
* now we can actually add entries to the combobox,
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
- String modelName = modelNames.getSelectedItem().toString();
+ String substitutionMatrix = modelNames.getSelectedItem().toString();
SimilarityParamsI params = getSimilarityParameters(doPCA);
if (doPCA)
{
- openPcaPanel(modelName, params);
+ openPcaPanel(substitutionMatrix, params);
}
else
{
- openTreePanel(modelName, params);
+
+ String treeAlgo = determineTreeAlgo();
+ // TreeCalculator calculateTree = new TreeCalculator(treeAlgo,
+ // substitutionMatrix, params);
+
+ openTreePanel(treeAlgo, substitutionMatrix, params);
}
// closeFrame();
}
- /**
- * Open a new Tree panel on the desktop
- *
- * @param modelName
- * @param params
- */
- protected void openTreePanel(String modelName, SimilarityParamsI params)
+ protected String determineTreeAlgo() // to be modified & expanded
+ {
+ String treeAlgorithm = neighbourJoining.isSelected()
+ ? TreeBuilder.NEIGHBOUR_JOINING
+ : TreeBuilder.AVERAGE_DISTANCE;
+
+ return treeAlgorithm;
+
+ }
+
+ protected void checkEnoughSequences(AlignViewport viewport)
{
- /*
- * gui validation shouldn't allow insufficient sequences here, but leave
- * this check in in case this method gets exposed programmatically in future
- */
- AlignViewport viewport = af.getViewport();
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
JvOptionPane.WARNING_MESSAGE);
return;
}
+ }
- String treeType = neighbourJoining.isSelected()
- ? TreeBuilder.NEIGHBOUR_JOINING
- : TreeBuilder.AVERAGE_DISTANCE;
- af.newTreePanel(treeType, modelName, params);
+ /**
+ * Open a new Tree panel on the desktop
+ *
+ */
+ protected void openTreePanel(String treeType, String substitutionMatrix,
+ SimilarityParamsI params)
+ {
+ /*
+ * gui validation shouldn't allow insufficient sequences here, but leave
+ * this check in in case this method gets exposed programmatically in future
+ */
+ checkEnoughSequences(af.getViewport());
+
+
+
+ af.newTreePanel(treeType, substitutionMatrix, params);
}
/**
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
+
return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
matchOnShortestLength);
}