sn.setElement(sequences[i]);
sn.setName(sequences[i].getName());
node.addElement(sn);
+
BitSet bs = new BitSet();
bs.set(i);
clusters.addElement(bs);
String treeType;
String scoreModelName; // if tree computed
+
/**
*
* @param treeAlgo
* @param substitutionMatrix
- * @param params
+ * @param calculateParams
*/
public TreeCalculator(String treeAlgo, String substitutionMatrix,
SimilarityParamsI calculateParams)
this.similarityParams = calculateParams;
}
+ /**
+ *
+ * @param alignViewport
+ * @return
+ */
public TreeBuilder makeTree(AlignViewport alignViewport)
{
ScoreModelI sm = ScoreModels.getInstance().getScoreModel(scoreModelName,
package jalview.ext.archaeopteryx;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
+import jalview.datamodel.SequenceI;
+import jalview.math.MatrixI;
import org.forester.phylogeny.Phylogeny;
-import org.forester.phylogeny.PhylogenyNode;
-public class ArchaeopteryxTreeBuilder extends Phylogeny
+public class ArchaeopteryxTreeBuilder extends Phylogeny // cannot inherit
+ // TreeBuilder as that
+ // demands the use of
+ // SequenceNode (instead
+ // of PhylogenyNode)
{
- List<PhylogenyNode> nodes = Collections
- .synchronizedList(new ArrayList<PhylogenyNode>());
+ protected SequenceI[] sequences;
+
+ protected MatrixI distances;
+
+ public ArchaeopteryxTreeBuilder(TreeModel treeModel)
+ {
+
+ }
+
+ public ArchaeopteryxTreeBuilder(TreeBuilder tree)
+ {
+
+ }
}
TreeModel tree = new TreeModel(calculatedTree);
openTreePanel(tree, treeAlgo, substitutionMatrix);
- ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
+ ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder(
+ tree);
}
*
* @param ap
* @param tree
+ * @param treeType
+ * @param substitutionMatrix
*/
public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
String substitutionMatrix)
* @param newtree
* @param theTitle
* @param inputData
- * @param viewport
*/
public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
String theTitle, AlignmentView inputData)