-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.analysis.AAFrequency;
-import jalview.analysis.AlignmentAnnotationUtils;
-import jalview.analysis.AlignmentUtils;
-import jalview.analysis.Conservation;
-import jalview.bin.JalviewLite;
-import jalview.commands.ChangeCaseCommand;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.util.UrlLink;
-
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JFrame;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.JPopupMenu;
-
-public class APopupMenu extends JPopupMenu implements
- ActionListener, ItemListener
-{
- private static final String ALL_ANNOTATIONS = "All";
-
- JMenu groupMenu = new JMenu();
-
- JMenuItem editGroupName = new JMenuItem();
-
- protected JMenuItem clustalColour = new JMenuItem();
-
- protected JMenuItem zappoColour = new JMenuItem();
-
- protected JMenuItem taylorColour = new JMenuItem();
-
- protected JMenuItem hydrophobicityColour = new JMenuItem();
-
- protected JMenuItem helixColour = new JMenuItem();
-
- protected JMenuItem strandColour = new JMenuItem();
-
- protected JMenuItem turnColour = new JMenuItem();
-
- protected JMenuItem buriedColour = new JMenuItem();
-
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
-
- protected JMenuItem userDefinedColour = new JMenuItem();
-
- protected JMenuItem PIDColour = new JMenuItem();
-
- protected JMenuItem BLOSUM62Colour = new JMenuItem();
-
- JMenuItem noColourmenuItem = new JMenuItem();
-
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
- final AlignmentPanel ap;
-
- JMenuItem unGroupMenuItem = new JMenuItem();
-
- JMenuItem createGroupMenuItem = new JMenuItem();
-
- JMenuItem nucleotideMenuItem = new JMenuItem();
-
- JMenu colourMenu = new JMenu();
-
- JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
- JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
-
- JMenu seqShowAnnotationsMenu = new JMenu(
- MessageManager.getString("label.show_annotations"));
-
- JMenu seqHideAnnotationsMenu = new JMenu(
- MessageManager.getString("label.hide_annotations"));
-
- JMenuItem seqAddReferenceAnnotations = new JMenuItem(
- MessageManager.getString("label.add_reference_annotations"));
-
- JMenu groupShowAnnotationsMenu = new JMenu(
- MessageManager.getString("label.show_annotations"));
-
- JMenu groupHideAnnotationsMenu = new JMenu(
- MessageManager.getString("label.hide_annotations"));
-
- JMenuItem groupAddReferenceAnnotations = new JMenuItem(
- MessageManager.getString("label.add_reference_annotations"));
-
- JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
-
- JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
-
- JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
-
- JMenuItem toUpper = new JMenuItem(
- MessageManager.getString("label.to_upper_case"));
-
- JMenuItem toLower = new JMenuItem(
- MessageManager.getString("label.to_lower_case"));
-
- JMenuItem toggleCase = new JMenuItem(
- MessageManager.getString("label.toggle_case"));
-
- JMenu outputmenu = new JMenu();
-
- JMenu seqMenu = new JMenu();
-
- JMenuItem pdb = new JMenuItem();
-
- JMenuItem hideSeqs = new JMenuItem();
-
- JMenuItem repGroup = new JMenuItem();
-
- JMenuItem sequenceName = new JMenuItem(
- MessageManager.getString("label.edit_name_description"));
-
- JMenuItem sequenceFeature = new JMenuItem(
- MessageManager.getString("label.create_sequence_feature"));
-
- JMenuItem editSequence = new JMenuItem(
- MessageManager.getString("label.edit_sequence"));
-
- JMenuItem sequenceDetails = new JMenuItem(
- MessageManager.getString("label.sequence_details") + "...");
-
- JMenuItem selSeqDetails = new JMenuItem(
- MessageManager.getString("label.sequence_details") + "...");
-
- JMenuItem makeReferenceSeq = new JMenuItem();
-
- SequenceI seq;
-
- JMenuItem revealAll = new JMenuItem();
-
- JMenuItem revealSeq = new JMenuItem();
-
- /**
- * index of sequence to be revealed
- */
- int revealSeq_index = -1;
-
- JMenu menu1 = new JMenu();
-
- public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
- Vector<String> links)
- {
- // /////////////////////////////////////////////////////////
- // If this is activated from the sequence panel, the user may want to
- // edit or annotate a particular residue. Therefore display the residue menu
- //
- // If from the IDPanel, we must display the sequence menu
- // ////////////////////////////////////////////////////////
-
- this.ap = apanel;
- this.seq = seq;
-
- try
- {
- jbInit();
- } catch (Exception e)
- {
- e.printStackTrace();
- }
-
- for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
- {
- JMenuItem item = new JMenuItem(
-AppletFormatAdapter.WRITEABLE_FORMATS[i]);
-
- item.addActionListener(this);
- outputmenu.add(item);
- }
-
- buildAnnotationSubmenus();
-
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg != null && sg.getSize() > 0)
- {
- editGroupName.setLabel(MessageManager.formatMessage(
- "label.name_param", new Object[]
- { sg.getName() }));
- showText.setState(sg.getDisplayText());
- showColourText.setState(sg.getColourText());
- showBoxes.setState(sg.getDisplayBoxes());
- displayNonconserved.setState(sg.getShowNonconserved());
- if (!ap.av.getAlignment().getGroups().contains(sg))
- {
- menu1.setLabel(MessageManager.getString("action.edit_new_group"));
- groupMenu.remove(unGroupMenuItem);
- }
- else
- {
- menu1.setLabel(MessageManager.getString("action.edit_group"));
- groupMenu.remove(createGroupMenuItem);
- }
-
- }
- else
- {
- remove(hideSeqs);
- remove(groupMenu);
- }
-
- if (links != null && links.size() > 0)
- {
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- for (int i = 0; i < links.size(); i++)
- {
- String link = links.elementAt(i);
- UrlLink urlLink = new UrlLink(link);
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- continue;
- }
- final String target = urlLink.getTarget(); // link.substring(0,
- // link.indexOf("|"));
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
- {
-
- // collect matching db-refs
- DBRefEntry[] dbr = DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- { target });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
- 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)
- {
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- }
- }
- }
- if (id != 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)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- // addshowLink(linkMenu, target, url_pref + id + url_suff);
- }
- // Now construct URLs from description but only try to do it for regex
- // URL links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description only if regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- else
- {
- addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
- }
- /*
- * final String url;
- *
- * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
- * string and any matching database reference accessions String url_pref
- * = link.substring(link.indexOf("|") + 1,
- * link.indexOf("$SEQUENCE_ID$"));
- *
- * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
- * // collect matching db-refs DBRefEntry[] dbr =
- * DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target}); //
- * collect id string too String id = seq.getName(); if (id.indexOf("|")
- * > -1) { id = id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null)
- * { for (int r=0;r<dbr.length; r++) { if
- * (dbr[r].getAccessionId().equals(id)) { // suppress duplicate link
- * creation for the bare sequence ID string with this link id = null; }
- * addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
- * target, url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null)
- * { // create Bare ID link for this RUL addshowLink(linkMenu, target,
- * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
- * link.substring(link.lastIndexOf("|")+1)); }
- */
- }
- if (linkMenu.getItemCount() > 0)
- {
- if (seq != null)
- {
- seqMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
- }
- }
- }
- // TODO: add group link menu entry here
- if (seq != null)
- {
- seqMenu.setLabel(seq.getName());
- if (seq == ap.av.getAlignment().getSeqrep())
- {
- makeReferenceSeq.setLabel(MessageManager
- .getString("action.unmark_as_reference"));// Unmark
- // representative");
- }
- else
- {
- makeReferenceSeq.setLabel(MessageManager
- .getString("action.set_as_reference")); // );
- }
- repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { seq.getName() }));
- }
- else
- {
- remove(seqMenu);
- }
-
- if (!ap.av.hasHiddenRows())
- {
- remove(revealAll);
- remove(revealSeq);
- }
- else
- {
- final int index = ap.av.getAlignment().findIndex(seq);
-
- if (ap.av.adjustForHiddenSeqs(index)
- - ap.av.adjustForHiddenSeqs(index - 1) > 1)
- {
- revealSeq_index = index;
- }
- else
- {
- remove(revealSeq);
- }
- }
- }
-
- /**
- * Build menus for annotation types that may be shown or hidden, and for
- * 'reference annotations' that may be added to the alignment.
- */
- private void buildAnnotationSubmenus()
- {
- /*
- * First for the currently selected sequence (if there is one):
- */
- final List<SequenceI> selectedSequence = (seq == null ? Collections
- .<SequenceI> emptyList() : Arrays.asList(seq));
- buildAnnotationTypesMenus(seqShowAnnotationsMenu,
- seqHideAnnotationsMenu, selectedSequence);
- configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
- selectedSequence);
-
- /*
- * and repeat for the current selection group (if there is one):
- */
- final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
- .<SequenceI> emptyList() : ap.av.getSelectionGroup()
- .getSequences());
- buildAnnotationTypesMenus(groupShowAnnotationsMenu,
- groupHideAnnotationsMenu, selectedGroup);
- configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
- selectedGroup);
- }
-
- /**
- * Determine whether or not to enable 'add reference annotations' menu item.
- * It is enable if there are any annotations, on any of the selected
- * sequences, which are not yet on the alignment (visible or not).
- *
- * @param menu
- * @param forSequences
- */
- private void configureReferenceAnnotationsMenu(JMenuItem menuItem,
- List<SequenceI> forSequences)
- {
- menuItem.setEnabled(false);
-
- /*
- * Temporary store to hold distinct calcId / type pairs for the tooltip.
- * Using TreeMap means calcIds are shown in alphabetical order.
- */
- Map<String, String> tipEntries = new TreeMap<String, String>();
- final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
- AlignmentI al = this.ap.av.getAlignment();
- AlignmentUtils.findAddableReferenceAnnotations(forSequences,
- tipEntries, candidates, al);
- if (!candidates.isEmpty())
- {
- StringBuilder tooltip = new StringBuilder(64);
- tooltip.append(MessageManager.getString("label.add_annotations_for"));
-
- /*
- * Found annotations that could be added. Enable the menu item, and
- * configure its action.
- */
- menuItem.setEnabled(true);
-
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- addReferenceAnnotations_actionPerformed(candidates);
- }
- });
- }
- }
-
- /**
- * Add annotations to the sequences and to the alignment.
- *
- * @param candidates
- * a map whose keys are sequences on the alignment, and values a list
- * of annotations to add to each sequence
- */
- protected void addReferenceAnnotations_actionPerformed(
- Map<SequenceI, List<AlignmentAnnotation>> candidates)
- {
- final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
- final AlignmentI alignment = this.ap.getAlignment();
- AlignmentUtils.addReferenceAnnotations(candidates, alignment,
- selectionGroup);
- refresh();
- }
-
- /**
- * add a show URL menu item to the given linkMenu
- *
- * @param linkMenu
- * @param target
- * - menu label string
- * @param url
- * - url to open
- */
- private void addshowLink(JMenu linkMenu, final String target,
- final String url)
- {
- addshowLink(linkMenu, target, target, url);
- }
-
- /**
- * add a show URL menu item to the given linkMenu
- *
- * @param linkMenu
- * @param target
- * - URL target window
- * @param label
- * - menu label string
- * @param url
- * - url to open
- */
- private void addshowLink(JMenu linkMenu, final String target,
- final String label, final String url)
- {
- JMenuItem item = new JMenuItem(label);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ap.alignFrame.showURL(url, target);
- }
- });
- linkMenu.add(item);
- }
-
- public void itemStateChanged(ItemEvent evt)
- {
- if (evt.getSource() == abovePIDColour)
- {
- abovePIDColour_itemStateChanged();
- }
- else if (evt.getSource() == showColourText)
- {
- showColourText_itemStateChanged();
- }
- else if (evt.getSource() == showText)
- {
- showText_itemStateChanged();
- }
- else if (evt.getSource() == showBoxes)
- {
- showBoxes_itemStateChanged();
- }
- else if (evt.getSource() == displayNonconserved)
- {
- this.showNonconserved_itemStateChanged();
- }
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- Object source = evt.getSource();
- if (source == clustalColour)
- {
- clustalColour_actionPerformed();
- }
- else if (source == zappoColour)
- {
- zappoColour_actionPerformed();
- }
- else if (source == taylorColour)
- {
- taylorColour_actionPerformed();
- }
- else if (source == hydrophobicityColour)
- {
- hydrophobicityColour_actionPerformed();
- }
- else if (source == helixColour)
- {
- helixColour_actionPerformed();
- }
- else if (source == strandColour)
- {
- strandColour_actionPerformed();
- }
- else if (source == turnColour)
- {
- turnColour_actionPerformed();
- }
- else if (source == buriedColour)
- {
- buriedColour_actionPerformed();
- }
- else if (source == nucleotideMenuItem)
- {
- nucleotideMenuItem_actionPerformed();
- }
-
- else if (source == userDefinedColour)
- {
- userDefinedColour_actionPerformed();
- }
- else if (source == PIDColour)
- {
- PIDColour_actionPerformed();
- }
- else if (source == BLOSUM62Colour)
- {
- BLOSUM62Colour_actionPerformed();
- }
- else if (source == noColourmenuItem)
- {
- noColourmenuItem_actionPerformed();
- }
- else if (source == conservationMenuItem)
- {
- conservationMenuItem_itemStateChanged();
- }
- else if (source == unGroupMenuItem)
- {
- unGroupMenuItem_actionPerformed();
- }
-
- else if (source == createGroupMenuItem)
- {
- createGroupMenuItem_actionPerformed();
- }
-
- else if (source == sequenceName)
- {
- editName();
- }
- else if (source == makeReferenceSeq)
- {
- makeReferenceSeq_actionPerformed();
- }
- else if (source == sequenceDetails)
- {
- showSequenceDetails();
- }
- else if (source == selSeqDetails)
- {
- showSequenceSelectionDetails();
- }
- else if (source == pdb)
- {
- addPDB();
- }
- else if (source == hideSeqs)
- {
- hideSequences(false);
- }
- else if (source == repGroup)
- {
- hideSequences(true);
- }
- else if (source == revealSeq)
- {
- ap.av.showSequence(revealSeq_index);
- }
- else if (source == revealAll)
- {
- ap.av.showAllHiddenSeqs();
- }
-
- else if (source == editGroupName)
- {
- EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
- getGroup().getDescription(), " Group Name",
- "Group Description", ap.alignFrame,
- "Edit Group Name / Description", 500, 100, true);
-
- if (dialog.accept)
- {
- getGroup().setName(dialog.getName().replace(' ', '_'));
- getGroup().setDescription(dialog.getDescription());
- }
-
- }
- else if (source == copy)
- {
- ap.alignFrame.copy_actionPerformed();
- }
- else if (source == cut)
- {
- ap.alignFrame.cut_actionPerformed();
- }
- else if (source == editSequence)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- if (sg != null)
- {
- if (seq == null)
- {
- seq = sg.getSequenceAt(0);
- }
-
- EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
- sg.getStartRes(), sg.getEndRes() + 1), null,
- "Edit Sequence ", null,
-
- ap.alignFrame, "Edit Sequence", 500, 100, true);
-
- if (dialog.accept)
- {
- 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());
- }
- }
- }
- else if (source == toUpper || source == toLower || source == toggleCase)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg != null)
- {
- List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
- sg.getStartRes(), sg.getEndRes() + 1);
-
- String description;
- int caseChange;
-
- if (source == toggleCase)
- {
- description = "Toggle Case";
- caseChange = ChangeCaseCommand.TOGGLE_CASE;
- }
- else if (source == toUpper)
- {
- description = "To Upper Case";
- caseChange = ChangeCaseCommand.TO_UPPER;
- }
- else
- {
- description = "To Lower Case";
- caseChange = ChangeCaseCommand.TO_LOWER;
- }
-
- 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());
-
- }
- }
- else if (source == sequenceFeature)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null)
- {
- return;
- }
-
- int rsize = 0, gSize = sg.getSize();
- SequenceI[] rseqs, seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
-
- for (int i = 0; i < gSize; i++)
- {
- int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
- int end = sg.findEndRes(sg.getSequenceAt(i));
- if (start <= end)
- {
- seqs[rsize] = sg.getSequenceAt(i);
- features[rsize] = new SequenceFeature(null, null, null, start,
- end, "Jalview");
- rsize++;
- }
- }
- rseqs = new SequenceI[rsize];
- tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs, 0, rseqs, 0, rsize);
- System.arraycopy(features, 0, tfeatures, 0, rsize);
- features = tfeatures;
- seqs = rseqs;
-
- if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
- features, true, ap))
- {
- ap.alignFrame.sequenceFeatures.setState(true);
- ap.av.setShowSequenceFeatures(true);;
- ap.highlightSearchResults(null);
- }
- }
- else
- {
- outputText(evt);
- }
-
- }
-
- void outputText(ActionEvent e)
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
-
- JFrame frame = new JFrame();
- frame.add(cap);
- JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.selection_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
- // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
- // now returns a full copy of sequence data
- // TODO consider using getSequenceSelection instead here
-
- cap.setText(new AppletFormatAdapter().formatSequences(
- e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
-
- }
-
- protected void showSequenceSelectionDetails()
- {
- createSequenceDetailsReport(ap.av.getSequenceSelection());
- }
-
- protected void showSequenceDetails()
- {
- createSequenceDetailsReport(new SequenceI[]
- { seq });
- }
-
- public void createSequenceDetailsReport(SequenceI[] sequences)
- {
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
-
- StringBuffer contents = new StringBuffer();
- for (SequenceI seq : sequences)
- {
- contents.append(MessageManager.formatMessage(
- "label.annotation_for_displayid", new Object[]
- { seq.getDisplayId(true) }));
- new SequenceAnnotationReport(null)
- .createSequenceAnnotationReport(
- contents,
- seq,
- true,
- true,
- false,
- (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
- : null);
- contents.append("</p>");
- }
- JFrame frame = new JFrame();
- frame.add(cap);
- JalviewLite.addFrame(frame, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "Selection"), 600, 500);
- cap.setText(MessageManager.formatMessage("label.html_content",
- new Object[]
- { contents.toString() }));
- }
-
- void editName()
- {
- EditNameDialog dialog = new EditNameDialog(seq.getName(),
- seq.getDescription(), " Sequence Name",
- "Sequence Description", ap.alignFrame,
- "Edit Sequence Name / Description", 500, 100, true);
-
- if (dialog.accept)
- {
- seq.setName(dialog.getName());
- seq.setDescription(dialog.getDescription());
- ap.paintAlignment(false);
- }
- }
-
- void addPDB()
- {
- if (seq.getPDBId() != null)
- {
- PDBEntry entry = seq.getPDBId().firstElement();
-
-// if (ap.av.applet.jmolAvailable)
-// {
- new AppletJmol(entry, new SequenceI[]
- { seq }, null, ap, AppletFormatAdapter.URL);
-// }
-// else
-// {
-// new MCview.AppletPDBViewer(entry, new SequenceI[]
-// { seq }, null, ap, AppletFormatAdapter.URL);
-// }
-
- }
- else
- {
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
- cap.setText(MessageManager.getString("label.paste_pdb_file"));
- cap.setPDBImport(seq);
- JFrame frame = new JFrame();
- frame.add(cap);
- JalviewLite.addFrame(frame, MessageManager.formatMessage(
- "label.paste_pdb_file_for_sequence", new Object[]
- { seq.getName() }), 400, 300);
- }
- }
-
- private void jbInit() throws Exception
- {
- groupMenu.setLabel(MessageManager.getString("label.selection"));
- sequenceFeature.addActionListener(this);
-
- editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel(MessageManager
- .getString("action.remove_group"));
- unGroupMenuItem.addActionListener(this);
-
- createGroupMenuItem.setLabel(MessageManager
- .getString("action.create_group"));
- createGroupMenuItem.addActionListener(this);
-
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- abovePIDColour.addItemListener(this);
- colourMenu.setLabel(MessageManager.getString("label.group_colour"));
- showBoxes.setLabel(MessageManager.getString("action.boxes"));
- showBoxes.setState(true);
- showBoxes.addItemListener(this);
- sequenceName.addActionListener(this);
- sequenceDetails.addActionListener(this);
- selSeqDetails.addActionListener(this);
- displayNonconserved.setLabel(MessageManager
- .getString("label.show_non_conversed"));
- displayNonconserved.setState(false);
- displayNonconserved.addItemListener(this);
- showText.setLabel(MessageManager.getString("action.text"));
- showText.addItemListener(this);
- showColourText.setLabel(MessageManager.getString("label.colour_text"));
- showColourText.addItemListener(this);
- outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
- seqMenu.setLabel(MessageManager.getString("label.sequence"));
- pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
- hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
- repGroup.setLabel(MessageManager.formatMessage(
- "label.represent_group_with", new Object[]
- { "" }));
- revealAll.setLabel(MessageManager.getString("action.reveal_all"));
- revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
- menu1.setLabel(MessageManager.getString("label.group") + ":");
- add(groupMenu);
- this.add(seqMenu);
- this.add(hideSeqs);
- this.add(revealSeq);
- this.add(revealAll);
- // groupMenu.add(selSeqDetails);
- groupMenu.add(groupShowAnnotationsMenu);
- groupMenu.add(groupHideAnnotationsMenu);
- groupMenu.add(groupAddReferenceAnnotations);
- groupMenu.add(editMenu);
- groupMenu.add(outputmenu);
- groupMenu.add(sequenceFeature);
- groupMenu.add(createGroupMenuItem);
- groupMenu.add(unGroupMenuItem);
- groupMenu.add(menu1);
-
- 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);
- colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
-
- noColourmenuItem.setLabel(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(this);
-
- clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
- clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(this);
- hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(this);
- strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
- strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
-
- userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
- userDefinedColour.addActionListener(this);
- PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
- PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62");
- BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
-
- editMenu.add(copy);
- copy.addActionListener(this);
- editMenu.add(cut);
- cut.addActionListener(this);
-
- editMenu.add(editSequence);
- editSequence.addActionListener(this);
-
- editMenu.add(toUpper);
- toUpper.addActionListener(this);
- editMenu.add(toLower);
- toLower.addActionListener(this);
- editMenu.add(toggleCase);
- seqMenu.add(seqShowAnnotationsMenu);
- seqMenu.add(seqHideAnnotationsMenu);
- seqMenu.add(seqAddReferenceAnnotations);
- seqMenu.add(sequenceName);
- seqMenu.add(makeReferenceSeq);
- // seqMenu.add(sequenceDetails);
-
- if (!ap.av.applet.useXtrnalSviewer)
- {
- seqMenu.add(pdb);
- }
- seqMenu.add(repGroup);
- menu1.add(editGroupName);
- menu1.add(colourMenu);
- menu1.add(showBoxes);
- menu1.add(showText);
- menu1.add(showColourText);
- menu1.add(displayNonconserved);
- toggleCase.addActionListener(this);
- pdb.addActionListener(this);
- hideSeqs.addActionListener(this);
- repGroup.addActionListener(this);
- revealAll.addActionListener(this);
- revealSeq.addActionListener(this);
- makeReferenceSeq.addActionListener(this);
- }
-
- void refresh()
- {
- ap.paintAlignment(true);
- }
-
- protected void clustalColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
- refresh();
- }
-
- protected void zappoColour_actionPerformed()
- {
- getGroup().cs = new ZappoColourScheme();
- refresh();
- }
-
- protected void taylorColour_actionPerformed()
- {
- getGroup().cs = new TaylorColourScheme();
- refresh();
- }
-
- protected void hydrophobicityColour_actionPerformed()
- {
- getGroup().cs = new HydrophobicColourScheme();
- refresh();
- }
-
- protected void helixColour_actionPerformed()
- {
- getGroup().cs = new HelixColourScheme();
- refresh();
- }
-
- protected void strandColour_actionPerformed()
- {
- getGroup().cs = new StrandColourScheme();
- refresh();
- }
-
- protected void turnColour_actionPerformed()
- {
- getGroup().cs = new TurnColourScheme();
- refresh();
- }
-
- protected void buriedColour_actionPerformed()
- {
- getGroup().cs = new BuriedColourScheme();
- refresh();
- }
-
- public void nucleotideMenuItem_actionPerformed()
- {
- getGroup().cs = new NucleotideColourScheme();
- refresh();
- }
-
- protected void abovePIDColour_itemStateChanged()
- {
- SequenceGroup sg = getGroup();
- if (sg.cs == null)
- {
- return;
- }
-
- if (abovePIDColour.getState())
- {
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
- .getName());
-
- sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
-
- SliderPanel.showPIDSlider();
-
- }
- else
- // remove PIDColouring
- {
- sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
- }
-
- refresh();
-
- }
-
- protected void userDefinedColour_actionPerformed()
- {
- new UserDefinedColours(ap, getGroup());
- }
-
- protected void PIDColour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
- refresh();
- }
-
- protected void BLOSUM62Colour_actionPerformed()
- {
- SequenceGroup sg = getGroup();
-
- sg.cs = new Blosum62ColourScheme();
-
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
-
- refresh();
- }
-
- protected void noColourmenuItem_actionPerformed()
- {
- getGroup().cs = null;
- refresh();
- }
-
- protected void conservationMenuItem_itemStateChanged()
- {
- SequenceGroup sg = getGroup();
- if (sg.cs == null)
- {
- return;
- }
-
- if (conservationMenuItem.getState())
- {
-
- sg.cs.setConservation(Conservation.calculateConservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(ap.av
- .getHiddenRepSequences()), 0, ap.av.getAlignment()
- .getWidth(), false, ap.av.getConsPercGaps(), false));
- SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
- SliderPanel.showConservationSlider();
- }
- else
- // remove ConservationColouring
- {
- sg.cs.setConservation(null);
- }
-
- refresh();
- }
-
- SequenceGroup getGroup()
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
-
- // this method won't add a new group if it already exists
- if (sg != null)
- {
- ap.av.getAlignment().addGroup(sg);
- }
-
- return sg;
- }
-
- void unGroupMenuItem_actionPerformed()
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.getAlignment().deleteGroup(sg);
- ap.av.setSelectionGroup(null);
- ap.paintAlignment(true);
- }
-
- void createGroupMenuItem_actionPerformed()
- {
- getGroup(); // implicitly create group
- refresh();
- }
-
- public void showColourText_itemStateChanged()
- {
- getGroup().setColourText(showColourText.getState());
- refresh();
- }
-
- public void showText_itemStateChanged()
- {
- getGroup().setDisplayText(showText.getState());
- refresh();
- }
- public void makeReferenceSeq_actionPerformed()
- {
- if (!ap.av.getAlignment().hasSeqrep())
- {
- // initialise the display flags so the user sees something happen
- ap.av.setDisplayReferenceSeq(true);
- ap.av.setColourByReferenceSeq(true);
- ap.av.getAlignment().setSeqrep(seq);
- }
- else
- {
- if (ap.av.getAlignment().getSeqrep() == seq)
- {
- ap.av.getAlignment().setSeqrep(null);
- }
- else
- {
- ap.av.getAlignment().setSeqrep(seq);
- }
- }
- refresh();
- }
-
- public void showNonconserved_itemStateChanged()
- {
- getGroup().setShowNonconserved(this.displayNonconserved.getState());
- refresh();
- }
-
- public void showBoxes_itemStateChanged()
- {
- getGroup().setDisplayBoxes(showBoxes.getState());
- refresh();
- }
-
- void hideSequences(boolean representGroup)
- {
- SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null || sg.getSize() < 1)
- {
- ap.av.hideSequence(new SequenceI[]
- { seq });
- return;
- }
-
- ap.av.setSelectionGroup(null);
-
- if (representGroup)
- {
- ap.av.hideRepSequences(seq, 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();
- }
-
- /**
- * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
- * "All" is added first, followed by a separator. Then add any annotation
- * types associated with the current selection. Separate menus are built for
- * the selected sequence group (if any), and the selected sequence.
- * <p>
- * Some annotation rows are always rendered together - these can be identified
- * by a common graphGroup property > -1. Only one of each group will be marked
- * as visible (to avoid duplication of the display). For such groups we add a
- * composite type name, e.g.
- * <p>
- * IUPredWS (Long), IUPredWS (Short)
- *
- * @param seq
- */
- protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
- List<SequenceI> forSequences)
- {
- showMenu.removeAll();
- hideMenu.removeAll();
-
- final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
- addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
- addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
- false);
- showMenu.addSeparator();
- hideMenu.addSeparator();
-
- final AlignmentAnnotation[] annotations = ap.getAlignment()
- .getAlignmentAnnotation();
-
- /*
- * Find shown/hidden annotations types, distinguished by source (calcId),
- * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
- * the insertion order, which is the order of the annotations on the
- * alignment.
- */
- Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
- Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
- AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
- hiddenTypes,
- AlignmentAnnotationUtils.asList(annotations),
- forSequences);
-
- for (String calcId : hiddenTypes.keySet())
- {
- for (List<String> type : hiddenTypes.get(calcId))
- {
- addAnnotationTypeToShowHide(showMenu, forSequences,
- calcId, type, false, true);
- }
- }
- // grey out 'show annotations' if none are hidden
- showMenu.setEnabled(!hiddenTypes.isEmpty());
-
- for (String calcId : shownTypes.keySet())
- {
- for (List<String> type : shownTypes.get(calcId))
- {
- addAnnotationTypeToShowHide(hideMenu, forSequences,
- calcId, type, false, false);
- }
- }
- // grey out 'hide annotations' if none are shown
- hideMenu.setEnabled(!shownTypes.isEmpty());
- }
-
- /**
- * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
- * menus.
- *
- * @param showOrHideMenu
- * the menu to add to
- * @param forSequences
- * the sequences whose annotations may be shown or hidden
- * @param calcId
- * @param types
- * the label to add
- * @param allTypes
- * if true this is a special label meaning 'All'
- * @param actionIsShow
- * if true, the select menu item action is to show the annotation
- * type, else hide
- */
- protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
- final List<SequenceI> forSequences, String calcId,
- final List<String> types, final boolean allTypes,
- final boolean actionIsShow)
- {
- String label = types.toString(); // [a, b, c]
- label = label.substring(1, label.length() - 1);
- final JMenuItem item = new JMenuItem(label);
- item.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
- forSequences, allTypes, actionIsShow);
- refresh();
- }
- });
- showOrHideMenu.add(item);
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.analysis.AAFrequency;\r
+import jalview.analysis.AlignmentAnnotationUtils;\r
+import jalview.analysis.AlignmentUtils;\r
+import jalview.analysis.Conservation;\r
+import jalview.bin.JalviewLite;\r
+import jalview.commands.ChangeCaseCommand;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.EditCommand.Action;\r
+import jalview.datamodel.AlignmentAnnotation;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.SequenceAnnotationReport;\r
+import jalview.schemes.Blosum62ColourScheme;\r
+import jalview.schemes.BuriedColourScheme;\r
+import jalview.schemes.ClustalxColourScheme;\r
+import jalview.schemes.HelixColourScheme;\r
+import jalview.schemes.HydrophobicColourScheme;\r
+import jalview.schemes.NucleotideColourScheme;\r
+import jalview.schemes.PIDColourScheme;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.StrandColourScheme;\r
+import jalview.schemes.TaylorColourScheme;\r
+import jalview.schemes.TurnColourScheme;\r
+import jalview.schemes.ZappoColourScheme;\r
+import jalview.util.DBRefUtils;\r
+import jalview.util.MessageManager;\r
+import jalview.util.UrlLink;\r
+\r
+import javax.swing.JCheckBoxMenuItem;\r
+import javax.swing.JFrame;\r
+import javax.swing.JMenu;\r
+import javax.swing.JMenuItem;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.util.Arrays;\r
+import java.util.Collections;\r
+import java.util.LinkedHashMap;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.TreeMap;\r
+import java.util.Vector;\r
+\r
+import javax.swing.JPopupMenu;\r
+\r
+public class APopupMenu extends JPopupMenu implements\r
+ ActionListener, ItemListener\r
+{\r
+ private static final String ALL_ANNOTATIONS = "All";\r
+\r
+ JMenu groupMenu = new JMenu();\r
+\r
+ JMenuItem editGroupName = new JMenuItem();\r
+\r
+ protected JMenuItem clustalColour = new JMenuItem();\r
+\r
+ protected JMenuItem zappoColour = new JMenuItem();\r
+\r
+ protected JMenuItem taylorColour = new JMenuItem();\r
+\r
+ protected JMenuItem hydrophobicityColour = new JMenuItem();\r
+\r
+ protected JMenuItem helixColour = new JMenuItem();\r
+\r
+ protected JMenuItem strandColour = new JMenuItem();\r
+\r
+ protected JMenuItem turnColour = new JMenuItem();\r
+\r
+ protected JMenuItem buriedColour = new JMenuItem();\r
+\r
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
+\r
+ protected JMenuItem userDefinedColour = new JMenuItem();\r
+\r
+ protected JMenuItem PIDColour = new JMenuItem();\r
+\r
+ protected JMenuItem BLOSUM62Colour = new JMenuItem();\r
+\r
+ JMenuItem noColourmenuItem = new JMenuItem();\r
+\r
+ protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
+\r
