startEnd = ap.av.getVisibleRegionBoundaries(
sg.getStartRes(), sg.getEndRes() + 1);
String description;
@@ -641,7 +805,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.showSequenceFeatures(true);
+ ap.av.setShowSequenceFeatures(true);
+ ;
ap.highlightSearchResults(null);
}
}
@@ -658,16 +823,15 @@ public class APopupMenu extends java.awt.PopupMenu implements
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500);
+ jalview.bin.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
cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(),
- new Alignment(ap.av.getSelectionAsNewSequence()),
- ap.av.showJVSuffix));
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
}
@@ -678,8 +842,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
protected void showSequenceDetails()
{
- createSequenceDetailsReport(new SequenceI[]
- { seq });
+ createSequenceDetailsReport(new SequenceI[] { seq });
}
public void createSequenceDetailsReport(SequenceI[] sequences)
@@ -690,16 +853,17 @@ public class APopupMenu extends java.awt.PopupMenu implements
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
- : null);
+ contents.append(MessageManager.formatMessage(
+ "label.annotation_for_displayid",
+ new Object[] { seq.getDisplayId(true) }));
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
+ .getMinMax() : null);
contents.append("");
}
Frame frame = new Frame();
@@ -707,7 +871,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
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 String[]{contents.toString()}));
+ cap.setText(MessageManager.formatMessage("label.html_content",
+ new Object[] { contents.toString() }));
}
void editName()
@@ -727,16 +892,20 @@ public class APopupMenu extends java.awt.PopupMenu implements
void addPDB()
{
- if (seq.getPDBId() != null)
+ if (seq.getAllPDBEntries() != null)
{
- PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
+ PDBEntry entry = seq.getAllPDBEntries().firstElement();
if (ap.av.applet.jmolAvailable)
- new jalview.appletgui.AppletJmol(entry, new Sequence[]
- { seq }, null, ap, AppletFormatAdapter.URL);
+ {
+ new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
+ null, ap, AppletFormatAdapter.URL);
+ }
else
- new MCview.AppletPDBViewer(entry, new Sequence[]
- { seq }, null, ap, AppletFormatAdapter.URL);
+ {
+ new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, AppletFormatAdapter.URL);
+ }
}
else
@@ -746,8 +915,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence",
+ new Object[] { seq.getName() }), 400, 300);
}
}
@@ -757,27 +927,31 @@ public class APopupMenu extends java.awt.PopupMenu implements
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.setLabel(MessageManager
+ .getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(this);
conservationMenuItem.addItemListener(this);
abovePIDColour.addItemListener(this);
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
- showBoxes.setLabel(MessageManager.getString("label.boxes"));
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addItemListener(this);
sequenceName.addActionListener(this);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
- displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setLabel(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
- showText.setLabel(MessageManager.getString("label.text"));
+ showText.setLabel(MessageManager.getString("action.text"));
showText.addItemListener(this);
showColourText.setLabel(MessageManager.getString("label.colour_text"));
showColourText.addItemListener(this);
@@ -785,16 +959,20 @@ public class APopupMenu extends java.awt.PopupMenu implements
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 String[]{""}));
+ 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")+":");
+ menu1.setLabel(MessageManager.getString("label.group") + ":");
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
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);
@@ -819,34 +997,42 @@ public class APopupMenu extends java.awt.PopupMenu implements
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- noColourmenuItem.setLabel("None");
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(this);
- clustalColour.setLabel("Clustalx colours");
+ clustalColour.setLabel(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(this);
- zappoColour.setLabel("Zappo");
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(this);
- taylorColour.setLabel("Taylor");
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel("Hydrophobicity");
+ hydrophobicityColour.setLabel(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel("Helix propensity");
+ helixColour
+ .setLabel(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(this);
- strandColour.setLabel("Strand propensity");
+ strandColour.setLabel(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(this);
- turnColour.setLabel("Turn propensity");
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(this);
- buriedColour.setLabel("Buried Index");
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(this);
- abovePIDColour.setLabel("Above % Identity");
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_percentage"));
- userDefinedColour.setLabel("User Defined");
+ userDefinedColour.setLabel(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(this);
- PIDColour.setLabel("Percentage Identity");
+ PIDColour.setLabel(MessageManager
+ .getString("label.percentage_identity"));
PIDColour.addActionListener(this);
BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel("Conservation");
+ conservationMenuItem.setLabel(MessageManager
+ .getString("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
@@ -861,6 +1047,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
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);
@@ -960,7 +1149,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
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();
@@ -968,7 +1157,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
else
// remove PIDColouring
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
refresh();
@@ -1072,6 +1261,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
getGroup().setDisplayText(showText.getState());
refresh();
}
+
public void makeReferenceSeq_actionPerformed()
{
if (!ap.av.getAlignment().hasSeqrep())
@@ -1112,8 +1302,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null || sg.getSize() < 1)
{
- ap.av.hideSequence(new SequenceI[]
- { seq });
+ ap.av.hideSequence(new SequenceI[] { seq });
return;
}
@@ -1141,4 +1330,107 @@ public class APopupMenu extends java.awt.PopupMenu implements
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.
+ *
+ * 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.
+ *
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
+ List forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List 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>> shownTypes = new LinkedHashMap>>();
+ Map>> hiddenTypes = new LinkedHashMap>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List 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 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 forSequences, String calcId,
+ final List 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);
+ }
+
}