import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
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.ColourSchemes;
import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
import java.awt.Color;
-import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.ArrayList;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.TreeMap;
import java.util.Vector;
-import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.118 $
*/
-public class PopupMenu extends JPopupMenu
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
{
JMenu groupMenu = new JMenu();
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 JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
- JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
- protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
- // protected JRadioButtonMenuItem RNAInteractionColour;
-
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JMenuItem modifyPID = new JMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
+
AlignmentPanel ap;
JMenu sequenceMenu = new JMenu();
this.ap = ap;
sequence = seq;
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
add(menuItem);
}
-
}
SequenceGroup sg = ap.av.getSelectionGroup();
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
- setColourSelected(sg.cs);
+ ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
+
+ conservationMenuItem.setEnabled(!sg.isNucleotide());
- if (sg.cs != null && sg.cs.conservationApplied())
+ if (sg.cs != null)
{
- conservationMenuItem.setSelected(true);
+ if (sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
}
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
+ modifyPID.setEnabled(abovePIDColour.isSelected());
displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : ap.av.getSequenceSelection())
{
void addFeatureLinks(final SequenceI seq, List<String> links)
{
JMenu linkMenu = new JMenu(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)
{
}
-
-
/**
* Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
* "All" is added first, followed by a separator. Then add any annotation
* 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);
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
+ Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
for (int sq = 0; sq < seqs.length; sq++)
{
});
sequenceSelDetails.setText(MessageManager
.getString("label.sequence_details"));
- sequenceSelDetails
-.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sequenceSelectionDetails_actionPerformed();
- }
- });
- PIDColour.setFocusPainted(false);
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
+
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new ActionListener()
});
createGroupMenuItem.setText(MessageManager
.getString("action.create_group"));
- createGroupMenuItem
-.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ createGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new ActionListener()
hideInsertions_actionPerformed(e);
}
});
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
+
groupMenu.add(sequenceSelDetails);
add(groupMenu);
add(sequenceMenu);
sequenceMenu.add(sequenceDetails);
sequenceMenu.add(makeReferenceSeq);
+ initColourMenu();
buildColourMenu();
editMenu.add(copy);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
-
- initColourMenu();
}
-
+
/**
* Constructs the entries for the colour menu
*/
textColour_actionPerformed();
}
});
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
- clustalColour.setText(MessageManager
- .getString("label.colourScheme_clustal"));
- clustalColour.setName(JalviewColourScheme.Clustal.toString());
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText(MessageManager
- .getString("label.colourScheme_zappo"));
- zappoColour.setName(JalviewColourScheme.Zappo.toString());
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText(MessageManager
- .getString("label.colourScheme_taylor"));
- taylorColour.setName(JalviewColourScheme.Taylor.toString());
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.colourScheme_hydrophobic"));
- hydrophobicityColour
- .setName(JalviewColourScheme.Hydrophobic.toString());
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText(MessageManager
- .getString("label.colourScheme_helix_propensity"));
- helixColour.setName(JalviewColourScheme.Helix.toString());
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText(MessageManager
- .getString("label.colourScheme_strand_propensity"));
- strandColour.setName(JalviewColourScheme.Strand.toString());
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText(MessageManager
- .getString("label.colourScheme_turn_propensity"));
- turnColour.setName(JalviewColourScheme.Turn.toString());
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText(MessageManager
- .getString("label.colourScheme_buried_index"));
- buriedColour.setName(JalviewColourScheme.Buried.toString());
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed();
- }
- });
abovePIDColour.setText(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDColour_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.colourScheme_%_identity"));
- PIDColour.setName(JalviewColourScheme.PID.toString());
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour
-.setText(MessageManager
- .getString("label.colourScheme_blosum62"));
- BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
}
});
- nucleotideColour.setText(MessageManager
- .getString("label.colourScheme_nucleotide"));
- nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
- nucleotideColour.addActionListener(new ActionListener()
+
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- nucleotideMenuItem_actionPerformed();
+ modifyPID_actionPerformed();
}
});
- purinePyrimidineColour.setText(MessageManager
- .getString("label.colourScheme_purine/pyrimidine"));
- purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
- .toString());
- purinePyrimidineColour.addActionListener(new ActionListener()
+
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- purinePyrimidineColour_actionPerformed();
+ conservationMenuItem_actionPerformed(conservationMenuItem
+ .isSelected());
}
});
- tcoffeeColour.setText(MessageManager
- .getString("label.colourScheme_t-coffee_scores"));
- tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString());
- tcoffeeColour.addActionListener(new ActionListener()
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- tcoffeeColorScheme_actionPerformed();
+ modifyConservation_actionPerformed();
}
});
-
- /*
- * covariationColour.addActionListener(new ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
-
- conservationMenuItem.setText(MessageManager
- .getString("action.by_conservation"));
- conservationMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
}
/**
*/
protected void buildColourMenu()
{
- SequenceGroup sg = getGroup();
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
colourMenu.removeAll();
colourMenu.add(textColour);
colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- // in Java 8, isApplicableTo can be a static method on the interface
- clustalColour.setEnabled(new ClustalxColourScheme(sg, null)
- .isApplicableTo(sg));
- colourMenu.add(BLOSUM62Colour);
- BLOSUM62Colour
- .setEnabled(new Blosum62ColourScheme().isApplicableTo(sg));
- colourMenu.add(PIDColour);
- PIDColour.setEnabled(new PIDColourScheme().isApplicableTo(sg));
- colourMenu.add(zappoColour);
- zappoColour.setEnabled(new ZappoColourScheme().isApplicableTo(sg));
- colourMenu.add(taylorColour);
- taylorColour.setEnabled(new TaylorColourScheme().isApplicableTo(sg));
- colourMenu.add(hydrophobicityColour);
- hydrophobicityColour.setEnabled(new HydrophobicColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(helixColour);
- helixColour.setEnabled(new HelixColourScheme().isApplicableTo(sg));
- colourMenu.add(strandColour);
- strandColour.setEnabled(new StrandColourScheme().isApplicableTo(sg));
- colourMenu.add(turnColour);
- turnColour.setEnabled(new TurnColourScheme().isApplicableTo(sg));
- colourMenu.add(buriedColour);
- buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(sg));
- colourMenu.add(nucleotideColour);
- nucleotideColour.setEnabled(new NucleotideColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(purinePyrimidineColour);
- purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(tcoffeeColour);
- tcoffeeColour
- .setEnabled(new TCoffeeColourScheme(sg).isApplicableTo(sg));
-
- /*
- * add some of these items to a ButtonGroup so their
- * selection is mutually exclusive
- */
- ButtonGroup colours = new ButtonGroup();
- /*
- * add any user-defined colours loaded on startup or
- * during the application session
- */
- SortedMap<String, UserColourScheme> userColourSchemes = UserDefinedColours
- .getUserColourSchemes();
- if (userColourSchemes != null)
- {
- for (String userColour : userColourSchemes.keySet())
- {
- JRadioButtonMenuItem item = new JRadioButtonMenuItem(userColour);
- item.setName(userColour); // button name identifies selected colour
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- colours.add(item);
- }
- }
- colourMenu.add(userDefinedColour);
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(BLOSUM62Colour);
- colours.add(PIDColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(purinePyrimidineColour);
- colours.add(tcoffeeColour);
- colours.add(nucleotideColour);
- colours.add(userDefinedColour);
- colours.add(abovePIDColour);
- // colours.add(RNAInteractionColour);
+ 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();
+ }
}
/**
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- SortedMap<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);
protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
{
- if (sequence != null)
+
+ HiddenColumns hidden = new HiddenColumns();
+ BitSet inserts = new BitSet(), mask = new BitSet();
+
+ // set mask to preserve existing hidden columns outside selected group
+ if (ap.av.hasHiddenColumns())
+ {
+ ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
+ }
+
+ boolean markedPopup = false;
+ // mark inserts in current selection
+ if (ap.av.getSelectionGroup() != null)
{
- ColumnSelection cs = ap.av.getColumnSelection();
- if (cs == null)
+ // mark just the columns in the selection group to be hidden
+ inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av
+ .getSelectionGroup().getEndRes() + 1);
+
+ // and clear that part of the mask
+ mask.andNot(inserts);
+
+ // now clear columns without gaps
+ for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
{
- cs = new ColumnSelection();
+ if (sq == sequence)
+ {
+ markedPopup = true;
+ }
+ inserts.and(sq.getInsertionsAsBits());
}
- cs.hideInsertionsFor(sequence);
- ap.av.setColumnSelection(cs);
}
+ else
+ {
+ // initially, mark all columns to be hidden
+ inserts.set(0, ap.av.getAlignment().getWidth());
+
+ // and clear out old hidden regions completely
+ mask.clear();
+ }
+
+ // now mark for sequence under popup if we haven't already done it
+ if (!markedPopup && sequence != null)
+ {
+ inserts.and(sequence.getInsertionsAsBits());
+ }
+
+ // finally, preserve hidden regions outside selection
+ inserts.or(mask);
+
+ // and set hidden columns accordingly
+ hidden.hideMarkedBits(inserts);
+
+ ap.av.getAlignment().setHiddenColumns(hidden);
refresh();
}
void refresh()
{
ap.updateAnnotation();
- ap.paintAlignment(true);
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void buriedColour_actionPerformed()
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void nucleotideMenuItem_actionPerformed()
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- protected void purinePyrimidineColour_actionPerformed()
- {
- getGroup().cs = new PurinePyrimidineColourScheme();
- refresh();
- }
-
- protected void tcoffeeColorScheme_actionPerformed()
- {
- getGroup().cs = new TCoffeeColourScheme(getGroup());
- refresh();
- }
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
/**
* DOCUMENT ME!
