import jalview.api.FeatureSettingsControllerI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
*
*/
void newTreePanel(TreeModel tree, String treeAlgo,
- SimilarityParamsI params)
+ String substitutionMatrix)
{
String frameTitle = "";
TreePanel tp;
}
}
- tp = new TreePanel(alignPanel, tree, treeAlgo, params);
+ tp = new TreePanel(alignPanel, tree, treeAlgo, substitutionMatrix);
frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
frameTitle += " from ";
TreeBuilder calculatedTree = treeCalculator
.makeTree(af.getViewport());
TreeModel tree = new TreeModel(calculatedTree);
- openTreePanel(tree, treeAlgo, params);
+ openTreePanel(tree, treeAlgo, substitutionMatrix);
ArchaeopteryxTreeBuilder aptxTree = new ArchaeopteryxTreeBuilder();
* @param treeAlgo
*/
protected void openTreePanel(TreeModel tree, String treeAlgo,
- SimilarityParamsI params)
+ String substitutionMatrix)
{
/*
* gui validation shouldn't allow insufficient sequences here, but leave
*/
checkEnoughSequences(af.getViewport());
- af.newTreePanel(tree, treeAlgo, params);
+ af.newTreePanel(tree, treeAlgo, substitutionMatrix);
}
/**
import jalview.analysis.AlignmentSorter;
import jalview.analysis.TreeModel;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
*/
public class TreePanel extends GTreePanel
{
-
- SimilarityParamsI similarityParams;
+ String substitutionMatrix;
String treeType;
- String scoreModelName; // if tree computed
-
String treeTitle; // if tree loaded
TreeCanvas treeCanvas;
* @param tree
*/
public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
- SimilarityParamsI params)
+ String substitutionMatrix)
{
super();
this.treeType = treeType;
- this.similarityParams = params;
+ this.substitutionMatrix = substitutionMatrix;
this.tree = tree;
initNewTreePanel(ap, tree);
/*
* short score model name (long description can be too long)
*/
- String smn = scoreModelName;
+ String smn = substitutionMatrix;
/*
* put them together as <method> Using <model>