import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
-import jalview.io.FileFormat;
+import jalview.io.FileFormats;
import jalview.util.MessageManager;
import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Component;
import java.awt.GridLayout;
import java.awt.Toolkit;
import java.awt.event.ActionEvent;
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu colourMenu = new JMenu();
-
protected JMenu webService = new JMenu();
+ protected JMenu hmmerMenu = new JMenu();
+
+ protected JCheckBoxMenuItem autoAlignSeqs = new JCheckBoxMenuItem();
+
+ protected JMenuItem hmmAlign = new JMenuItem();
+
+ protected JMenuItem hmmSearch = new JMenuItem();
+
+ protected JMenuItem hmmBuild = new JCheckBoxMenuItem();
+
protected JMenuItem webServiceNoServices;
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JMenu outputTextboxMenu = new JMenu();
- protected JRadioButtonMenuItem textColour;
-
- protected JRadioButtonMenuItem userDefinedColour;
-
protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem;
-
- protected JRadioButtonMenuItem noColourmenuItem;
-
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem abovePIDThreshold;
-
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
JMenuItem copy = new JMenuItem();
JMenu pasteMenu = new JMenu();
- protected JCheckBoxMenuItem applyToAllGroups;
-
protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem modifyPID;
+ protected JCheckBoxMenuItem applyToAllGroups;
+
+ protected JMenu colourMenu = new JMenu();
+
+ protected JMenuItem textColour;
+
+ protected JCheckBoxMenuItem conservationMenuItem;
protected JMenuItem modifyConservation;
+ protected JCheckBoxMenuItem abovePIDThreshold;
+
+ protected JMenuItem modifyPID;
+
protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JMenu sort = new JMenu();
- protected JMenu calculateTree = new JMenu();
+ protected JMenuItem calculateTree = new JMenuItem();
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private SequenceAnnotationOrder annotationSortOrder;
private boolean showAutoCalculatedAbove = false;
- private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
private SplitContainerI splitFrame;
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
}
}
- /**
- * Marks as selected the colour menu item matching the given name, or the
- * first item ('None') if no match is found
- *
- * @param colourName
- */
- protected void setColourSelected(String colourName)
- {
- noColourmenuItem.setSelected(true);
- if (colourName == null)
- {
- return;
- }
-
- /*
- * look for a radio button with a name that matches the colour name
- * (note the button text may not as it may be internationalised)
- */
- for (Component menuItem : colourMenu.getMenuComponents())
- {
- if (menuItem instanceof JRadioButtonMenuItem)
- {
- if (colourName.equals(((JRadioButtonMenuItem) menuItem).getName()))
- {
- ((JRadioButtonMenuItem) menuItem).setSelected(true);
- return;
- }
- }
- }
- }
-
private void jbInit() throws Exception
{
initColourMenu();
+ initHMMERMenu();
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
JMenu calculateMenu = new JMenu(
MessageManager.getString("action.calculate"));
webService.setText(MessageManager.getString("action.web_service"));
+ hmmerMenu.setText(MessageManager.getString("action.hmmer"));
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- JMenuItem PCAMenuItem = new JMenuItem(
- MessageManager.getString("label.principal_component_analysis"));
- PCAMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PCAMenuItem_actionPerformed(e);
- }
- });
- JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_identity"));
- averageDistanceTreeMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- averageDistanceTreeMenuItem_actionPerformed(e);
- }
- });
- JMenuItem neighbourTreeMenuItem = new JMenuItem(
- MessageManager.getString("label.neighbour_joining_identity"));
- neighbourTreeMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- neighbourTreeMenuItem_actionPerformed(e);
- }
- });
this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
outputTextboxMenu.setText(MessageManager
.getString("label.out_to_textbox"));
-
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.average_distance_blosum62"));
- avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- avTreeBlosumMenuItem_actionPerformed(e);
- }
- });
- JMenuItem njTreeBlosumMenuItem = new JMenuItem(
- MessageManager.getString("label.neighbour_blosum62"));
- njTreeBlosumMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- njTreeBlosumMenuItem_actionPerformed(e);
- }
- });
annotationPanelMenuItem.setActionCommand("");
annotationPanelMenuItem.setText(MessageManager
.getString("label.show_annotations"));
});
JMenuItem createGroup = new JMenuItem(
- MessageManager.getString("action.create_groups"));
+ MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
@Override
public void menuSelected(MenuEvent e)
{
- buildTreeMenu();
+ buildTreeSortMenu();
}
@Override
});
sortByAnnotScore.setVisible(false);
- calculateTree
- .setText(MessageManager.getString("action.calculate_tree"));
+ calculateTree.setText(MessageManager
+ .getString("action.calculate_tree_pca"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
padGapsMenuitem.setState(jalview.bin.Cache
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
idRightAlign.setText(MessageManager
.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
+ alignFrameMenuBar.add(hmmerMenu);
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
calculateMenu.add(showReverse);
/**
* Constructs the entries on the Colour menu (but does not add them to the
- * menu). The 'name' property of each item is set to the canonical name of the
- * corresponding colour scheme (may not match the display name), to allow
- * selection of items by colour scheme name.
+ * menu).
*/
- protected void initColourMenu()
+ protected void initHMMERMenu()
{
- applyToAllGroups = new JCheckBoxMenuItem(
- MessageManager.getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.addActionListener(new ActionListener()
+ autoAlignSeqs = new JCheckBoxMenuItem(
+ MessageManager.getString("label.auto_align_seqs"));
+ hmmAlign = new JMenuItem(MessageManager.getString("label.hmmalign"));
+ hmmBuild = new JMenuItem(MessageManager.getString("label.hmmbuild"));
+ hmmSearch = new JMenuItem(MessageManager.getString("label.hmmsearch"));
+ autoAlignSeqs.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed();
+ autoAlignSeqs_actionPerformed(autoAlignSeqs.isSelected());
}
});
- textColour = new JRadioButtonMenuItem(
- MessageManager.getString("action.set_text_colour"));
- textColour.addActionListener(new ActionListener()
+ }
+ protected void initColourMenu()
+ {
+ applyToAllGroups = new JCheckBoxMenuItem(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- textColour_actionPerformed();
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
}
});
- userDefinedColour = new JRadioButtonMenuItem(
- MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
+ textColour = new JMenuItem(
+ MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- userDefinedColour_actionPerformed(e);
+ textColour_actionPerformed();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed();
- }
- });
- noColourmenuItem = new JRadioButtonMenuItem(
- MessageManager.getString("label.none"));
- noColourmenuItem.setName("None");
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
+ conservationMenuItem_actionPerformed(conservationMenuItem
+ .isSelected());
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDThreshold_actionPerformed();
+ abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
}
});
modifyPID = new JMenuItem(
{
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
- {
- }
-
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- }
-
-
-
- /*
- * protected void covariationColour_actionPerformed() { }
- */
-
- protected void noColourmenuItem_actionPerformed()
- {
- }
-
- protected void conservationMenuItem_actionPerformed()
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
{
}
- protected void abovePIDThreshold_actionPerformed()
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
{
}
- protected void applyToAllGroups_actionPerformed()
+ protected void applyToAllGroups_actionPerformed(boolean selected)
+ {
+ }
+
+ protected void autoAlignSeqs_actionPerformed(boolean selected)
+ {
+ }
+
+ protected void hmmAlign_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void hmmBuild_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void hmmSearch_actionPerformed(ActionEvent e)
{
}
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
protected void showComplement_actionPerformed(boolean complement)
{
}
+
+ protected void showInformationHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void normaliseHMMSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff