features)
+ {
+ JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
+
+ // only add link menu if it has entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ if (forIdPanel)
{
- clustalColour.setSelected(true);
+ sequenceMenu.add(linkMenu);
}
else
{
- noColourmenuItem.setSelected(true);
+ add(linkMenu);
}
+ }
+ }
+
+ /**
+ * 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(JMenu showMenu, JMenu hideMenu,
+ List forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ 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);
- if (sg.cs != null && sg.cs.conservationApplied())
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List type : hiddenTypes.get(calcId))
{
- conservationMenuItem.setSelected(true);
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
}
- displayNonconserved.setSelected(sg.getShowunconserved());
- showText.setSelected(sg.getDisplayText());
- showColourText.setSelected(sg.getColourText());
- showBoxes.setSelected(sg.getDisplayBoxes());
}
- else
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
{
- groupMenu.setVisible(false);
- editMenu.setVisible(false);
+ 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());
+ }
- if (!ap.av.alignment.getGroups().contains(sg))
+ /**
+ * Returns a list of sequences - either the current selection group (if there
+ * is one), else the specified single sequence.
+ *
+ * @param seq
+ * @return
+ */
+ protected List getSequenceScope(SequenceI seq)
+ {
+ List forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
{
- unGroupMenuItem.setVisible(false);
+ forSequences = selectionGroup.getSequences();
}
-
- if (seq == null)
+ else
{
- sequenceMenu.setVisible(false);
- structureMenu.setVisible(false);
+ forSequences = seq == null ? Collections. emptyList()
+ : Arrays.asList(seq);
}
+ return forSequences;
+ }
- if (links != null && links.size() > 0)
+ /**
+ * 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(JMenu 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); // a, b, c
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new ActionListener()
{
- JMenu linkMenu = new JMenu("Link");
- Vector linkset = new Vector();
- for (int i = 0; i < links.size(); i++)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- String link = links.elementAt(i).toString();
- UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for URLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- if (urlLink.isDynamic())
- {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
- .getDBRef(), new String[]
- { urlLink.getTarget() });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr!=null && descr.length()<1)
- {
- descr = null;
- }
+ private void buildGroupURLMenu(SequenceGroup sg, List groupLinks)
+ {
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
- true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
- {
- linkset.addElement(urls[u]+"|"+urls[u+1]);
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- }
- }
- }
- }
- if (id != null)
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
+ // sequence only URLs
+ // ID/regex match URLs
+ JMenu groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ // three types of url that might be created.
+ JMenu[] linkMenus = new JMenu[] { null,
+ new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);
+ Hashtable commonDbrefs = new Hashtable<>();
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
+
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
+ // just collect ids from dataset sequence
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
+ SequenceI sqi = seqs[sq];
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
+ List dbr = sqi.getDBRefs();
+ int nd;
+ if (dbr != null && (nd = dbr.size()) > 0)
+ {
+ for (int d = 0; d < nd; d++)
+ {
+ DBRefEntry e = dbr.get(d);
+ String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
+ Object[] sarray = commonDbrefs.get(src);
+ if (sarray == null)
{
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
- {
- linkset.addElement(urls[u]+"|"+urls[u+1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
+ sarray = new Object[2];
+ sarray[0] = new int[] { 0 };
+ sarray[1] = new String[seqs.length];
+
+ commonDbrefs.put(src, sarray);
}
- // Create urls from description but only for URL links which are regex links
- if (descr != null && urlLink.getRegexReplace()!=null)
- {
- // create link for this URL from description where regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
- {
- linkset.addElement(urls[u]+"|"+urls[u+1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!e.hasMap()
+ || (e.getMap().locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = e.getAccessionId();
+ ((int[]) sarray[0])[0]++;
}
}
}
- else
+ }
+ }
+ // now create group links for all distinct ID/sequence sets.
+ boolean addMenu = false; // indicates if there are any group links to give
+ // to user
+ for (String link : groupLinks)
+ {
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ Console.error("Exception for GroupURLLink '" + link + "'", foo);
+ continue;
+ }
+ if (!urlLink.isValid())
+ {
+ Console.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
+ String[] seqstr, ids; // input to makeUrl
+ if (idset != null)
+ {
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
- if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
+ if (allids[sq] != null)
{
- linkset.addElement(label+"|"+urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
}
}
}
- if (sequence != null)
+ else
{
- sequenceMenu.add(linkMenu);
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames = true;
}
- else
+ // and try and make the groupURL!
+
+ Object[] urlset = null;
+ try
{
- add(linkMenu);
+ urlset = urlLink.makeUrlStubs(ids, seqstr,
+ "FromJalview" + System.currentTimeMillis(), false);
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(linkMenus[type],
+ label + (((type & 1) == 1)
+ ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+ : ""),
+ urlLink, urlset);
+ addMenu = true;
}
}
- }
-
- /**
- * add a show URL menu item to the given linkMenu
- *
- * @param linkMenu
- * @param label -
- * menu label string
- * @param url -
- * url to open
- */
- private void addshowLink(JMenu linkMenu, String label, final String url)
- {
- JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL: " + url);
- item.addActionListener(new java.awt.event.ActionListener()
+ if (addMenu)
{
- public void actionPerformed(ActionEvent e)
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ for (int m = 0; m < linkMenus.length; m++)
{
- new Thread(new Runnable()
+ if (linkMenus[m] != null
+ && linkMenus[m].getMenuComponentCount() > 0)
{
-
- public void run()
- {
- showLink(url);
- }
-
- }).start();
+ groupLinksMenu.add(linkMenus[m]);
+ }
}
- });
- linkMenu.add(item);
+ groupMenu.add(groupLinksMenu);
+ }
}
/**
* DOCUMENT ME!
*
* @throws Exception
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("Name");
- groupName.addActionListener(new java.awt.event.ActionListener()
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
+ groupName.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
}
});
- sequenceMenu.setText("Sequence");
- sequenceName.setText("Edit Name/Description");
- sequenceName.addActionListener(new java.awt.event.ActionListener()
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+
+ JMenuItem sequenceName = new JMenuItem(
+ MessageManager.getString("label.edit_name_description"));
+ sequenceName.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
- PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem chooseAnnotations = new JMenuItem(
+ MessageManager.getString("action.choose_annotations"));
+ chooseAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- unGroupMenuItem_actionPerformed();
+ chooseAnnotations_actionPerformed(e);
+ }
+ });
+ JMenuItem sequenceDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
+ sequenceDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSequenceDetailsReport(new SequenceI[] { sequence });
+ }
+ });
+ JMenuItem sequenceSelDetails = new JMenuItem(
+ MessageManager.getString("label.sequence_details"));
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
}
});
- outline.setText("Border colour");
- outline.addActionListener(new java.awt.event.ActionListener()
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- outline_actionPerformed();
+ unGroupMenuItem_actionPerformed();
+ }
+ });
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
}
});
- nucleotideMenuItem.setText("Nucleotide");
- nucleotideMenuItem.addActionListener(new ActionListener()
+
+ JMenuItem outline = new JMenuItem(
+ MessageManager.getString("action.border_colour"));
+ outline.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- nucleotideMenuItem_actionPerformed();
+ outline_actionPerformed();
}
});
- colourMenu.setText("Group Colour");
- showBoxes.setText("Boxes");
+ showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
}
});
- showText.setText("Text");
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
- displayNonconserved.setText("Show Nonconserved");
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText("Edit");
- cut.setText("Cut");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
}
});
- upperCase.setText("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("Copy");
+ JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
- lowerCase.setText("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("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("From File");
- pdbFromFile.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- pdbFromFile_actionPerformed();
- }
- });
- enterPDB.setText("Enter PDB Id");
- enterPDB.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- enterPDB_actionPerformed();
- }
- });
- discoverPDB.setText("Discover PDB ids");
- discoverPDB.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- discoverPDB_actionPerformed();
- }
- });
- outputMenu.setText("Output to Textbox...");
- sequenceFeature.setText("Create Sequence Feature");
+ outputMenu.setText(
+ MessageManager.getString("label.out_to_textbox") + "...");
+ seqShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ seqHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ groupShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ groupHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ JMenuItem sequenceFeature = new JMenuItem(
+ MessageManager.getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
- textColour.setText("Text Colour");
- textColour.addActionListener(new ActionListener()
+ editGroupMenu.setText(MessageManager.getString("label.group"));
+ chooseStructure.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
+ chooseStructure.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
{
- textColour_actionPerformed();
+ SequenceI[] selectedSeqs = new SequenceI[] { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
}
});
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("View Structure");
+
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
+
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText("Edit Sequence...");
+ JMenuItem editSequence = new JMenuItem(
+ MessageManager.getString("label.edit_sequence") + "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
- editSequence_actionPerformed(actionEvent);
+ editSequence_actionPerformed();
}
});
- /*
- * annotationMenuItem.setText("By Annotation");
- * annotationMenuItem.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent actionEvent) {
- * annotationMenuItem_actionPerformed(actionEvent); } });
- */
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
+ makeReferenceSeq.addActionListener(new ActionListener()
+ {
- add(groupMenu);
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ makeReferenceSeq_actionPerformed(actionEvent);
+
+ }
+ });
+ groupMenu.add(sequenceSelDetails);
+ add(groupMenu);
add(sequenceMenu);
- this.add(structureMenu);
+ add(rnaStructureMenu);
+ add(chooseStructure);
+ if (forIdPanel)
+ {
+ JMenuItem hideInsertions = new JMenuItem(
+ MessageManager.getString("label.hide_insertions"));
+ hideInsertions.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideInsertions_actionPerformed(e);
+ }
+ });
+ add(hideInsertions);
+ }
+ // annotations configuration panel suppressed for now
+ // groupMenu.add(chooseAnnotations);
+
+ /*
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
+ */
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
- groupMenu.add(jMenu1);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
+ groupMenu.add(editGroupMenu);
sequenceMenu.add(sequenceName);
- colourMenu.add(textColour);
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
- colourMenu.add(userDefinedColour);
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- JMenuItem item = new JMenuItem(userColours.nextElement().toString());
- item.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- }
- }
+ sequenceMenu.add(sequenceDetails);
+ sequenceMenu.add(makeReferenceSeq);
+
+ initColourMenu();
+ buildColourMenu();
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
editMenu.add(upperCase);
editMenu.add(lowerCase);
editMenu.add(toggle);
- pdbMenu.add(pdbFromFile);
- pdbMenu.add(enterPDB);
- pdbMenu.add(discoverPDB);
- jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
- jMenu1.add(colourMenu);
- jMenu1.add(showBoxes);
- jMenu1.add(showText);
- jMenu1.add(showColourText);
- jMenu1.add(outline);
- jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed();
- }
- });
+ editGroupMenu.add(groupName);
+ editGroupMenu.add(colourMenu);
+ editGroupMenu.add(showBoxes);
+ editGroupMenu.add(showText);
+ editGroupMenu.add(showColourText);
+ editGroupMenu.add(outline);
+ editGroupMenu.add(displayNonconserved);
+ }
- clustalColour.setText("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed();
- }
- });
- zappoColour.setText("Zappo");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed();
- }
- });
- taylorColour.setText("Taylor");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed();
- }
- });
- hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
- helixColour.setText("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed();
- }
- });
- strandColour.setText("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed();
- }
- });
- turnColour.setText("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed();
- }
- });
- buriedColour.setText("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ /**
+ * Constructs the entries for the colour menu
+ */
+ protected void initColourMenu()
+ {
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- buriedColour_actionPerformed();
+ textColour_actionPerformed();
}
});
- abovePIDColour.setText("Above % Identity");
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- abovePIDColour_actionPerformed();
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
}
});
- userDefinedColour.setText("User Defined...");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- userDefinedColour_actionPerformed(e);
+ modifyPID_actionPerformed();
}
});
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- PIDColour_actionPerformed();
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
}
});
- BLOSUM62Colour.setText("BLOSUM62");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+
+ annotationColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+ annotationColour.setEnabled(false);
+ annotationColour.setToolTipText(
+ MessageManager.getString("label.by_annotation_tooltip"));
+
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- BLOSUM62Colour_actionPerformed();
+ modifyConservation_actionPerformed();
}
});
- conservationMenuItem.setText("Conservation");
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
- }
-
- protected void showNonconserved_actionPerformed()
- {
- getGroup().setShowunconserved(displayNonconserved.isSelected());
- refresh();
- }
-
- /**
- * call to refresh view after settings change
- */
- void refresh()
- {
- ap.paintAlignment(true);
-
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
- .getWidth());
- refresh();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
*/
- protected void zappoColour_actionPerformed()
+ protected void buildColourMenu()
{
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
+ false);
+ bg.add(annotationColour);
+ colourMenu.add(annotationColour);
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void helixColour_actionPerformed()
+ protected void modifyConservation_actionPerformed()
{
- getGroup().cs = new HelixColourScheme();
- refresh();
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void strandColour_actionPerformed()
+ protected void modifyPID_actionPerformed()
{
- getGroup().cs = new StrandColourScheme();
- refresh();
+ 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();
+ }
}
/**
- * DOCUMENT ME!
+ * 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 alignment annotation on the alignment, matched on
+ * calcId, label and sequenceRef.
*
- * @param e
- * DOCUMENT ME!
- */
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- /**
- * DOCUMENT ME!
+ * A tooltip is also constructed that displays the source (calcId) and type
+ * (label) of the annotations that can be added.
*
- * @param e
- * DOCUMENT ME!
+ * @param menuItem
+ * @param forSequences
*/
- protected void buriedColour_actionPerformed()
+ protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
+ List forSequences)
{
- getGroup().cs = new BuriedColourScheme();
- refresh();
+ menuItem.setEnabled(false);
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ SortedMap tipEntries = new TreeMap<>();
+ final Map> candidates = new LinkedHashMap<>();
+ 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 tooltip and action.
+ */
+ menuItem.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("
" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ menuItem.setToolTipText(tooltipText);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
}
/**
- * DOCUMENT ME!
+ * Add annotations to the sequences and to the alignment.
*
- * @param e
- * DOCUMENT ME!
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
*/
- public void nucleotideMenuItem_actionPerformed()
+ protected void addReferenceAnnotations_actionPerformed(
+ Map> candidates)
{
- getGroup().cs = new NucleotideColourScheme();
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
refresh();
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void abovePIDColour_actionPerformed()
+ protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
{
- SequenceGroup sg = getGroup();
- if (sg.cs == null)
+ if (!ap.av.getAlignment().hasSeqrep())
{
- return;
+ // initialise the display flags so the user sees something happen
+ ap.av.setDisplayReferenceSeq(true);
+ ap.av.setColourByReferenceSeq(true);
+ ap.av.getAlignment().setSeqrep(sequence);
}
-
- if (abovePIDColour.isSelected())
+ else
{
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ if (ap.av.getAlignment().getSeqrep() == sequence)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ }
+ refresh();
+ }
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
+ protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
+ {
+ HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+ BitSet inserts = new BitSet();
- sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
+ boolean markedPopup = false;
+ // mark inserts in current selection
+ if (ap.av.getSelectionGroup() != null)
+ {
+ // mark just the columns in the selection group to be hidden
+ inserts.set(ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
- SliderPanel.showPIDSlider();
+ // now clear columns without gaps
+ for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
+ {
+ if (sq == sequence)
+ {
+ markedPopup = true;
+ }
+ inserts.and(sq.getInsertionsAsBits());
+ }
+ hidden.clearAndHideColumns(inserts,
+ ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes());
}
- else
- // remove PIDColouring
+
+ // now mark for sequence under popup if we haven't already done it
+ else if (!markedPopup && sequence != null)
{
- sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
- }
+ inserts.or(sequence.getInsertionsAsBits());
+ // and set hidden columns accordingly
+ hidden.hideColumns(inserts);
+ }
refresh();
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ protected void sequenceSelectionDetails_actionPerformed()
{
- SequenceGroup sg = getGroup();
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
- if (e.getActionCommand().equals("User Defined..."))
- {
- new UserDefinedColours(ap, sg);
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ StringBuilder contents = new StringBuilder(128);
+ contents.append("");
+ for (SequenceI seq : sequences)
+ {
+ contents.append("" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "
\n");
+ new SequenceAnnotationReport(false).createSequenceAnnotationReport(
+ contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
+ contents.append("
");
+ }
+ contents.append("");
+ String report = contents.toString();
+
+ JInternalFrame frame;
+ if (Platform.isJS())
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(report);
+ textLabel.setBackground(Color.WHITE);
+ JPanel pane = new JPanel(new BorderLayout());
+ pane.setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ pane.add(textLabel, BorderLayout.NORTH);
+ frame = new JInternalFrame();
+ frame.getContentPane().add(new JScrollPane(pane));
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
- .getUserColourSchemes().get(e.getActionCommand());
-
- sg.cs = udc;
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ cap.setText(report);
+ frame = cap;
}
+
+ Desktop.addInternalFrame(frame,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
+ }
+
+ protected void showNonconserved_actionPerformed()
+ {
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
refresh();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * call to refresh view after settings change
*/
- protected void PIDColour_actionPerformed()
+ void refresh()
{
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
- refresh();
+ ap.updateAnnotation();
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
}
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
/**
* DOCUMENT ME!
*
+ * @param selected
+ *
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- protected void BLOSUM62Colour_actionPerformed()
+ public void abovePIDColour_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (selected)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup().getName());
- sg.cs = new Blosum62ColourScheme();
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ SliderPanel.showPIDSlider();
+ }
+ else
+ // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
+ }
+ modifyPID.setEnabled(selected);
refresh();
}
/**
- * DOCUMENT ME!
+ * Open a panel where the user can choose which types of sequence annotation
+ * to show or hide.
*
* @param e
- * DOCUMENT ME!
*/
- protected void noColourmenuItem_actionPerformed()
+ protected void chooseAnnotations_actionPerformed(ActionEvent e)
{
- getGroup().cs = null;
- refresh();
+ // todo correct way to guard against opening a duplicate panel?
+ new AnnotationChooser(ap);
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- protected void conservationMenuItem_actionPerformed()
+ public void conservationMenuItem_actionPerformed(boolean selected)
{
SequenceGroup sg = getGroup();
if (sg.cs == null)
@@ -1177,75 +1949,60 @@ public class PopupMenu extends JPopupMenu
return;
}
- if (conservationMenuItem.isSelected())
+ if (selected)
{
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(ap.av.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
-
+ 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.predefinedColours = true;
- sg.cs = acg;
+ modifyConservation.setEnabled(selected);
refresh();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a dialog where group name and description may be edited
*/
protected void groupName_actionPerformed()
{
-
SequenceGroup sg = getGroup();
- EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
- .getDescription(), " Group Name ", "Group Description ",
- "Edit Group Name/Description");
-
- if (!dialog.accept)
- {
- return;
- }
-
- sg.setName(dialog.getName());
- sg.setDescription(dialog.getDescription());
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),
+ sg.getDescription(),
+ MessageManager.getString("label.group_name"),
+ MessageManager.getString("label.group_description"));
+ dialog.showDialog(ap.alignFrame,
+ MessageManager.getString("label.edit_group_name_description"),
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ }
+ });
}
/**
- * DOCUMENT ME!
+ * Get selection group - adding it to the alignment if necessary.
*
- * @return DOCUMENT ME!
+ * @return sequence group to operate on
*/
SequenceGroup getGroup()
{
@@ -1253,89 +2010,95 @@ public class PopupMenu extends JPopupMenu
// this method won't add a new group if it already exists
if (sg != null)
{
- ap.av.alignment.addGroup(sg);
+ ap.av.getAlignment().addGroup(sg);
}
return sg;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Shows a dialog where the sequence name and description may be edited. If a
+ * name containing spaces is entered, these are converted to underscores, with
+ * a warning message.
*/
void sequenceName_actionPerformed()
{
- EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
- .getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description");
-
- if (!dialog.accept)
- {
- return;
- }
-
- if (dialog.getName() != null)
- {
- if (dialog.getName().indexOf(" ") > -1)
- {
- JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in Sequence Name",
- JOptionPane.WARNING_MESSAGE);
- }
-
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false);
- }
-
- sequence.setDescription(dialog.getDescription());
-
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
-
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+ sequence.getDescription(),
+ MessageManager.getString("label.sequence_name"),
+ MessageManager.getString("label.sequence_description"));
+ dialog.showDialog(ap.alignFrame, MessageManager.getString(
+ "label.edit_sequence_name_description"), new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager.getString(
+ "label.spaces_converted_to_underscores"),
+ MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false, false);
+ }
+ sequence.setDescription(dialog.getDescription());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+ });
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
refresh();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
+ refresh();
+ }
+
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Offers a colour chooser and sets the selected colour as the group outline
*/
protected void outline_actionPerformed()
{
- SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
- Color.BLUE);
-
- if (col != null)
+ String title = MessageManager.getString("label.select_outline_colour");
+ ColourChooserListener listener = new ColourChooserListener()
{
- sg.setOutlineColour(col);
- }
-
- refresh();
+ @Override
+ public void colourSelected(Color c)
+ {
+ getGroup().setOutlineColour(c);
+ refresh();
+ }
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
+ Color.BLUE, listener);
}
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showBoxes_actionPerformed()
{
@@ -1347,7 +2110,7 @@ public class PopupMenu extends JPopupMenu
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showText_actionPerformed()
{
@@ -1359,7 +2122,7 @@ public class PopupMenu extends JPopupMenu
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showColourText_actionPerformed()
{
@@ -1367,66 +2130,19 @@ public class PopupMenu extends JPopupMenu
refresh();
}
- public void showLink(String url)
- {
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "Web browser not found", JOptionPane.WARNING_MESSAGE);
-
- ex.printStackTrace();
- }
- }
-
void hideSequences(boolean representGroup)
{
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[]
- { sequence });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(sequence, sg);
-
- return;
- }
-
- int gsize = sg.getSize();
- SequenceI[] hseqs;
-
- hseqs = new SequenceI[gsize];
-
- int index = 0;
- for (int i = 0; i < gsize; i++)
- {
- hseqs[index++] = sg.getSequenceAt(i);
- }
-
- ap.av.hideSequence(hseqs);
- ap.av.sendSelection();
+ ap.av.hideSequences(sequence, representGroup);
}
public void copy_actionPerformed()
{
- ap.alignFrame.copy_actionPerformed(null);
+ ap.alignFrame.copy_actionPerformed();
}
public void cut_actionPerformed()
{
- ap.alignFrame.cut_actionPerformed(null);
+ ap.alignFrame.cut_actionPerformed();
}
void changeCase(ActionEvent e)
@@ -1436,36 +2152,36 @@ public class PopupMenu extends JPopupMenu
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
- sg.getEndRes() + 1);
+ List startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
if (source == toggle)
{
- description = "Toggle Case";
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = "To Upper Case";
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = "To Lower Case";
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
- .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
@@ -1474,109 +2190,20 @@ public class PopupMenu extends JPopupMenu
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + e.getActionCommand(), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { 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.alignment.getAlignmentAnnotation();
- 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;
- }
-
- public void pdbFromFile_actionPerformed()
- {
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file");
- chooser.setToolTipText("Load a PDB file");
-
- int value = chooser.showOpenDialog(null);
-
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- PDBEntry entry = new PDBEntry();
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- try
- {
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
- jalview.io.AppletFormatAdapter.FILE);
+ // or we simply trust the user wants
+ // wysiwig behaviour
- if (pdbfile.id == null)
- {
- String reply = JOptionPane
- .showInternalInputDialog(
- Desktop.desktop,
- "Couldn't find a PDB id in the file supplied."
