1 && reppdb.size() < pdbe.size())
{
- structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
- rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ .formatMessage(
+ "label.view_all_representative_structures",
+ new String[]
+ { new Integer(reppdb.size()).toString() })));
+ rpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
rpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pr, ap.av.collateForPDB(pr));
}
});
}
@@ -541,11 +658,13 @@ public class PopupMenu extends JPopupMenu
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- jMenu1.setText(MessageManager.getString("action.edit_new_group"));
- } else {
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
- jMenu1.setText(MessageManager.getString("action.edit_group"));
+ jMenu1.setText(MessageManager.getString("action.edit_group"));
}
if (seq == null)
@@ -557,7 +676,7 @@ public class PopupMenu extends JPopupMenu
if (links != null && links.size() > 0)
{
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
@@ -677,6 +796,307 @@ public class PopupMenu extends JPopupMenu
}
}
+ /**
+ * Add annotation types to a 'Show annotations' or 'Hide annotations' menu.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection.
+ *
+ * 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)
+ */
+ protected void buildAnnotationTypesMenus()
+ {
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup == null)
+ {
+ // this menu option is only for a selection
+ return;
+ }
+
+ showAnnotationsMenu.removeAll();
+ hideAnnotationsMenu.removeAll();
+ final List all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showAnnotationsMenu, "", all, true, true);
+ addAnnotationTypeToShowHide(hideAnnotationsMenu, "", all, true, false);
+ showAnnotationsMenu.addSeparator();
+ hideAnnotationsMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+ BitSet visibleGraphGroups = PopupMenu
+ .getVisibleLineGraphGroups(annotations);
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup.
+ */
+ Map>> shownTypes = new HashMap>>();
+ Map>> hiddenTypes = new HashMap>>();
+ PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes,
+ visibleGraphGroups, annotations, selectionGroup);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showAnnotationsMenu, calcId, type,
+ false, true);
+ }
+ }
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideAnnotationsMenu, calcId, type,
+ false, false);
+ }
+ }
+ }
+
+ /**
+ * Helper method to populate lists of annotation types for the Show/Hide
+ * Annotations menus. If sequenceGroup is not null, this is restricted to
+ * annotations which are associated with sequences in the selection group.
+ *
+ * If an annotation row is currently visible, its type (label) is added (once
+ * only per type), to the shownTypes list. If it is currently hidden, it is
+ * added to the hiddenTypesList.
+ *
+ * For rows that belong to a line graph group, so are always rendered
+ * together:
+ *
+ * - Treat all rows in the group as visible, if at least one of them is
+ * - Build a comma-separated label with all the types that belong to the
+ * group
+ *
+ *
+ * @param shownTypes
+ * a map, keyed by calcId (annotation source), whose entries are the
+ * lists of annotation types found for the calcId; each annotation
+ * type in turn may be a list (in the case of grouped annotations)
+ * @param hiddenTypes
+ * a map, similar to shownTypes, but for hidden annotation types
+ * @param visibleGraphGroups
+ * a lookup keyed by graphGroup identifier
+ * @param annotations
+ * the annotations on the alignment to scan
+ * @param sequenceGroup
+ * the sequence group to restrict search to
+ */
+ public static void getAnnotationTypesForShowHide(
+ Map>> shownTypes,
+ Map>> hiddenTypes,
+ BitSet visibleGraphGroups, AlignmentAnnotation[] annotations,
+ SequenceGroup sequenceGroup)
+ {
+ /*
+ * Build a lookup, by calcId (annotation source), of all annotation types in
+ * each graph group.
+ */
+ Map>> groupLabels = new HashMap>>();
+
+ // trackers for which calcId!label combinations we have dealt with
+ List addedToShown = new ArrayList();
+ List addedToHidden = new ArrayList();
+
+ for (AlignmentAnnotation aa : annotations)
+ {
+
+ if (sequenceGroup == null
+ || (aa.sequenceRef != null && sequenceGroup.getSequences()
+ .contains(aa.sequenceRef)))
+ {
+ String calcId = aa.getCalcId();
+
+ /*
+ * Build a 'composite label' for types in line graph groups.
+ */
+ final List labelAsList = new ArrayList();
+ final String displayLabel = aa.label;
+ labelAsList.add(displayLabel);
+ if (aa.graph == AlignmentAnnotation.LINE_GRAPH
+ && aa.graphGroup > -1)
+ {
+ if (!groupLabels.containsKey(calcId))
+ {
+ groupLabels.put(calcId, new HashMap>());
+ }
+ Map> groupLabelsForCalcId = groupLabels
+ .get(calcId);
+ if (groupLabelsForCalcId.containsKey(aa.graphGroup))
+ {
+ if (!groupLabelsForCalcId.get(aa.graphGroup).contains(
+ displayLabel))
+ {
+ groupLabelsForCalcId.get(aa.graphGroup).add(displayLabel);
+ }
+ }
+ else
+ {
+ groupLabelsForCalcId.put(aa.graphGroup, labelAsList);
+ }
+ }
+ else
+ /*
+ * 'Simple case' - not a grouped annotation type - list of one label
+ * only
+ */
+ {
+ String rememberAs = calcId + "!" + displayLabel;
+ if (aa.visible && !addedToShown.contains(rememberAs))
+ {
+ if (!shownTypes.containsKey(calcId))
+ {
+ shownTypes.put(calcId, new ArrayList>());
+ }
+ shownTypes.get(calcId).add(labelAsList);
+ addedToShown.add(rememberAs);
+ }
+ else
+ {
+ if (!aa.visible && !addedToHidden.contains(rememberAs))
+ {
+ if (!hiddenTypes.containsKey(calcId))
+ {
+ hiddenTypes.put(calcId, new ArrayList>());
+ }
+ hiddenTypes.get(calcId).add(labelAsList);
+ addedToHidden.add(rememberAs);
+ }
+ }
+ }
+ }
+ }
+ /*
+ * finally add the 'composite group labels' to the appropriate lists,
+ * depending on whether the group is identified as visible or hidden
+ */
+ for (String calcId : groupLabels.keySet())
+ {
+ for (int group : groupLabels.get(calcId).keySet())
+ {
+ final List groupLabel = groupLabels.get(calcId).get(group);
+ if (visibleGraphGroups.get(group))
+ {
+ if (!shownTypes.containsKey(calcId))
+ {
+ shownTypes.put(calcId, new ArrayList>());
+ }
+ shownTypes.get(calcId).add(groupLabel);
+ }
+ else
+ {
+ if (!hiddenTypes.containsKey(calcId))
+ {
+ hiddenTypes.put(calcId, new ArrayList>());
+ }
+ hiddenTypes.get(calcId).add(groupLabel);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns a BitSet (possibly empty) of those graphGroups for line graph
+ * annotations, which have at least one member annotation row marked visible.
+ * The logic is that only one row in the group is marked visible, but when it
+ * is drawn, so are all the other rows in the same group.
+ *
+ * This lookup set allows us to check whether rows marked not visible are in
+ * fact shown.
+ *
+ * @see AnnotationRenderer#drawComponent
+ * @param annotations
+ * @return
+ */
+ public static BitSet getVisibleLineGraphGroups(
+ AlignmentAnnotation[] annotations)
+ {
+ // todo move to a utility class
+ BitSet result = new BitSet();
+ for (AlignmentAnnotation ann : annotations)
+ {
+ if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible)
+ {
+ int gg = ann.graphGroup;
+ if (gg > -1)
+ {
+ result.set(gg);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @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(JMenu showOrHideMenu,
+ 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 JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(types, allTypes, actionIsShow);
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ /**
+ * Action on selecting a list of annotation type (or the 'all types' values)
+ * to show or hide for the selection.
+ *
+ * @param types
+ * @param anyType
+ * @param doShow
+ */
+ protected void showHideAnnotation_actionPerformed(
+ Collection types, boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ // TODO: select by calcId (source of annotation) as well as label
+ // e.g. by refactoring of buildAnnotationTypeMenus to as
+ // to construct the actionPerformed methods as the calcId/labels are found
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && ap.av.getSelectionGroup().getSequences()
+ .contains(aa.sequenceRef))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ refresh();
+ }
+
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
@@ -684,11 +1104,18 @@ public class PopupMenu extends JPopupMenu
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
JMenu[] linkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
- new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
- // created.
+ { null, new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
+ // types
+ // of url
+ // that
+ // might
+ // be
+ // created.
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
@@ -810,7 +1237,8 @@ public class PopupMenu extends JPopupMenu
}
if (addMenu)
{
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
@@ -836,14 +1264,18 @@ public class PopupMenu extends JPopupMenu
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_param", new String[]
+ { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
showLink(url);
@@ -871,15 +1303,21 @@ public class PopupMenu extends JPopupMenu
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
- // TODO: put in info about what is being sent.
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_seqs_param",
+ new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // TODO: put in info about what is being sent.
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
@@ -905,202 +1343,279 @@ public class PopupMenu extends JPopupMenu
*/
private void jbInit() throws Exception
{
- groupMenu.setText(MessageManager.getString("label.group"));
- groupMenu.setText(MessageManager.getString("label.selection"));
- groupName.setText(MessageManager.getString("label.name"));
+ groupMenu.setText(MessageManager.getString("label.group"));
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
}
});
- sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager.getString("label.edit_name_description"));
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+ sequenceName.setText(MessageManager
+ .getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ chooseAnnotations.setText(MessageManager
+ .getString("label.choose_annotations") + "...");
+ chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ chooseAnnotations_actionPerformed(e);
+ }
+ });
+ sequenceDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ sequenceSelDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceSelectionDetails_actionPerformed();
}
});
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ createGroupMenuItem.setText(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
- outline.setText(MessageManager.getString("action.border_colour"));
+ outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
}
});
- colourMenu.setText(MessageManager.getString("label.group_colour"));
- showBoxes.setText(MessageManager.getString("action.boxes"));
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
}
});
- showText.setText(MessageManager.getString("action.text"));
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
- showColourText.setText(MessageManager.getString("label.colour_text"));
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setText(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText(MessageManager.getString("action.edit"));
- cut.setText(MessageManager.getString("action.cut"));
+ editMenu.setText(MessageManager.getString("action.edit"));
+ cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
}
});
- upperCase.setText(MessageManager.getString("label.to_upper_case"));
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- copy.setText(MessageManager.getString("action.copy"));
+ copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
- lowerCase.setText(MessageManager.getString("label.to_lower_case"));
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- toggle.setText(MessageManager.getString("label.toggle_case"));
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
- pdbFromFile.setText(MessageManager.getString("label.from_file"));
+ pdbMenu.setText(MessageManager
+ .getString("label.associate_structure_with_sequence"));
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pdbFromFile_actionPerformed();
}
});
- enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
+ // RNAFold.setText("From RNA Fold with predict2D");
+ // RNAFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // RNAFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // ContraFold.setText("From Contra Fold with predict2D");
+ // ContraFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // ContraFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
enterPDB_actionPerformed();
}
});
- discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
discoverPDB_actionPerformed();
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
- sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
+ showAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ hideAnnotationsMenu.setText(MessageManager
+ .getString("label.hide_annotations"));
+ configureReferenceAnnotationsMenu();
+ sequenceFeature.setText(MessageManager
+ .getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
- textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
}
});
- jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
- viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
+ jMenu1.setText(MessageManager.getString("label.group"));
+ structureMenu.setText(MessageManager.getString("label.structure"));
+ viewStructureMenu.setText(MessageManager
+ .getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed(actionEvent);
@@ -1117,6 +1632,10 @@ public class PopupMenu extends JPopupMenu
add(groupMenu);
add(sequenceMenu);
this.add(structureMenu);
+ // groupMenu.add(chooseAnnotations);
+ groupMenu.add(showAnnotationsMenu);
+ groupMenu.add(hideAnnotationsMenu);
+ groupMenu.add(addDatasequenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
@@ -1140,6 +1659,8 @@ public class PopupMenu extends JPopupMenu
colourMenu.add(nucleotideMenuItem);
if (ap.getAlignment().isNucleotide())
{
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
@@ -1155,6 +1676,7 @@ public class PopupMenu extends JPopupMenu
JMenuItem item = new JMenuItem(userColours.nextElement().toString());
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
@@ -1175,6 +1697,10 @@ public class PopupMenu extends JPopupMenu
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
+ // JBPNote: These shouldn't be added here - should appear in a generic
+ // 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
@@ -1187,131 +1713,155 @@ public class PopupMenu extends JPopupMenu
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
- noColourmenuItem.setText(MessageManager.getString("label.none"));
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
}
});
- clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
+ clustalColour.setText(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed();
}
});
- zappoColour.setText(MessageManager.getString("label.zappo"));
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed();
}
});
- taylorColour.setText(MessageManager.getString("label.taylor"));
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed();
}
});
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed();
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed();
}
});
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed();
}
});
- buriedColour.setText(MessageManager.getString("label.buried_index"));
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
+ abovePIDColour.setText(MessageManager
+ .getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed();
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed();
}
});
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
- conservationMenuItem.setText(MessageManager.getString("label.conservation"));
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
@@ -1319,6 +1869,138 @@ public class PopupMenu extends JPopupMenu
});
}
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not on the alignment. If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an annotation that matches on
+ * sequenceRef.datasetSequence, calcId and label.
+ */
+ protected void configureReferenceAnnotationsMenu()
+ {
+ addDatasequenceAnnotations.setText(MessageManager
+ .getString("label.add_reference_annotations"));
+ addDatasequenceAnnotations.setEnabled(false);
+
+ /*
+ * Temporary store so we can write distinct calcId / type pairs on the
+ * tooltip.
+ */
+ Map tipEntries = new HashMap();
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ // this menu option only applies for a Selection
+ if (this.ap.av.getSelectionGroup() == null)
+ {
+ return;
+ }
+
+ /*
+ * For each sequence selected in the alignment, make a list of any
+ * annotations on the underlying dataset sequence which are not already on
+ * the sequence in the alignment.
+ *
+ * Build a map of { alignmentSequence, }
+ */
+ final Map> candidates = new HashMap>();
+ for (SequenceI seq : this.ap.av.getSelectionGroup().getSequences())
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List result = new ArrayList();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * If the sequence has no annotation that matches this one, then add
+ * this one to the results list.
+ */
+ if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label)
+ .isEmpty())
+ {
+ result.add(dsann);
+ tipEntries.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ if (!candidates.isEmpty())
+ {
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its tooltip and action.
+ */
+ addDatasequenceAnnotations.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("
" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ addDatasequenceAnnotations.setToolTipText(tooltipText);
+
+ addDatasequenceAnnotations.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> candidates)
+ {
+ for (SequenceI seq : candidates.keySet())
+ {
+ for (AlignmentAnnotation ann : candidates.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ // add to the sequence (sets correct copyAnn.datasetSequence)
+ seq.addAlignmentAnnotation(copyAnn);
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ this.ap.getAlignment().addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ refresh();
+ }
+
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
@@ -1336,8 +2018,12 @@ public class PopupMenu extends JPopupMenu
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
- + "
");
+ contents.append("
"
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new String[]
+ { seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
@@ -1351,8 +2037,11 @@ public class PopupMenu extends JPopupMenu
}
cap.setText("" + contents.toString() + "");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))
- ,500, 400);
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequece_details_for",
+ (sequences.length == 1 ? new String[]
+ { sequences[0].getDisplayId(true) } : new String[]
+ { MessageManager.getString("label.selection") })), 500, 400);
}
@@ -1538,7 +2227,7 @@ public class PopupMenu extends JPopupMenu
{
SequenceGroup sg = getGroup();
- if (e.getSource().equals(userDefinedColour))
+ if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
@@ -1553,6 +2242,18 @@ public class PopupMenu extends JPopupMenu
}
/**
+ * Open a panel where the user can choose which types of sequence annotation
+ * to show or hide.
+ *
+ * @param e
+ */
+ protected void chooseAnnotations_actionPerformed(ActionEvent e)
+ {
+ // todo correct way to guard against opening a duplicate panel?
+ new AnnotationChooser(ap);
+ }
+
+ /**
* DOCUMENT ME!
*
* @param e
@@ -1615,7 +2316,7 @@ public class PopupMenu extends JPopupMenu
if (conservationMenuItem.isSelected())
{
- // JBPNote: Conservation name shouldn't be i18n translated
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
@@ -1667,8 +2368,10 @@ public class PopupMenu extends JPopupMenu
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",
- MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
+ sg.getDescription(), " "
+ + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -1707,8 +2410,12 @@ public class PopupMenu extends JPopupMenu
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",
- MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
+ sequence.getDescription(),
+ " " + MessageManager.getString("label.sequence_name")
+ + " ",
+ MessageManager.getString("label.sequence_description") + " ",
+ MessageManager
+ .getString("label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -1720,10 +2427,14 @@ public class PopupMenu extends JPopupMenu
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- MessageManager.getString("label.spaces_converted_to_backslashes"),
- MessageManager.getString("label.no_spaces_allowed_sequence_name"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
@@ -1750,9 +2461,11 @@ public class PopupMenu extends JPopupMenu
ap.av.setSelectionGroup(null);
refresh();
}
+
void createGroupMenuItem_actionPerformed()
{
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
refresh();
}
@@ -1765,7 +2478,8 @@ public class PopupMenu extends JPopupMenu
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
@@ -1819,11 +2533,10 @@ public class PopupMenu extends JPopupMenu
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
@@ -1889,17 +2602,17 @@ public class PopupMenu extends JPopupMenu
if (source == toggle)
{
- description = MessageManager.getString("label.toggle_case");
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = MessageManager.getString("label.to_upper_case");
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = MessageManager.getString("label.to_lower_case");
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
@@ -1919,31 +2632,18 @@ public class PopupMenu extends JPopupMenu
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
- SequenceGroup sg = ap.av.getSelectionGroup();
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
- omitHidden = ap.av.getViewAsString(true);
- Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
- {
- for (int i = 0; i < nala.length; i++)
- {
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
- }
- }
+
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
+ ap.av, true));
}
public void pdbFromFile_actionPerformed()
@@ -1951,8 +2651,12 @@ public class PopupMenu extends JPopupMenu
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
- chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
@@ -1966,10 +2670,24 @@ public class PopupMenu extends JPopupMenu
}
+ // JBNote: commented out - these won't be instantiated here...!
+ // public void RNAFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromRNAFold("toto");
+ // }
+ //
+ // public void ContraFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromContraFold("toto");
+ // }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
@@ -1987,6 +2705,7 @@ public class PopupMenu extends JPopupMenu
: ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
+ @Override
public void run()
{
@@ -2071,16 +2790,19 @@ public class PopupMenu extends JPopupMenu
if (sg != null)
{
if (sequence == null)
- sequence = (Sequence) sg.getSequenceAt(0);
+ sequence = sg.getSequenceAt(0);
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
- MessageManager.getString("label.edit_sequence"), ap.alignFrame);
+ sg.getEndRes() + 1), null,
+ MessageManager.getString("label.edit_sequence"), null,
+ MessageManager.getString("label.edit_sequence"),
+ ap.alignFrame);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),