+ final AlignmentPanel ap;\r
+\r
+ JMenuItem unGroupMenuItem = new JMenuItem();\r
+\r
+ JMenuItem createGroupMenuItem = new JMenuItem();\r
+\r
+ JMenuItem nucleotideMenuItem = new JMenuItem();\r
+\r
+ JMenu colourMenu = new JMenu();\r
+\r
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
+\r
+ JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();\r
+\r
+ JMenu seqShowAnnotationsMenu = new JMenu(\r
+ MessageManager.getString("label.show_annotations"));\r
+\r
+ JMenu seqHideAnnotationsMenu = new JMenu(\r
+ MessageManager.getString("label.hide_annotations"));\r
+\r
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem(\r
+ MessageManager.getString("label.add_reference_annotations"));\r
+\r
+ JMenu groupShowAnnotationsMenu = new JMenu(\r
+ MessageManager.getString("label.show_annotations"));\r
+\r
+ JMenu groupHideAnnotationsMenu = new JMenu(\r
+ MessageManager.getString("label.hide_annotations"));\r
+\r
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem(\r
+ MessageManager.getString("label.add_reference_annotations"));\r
+\r
+ JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));\r
+\r
+ JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));\r
+\r
+ JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));\r
+\r
+ JMenuItem toUpper = new JMenuItem(\r
+ MessageManager.getString("label.to_upper_case"));\r
+\r
+ JMenuItem toLower = new JMenuItem(\r
+ MessageManager.getString("label.to_lower_case"));\r
+\r
+ JMenuItem toggleCase = new JMenuItem(\r
+ MessageManager.getString("label.toggle_case"));\r
+\r
+ JMenu outputmenu = new JMenu();\r
+\r
+ JMenu seqMenu = new JMenu();\r
+\r
+ JMenuItem pdb = new JMenuItem();\r
+\r
+ JMenuItem hideSeqs = new JMenuItem();\r
+\r
+ JMenuItem repGroup = new JMenuItem();\r
+\r
+ JMenuItem sequenceName = new JMenuItem(\r
+ MessageManager.getString("label.edit_name_description"));\r
+\r
+ JMenuItem sequenceFeature = new JMenuItem(\r
+ MessageManager.getString("label.create_sequence_feature"));\r
+\r
+ JMenuItem editSequence = new JMenuItem(\r
+ MessageManager.getString("label.edit_sequence"));\r
+\r
+ JMenuItem sequenceDetails = new JMenuItem(\r
+ MessageManager.getString("label.sequence_details") + "...");\r
+\r
+ JMenuItem selSeqDetails = new JMenuItem(\r
+ MessageManager.getString("label.sequence_details") + "...");\r
+\r
+ JMenuItem makeReferenceSeq = new JMenuItem();\r
+ \r
+ SequenceI seq;\r
+\r
+ JMenuItem revealAll = new JMenuItem();\r
+\r
+ JMenuItem revealSeq = new JMenuItem();\r
+\r
+ /**\r
+ * index of sequence to be revealed\r
+ */\r
+ int revealSeq_index = -1;\r
+\r
+ JMenu menu1 = new JMenu();\r
+\r
+ public APopupMenu(AlignmentPanel apanel, final SequenceI seq,\r
+ Vector<String> links)\r
+ {\r
+ // /////////////////////////////////////////////////////////\r
+ // If this is activated from the sequence panel, the user may want to\r
+ // edit or annotate a particular residue. Therefore display the residue menu\r
+ //\r
+ // If from the IDPanel, we must display the sequence menu\r
+ // ////////////////////////////////////////////////////////\r
+\r
+ this.ap = apanel;\r
+ this.seq = seq;\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+ JMenuItem item = new JMenuItem(\r
+AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(this);\r
+ outputmenu.add(item);\r
+ }\r
+\r
+ buildAnnotationSubmenus();\r
+\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null && sg.getSize() > 0)\r
+ {\r
+ editGroupName.setLabel(MessageManager.formatMessage(\r
+ "label.name_param", new Object[]\r
+ { sg.getName() }));\r
+ showText.setState(sg.getDisplayText());\r
+ showColourText.setState(sg.getColourText());\r
+ showBoxes.setState(sg.getDisplayBoxes());\r
+ displayNonconserved.setState(sg.getShowNonconserved());\r
+ if (!ap.av.getAlignment().getGroups().contains(sg))\r
+ {\r
+ menu1.setLabel(MessageManager.getString("action.edit_new_group"));\r
+ groupMenu.remove(unGroupMenuItem);\r
+ }\r
+ else\r
+ {\r
+ menu1.setLabel(MessageManager.getString("action.edit_group"));\r
+ groupMenu.remove(createGroupMenuItem);\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ remove(hideSeqs);\r
+ remove(groupMenu);\r
+ }\r
+\r
+ if (links != null && links.size() > 0)\r
+ {\r
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
+ for (int i = 0; i < links.size(); i++)\r
+ {\r
+ String link = links.elementAt(i);\r
+ UrlLink urlLink = new UrlLink(link);\r
+ if (!urlLink.isValid())\r
+ {\r
+ System.err.println(urlLink.getInvalidMessage());\r
+ continue;\r
+ }\r
+ final String target = urlLink.getTarget(); // link.substring(0,\r
+ // link.indexOf("|"));\r
+ final String label = urlLink.getLabel();\r
+ if (seq != null && urlLink.isDynamic())\r
+ {\r
+\r
+ // collect matching db-refs\r
+ DBRefEntry[] dbr = DBRefUtils.selectRefs(\r
+ seq.getDBRef(), new String[]\r
+ { target });\r
+ // collect id string too\r
+ String id = seq.getName();\r
+ String descr = seq.getDescription();\r
+ if (descr != null && descr.length() < 1)\r
+ {\r
+ descr = null;\r
+ }\r
+ if (dbr != null)\r
+ {\r
+ for (int r = 0; r < dbr.length; r++)\r
+ {\r
+ if (id != null && dbr[r].getAccessionId().equals(id))\r
+ {\r
+ // suppress duplicate link creation for the bare sequence ID\r
+ // string with this link\r
+ id = null;\r
+ }\r
+ // create Bare ID link for this RUL\r
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),\r
+ true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (id != null)\r
+ {\r
+ // create Bare ID link for this RUL\r
+ String[] urls = urlLink.makeUrls(id, true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ addshowLink(linkMenu, label, urls[u + 1]);\r
+ }\r
+ }\r
+ // addshowLink(linkMenu, target, url_pref + id + url_suff);\r
+ }\r
+ // Now construct URLs from description but only try to do it for regex\r
+ // URL links\r
+ if (descr != null && urlLink.getRegexReplace() != null)\r
+ {\r
+ // create link for this URL from description only if regex matches\r
+ String[] urls = urlLink.makeUrls(descr, true);\r
+ if (urls != null)\r
+ {\r
+ for (int u = 0; u < urls.length; u += 2)\r
+ {\r
+ addshowLink(linkMenu, label, urls[u + 1]);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));\r
+ }\r
+ /*\r
+ * final String url;\r
+ * \r
+ * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID\r
+ * string and any matching database reference accessions String url_pref\r
+ * = link.substring(link.indexOf("|") + 1,\r
+ * link.indexOf("$SEQUENCE_ID$"));\r
+ * \r
+ * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+ * // collect matching db-refs DBRefEntry[] dbr =\r
+ * DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target}); //\r
+ * collect id string too String id = seq.getName(); if (id.indexOf("|")\r
+ * > -1) { id = id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null)\r
+ * { for (int r=0;r<dbr.length; r++) { if\r
+ * (dbr[r].getAccessionId().equals(id)) { // suppress duplicate link\r
+ * creation for the bare sequence ID string with this link id = null; }\r
+ * addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),\r
+ * target, url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null)\r
+ * { // create Bare ID link for this RUL addshowLink(linkMenu, target,\r
+ * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,\r
+ * link.substring(link.lastIndexOf("|")+1)); }\r
+ */\r
+ }\r
+ if (linkMenu.getItemCount() > 0)\r
+ {\r
+ if (seq != null)\r
+ {\r
+ seqMenu.add(linkMenu);\r
+ }\r
+ else\r
+ {\r
+ add(linkMenu);\r
+ }\r
+ }\r
+ }\r
+ // TODO: add group link menu entry here\r
+ if (seq != null)\r
+ {\r
+ seqMenu.setLabel(seq.getName());\r
+ if (seq == ap.av.getAlignment().getSeqrep())\r
+ {\r
+ makeReferenceSeq.setLabel(MessageManager\r
+ .getString("action.unmark_as_reference"));// Unmark\r
+ // representative");\r
+ }\r
+ else\r
+ {\r
+ makeReferenceSeq.setLabel(MessageManager\r
+ .getString("action.set_as_reference")); // );\r
+ }\r
+ repGroup.setLabel(MessageManager.formatMessage(\r
+ "label.represent_group_with", new Object[]\r
+ { seq.getName() }));\r
+ }\r
+ else\r
+ {\r
+ remove(seqMenu);\r
+ }\r
+\r
+ if (!ap.av.hasHiddenRows())\r
+ {\r
+ remove(revealAll);\r
+ remove(revealSeq);\r
+ }\r
+ else\r
+ {\r
+ final int index = ap.av.getAlignment().findIndex(seq);\r
+\r
+ if (ap.av.adjustForHiddenSeqs(index)\r
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
+ {\r
+ revealSeq_index = index;\r
+ }\r
+ else\r
+ {\r
+ remove(revealSeq);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Build menus for annotation types that may be shown or hidden, and for\r
+ * 'reference annotations' that may be added to the alignment.\r
+ */\r