- + "Please enter an Id to identify this structure.",
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
- if (reply == null)
- {
- return;
- }
-
- entry.setId(reply);
- }
- else
- {
- entry.setId(pdbfile.id);
- }
- } catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
-
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
- }
-
- }
-
- public void enterPDB_actionPerformed()
- {
- String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
-
- if (id != null && id.length() > 0)
- {
- PDBEntry entry = new PDBEntry();
- entry.setId(id.toUpperCase());
- sequence.getDatasetSequence().addPDBId(entry);
- }
- }
-
- public void discoverPDB_actionPerformed()
- {
-
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
- { sequence }
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
- Thread discpdb = new Thread(new Runnable()
- {
- public void run()
- {
-
- new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
- .fetchDBRefs(false);
- }
-
- });
- discpdb.start();
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
public void sequenceFeature_actionPerformed()
@@ -1587,24 +2214,31 @@ public class PopupMenu extends JPopupMenu
return;
}
- int gSize = sg.getSize();
- SequenceI[] seqs = new SequenceI[gSize];
- SequenceFeature[] features = new SequenceFeature[gSize];
+ List seqs = new ArrayList<>();
+ List 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++)
{
- seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
- features[i] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
+ if (start <= end)
+ {
+ seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+ features.add(new SequenceFeature(null, null, start, end, null));
+ }
}
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
+ /*
+ * an entirely gapped region will generate empty lists of sequence / features
+ */
+ if (!seqs.isEmpty())
{
- ap.alignFrame.setShowSeqFeatures(true);
- ap.highlightSearchResults(null);
+ new FeatureEditor(ap, seqs, features, true).showDialog();
}
}
@@ -1617,53 +2251,76 @@ public class PopupMenu extends JPopupMenu
}
}
- public void colourByStructure(String pdbid)
- {
- Annotation[] anots = jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().colourSequenceFromStructure(
- sequence, pdbid);
-
- AlignmentAnnotation an = new AlignmentAnnotation("Structure",
- "Coloured by " + pdbid, anots);
-
- ap.av.alignment.addAnnotation(an);
- an.createSequenceMapping(sequence, 0, true);
- // an.adjustForAlignment();
- ap.av.alignment.setAnnotationIndex(an, 0);
-
- ap.adjustAnnotationHeight();
-
- sequence.addAlignmentAnnotation(an);
-
- }
-
- public void editSequence_actionPerformed(ActionEvent actionEvent)
+ /**
+ * Shows a dialog where sequence characters may be edited. Any changes are
+ * applied, and added as an available 'Undo' item in the edit commands
+ * history.
+ */
+ public void editSequence_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
+ SequenceI seq = sequence;
if (sg != null)
{
- if (sequence == null)
- sequence = (Sequence) sg.getSequenceAt(0);
-
- EditNameDialog dialog = new EditNameDialog(sequence
- .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
- null, "Edit Sequence ", null, "Edit Sequence");
-
- if (dialog.accept)
+ if (seq == null)
{
- EditCommand editCommand = new EditCommand("Edit Sequences",
- EditCommand.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()), sg
- .getSequencesAsArray(ap.av.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+ seq = sg.getSequenceAt(0);
+ }
- ap.alignFrame.addHistoryItem(editCommand);
+ EditNameDialog dialog = new EditNameDialog(
+ seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null);
+ dialog.showDialog(ap.alignFrame,
+ MessageManager.getString("label.edit_sequence"),
+ new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(
+ ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+ ap.alignFrame.addHistoryItem(editCommand);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+ });
+ }
+ }
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
- }
+ /**
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
+ *
+ * @return
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ SequenceGroup sg = getGroup();
+ /*
+ * switch to the chosen colour scheme (or null for None)
+ */
+ ColourSchemeI colourScheme = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, ap.av, sg,
+ ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
}
+
+ refresh();
}
}