*
+ * @param selected
+ *
* @param e
* DOCUMENT ME!
*/
- protected void abovePIDColour_actionPerformed()
+ public void abovePIDColour_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- if (abovePIDColour.isSelected())
+ if (selected)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
sg.getStartRes(), sg.getEndRes() + 1));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup()
.getName());
sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
// remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
}
+ modifyPID.setEnabled(selected);
refresh();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
- {
- SequenceGroup sg = getGroup();
-
- if (e.getSource().equals(userDefinedColour))
- {
- new UserDefinedColours(ap, sg);
- }
- else
- {
- UserColourScheme udc = UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
- }
- refresh();
- }
-
- /**
* Open a panel where the user can choose which types of sequence annotation
* to show or hide.
*
* @param e
* DOCUMENT ME!
*/
- protected void PIDColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void BLOSUM62Colour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(
- sg.getSequences(ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1));
-
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void noColourmenuItem_actionPerformed()
- {
- getGroup().cs = null;
- refresh();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
return;
}
- if (conservationMenuItem.isSelected())
+ if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group", sg.getSequences(ap.av
c.calculate();
c.verdict(false, ap.av.getConsPercGaps());
-
sg.cs.setConservation(c);
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+ sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
sg.cs.setConservation(null);
+ SliderPanel.hideConservationSlider();
}
-
- refresh();
- }
-
- public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
- {
- SequenceGroup sg = getGroup();
- if (sg == null)
- {
- return;
- }
-
- AnnotationColourGradient acg = new AnnotationColourGradient(
- sequence.getAnnotation()[0], null,
- AnnotationColourGradient.NO_THRESHOLD);
-
- acg.setPredefinedColours(true);
- sg.cs = acg;
+ modifyConservation.setEnabled(selected);
refresh();
}
// or we simply trust the user wants
// wysiwig behaviour
- FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+ FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
return;
}
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ int gSize = sg.getSize();
for (int i = 0; i < gSize; i++)
{
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
if (start <= end)
{
- seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
- features[rsize] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
- rsize++;
+ seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+ features.add(new SequenceFeature(null, null, null, start, end, null));
}
}
- 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.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
- {
- ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+
+ /*
+ * an entirely gapped region will generate empty lists of sequence / features
+ */
+ if (!seqs.isEmpty())
+ {
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(
+ seqs, features, true, ap))
+ {
+ ap.alignFrame.setShowSeqFeatures(true);
+ ap.highlightSearchResults(null);
+ }
}
}
}
/**
- * Marks as selected the colour menu item matching the given name, or the
- * first item ('None') if no match is found
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
*
- * @param cs
+ * @return
*/
- protected void setColourSelected(ColourSchemeI cs)
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
{
- noColourmenuItem.setSelected(true);
- if (cs == null)
- {
- return;
- }
-
- String schemeName = cs.getSchemeName();
+ SequenceGroup sg = getGroup();
/*
- * look for a radio button with a name that matches the colour name
- * (note the button text may not as it may be internationalised)
+ * switch to the chosen colour scheme (or null for None)
*/
- for (Component menuItem : colourMenu.getMenuComponents())
+ ColourSchemeI colourScheme = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, sg,
+ ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
{
- if (menuItem instanceof JRadioButtonMenuItem)
- {
- if (schemeName.equals(((JRadioButtonMenuItem) menuItem).getName()))
- {
- ((JRadioButtonMenuItem) menuItem).setSelected(true);
- return;
- }
- }
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
+
+ refresh();
}
}
git://source.jalview.org / jalview.git / blobdiff