import jalview.io.NewickFile;
import jalview.jbgui.GTreePanel;
import jalview.schemes.ResidueProperties;
+import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
{
NewickFile newtree;
- jalview.datamodel.AlignmentView odata = null;
+ AlignmentView odata = null;
public TreeLoader(NewickFile newtree)
{
buffer.append("PID");
}
- jalview.io.NewickFile fout = new jalview.io.NewickFile(
- tree.getTopNode());
+ NewickFile fout = new NewickFile(tree.getTopNode());
try
{
cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
public void saveAsNewick_actionPerformed(ActionEvent e)
{
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"));
chooser.setToolTipText(MessageManager.getString("action.save"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
try
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(
- tree.getTopNode());
+ NewickFile fout = new NewickFile(tree.getTopNode());
String output = fout.print(tree.isHasBootstrap(),
tree.isHasDistances(), tree.isHasRootDistance());
java.io.PrintWriter out = new java.io.PrintWriter(
{
if (!tree.hasOriginalSequenceData())
{
- jalview.bin.Cache.log
+ Cache.log
.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
{
boolean accurateText = true;
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+ String renderStyle = Cache.getDefault("EPS_RENDERING",
"Prompt each time");
// If we need to prompt, and if the GUI is visible then
try
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "eps" }, new String[]
{ "Encapsulated Postscript" }, "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
int value = chooser.showSaveDialog(this);
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
try
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"), new String[]
{ "png" }, new String[]
{ "Portable network graphics" }, "Portable network graphics");
- chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ Cache.setProperty("LAST_DIRECTORY", chooser
.getSelectedFile().getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
if (sq != null)
{
// search dbrefs, features and annotation
- DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+ DBRefEntry[] refs = DBRefUtils.selectRefs(
sq.getDBRef(), new String[]
{ labelClass.toUpperCase() });
if (refs != null)