import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
- buildTreeMenu();
+ calculateTree.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new TreeChooser(AlignFrame.this);
+ }
+ });
buildColourMenu();
if (Desktop.desktop != null)
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "PID", "Average distance tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "PID", "Neighbour joining tree using PID");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- @Override
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- newTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
- }
-
- /**
- * DOCUMENT ME!
- *
* @param type
* DOCUMENT ME!
* @param pwType
* call. Listeners are added to remove the menu item when the treePanel is
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
- *
- * @param treePanel
- * Displayed tree window.
- * @param title
- * SortBy menu item title.
*/
@Override
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
- calculateTree.removeAll();
- // build the calculate menu
-
- for (final String type : new String[] { "NJ", "AV" })
- {
- String treecalcnm = MessageManager.getString("label.tree_calc_"
- + type.toLowerCase());
- for (final String pwtype : ResidueProperties.scoreMatrices.keySet())
- {
- JMenuItem tm = new JMenuItem();
- ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
- if (sm.isDNA() == viewport.getAlignment().isNucleotide()
- || sm.isProtein() == !viewport.getAlignment()
- .isNucleotide())
- {
- String smn = MessageManager.getStringOrReturn(
- "label.score_model_", sm.getName());
- final String title = MessageManager.formatMessage(
- "label.treecalc_title", treecalcnm, smn);
- tm.setText(title);//
- tm.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- newTreePanel(type, pwtype, title);
- }
- });
- calculateTree.add(tm);
- }
-
- }
- }
sortByTreeMenu.removeAll();
List<Component> comps = PaintRefresher.components.get(viewport
ColourMenuHelper.setColourSelected(colourMenu, schemeName);
}
+
+ public void newTreePanel(String treeType, ScoreModelI sm)
+ {
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + treeType.toLowerCase());
+ String smn = MessageManager.getStringOrReturn("label.score_model_",
+ sm.getName());
+ final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ treecalcnm, smn);
+ newTreePanel(treeType, sm.getName(), ttl);
+ }
}
class PrintThread extends Thread