*/
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.Arrays;
+import java.util.Collections;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
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.Vector;
-
public class APopupMenu extends java.awt.PopupMenu implements
ActionListener, ItemListener
{
+ private static final String ALL_ANNOTATIONS = "All";
+
Menu groupMenu = new Menu();
MenuItem editGroupName = new MenuItem();
CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
+ Menu seqShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu seqHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem seqAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
+ Menu groupShowAnnotationsMenu = new Menu(
+ MessageManager.getString("label.show_annotations"));
+
+ Menu groupHideAnnotationsMenu = new Menu(
+ MessageManager.getString("label.hide_annotations"));
+
+ MenuItem groupAddReferenceAnnotations = new MenuItem(
+ MessageManager.getString("label.add_reference_annotations"));
+
Menu editMenu = new Menu(MessageManager.getString("action.edit"));
- MenuItem copy = new MenuItem(
- MessageManager.getString("label.jalview_copy"));
+ MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
- MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
+ MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
MenuItem toUpper = new MenuItem(
MessageManager.getString("label.to_upper_case"));
MenuItem makeReferenceSeq = new MenuItem();
- Sequence seq;
+ SequenceI seq;
MenuItem revealAll = new MenuItem();
Menu menu1 = new Menu();
- public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
+ public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
+ Vector<String> links)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
outputmenu.add(item);
}
- SequenceGroup sg = ap.av.getSelectionGroup();
+ buildAnnotationSubmenus();
+ SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null && sg.getSize() > 0)
{
editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new String[]
+ "label.name_param", new Object[]
{ sg.getName() }));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
if (links != null && links.size() > 0)
{
Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- String link;
for (int i = 0; i < links.size(); i++)
{
- link = links.elementAt(i).toString();
+ String link = links.elementAt(i);
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
.getString("action.set_as_reference")); // );
}
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ seq.getName() }));
}
else
}
/**
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment.
+ */
+ private void buildAnnotationSubmenus()
+ {
+ /*
+ * First for the currently selected sequence (if there is one):
+ */
+ final List<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * 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());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
+ }
+
+ /**
+ * Determine whether or not to enable 'add reference annotations' menu item.
+ * It is enable if there are any annotations, on any of the selected
+ * sequences, which are not yet on the alignment (visible or not).
+ *
+ * @param menu
+ * @param forSequences
+ */
+ private void configureReferenceAnnotationsMenu(MenuItem menuItem,
+ List<SequenceI> forSequences)
+ {
+ menuItem.setEnabled(false);
+
+ /*
+ * 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>>();
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,
+ tipEntries, candidates, al);
+ if (!candidates.isEmpty())
+ {
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its action.
+ */
+ menuItem.setEnabled(true);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
+ refresh();
+ }
+
+ /**
* add a show URL menu item to the given linkMenu
*
* @param linkMenu
{
if (seq == null)
{
- seq = (Sequence) sg.getSequenceAt(0);
+ seq = sg.getSequenceAt(0);
}
EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
else if (source == toUpper || source == toLower || source == toggleCase)
{
SequenceGroup sg = ap.av.getSelectionGroup();
- Vector regions = new Vector();
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
sg.getStartRes(), sg.getEndRes() + 1);
String description;
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command", new String[]
+ "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
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(),
- ap.av.showJVSuffix, ap.av, true));
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true));
}
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid", new String[]
+ "label.annotation_for_displayid", new Object[]
{ seq.getDisplayId(true) }));
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
+ (sequences.length == 1 ? sequences[0].getDisplayId(true)
: "Selection"), 600, 500);
cap.setText(MessageManager.formatMessage("label.html_content",
- new String[]
+ new Object[]
{ contents.toString() }));
}
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new Sequence[]
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[]
{ seq }, null, ap, AppletFormatAdapter.URL);
}
else
{
- new MCview.AppletPDBViewer(entry, new Sequence[]
+ new MCview.AppletPDBViewer(entry, new SequenceI[]
{ seq }, null, ap, AppletFormatAdapter.URL);
}
Frame frame = new Frame();
frame.add(cap);
jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence", new String[]
+ "label.paste_pdb_file_for_sequence", new Object[]
{ seq.getName() }), 400, 300);
}
}
pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ "" }));
revealAll.setLabel(MessageManager.getString("action.reveal_all"));
revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
this.add(revealSeq);
this.add(revealAll);
// groupMenu.add(selSeqDetails);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputmenu);
groupMenu.add(sequenceFeature);
editMenu.add(toLower);
toLower.addActionListener(this);
editMenu.add(toggleCase);
+ seqMenu.add(seqShowAnnotationsMenu);
+ seqMenu.add(seqHideAnnotationsMenu);
+ seqMenu.add(seqAddReferenceAnnotations);
seqMenu.add(sequenceName);
seqMenu.add(makeReferenceSeq);
// seqMenu.add(sequenceDetails);
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
ap.av.sendSelection();
}
+ /**
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
+ * <p>
+ * Some annotation rows are always rendered together - these can be identified
+ * by a common graphGroup property > -1. Only one of each group will be marked
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * 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>>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
+ hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations),
+ forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences,
+ calcId, type, false, true);
+ }
+ }
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences,
+ calcId, type, false, false);
+ }
+ }
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(Menu showOrHideMenu,
+ final List<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
+ forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff