import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.JalviewColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
MenuItem editGroupName = new MenuItem();
- protected MenuItem clustalColour = new MenuItem();
+ CheckboxMenuItem noColour = new CheckboxMenuItem();
- protected MenuItem zappoColour = new MenuItem();
+ protected CheckboxMenuItem clustalColour = new CheckboxMenuItem();
- protected MenuItem taylorColour = new MenuItem();
+ protected CheckboxMenuItem zappoColour = new CheckboxMenuItem();
- protected MenuItem hydrophobicityColour = new MenuItem();
+ protected CheckboxMenuItem taylorColour = new CheckboxMenuItem();
- protected MenuItem helixColour = new MenuItem();
+ protected CheckboxMenuItem hydrophobicityColour = new CheckboxMenuItem();
- protected MenuItem strandColour = new MenuItem();
+ protected CheckboxMenuItem helixColour = new CheckboxMenuItem();
- protected MenuItem turnColour = new MenuItem();
+ protected CheckboxMenuItem strandColour = new CheckboxMenuItem();
- protected MenuItem buriedColour = new MenuItem();
+ protected CheckboxMenuItem turnColour = new CheckboxMenuItem();
- protected MenuItem userDefinedColour = new MenuItem();
+ protected CheckboxMenuItem buriedColour = new CheckboxMenuItem();
- protected MenuItem PIDColour = new MenuItem();
+ protected CheckboxMenuItem PIDColour = new CheckboxMenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
+ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
- MenuItem noColourmenuItem = new MenuItem();
+ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
+
+ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
+
+ protected MenuItem userDefinedColour = new MenuItem();
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();
MenuItem createGroupMenuItem = new MenuItem();
- MenuItem nucleotideMenuItem = new MenuItem();
-
Menu colourMenu = new Menu();
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
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
{
}
/**
+ * Select the menu item (if any) matching the current colour scheme. This
+ * works by matching the menu item name (not display text) to the canonical
+ * name of the colour scheme.
+ *
+ * @param cs
+ */
+ protected void setSelectedColour(ColourSchemeI cs)
+ {
+ if (cs == null)
+ {
+ noColour.setState(true);
+ }
+ else
+ {
+ for (int i = 0; i < colourMenu.getItemCount(); i++)
+ {
+ MenuItem item = colourMenu.getItem(i);
+ if (item instanceof CheckboxMenuItem)
+ {
+ if (cs.getSchemeName().equals(item.getName()))
+ {
+ ((CheckboxMenuItem) item).setState(true);
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
*
* @param seq
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- Map<String, String> tipEntries = new TreeMap<String, String>();
+ SortedMap<String, String> tipEntries = new TreeMap<String, String>();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences,
linkMenu.add(item);
}
+ /**
+ * Actions on selecting / unselecting a checkbox menu item
+ */
@Override
public void itemStateChanged(ItemEvent evt)
{
Object source = evt.getSource();
- if (source == abovePIDColour)
+ if (source == noColour)
{
- abovePIDColour_itemStateChanged();
- }
- else if (source == conservationMenuItem)
- {
- conservationMenuItem_itemStateChanged();
- }
- else if (source == showColourText)
- {
- showColourText_itemStateChanged();
+ noColourmenuItem_actionPerformed();
}
- else if (source == showText)
+ else if (source == clustalColour)
{
- showText_itemStateChanged();
- }
- else if (source == showBoxes)
- {
- showBoxes_itemStateChanged();
+ clustalColour_actionPerformed();
}
- else if (source == displayNonconserved)
+ else if (source == BLOSUM62Colour)
{
- this.showNonconserved_itemStateChanged();
+ BLOSUM62Colour_actionPerformed();
}
- }
-
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- Object source = evt.getSource();
- if (source == clustalColour)
+ else if (source == PIDColour)
{
- clustalColour_actionPerformed();
+ PIDColour_actionPerformed();
}
else if (source == zappoColour)
{
{
buriedColour_actionPerformed();
}
- else if (source == nucleotideMenuItem)
+ else if (source == nucleotideColour)
{
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)
{
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);
}
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- abovePIDColour.addItemListener(this);
- modifyPID.setLabel(MessageManager
- .getString("label.modify_identity_threshold"));
- modifyPID.addActionListener(this);
- modifyConservation.setLabel(MessageManager
- .getString("label.modify_conservation_threshold"));
- modifyPID.setEnabled(abovePIDColour.getState());
- modifyConservation.setEnabled(conservationMenuItem.getState());
- modifyConservation.addActionListener(this);
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
displayNonconserved.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
showText.setLabel(MessageManager.getString("action.text"));
groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
- colourMenu.add(noColourmenuItem);
+ colourMenu.add(noColour);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
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(conservationMenuItem);
+ colourMenu.add(conservationColour);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
colourMenu.add(modifyPID);
- 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"));
+
+ 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("action.by_conservation"));
+ conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
+
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("action.by_conservation"));
editMenu.add(copy);
copy.addActionListener(this);
refresh();
}
+ public void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+
protected void abovePIDColour_itemStateChanged()
{
SequenceGroup sg = getGroup();
return;
}
- if (conservationMenuItem.getState())
+ if (conservationColour.getState())
{
sg.cs.setConservation(Conservation.calculateConservation("Group", sg
.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
- modifyConservation.setEnabled(conservationMenuItem.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
git://source.jalview.org / jalview.git / blobdiff