+ private void buildAnnotationSubmenus()\r
+ {\r
+ /*\r
+ * First for the currently selected sequence (if there is one):\r
+ */\r
+ final List<SequenceI> selectedSequence = (seq == null ? Collections\r
+ .<SequenceI> emptyList() : Arrays.asList(seq));\r
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,\r
+ seqHideAnnotationsMenu, selectedSequence);\r
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,\r
+ selectedSequence);\r
+\r
+ /*\r
+ * and repeat for the current selection group (if there is one):\r
+ */\r
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections\r
+ .<SequenceI> emptyList() : ap.av.getSelectionGroup()\r
+ .getSequences());\r
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,\r
+ groupHideAnnotationsMenu, selectedGroup);\r
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,\r
+ selectedGroup);\r
+ }\r
+\r
+ /**\r
+ * Determine whether or not to enable 'add reference annotations' menu item.\r
+ * It is enable if there are any annotations, on any of the selected\r
+ * sequences, which are not yet on the alignment (visible or not).\r
+ * \r
+ * @param menu\r
+ * @param forSequences\r
+ */\r
+ private void configureReferenceAnnotationsMenu(JMenuItem menuItem,\r
+ List<SequenceI> forSequences)\r
+ {\r
+ menuItem.setEnabled(false);\r
+\r
+ /*\r
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.\r
+ * Using TreeMap means calcIds are shown in alphabetical order.\r
+ */\r
+ Map<String, String> tipEntries = new TreeMap<String, String>();\r
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();\r
+ AlignmentI al = this.ap.av.getAlignment();\r
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences,\r
+ tipEntries, candidates, al);\r
+ if (!candidates.isEmpty())\r
+ {\r
+ StringBuilder tooltip = new StringBuilder(64);\r
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));\r
+\r
+ /*\r
+ * Found annotations that could be added. Enable the menu item, and\r
+ * configure its action.\r
+ */\r
+ menuItem.setEnabled(true);\r
+\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addReferenceAnnotations_actionPerformed(candidates);\r
+ }\r
+ });\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Add annotations to the sequences and to the alignment.\r
+ * \r
+ * @param candidates\r
+ * a map whose keys are sequences on the alignment, and values a list\r
+ * of annotations to add to each sequence\r
+ */\r
+ protected void addReferenceAnnotations_actionPerformed(\r
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)\r
+ {\r
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();\r
+ final AlignmentI alignment = this.ap.getAlignment();\r
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,\r
+ selectionGroup);\r
+ refresh();\r
+ }\r
+\r
+ /**\r
+ * add a show URL menu item to the given linkMenu\r
+ * \r
+ * @param linkMenu\r
+ * @param target\r
+ * - menu label string\r
+ * @param url\r
+ * - url to open\r
+ */\r
+ private void addshowLink(JMenu linkMenu, final String target,\r
+ final String url)\r
+ {\r
+ addshowLink(linkMenu, target, target, url);\r
+ }\r
+\r
+ /**\r
+ * add a show URL menu item to the given linkMenu\r
+ * \r
+ * @param linkMenu\r
+ * @param target\r
+ * - URL target window\r
+ * @param label\r
+ * - menu label string\r
+ * @param url\r
+ * - url to open\r
+ */\r
+ private void addshowLink(JMenu linkMenu, final String target,\r
+ final String label, final String url)\r
+ {\r
+ JMenuItem item = new JMenuItem(label);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+ });\r
+ linkMenu.add(item);\r
+ }\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (evt.getSource() == abovePIDColour)\r
+ {\r
+ abovePIDColour_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == showColourText)\r
+ {\r
+ showColourText_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == showText)\r
+ {\r
+ showText_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == showBoxes)\r
+ {\r
+ showBoxes_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == displayNonconserved)\r
+ {\r
+ this.showNonconserved_itemStateChanged();\r
+ }\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+ if (source == clustalColour)\r
+ {\r
+ clustalColour_actionPerformed();\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
+ zappoColour_actionPerformed();\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
+ taylorColour_actionPerformed();\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
+ hydrophobicityColour_actionPerformed();\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
+ helixColour_actionPerformed();\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
+ strandColour_actionPerformed();\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
+ turnColour_actionPerformed();\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
+ buriedColour_actionPerformed();\r
+ }\r
+ else if (source == nucleotideMenuItem)\r
+ {\r
+ nucleotideMenuItem_actionPerformed();\r
+ }\r
+\r
+ else if (source == userDefinedColour)\r
+ {\r
+ userDefinedColour_actionPerformed();\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ PIDColour_actionPerformed();\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
+ BLOSUM62Colour_actionPerformed();\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
+ noColourmenuItem_actionPerformed();\r
+ }\r
+ else if (source == conservationMenuItem)\r
+ {\r
+ conservationMenuItem_itemStateChanged();\r
+ }\r
+ else if (source == unGroupMenuItem)\r
+ {\r
+ unGroupMenuItem_actionPerformed();\r
+ }\r
+\r
+ else if (source == createGroupMenuItem)\r
+ {\r
+ createGroupMenuItem_actionPerformed();\r
+ }\r
+\r
+ else if (source == sequenceName)\r
+ {\r
+ editName();\r
+ }\r
+ else if (source == makeReferenceSeq)\r
+ {\r
+ makeReferenceSeq_actionPerformed();\r
+ }\r
+ else if (source == sequenceDetails)\r
+ {\r
+ showSequenceDetails();\r
+ }\r
+ else if (source == selSeqDetails)\r
+ {\r
+ showSequenceSelectionDetails();\r
+ }\r
+ else if (source == pdb)\r
+ {\r
+ addPDB();\r
+ }\r
+ else if (source == hideSeqs)\r
+ {\r
+ hideSequences(false);\r
+ }\r
+ else if (source == repGroup)\r
+ {\r
+ hideSequences(true);\r
+ }\r
+ else if (source == revealSeq)\r
+ {\r
+ ap.av.showSequence(revealSeq_index);\r
+ }\r
+ else if (source == revealAll)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ }\r
+\r
+ else if (source == editGroupName)\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(getGroup().getName(),\r
+ getGroup().getDescription(), " Group Name",\r
+ "Group Description", ap.alignFrame,\r
+ "Edit Group Name / Description", 500, 100, true);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ getGroup().setName(dialog.getName().replace(' ', '_'));\r
+ getGroup().setDescription(dialog.getDescription());\r
+ }\r
+\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ ap.alignFrame.copy_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ ap.alignFrame.cut_actionPerformed();\r
+ }\r
+ else if (source == editSequence)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ if (sg != null)\r
+ {\r
+ if (seq == null)\r
+ {\r
+ seq = sg.getSequenceAt(0);\r
+ }\r
+\r
+ EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(\r
+ sg.getStartRes(), sg.getEndRes() + 1), null,\r
+ "Edit Sequence ", null,\r
+\r
+ ap.alignFrame, "Edit Sequence", 500, 100, true);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
+ Action.REPLACE, dialog.getName().replace(' ',\r
+ ap.av.getGapCharacter()),\r
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
+ sg.getStartRes(), sg.getEndRes() + 1,\r
+ ap.av.getAlignment());\r
+\r
+ ap.alignFrame.addHistoryItem(editCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
+ }\r
+ }\r
+ }\r
+ else if (source == toUpper || source == toLower || source == toggleCase)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null)\r
+ {\r
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(\r
+ sg.getStartRes(), sg.getEndRes() + 1);\r
+\r
+ String description;\r
+ int caseChange;\r
+\r
+ if (source == toggleCase)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if (source == toUpper)\r
+ {\r
+ description = "To Upper Case";\r
+ caseChange = ChangeCaseCommand.TO_UPPER;\r
+ }\r
+ else\r
+ {\r
+ description = "To Lower Case";\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
+ }\r
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,\r
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
+ startEnd, caseChange);\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
+ .getSequences());\r
+\r
+ }\r
+ }\r
+ else if (source == sequenceFeature)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ int rsize = 0, gSize = sg.getSize();\r
