*/
package jalview.appletgui;
+import java.awt.CheckboxMenuItem;
+import java.awt.Frame;
+import java.awt.Menu;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+import java.util.Vector;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.io.FileFormatI;
import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
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 jalview.util.MessageManager;
import jalview.util.UrlLink;
-import java.awt.CheckboxMenuItem;
-import java.awt.Frame;
-import java.awt.Menu;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-public class APopupMenu extends java.awt.PopupMenu implements
- ActionListener, ItemListener
+public class APopupMenu extends java.awt.PopupMenu
+ implements ActionListener, ItemListener
{
Menu groupMenu = new Menu();
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 CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ protected CheckboxMenuItem buriedColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem PIDColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
+
+ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
+
+ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
protected MenuItem userDefinedColour = new MenuItem();
- protected MenuItem PIDColour = new MenuItem();
+ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
+ MenuItem modifyPID = new MenuItem();
- MenuItem noColourmenuItem = new MenuItem();
+ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+ MenuItem modifyConservation = new MenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
final AlignmentPanel ap;
MenuItem createGroupMenuItem = new MenuItem();
- MenuItem nucleotideMenuItem = new MenuItem();
-
Menu colourMenu = new Menu();
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
- Vector<String> links)
+ List<String> links)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new Object[] { sg.getName() }));
+ if (sg.isNucleotide())
+ {
+ conservationColour.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
+ }
+ else
+ {
+ purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
+ }
+ editGroupName.setLabel(
+ MessageManager.formatMessage("label.name_param", new Object[]
+ { sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
if (sg.cs != null)
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
- conservationMenuItem.setState(sg.cs.conservationApplied());
+ conservationColour.setState(sg.cs.conservationApplied());
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
}
}
+ setSelectedColour(sg.cs);
}
else
{
seqMenu.setLabel(seq.getName());
if (seq == ap.av.getAlignment().getSeqrep())
{
- makeReferenceSeq.setLabel(MessageManager
- .getString("action.unmark_as_reference"));// Unmark
- // representative");
+ makeReferenceSeq.setLabel(
+ MessageManager.getString("action.unmark_as_reference"));// Unmark
+ // representative");
}
else
{
- makeReferenceSeq.setLabel(MessageManager
- .getString("action.set_as_reference")); // );
+ makeReferenceSeq.setLabel(
+ MessageManager.getString("action.set_as_reference")); // );
}
- repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[] { seq.getName() }));
+ repGroup.setLabel(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { seq.getName() }));
}
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(ResidueShaderI cs)
+ {
+ if (cs == null || cs.getColourScheme() == null)
+ {
+ noColour.setState(true);
+ }
+ else
+ {
+ String name = cs.getColourScheme().getSchemeName();
+ for (int i = 0; i < colourMenu.getItemCount(); i++)
+ {
+ MenuItem item = colourMenu.getItem(i);
+ if (item instanceof CheckboxMenuItem)
+ {
+ if (name.equals(item.getName()))
+ {
+ ((CheckboxMenuItem) item).setState(true);
+ }
+ }
+ }
+ }
+ }
+
+ /**
* Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
*
* @param seq
void addFeatureLinks(final SequenceI seq, List<String> links)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+ Map<String, List<String>> linkset = new LinkedHashMap<>();
for (String link : links)
{
/*
* First for the currently selected sequence (if there is one):
*/
- final List<SequenceI> selectedSequence = (seq == null ? Collections
- .<SequenceI> emptyList() : Arrays.asList(seq));
+ final List<SequenceI> selectedSequence = (seq == null
+ ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq));
buildAnnotationTypesMenus(seqShowAnnotationsMenu,
seqHideAnnotationsMenu, selectedSequence);
configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
/*
* and repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
- .<SequenceI> emptyList() : ap.av.getSelectionGroup()
- .getSequences());
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : ap.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
* 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>();
- final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ SortedMap<String, String> tipEntries = new TreeMap<>();
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
AlignmentI al = this.ap.av.getAlignment();
- AlignmentUtils.findAddableReferenceAnnotations(forSequences,
- tipEntries, candidates, al);
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
if (!candidates.isEmpty())
{
StringBuilder tooltip = new StringBuilder(64);
