- /**
- * Open a new Tree panel on the desktop
- *
- * @param modelName
- * @param params
- */
- protected void openTreePanel(String modelName, SimilarityParamsI params)
+ 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
+ {
+ String treeAlgorithm = neighbourJoining.isSelected()
+ ? TreeBuilder.NEIGHBOUR_JOINING
+ : TreeBuilder.AVERAGE_DISTANCE;
+
+ return treeAlgorithm;
+
+ }
+
+ protected void checkEnoughSequences(AlignViewport viewport)