label.style = Style:
label.calculating = Calculating....
label.modify_conservation_visibility = Modify conservation visibility
- label.colour_residues_above_occurence = Colour residues above % occurence
-label.colour_residues_above_occurence = Colour residues above % occurrence
++label.colour_residues_above_occurrence = Colour residues above % occurrence
label.set_this_label_text = set this label text
label.sequences_from = Sequences from {0}
label.successfully_loaded_file = Successfully loaded file {0}
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ MenuItem modifyPID = new MenuItem();
+
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
+ MenuItem modifyConservation = new MenuItem();
+
++ MenuItem noColourmenuItem = new MenuItem();
++
final AlignmentPanel ap;
MenuItem unGroupMenuItem = new MenuItem();
if (sg.cs != null)
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
+ conservationColour.setState(sg.cs.conservationApplied());
+ modifyPID.setEnabled(abovePIDColour.getState());
- conservationMenuItem.setState(sg.cs.conservationApplied());
- modifyConservation.setEnabled(conservationMenuItem.getState());
++ modifyConservation.setEnabled(conservationColour.getState());
}
}
+ setSelectedColour(sg.cs);
}
else
{
{
nucleotideMenuItem_actionPerformed();
}
-
- else if (source == userDefinedColour)
+ else if (source == purinePyrimidineColour)
{
- userDefinedColour_actionPerformed();
+ purinePyrimidineColour_actionPerformed();
}
- else if (source == PIDColour)
+ else if (source == abovePIDColour)
{
- PIDColour_actionPerformed();
+ abovePIDColour_itemStateChanged();
}
- else if (source == BLOSUM62Colour)
+ else if (source == conservationColour)
{
- BLOSUM62Colour_actionPerformed();
+ conservationMenuItem_itemStateChanged();
}
- else if (source == noColourmenuItem)
+ else if (source == showColourText)
{
- noColourmenuItem_actionPerformed();
+ showColourText_itemStateChanged();
+ }
+ else if (source == showText)
+ {
+ showText_itemStateChanged();
+ }
+ else if (source == showBoxes)
+ {
+ showBoxes_itemStateChanged();
+ }
+ else if (source == displayNonconserved)
+ {
+ this.showNonconserved_itemStateChanged();
+ }
+ }
+
+ /**
+ * Actions on clicking a menu item
+ */
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+ if (source == userDefinedColour)
+ {
+ userDefinedColour_actionPerformed();
}
+ else if (source == modifyConservation)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == modifyPID)
+ {
+ abovePIDColour_itemStateChanged();
+ }
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
void addPDB()
{
Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
-- if (pdbs != null&& !pdbs.isEmpty())
++ if (pdbs != null && !pdbs.isEmpty())
{
PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
-- new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
-- null, ap, DataSourceType.URL);
++ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
++ DataSourceType.URL);
}
else
{
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
-- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
++ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
colourMenu.add(strandColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
+ colourMenu.add(conservationColour);
++ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- noColourmenuItem.setLabel(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(this);
+ noColour.setLabel(MessageManager.getString("label.none"));
+ noColour.addItemListener(this);
+ /*
+ * setName allows setSelectedColour to do its thing
+ */
clustalColour.setLabel(MessageManager
- .getString("label.clustalx_colours"));
- clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(this);
+ .getString("label.colourScheme_clustal"));
+ clustalColour.setName(JalviewColourScheme.Clustal.toString());
+ clustalColour.addItemListener(this);
+ BLOSUM62Colour.setLabel(MessageManager
+ .getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
+ BLOSUM62Colour.addItemListener(this);
+ PIDColour.setLabel(MessageManager
+ .getString("label.colourScheme_%_identity"));
+ PIDColour.setName(JalviewColourScheme.PID.toString());
+ PIDColour.addItemListener(this);
+ zappoColour.setLabel(MessageManager
+ .getString("label.colourScheme_zappo"));
+ zappoColour.setName(JalviewColourScheme.Zappo.toString());
+ zappoColour.addItemListener(this);
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
+ taylorColour.setName(JalviewColourScheme.Taylor.toString());
+ taylorColour.addItemListener(this);
hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(this);
+ .getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
+ helixColour.setName(JalviewColourScheme.Helix.toString());
+ helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager
- .getString("label.above_identity_percentage"));
+ .getString("label.colourScheme_strand_propensity"));
+ strandColour.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
+ buriedColour.setName(JalviewColourScheme.Buried.toString());
+ buriedColour.addItemListener(this);
+ nucleotideColour.setLabel(MessageManager
+ .getString("label.colourScheme_nucleotide"));
+ nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
+ nucleotideColour.addItemListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.colourScheme_purine/pyrimidine"));
+ purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
+ .toString());
+ purinePyrimidineColour.addItemListener(this);
userDefinedColour.setLabel(MessageManager
.getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager
- .getString("label.percentage_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62");
- BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("label.conservation"));
+
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDColour.addItemListener(this);
++ modifyPID.setLabel(MessageManager
++ .getString("label.modify_identity_threshold"));
++ modifyPID.addActionListener(this);
+ conservationColour.setLabel(MessageManager
- .getString("label.conservation"));
++ .getString("action.by_conservation"));
+ conservationColour.addItemListener(this);
++ modifyConservation.setLabel(MessageManager
++ .getString("label.modify_conservation_threshold"));
++ modifyConservation.addActionListener(this);
editMenu.add(copy);
copy.addActionListener(this);
else
// remove ConservationColouring
{
+ SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
