+ this.treeType = treeAlgo;
+ this.scoreModelName = substitutionMatrix;
+ this.similarityParams = calculateParams;
+ }
+
+ /**
+ *
+ * @param alignViewport
+ * @return
+ */
+ public TreeBuilder makeTree(AlignViewport alignViewport)
+ {
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
+ alignViewport.getAlignPanel());
+
+ TreeBuilder builtTree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(alignViewport, sm, similarityParams)
+ : new AverageDistanceTree(alignViewport, sm, similarityParams);
+
+ return builtTree;
+
+ }
+
+ public SimilarityParamsI getSimilarityParams()
+ {
+ return similarityParams;
+ }
+
+ public void setSimilarityParams(SimilarityParamsI similarityParams)
+ {
+ this.similarityParams = similarityParams;
+ }
+
+ public String getTreeType()
+ {
+ return treeType;
+ }
+
+ public void setTreeType(String treeType)
+ {
+ this.treeType = treeType;