import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
}
else
{
- ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName,
- treeCanvas.getAssociatedPanel());
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+ scoreModelName, treeCanvas.getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
{
// TODO: JAL-3048 save newick file for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_tree_as_newick"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
try
AlignmentView originalData = tree.getOriginalData();
if (originalData == null)
{
- jalview.bin.Cache.log.info(
+ Console.info(
"Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
}
else
{
- treeCanvas.getAssociatedPanel().alignFrame
- .addHistoryItem(
- sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+ treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
- exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
+ exporter.doExport(null, this, width, height,
+ tree.toLowerCase(Locale.ROOT));
}
/**
/*
* i18n description of Neighbour Joining or Average Distance method
*/
- String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
+ String treecalcnm = MessageManager.getString(
+ "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
/*
* short score model name (long description can be too long)
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
- FileOutputStream out = new FileOutputStream(
- outFile);
+ FileOutputStream out = new FileOutputStream(outFile);
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
height);
pg.setAccurateTextMode(!textOption);
ex.printStackTrace();
}
}
-
+
public AlignViewport getViewport()
{
return av;