-
- modifyConservation.setEnabled(conservationMenuItem.getState());
++ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
SliderPanel pid = null;
if (PIDSlider == null)
{
-- pid = new SliderPanel(ap, 50, false, cs);
++ pid = new SliderPanel(ap, cs.getThreshold(), false, cs);
PIDSlider = new Frame();
PIDSlider.add(pid);
}
}
++ /**
++ * Hides the PID slider panel if it is shown
++ */
+ public static void hidePIDSlider()
+ {
- PIDSlider.setVisible(false);
++ if (PIDSlider != null)
++ {
++ PIDSlider.setVisible(false);
++ }
+ PIDSlider = null;
+ }
+
++ /**
++ * Hides the Conservation slider panel if it is shown
++ */
+ public static void hideConservationSlider()
+ {
- conservationSlider.setVisible(false);
++ if (conservationSlider != null)
++ {
++ conservationSlider.setVisible(false);
++ }
+ conservationSlider = null;
+ }
public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
ColourSchemeI cs)
{
showReverse.setVisible(nucleotide);
showReverseComplement.setVisible(nucleotide);
conservationMenuItem.setEnabled(!nucleotide);
-- modifyConservation.setEnabled(!nucleotide);
++ modifyConservation.setEnabled(!nucleotide
++ && conservationMenuItem.isSelected());
showGroupConservation.setEnabled(!nucleotide);
- rnahelicesColour.setEnabled(nucleotide);
- nucleotideColour.setEnabled(nucleotide);
- purinePyrimidineColour.setEnabled(nucleotide);
- RNAInteractionColour.setEnabled(nucleotide);
+
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
JMenuItem groupName = new JMenuItem();
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
-
protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
+
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
+
AlignmentPanel ap;
JMenu sequenceMenu = new JMenu();
sequenceSelectionDetails_actionPerformed();
}
});
- PIDColour.setFocusPainted(false);
++
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new ActionListener()
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
-
- clustalColour.setText(MessageManager
- .getString("label.clustalx_colours"));
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed();
- }
- });
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour
- .setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
+ }
-
++
+ /**
+ * Constructs the entries for the colour menu
+ */
+ protected void initColourMenu()
+ {
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- purinePyrimidineColour_actionPerformed();
+ textColour_actionPerformed();
}
});
+
- /*
- * covariationColour.addActionListener(new ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
abovePIDColour.setText(MessageManager
- .getString("label.above_identity_percentage"));
+ .getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
{
@Override
}
});
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+
conservationMenuItem.setText(MessageManager
- .getString("label.conservation"));
+ .getString("action.by_conservation"));
conservationMenuItem.addActionListener(new ActionListener()
{
@Override
conservationMenuItem_actionPerformed();
}
});
+
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
}
+ /**
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
++ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
++ colourMenu.add(modifyPID);
++ }
++
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
+ SliderPanel.showPIDSlider();
+ }
}
/**
return sp.getValue();
}
+ /**
++ * Hides the PID slider panel if it is shown
++ */
+ public static void hidePIDSlider()
+ {
- try
- {
- PIDSlider.setClosed(true);
- PIDSlider = null;
- } catch (PropertyVetoException ex)
++ if (PIDSlider != null)
+ {
++ try
++ {
++ PIDSlider.setClosed(true);
++ PIDSlider = null;
++ } catch (PropertyVetoException ex)
++ {
++ }
+ }
+ }
+
++ /**
++ * Hides the conservation slider panel if it is shown
++ */
+ public static void hideConservationSlider()
+ {
- try
- {
- conservationSlider.setClosed(true);
- conservationSlider = null;
- } catch (PropertyVetoException ex)
++ if (conservationSlider != null)
+ {
++ try
++ {
++ conservationSlider.setClosed(true);
++ conservationSlider = null;
++ } catch (PropertyVetoException ex)
++ {
++ }
+ }
+ }
+
+ /**
* DOCUMENT ME!
*/
public static void showConservationSlider()
protected JMenuItem closeMenuItem = new JMenuItem();
-- protected JMenu colourMenu = new JMenu();
--
protected JMenu webService = new JMenu();
protected JMenuItem webServiceNoServices;
protected JMenu outputTextboxMenu = new JMenu();
- protected JRadioButtonMenuItem textColour;
-
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
-
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
protected JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem;
-
- public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
-
- public JCheckBoxMenuItem abovePIDThreshold = 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;
-
- public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+
- protected JMenuItem modifyPID;
++ protected JCheckBoxMenuItem applyToAllGroups;
++
++ protected JMenu colourMenu = new JMenu();
+
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
++ protected JRadioButtonMenuItem textColour;
+
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
++ protected JCheckBoxMenuItem conservationMenuItem;
- protected JMenuItem modifyConservation = new JMenuItem();
+ protected JMenuItem modifyConservation;
- protected JMenuItem modifyPID = new JMenuItem();
++ protected JCheckBoxMenuItem abovePIDThreshold;
++
++ protected JMenuItem modifyPID;
++
+ protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed(e);
- }
- });
++
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+ abovePIDThreshold.setText(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ });
++
showSeqFeatures.setText(MessageManager
.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
});
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
++
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
public ParseHtmlBodyAndLinks(String description, boolean removeHTML,
String newline)
{
-- StringBuilder sb = new StringBuilder(description.length());
if (description == null || description.length() == 0)
{
htmlContent = false;
return;
}
++ StringBuilder sb = new StringBuilder(description.length());
if (description.toUpperCase().indexOf("<HTML>") == -1)
{
htmlContent = false;
git://source.jalview.org / jalview.git / commitdiff