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];\r
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];\r
+\r
+ for (int i = 0; i < gSize; i++)\r
+ {\r
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
+ int end = sg.findEndRes(sg.getSequenceAt(i));\r
+ if (start <= end)\r
+ {\r
+ seqs[rsize] = sg.getSequenceAt(i);\r
+ features[rsize] = new SequenceFeature(null, null, null, start,\r
+ end, "Jalview");\r
+ rsize++;\r
+ }\r
+ }\r
+ rseqs = new SequenceI[rsize];\r
+ tfeatures = new SequenceFeature[rsize];\r
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);\r
+ System.arraycopy(features, 0, tfeatures, 0, rsize);\r
+ features = tfeatures;\r
+ seqs = rseqs;\r
+\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
+ features, true, ap))\r
+ {\r
+ ap.alignFrame.sequenceFeatures.setState(true);\r
+ ap.av.setShowSequenceFeatures(true);;\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ outputText(evt);\r
+ }\r
+\r
+ }\r
+\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+\r
+ JFrame frame = new JFrame();\r
+ frame.add(cap);\r
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(\r
+ "label.selection_output_command", new Object[]\r
+ { e.getActionCommand() }), 600, 500);\r
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this method\r
+ // now returns a full copy of sequence data\r
+ // TODO consider using getSequenceSelection instead here\r
+\r
+ cap.setText(new AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));\r
+\r
+ }\r
+\r
+ protected void showSequenceSelectionDetails()\r
+ {\r
+ createSequenceDetailsReport(ap.av.getSequenceSelection());\r
+ }\r
+\r
+ protected void showSequenceDetails()\r
+ {\r
+ createSequenceDetailsReport(new SequenceI[]\r
+ { seq });\r
+ }\r
+\r
+ public void createSequenceDetailsReport(SequenceI[] sequences)\r
+ {\r
+\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+\r
+ StringBuffer contents = new StringBuffer();\r
+ for (SequenceI seq : sequences)\r
+ {\r
+ contents.append(MessageManager.formatMessage(\r
+ "label.annotation_for_displayid", new Object[]\r
+ { seq.getDisplayId(true) }));\r
+ new SequenceAnnotationReport(null)\r
+ .createSequenceAnnotationReport(\r
+ contents,\r
+ seq,\r
+ true,\r
+ true,\r
+ false,\r
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()\r
+ : null);\r
+ contents.append("</p>");\r
+ }\r
+ JFrame frame = new JFrame();\r
+ frame.add(cap);\r
+ JalviewLite.addFrame(frame, "Sequence Details for "\r
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)\r
+ : "Selection"), 600, 500);\r
+ cap.setText(MessageManager.formatMessage("label.html_content",\r
+ new Object[]\r
+ { contents.toString() }));\r
+ }\r
+\r
+ void editName()\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(seq.getName(),\r
+ seq.getDescription(), " Sequence Name",\r
+ "Sequence Description", ap.alignFrame,\r
+ "Edit Sequence Name / Description", 500, 100, true);\r
+\r
+ if (dialog.accept)\r
+ {\r
+ seq.setName(dialog.getName());\r
+ seq.setDescription(dialog.getDescription());\r
+ ap.paintAlignment(false);\r
+ }\r
+ }\r
+\r
+ void addPDB()\r
+ {\r
+ if (seq.getPDBId() != null)\r
+ {\r
+ PDBEntry entry = seq.getPDBId().firstElement();\r
+\r
+// if (ap.av.applet.jmolAvailable)\r
+// {\r
+ new AppletJmol(entry, new SequenceI[]\r
+ { seq }, null, ap, AppletFormatAdapter.URL);\r
+// }\r
+// else\r
+// {\r
+// new MCview.AppletPDBViewer(entry, new SequenceI[]\r
+// { seq }, null, ap, AppletFormatAdapter.URL);\r
+// }\r
+\r
+ }\r
+ else\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+ cap.setText(MessageManager.getString("label.paste_pdb_file"));\r
+ cap.setPDBImport(seq);\r
+ JFrame frame = new JFrame();\r
+ frame.add(cap);\r
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(\r
+ "label.paste_pdb_file_for_sequence", new Object[]\r
+ { seq.getName() }), 400, 300);\r
+ }\r
+ }\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+ groupMenu.setLabel(MessageManager.getString("label.selection"));\r
+ sequenceFeature.addActionListener(this);\r
+\r
+ editGroupName.addActionListener(this);\r
+ unGroupMenuItem.setLabel(MessageManager\r
+ .getString("action.remove_group"));\r
+ unGroupMenuItem.addActionListener(this);\r
+\r
+ createGroupMenuItem.setLabel(MessageManager\r
+ .getString("action.create_group"));\r
+ createGroupMenuItem.addActionListener(this);\r
+\r
+ nucleotideMenuItem.setLabel(MessageManager\r
+ .getString("label.nucleotide"));\r
+ nucleotideMenuItem.addActionListener(this);\r
+ conservationMenuItem.addItemListener(this);\r
+ abovePIDColour.addItemListener(this);\r
+ colourMenu.setLabel(MessageManager.getString("label.group_colour"));\r
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));\r
+ showBoxes.setState(true);\r
+ showBoxes.addItemListener(this);\r
+ sequenceName.addActionListener(this);\r
+ sequenceDetails.addActionListener(this);\r
+ selSeqDetails.addActionListener(this);\r
+ displayNonconserved.setLabel(MessageManager\r
+ .getString("label.show_non_conversed"));\r
+ displayNonconserved.setState(false);\r
+ displayNonconserved.addItemListener(this);\r
+ showText.setLabel(MessageManager.getString("action.text"));\r
+ showText.addItemListener(this);\r
+ showColourText.setLabel(MessageManager.getString("label.colour_text"));\r
+ showColourText.addItemListener(this);\r
+ outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));\r
+ seqMenu.setLabel(MessageManager.getString("label.sequence"));\r
+ pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));\r
+ hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));\r
+ repGroup.setLabel(MessageManager.formatMessage(\r
+ "label.represent_group_with", new Object[]\r
+ { "" }));\r
+ revealAll.setLabel(MessageManager.getString("action.reveal_all"));\r
+ revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));\r
+ menu1.setLabel(MessageManager.getString("label.group") + ":");\r
+ add(groupMenu);\r
+ this.add(seqMenu);\r
+ this.add(hideSeqs);\r
+ this.add(revealSeq);\r
+ this.add(revealAll);\r
+ // groupMenu.add(selSeqDetails);\r
+ groupMenu.add(groupShowAnnotationsMenu);\r
+ groupMenu.add(groupHideAnnotationsMenu);\r
+ groupMenu.add(groupAddReferenceAnnotations);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputmenu);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(createGroupMenuItem);\r
+ groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(menu1);\r
+\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
+\r
+ noColourmenuItem.setLabel(MessageManager.getString("label.none"));\r
+ noColourmenuItem.addActionListener(this);\r
+\r
+ clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel(MessageManager.getString("label.zappo"));\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel(MessageManager.getString("label.taylor"));\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel(MessageManager.getString("label.helix_propensity"));\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel(MessageManager.getString("label.strand_propensity"));\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel(MessageManager.getString("label.turn_propensity"));\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel(MessageManager.getString("label.buried_index"));\r
+ buriedColour.addActionListener(this);\r
+ abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));\r
+\r
+ userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));\r
+\r
+ editMenu.add(copy);\r
+ copy.addActionListener(this);\r
+ editMenu.add(cut);\r
+ cut.addActionListener(this);\r
+\r
+ editMenu.add(editSequence);\r
+ editSequence.addActionListener(this);\r
+\r
+ editMenu.add(toUpper);\r
+ toUpper.addActionListener(this);\r
+ editMenu.add(toLower);\r
+ toLower.addActionListener(this);\r
+ editMenu.add(toggleCase);\r
+ seqMenu.add(seqShowAnnotationsMenu);\r
+ seqMenu.add(seqHideAnnotationsMenu);\r
+ seqMenu.add(seqAddReferenceAnnotations);\r
+ seqMenu.add(sequenceName);\r
+ seqMenu.add(makeReferenceSeq);\r
+ // seqMenu.add(sequenceDetails);\r
+\r
+ if (!ap.av.applet.useXtrnalSviewer)\r
+ {\r
+ seqMenu.add(pdb);\r
+ }\r
+ seqMenu.add(repGroup);\r
+ menu1.add(editGroupName);\r
+ menu1.add(colourMenu);\r
+ menu1.add(showBoxes);\r
+ menu1.add(showText);\r
+ menu1.add(showColourText);\r
+ menu1.add(displayNonconserved);\r
+ toggleCase.addActionListener(this);\r
+ pdb.addActionListener(this);\r
+ hideSeqs.addActionListener(this);\r
+ repGroup.addActionListener(this);\r
+ revealAll.addActionListener(this);\r
+ revealSeq.addActionListener(this);\r
+ makeReferenceSeq.addActionListener(this);\r
+ }\r
+\r
+ void refresh()\r
+ {\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ protected void clustalColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());\r