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();
- }
- else if (source == showText)
- {
- showText_itemStateChanged();
+ noColourmenuItem_actionPerformed();
}
- else if (source == showBoxes)
+ else if (source == clustalColour)
{
- 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 (evt.getSource() == 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)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == modifyPID)
+ {
+ abovePIDColour_itemStateChanged();
}
else if (source == unGroupMenuItem)
{
seq = sg.getSequenceAt(0);
}
- EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
- sg.getStartRes(), sg.getEndRes() + 1), null,
- "Edit Sequence ", null,
+ EditNameDialog dialog = new EditNameDialog(
+ seq.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1),
+ null, "Edit Sequence ", null,
ap.alignFrame, "Edit Sequence", 500, 100, true);
{
EditCommand editCommand = new EditCommand(
MessageManager.getString("label.edit_sequences"),
- Action.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
+ Action.REPLACE,
+ dialog.getName().replace(' ', ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1,
ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
return;
}
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+ int gSize = sg.getSize();
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
for (int i = 0; i < gSize; i++)
{
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
- seqs[rsize] = sg.getSequenceAt(i);
- features[rsize] = new SequenceFeature(null, null, null, start,
- end, "Jalview");
- rsize++;
+ seqs.add(sg.getSequenceAt(i));
+ features.add(
+ new SequenceFeature(null, null, start, end, "Jalview"));
}
}
- rseqs = new SequenceI[rsize];
- tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs, 0, rseqs, 0, rsize);
- System.arraycopy(features, 0, tfeatures, 0, rsize);
- features = tfeatures;
- seqs = rseqs;
-
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
+
+ if (!seqs.isEmpty())
{
- ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.setShowSequenceFeatures(true);
- ;
- ap.highlightSearchResults(null);
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.sequenceFeatures.setState(true);
+ ap.av.setShowSequenceFeatures(true);
+ ap.av.setSearchResults(null); // clear highlighting
+ ap.repaint(); // draw new/amended features
+ }
}
}
else
Frame frame = new Frame();
frame.add(cap);
- JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command",
- new Object[] { e.getActionCommand() }), 600, 500);
+ JalviewLite.addFrame(frame, MessageManager
+ .formatMessage("label.selection_output_command", new Object[]
+ { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- FileFormatI fileFormat = FileFormats.getInstance().forName(
- e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
ap.av.getShowJVSuffix(), ap, true));
StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
- contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid",
- new Object[] { seq.getDisplayId(true) }));
- new SequenceAnnotationReport(null).createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
- .getMinMax() : null);
+ contents.append(MessageManager
+ .formatMessage("label.annotation_for_displayid", new Object[]
+ { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.seqPanel.seqCanvas.fr);
contents.append("</p>");
}
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "Selection"), 600, 500);
- cap.setText(MessageManager.formatMessage("label.html_content",
- new Object[] { contents.toString() }));
+ jalview.bin.JalviewLite.addFrame(frame,
+ "Sequence Details for " + (sequences.length == 1
+ ? sequences[0].getDisplayId(true)
+ : "Selection"),
+ 600, 500);
+ cap.setText(
+ MessageManager.formatMessage("label.html_content", new Object[]
+ { contents.toString() }));
}
void editName()
{
seq.setName(dialog.getName());
seq.setDescription(dialog.getDescription());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
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
{
- new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
ap, DataSourceType.URL);
}
}
else
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true,
+ ap.alignFrame);
cap.setText(MessageManager.getString("label.paste_pdb_file"));
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence",
- new Object[] { seq.getName() }), 400, 300);
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence", new Object[]
+ { seq.getName() }), 400, 300);
}
}
sequenceFeature.addActionListener(this);
editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel(MessageManager
- .getString("action.remove_group"));
+ unGroupMenuItem
+ .setLabel(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
- createGroupMenuItem.setLabel(MessageManager
- .getString("action.create_group"));
+ createGroupMenuItem
+ .setLabel(MessageManager.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- abovePIDColour.addItemListener(this);
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
sequenceName.addActionListener(this);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
- displayNonconserved.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ displayNonconserved
+ .setLabel(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
showText.setLabel(MessageManager.getString("action.text"));
seqMenu.setLabel(MessageManager.getString("label.sequence"));
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
- repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[] { "" }));
+ repGroup.setLabel(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
menu1.setLabel(MessageManager.getString("label.group:"));
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(conservationColour);
+ colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
-
- noColourmenuItem.setLabel(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(this);
-
- 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);
- hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(this);
+ colourMenu.add(modifyPID);
+
+ noColour.setLabel(MessageManager.getString("label.none"));
+ noColour.addItemListener(this);
+
+ /*
+ * setName allows setSelectedColour to do its thing
+ */
+ clustalColour.setLabel(
+ MessageManager.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.colourScheme_hydrophobic"));
+ hydrophobicityColour
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
+ 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"));
-
- userDefinedColour.setLabel(MessageManager
- .getString("action.user_defined"));
+ .getString("label.colourScheme_strandpropensity"));
+ strandColour.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
+ turnColour.setLabel(
+ MessageManager.getString("label.colourScheme_turnpropensity"));
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
+ buriedColour.setLabel(
+ MessageManager.getString("label.colourScheme_buriedindex"));
+ 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("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
void refresh()
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
+ sg.cs = new ResidueShader(
+ new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
- getGroup().cs = new ZappoColourScheme();
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
refresh();
}
protected void taylorColour_actionPerformed()
{
- getGroup().cs = new TaylorColourScheme();
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
- getGroup().cs = new HydrophobicColourScheme();
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
refresh();
}
protected void helixColour_actionPerformed()
{
- getGroup().cs = new HelixColourScheme();
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
refresh();
}
protected void strandColour_actionPerformed()
{
- getGroup().cs = new StrandColourScheme();
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
refresh();
}
protected void turnColour_actionPerformed()
{
- getGroup().cs = new TurnColourScheme();
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
refresh();
}
protected void buriedColour_actionPerformed()
{
- getGroup().cs = new BuriedColourScheme();
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
- getGroup().cs = new NucleotideColourScheme();
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
+ refresh();
+ }
+
+ public void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new PurinePyrimidineColourScheme());
refresh();
}
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+ getGroup().getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
else
// remove PIDColouring
{
+ SliderPanel.hidePIDSlider();
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
-
+ modifyPID.setEnabled(abovePIDColour.getState());
refresh();
-
}
protected void userDefinedColour_actionPerformed()
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ sg.cs = new ResidueShader(new PIDColourScheme());
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
refresh();
}
{
SequenceGroup sg = getGroup();
- sg.cs = new Blosum62ColourScheme();
+ sg.cs = new ResidueShader(new Blosum62ColourScheme());
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
refresh();
}
return;
}
- if (conservationMenuItem.getState())
+ if (conservationColour.getState())
{
- sg.cs.setConservation(Conservation.calculateConservation("Group", sg
- .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
- .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
- false));
+ Conservation conservation = Conservation.calculateConservation(
+ "Group", sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth(), false,
+ ap.av.getConsPercGaps(), false);
+ sg.getGroupColourScheme().setConservation(conservation);
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
+ SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
-
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
SequenceGroup sg = ap.av.getSelectionGroup();
ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void createGroupMenuItem_actionPerformed()
showMenu.removeAll();
hideMenu.removeAll();
- final List<String> all = Arrays.asList(new String[] { MessageManager
- .getString("label.all") });
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ final List<String> all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
false);
showMenu.addSeparator();
* the insertion order, which is the order of the annotations on the
* alignment.
*/
- Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
AlignmentAnnotationUtils.asList(annotations), forSequences);
git://source.jalview.org / jalview.git / blobdiff