+ refresh();\r
+ }\r
+\r
+ protected void zappoColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new ZappoColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void taylorColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new TaylorColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void hydrophobicityColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new HydrophobicColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void helixColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new HelixColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void strandColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new StrandColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void turnColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new TurnColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void buriedColour_actionPerformed()\r
+ {\r
+ getGroup().cs = new BuriedColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ public void nucleotideMenuItem_actionPerformed()\r
+ {\r
+ getGroup().cs = new NucleotideColourScheme();\r
+ refresh();\r
+ }\r
+\r
+ protected void abovePIDColour_itemStateChanged()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (abovePIDColour.getState())\r
+ {\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av\r
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()\r
+ .getName());\r
+\r
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());\r
+\r
+ SliderPanel.showPIDSlider();\r
+\r
+ }\r
+ else\r
+ // remove PIDColouring\r
+ {\r
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());\r
+ }\r
+\r
+ refresh();\r
+\r
+ }\r
+\r
+ protected void userDefinedColour_actionPerformed()\r
+ {\r
+ new UserDefinedColours(ap, getGroup());\r
+ }\r
+\r
+ protected void PIDColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new PIDColourScheme();\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av\r
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));\r
+ refresh();\r
+ }\r
+\r
+ protected void BLOSUM62Colour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+\r
+ sg.cs = new Blosum62ColourScheme();\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av\r
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));\r
+\r
+ refresh();\r
+ }\r
+\r
+ protected void noColourmenuItem_actionPerformed()\r
+ {\r
+ getGroup().cs = null;\r
+ refresh();\r
+ }\r
+\r
+ protected void conservationMenuItem_itemStateChanged()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (conservationMenuItem.getState())\r
+ {\r
+\r
+ sg.cs.setConservation(Conservation.calculateConservation("Group",\r
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av\r
+ .getHiddenRepSequences()), 0, ap.av.getAlignment()\r
+ .getWidth(), false, ap.av.getConsPercGaps(), false));\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ else\r
+ // remove ConservationColouring\r
+ {\r
+ sg.cs.setConservation(null);\r
+ }\r
+\r
+ refresh();\r
+ }\r
+\r
+ SequenceGroup getGroup()\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ // this method won't add a new group if it already exists\r
+ if (sg != null)\r
+ {\r
+ ap.av.getAlignment().addGroup(sg);\r
+ }\r
+\r
+ return sg;\r
+ }\r
+\r
+ void unGroupMenuItem_actionPerformed()\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.getAlignment().deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ void createGroupMenuItem_actionPerformed()\r
+ {\r
+ getGroup(); // implicitly create group\r
+ refresh();\r
+ }\r
+\r
+ public void showColourText_itemStateChanged()\r
+ {\r
+ getGroup().setColourText(showColourText.getState());\r
+ refresh();\r
+ }\r
+\r
+ public void showText_itemStateChanged()\r
+ {\r
+ getGroup().setDisplayText(showText.getState());\r
+ refresh();\r
+ }\r
+ public void makeReferenceSeq_actionPerformed()\r
+ {\r
+ if (!ap.av.getAlignment().hasSeqrep())\r
+ {\r
+ // initialise the display flags so the user sees something happen\r
+ ap.av.setDisplayReferenceSeq(true);\r
+ ap.av.setColourByReferenceSeq(true);\r
+ ap.av.getAlignment().setSeqrep(seq);\r
+ }\r
+ else\r
+ {\r
+ if (ap.av.getAlignment().getSeqrep() == seq)\r
+ {\r
+ ap.av.getAlignment().setSeqrep(null);\r
+ }\r
+ else\r
+ {\r
+ ap.av.getAlignment().setSeqrep(seq);\r
+ }\r
+ }\r
+ refresh();\r
+ }\r
+\r
+ public void showNonconserved_itemStateChanged()\r
+ {\r
+ getGroup().setShowNonconserved(this.displayNonconserved.getState());\r
+ refresh();\r
+ }\r
+\r
+ public void showBoxes_itemStateChanged()\r
+ {\r
+ getGroup().setDisplayBoxes(showBoxes.getState());\r
+ refresh();\r
+ }\r
+\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null || sg.getSize() < 1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]\r
+ { seq });\r
+ return;\r
+ }\r
+\r
+ ap.av.setSelectionGroup(null);\r
+\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(seq, sg);\r
+\r
+ return;\r
+ }\r
+\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
+\r
+ hseqs = new SequenceI[gsize];\r
+\r
+ int index = 0;\r
+ for (int i = 0; i < gsize; i++)\r
+ {\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
+ ap.av.sendSelection();\r
+ }\r
+\r
+ /**\r
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.\r
+ * "All" is added first, followed by a separator. Then add any annotation\r
+ * types associated with the current selection. Separate menus are built for\r
+ * the selected sequence group (if any), and the selected sequence.\r
+ * <p>\r
+ * Some annotation rows are always rendered together - these can be identified\r
+ * by a common graphGroup property > -1. Only one of each group will be marked\r
+ * as visible (to avoid duplication of the display). For such groups we add a\r
+ * composite type name, e.g.\r
+ * <p>\r
+ * IUPredWS (Long), IUPredWS (Short)\r
+ * \r
+ * @param seq\r
+ */\r
+ protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,\r
+ List<SequenceI> forSequences)\r
+ {\r
+ showMenu.removeAll();\r
+ hideMenu.removeAll();\r
+ \r
+ final List<String> all = Arrays.asList(ALL_ANNOTATIONS);\r
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);\r
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,\r
+ false);\r
+ showMenu.addSeparator();\r
+ hideMenu.addSeparator();\r
+ \r
+ final AlignmentAnnotation[] annotations = ap.getAlignment()\r
+ .getAlignmentAnnotation();\r
+ \r
+ /*\r
+ * Find shown/hidden annotations types, distinguished by source (calcId),\r
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in\r
+ * the insertion order, which is the order of the annotations on the\r
+ * alignment.\r
+ */\r
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();\r
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();\r
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,\r
+ hiddenTypes,\r
+ AlignmentAnnotationUtils.asList(annotations),\r
+ forSequences);\r
+ \r
+ for (String calcId : hiddenTypes.keySet())\r
+ {\r
+ for (List<String> type : hiddenTypes.get(calcId))\r
+ {\r
+ addAnnotationTypeToShowHide(showMenu, forSequences,\r
+ calcId, type, false, true);\r
+ }\r
+ }\r
+ // grey out 'show annotations' if none are hidden\r
+ showMenu.setEnabled(!hiddenTypes.isEmpty());\r
+ \r
+ for (String calcId : shownTypes.keySet())\r
+ {\r
+ for (List<String> type : shownTypes.get(calcId))\r
+ {\r
+ addAnnotationTypeToShowHide(hideMenu, forSequences,\r
+ calcId, type, false, false);\r
+ }\r
+ }\r
+ // grey out 'hide annotations' if none are shown\r
+ hideMenu.setEnabled(!shownTypes.isEmpty());\r
+ }\r
+\r
+ /**\r
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'\r
+ * menus.\r
+ * \r
+ * @param showOrHideMenu\r
+ * the menu to add to\r
+ * @param forSequences\r
+ * the sequences whose annotations may be shown or hidden\r
+ * @param calcId\r
+ * @param types\r
+ * the label to add\r
+ * @param allTypes\r
+ * if true this is a special label meaning 'All'\r
+ * @param actionIsShow\r
+ * if true, the select menu item action is to show the annotation\r
+ * type, else hide\r
+ */\r
+ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,\r
+ final List<SequenceI> forSequences, String calcId,\r
+ final List<String> types, final boolean allTypes,\r
+ final boolean actionIsShow)\r
+ {\r
+ String label = types.toString(); // [a, b, c]\r
+ label = label.substring(1, label.length() - 1);\r
+ final JMenuItem item = new JMenuItem(label);\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ @Override\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,\r
+ forSequences, allTypes, actionIsShow);\r
+ refresh();\r
+ }\r
+ });\r
+ showOrHideMenu.add(item);\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff