X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=4b0ffad851283468ebb1d2458ac6415f153e9af7;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=5f6c55694a49bfc3e481a3aa50ccf67ac99cbe67;hpb=fe6b3fb39308b5c045849db2be75ba07824be776;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 5f6c556..abe9835 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,41 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AAFrequency; -import jalview.analysis.Conservation; -import jalview.commands.ChangeCaseCommand; -import jalview.commands.EditCommand; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.Annotation; -import jalview.datamodel.DBRefEntry; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.io.FormatAdapter; -import jalview.io.SequenceAnnotationReport; -import jalview.renderer.AnnotationRenderer; -import jalview.schemes.AnnotationColourGradient; -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.PurinePyrimidineColourScheme; -import jalview.schemes.ResidueProperties; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; -import jalview.util.GroupUrlLink; -import jalview.util.GroupUrlLink.UrlStringTooLongException; -import jalview.util.MessageManager; -import jalview.util.UrlLink; - import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -62,10 +27,14 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.BitSet; import java.util.Collection; +import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; +import java.util.Objects; +import java.util.SortedMap; +import java.util.TreeMap; import java.util.Vector; import javax.swing.ButtonGroup; @@ -73,83 +42,91 @@ import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPopupMenu; import javax.swing.JRadioButtonMenuItem; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.Conservation; +import jalview.api.AlignViewportI; +import jalview.bin.Cache; +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.HiddenColumns; +import jalview.datamodel.MappedFeatures; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ColourMenuHelper.ColourChangeListener; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.FormatAdapter; +import jalview.io.SequenceAnnotationReport; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueColourScheme; +import jalview.util.Comparison; +import jalview.util.GroupUrlLink; +import jalview.util.GroupUrlLink.UrlStringTooLongException; +import jalview.util.MessageManager; +import jalview.util.StringUtils; +import jalview.util.UrlLink; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; + /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision: 1.118 $ + * The popup menu that is displayed on right-click on a sequence id, or in the + * sequence alignment. */ -public class PopupMenu extends JPopupMenu +public class PopupMenu extends JPopupMenu implements ColourChangeListener { - private static final String ALL_ANNOTATIONS = "All"; - - private static final String COMMA = ","; - - JMenu groupMenu = new JMenu(); - - JMenuItem groupName = new JMenuItem(); - - protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); + /* + * maximum length of feature description to include in popup menu item text + */ + private static final int FEATURE_DESC_MAX = 40; - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); + /* + * true for ID Panel menu, false for alignment panel menu + */ + private final boolean forIdPanel; - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); + private final AlignmentPanel ap; - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); + /* + * the sequence under the cursor when clicked + * (additional sequences may be selected) + */ + private final SequenceI sequence; - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); + JMenu groupMenu = new JMenu(); - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); + JMenuItem groupName = new JMenuItem(); protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); - - // protected JRadioButtonMenuItem covariationColour = new - // JRadioButtonMenuItem(); - - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - AlignmentPanel ap; - - JMenu sequenceMenu = new JMenu(); - - JMenuItem sequenceName = new JMenuItem(); + protected JRadioButtonMenuItem annotationColour; - JMenuItem sequenceDetails = new JMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); - JMenuItem sequenceSelDetails = new JMenuItem(); - - JMenuItem chooseAnnotations = new JMenuItem(); + JMenu sequenceMenu = new JMenu(); - SequenceI sequence; + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); - JMenuItem outline = new JMenuItem(); - - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -162,111 +139,275 @@ public class PopupMenu extends JPopupMenu JMenu editMenu = new JMenu(); - JMenuItem cut = new JMenuItem(); - - JMenuItem copy = new JMenuItem(); - JMenuItem upperCase = new JMenuItem(); JMenuItem lowerCase = new JMenuItem(); JMenuItem toggle = new JMenuItem(); - JMenu pdbMenu = new JMenu(); + JMenu outputMenu = new JMenu(); - JMenuItem pdbFromFile = new JMenuItem(); + JMenu seqShowAnnotationsMenu = new JMenu(); - // JBPNote: Commented these out - Should add these services via the web - // services menu system. - // JMenuItem ContraFold = new JMenuItem(); + JMenu seqHideAnnotationsMenu = new JMenu(); - // JMenuItem RNAFold = new JMenuItem(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); - JMenuItem enterPDB = new JMenuItem(); + JMenu groupShowAnnotationsMenu = new JMenu(); - JMenuItem discoverPDB = new JMenuItem(); + JMenu groupHideAnnotationsMenu = new JMenu(); - JMenu outputMenu = new JMenu(); + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); - JMenu showAnnotationsMenu = new JMenu(); + JMenuItem textColour = new JMenuItem(); - JMenu hideAnnotationsMenu = new JMenu(); + JMenu editGroupMenu = new JMenu(); - JMenuItem addDatasequenceAnnotations = new JMenuItem(); + JMenuItem chooseStructure = new JMenuItem(); - JMenuItem sequenceFeature = new JMenuItem(); + JMenu rnaStructureMenu = new JMenu(); - JMenuItem textColour = new JMenuItem(); + /** + * Constructs a menu with sub-menu items for any hyperlinks for the sequence + * and/or features provided. Hyperlinks may include a lookup by sequence id, + * or database cross-references, depending on which links are enabled in user + * preferences. + * + * @param seq + * @param features + * @return + */ + protected static JMenu buildLinkMenu(final SequenceI seq, + List features) + { + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); + + List nlinks = null; + if (seq != null) + { + nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + UrlLink.sort(nlinks); + } + else + { + nlinks = new ArrayList<>(); + } + + if (features != null) + { + for (SequenceFeature sf : features) + { + if (sf.links != null) + { + for (String link : sf.links) + { + nlinks.add(link); + } + } + } + } + + /* + * instantiate the hyperlinklink templates from sequence data; + * note the order of the templates is preserved in the map + */ + Map> linkset = new LinkedHashMap<>(); + for (String link : nlinks) + { + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) + { + Cache.log.error("Exception for URLLink '" + link + "'", foo); + continue; + } + + if (!urlLink.isValid()) + { + Cache.log.error(urlLink.getInvalidMessage()); + continue; + } + + urlLink.createLinksFromSeq(seq, linkset); + } + + /* + * construct menu items for the hyperlinks (still preserving + * the order of the sorted templates) + */ + addUrlLinks(linkMenu, linkset.values()); + + return linkMenu; + } + + /** + * A helper method that builds menu items from the given links, with action + * handlers to open the link URL, and adds them to the linkMenu. Each provided + * link should be a list whose second item is the menu text, and whose fourth + * item is the URL to open when the menu item is selected. + * + * @param linkMenu + * @param linkset + */ + static private void addUrlLinks(JMenu linkMenu, + Collection> linkset) + { + for (List linkstrset : linkset) + { + final String url = linkstrset.get(3); + JMenuItem item = new JMenuItem(linkstrset.get(1)); + item.setToolTipText(MessageManager + .formatMessage("label.open_url_param", new Object[] + { url })); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + @Override + public void run() + { + showLink(url); + } + }).start(); + } + }); + linkMenu.add(item); + } + } - JMenu jMenu1 = new JMenu(); + /** + * Opens the provided url in the default web browser, or shows an error + * message if this fails + * + * @param url + */ + static void showLink(String url) + { + try + { + jalview.util.BrowserLauncher.openURL(url); + } catch (Exception ex) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JvOptionPane.WARNING_MESSAGE); - JMenu structureMenu = new JMenu(); + ex.printStackTrace(); + } + } - JMenu viewStructureMenu = new JMenu(); + /** + * add a late bound groupURL item to the given linkMenu + * + * @param linkMenu + * @param label + * - menu label string + * @param urlgenerator + * GroupURLLink used to generate URL + * @param urlstub + * Object array returned from the makeUrlStubs function. + */ + static void addshowLink(JMenu linkMenu, String label, + final GroupUrlLink urlgenerator, final Object[] urlstub) + { + JMenuItem item = new JMenuItem(label); + item.setToolTipText(MessageManager + .formatMessage("label.open_url_seqs_param", new Object[] + { urlgenerator.getUrl_prefix(), + urlgenerator.getNumberInvolved(urlstub) })); + // TODO: put in info about what is being sent. + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { - // JMenu colStructureMenu = new JMenu(); - JMenuItem editSequence = new JMenuItem(); + @Override + public void run() + { + try + { + showLink(urlgenerator.constructFrom(urlstub)); + } catch (UrlStringTooLongException e2) + { + } + } - // JMenuItem annotationMenuItem = new JMenuItem(); + }).start(); + } + }); - JMenu groupLinksMenu; + linkMenu.add(item); + } /** - * Creates a new PopupMenu object. + * Constructor for a PopupMenu for a click in the alignment panel (on a residue) * * @param ap - * DOCUMENT ME! + * the panel in which the mouse is clicked * @param seq - * DOCUMENT ME! + * the sequence under the mouse + * @throws NullPointerException + * if seq is null */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) + public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column) { - this(ap, seq, links, null); + this(false, ap, seq, column, null); } /** + * Constructor for a PopupMenu for a click in the sequence id panel * - * @param ap + * @param alignPanel + * the panel in which the mouse is clicked * @param seq - * @param links + * the sequence under the mouse click * @param groupLinks + * templates for sequence external links + * @throws NullPointerException + * if seq is null */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, - Vector links, Vector groupLinks) + public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, + List groupLinks) { - // ///////////////////////////////////////////////////////// - // 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 = ap; + this(true, alignPanel, seq, -1, groupLinks); + } + + /** + * Private constructor that constructs a popup menu for either sequence ID + * Panel, or alignment context + * + * @param fromIdPanel + * @param alignPanel + * @param seq + * @param column + * aligned column position (0...) + * @param groupLinks + */ + private PopupMenu(boolean fromIdPanel, + final AlignmentPanel alignPanel, + final SequenceI seq, final int column, List groupLinks) + { + Objects.requireNonNull(seq); + this.forIdPanel = fromIdPanel; + this.ap = alignPanel; sequence = seq; - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(purinePyrimidineColour); - colours.add(RNAInteractionColour); - // colours.add(covariationColour); - - for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) - { - JMenuItem item = new JMenuItem( - jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); - - item.addActionListener(new java.awt.event.ActionListener() + for (String ff : FileFormats.getInstance().getWritableFormats(true)) + { + JMenuItem item = new JMenuItem(ff); + + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -279,9 +420,28 @@ public class PopupMenu extends JPopupMenu } /* - * Build menus for annotation types that may be shown or hidden. + * Build menus for annotation types that may be shown or hidden, and for + * 'reference annotations' that may be added to the alignment. First for the + * currently selected sequence (if there is one): + */ + final List selectedSequence = (forIdPanel && seq != null + ? Arrays.asList(seq) + : Collections. emptyList()); + buildAnnotationTypesMenus(seqShowAnnotationsMenu, + seqHideAnnotationsMenu, selectedSequence); + configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, + selectedSequence); + + /* + * And repeat for the current selection group (if there is one): */ - buildAnnotationTypesMenus(); + final List selectedGroup = (alignPanel.av.getSelectionGroup() == null + ? Collections. emptyList() + : alignPanel.av.getSelectionGroup().getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); try { @@ -291,135 +451,97 @@ public class PopupMenu extends JPopupMenu e.printStackTrace(); } - JMenuItem menuItem; - if (seq != null) + if (forIdPanel) { + JMenuItem menuItem; sequenceMenu.setText(sequence.getName()); - - if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size() > 0) + if (seq == alignPanel.av.getAlignment().getSeqrep()) { - java.util.Enumeration e = seq.getDatasetSequence().getPDBId() - .elements(); - - while (e.hasMoreElements()) - { - final PDBEntry pdb = (PDBEntry) e.nextElement(); - - menuItem = new JMenuItem(); - menuItem.setText(pdb.getId()); - menuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO re JAL-860: optionally open dialog or provide a menu entry - // allowing user to open just one structure per sequence - // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] - // { pdb })[0], null, ap); - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(pdb, - ap.av.collateForPDB(new PDBEntry[] - { pdb })[0], null, ap); - } - }); - viewStructureMenu.add(menuItem); - - /* - * menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); - * menuItem.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * colourByStructure(pdb.getId()); } }); - * colStructureMenu.add(menuItem); - */ - } + makeReferenceSeq.setText( + MessageManager.getString("action.unmark_as_reference")); } else { - if (ap.av.getAlignment().isNucleotide() == false) - { - structureMenu.remove(viewStructureMenu); - } - // structureMenu.remove(colStructureMenu); + makeReferenceSeq.setText( + MessageManager.getString("action.set_as_reference")); } - if (ap.av.getAlignment().isNucleotide() == true) + if (!alignPanel.av.getAlignment().isNucleotide()) + { + remove(rnaStructureMenu); + } + else { - AlignmentAnnotation[] aa = ap.av.getAlignment() + int origCount = rnaStructureMenu.getItemCount(); + /* + * add menu items to 2D-render any alignment or sequence secondary + * structure annotation + */ + AlignmentAnnotation[] aas = alignPanel.av.getAlignment() .getAlignmentAnnotation(); - for (int i = 0; i < aa.length; i++) + if (aas != null) { - if (aa[i].getRNAStruc() != null) + for (final AlignmentAnnotation aa : aas) { - final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label; - menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", new String[] - { structureLine })); - menuItem.addActionListener(new java.awt.event.ActionListener() - + if (aa.isValidStruc() && aa.sequenceRef == null) { - @Override - public void actionPerformed(ActionEvent e) + /* + * valid alignment RNA secondary structure annotation + */ + menuItem = new JMenuItem(); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_structure_line", new Object[] + { aa.label })); + menuItem.addActionListener(new ActionListener() { - // System.out.println("1:"+structureLine); - System.out.println("1:sname" + seq.getName()); - System.out.println("2:seq" + seq); - - // System.out.println("3:"+seq.getSequenceAsString()); - System.out.println("3:strucseq" + rnastruc); - // System.out.println("4:struc"+seq.getRNA()); - System.out.println("5:name" + seq.getName()); - System.out.println("6:ap" + ap); - new AppVarna(structureLine, seq, seq.getSequenceAsString(), - rnastruc, seq.getName(), ap); - // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), - // seq.getName(), ap); - System.out.println("end"); - } - }); - viewStructureMenu.add(menuItem); + @Override + public void actionPerformed(ActionEvent e) + { + new AppVarna(seq, aa, alignPanel); + } + }); + rnaStructureMenu.add(menuItem); + } } } - // SequenceFeatures[] test = seq.getSequenceFeatures(); - if (seq.getAnnotation() != null) { - AlignmentAnnotation seqAnno[] = seq.getAnnotation(); - for (int i = 0; i < seqAnno.length; i++) + AlignmentAnnotation seqAnns[] = seq.getAnnotation(); + for (final AlignmentAnnotation aa : seqAnns) { - if (seqAnno[i].getRNAStruc() != null) + if (aa.isValidStruc()) { - final String rnastruc = seqAnno[i].getRNAStruc(); - + /* + * valid sequence RNA secondary structure annotation + */ // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", new String[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - - new AppVarna(seq.getName() + " structure", seq, seq - .getSequenceAsString(), rnastruc, seq.getName(), - ap); + new AppVarna(seq, aa, alignPanel); } }); - viewStructureMenu.add(menuItem); + rnaStructureMenu.add(menuItem); } } } - + if (rnaStructureMenu.getItemCount() == origCount) + { + remove(rnaStructureMenu); + } } menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -429,13 +551,13 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); - if (ap.av.getSelectionGroup() != null - && ap.av.getSelectionGroup().getSize() > 1) + if (alignPanel.av.getSelectionGroup() != null + && alignPanel.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] + menuItem = new JMenuItem(MessageManager + .formatMessage("label.represent_group_with", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -446,12 +568,12 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows()) + if (alignPanel.av.hasHiddenRows()) { - final int index = ap.av.getAlignment().findIndex(seq); + final int index = alignPanel.av.getAlignment().findIndex(seq); - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) + if (alignPanel.av.adjustForHiddenSeqs(index) + - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_sequences")); @@ -460,10 +582,10 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - ap.av.showSequence(index); - if (ap.overviewPanel != null) + alignPanel.av.showSequence(index); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); @@ -471,104 +593,66 @@ public class PopupMenu extends JPopupMenu } } } - // for the case when no sequences are even visible - if (ap.av.hasHiddenRows()) + + /* + * offer 'Reveal All' + * - in the IdPanel (seq not null) if any sequence is hidden + * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null) + */ + if (alignPanel.av.hasHiddenRows()) { + boolean addOption = seq != null; + if (!addOption && alignPanel.av.getAlignment().getHeight() == 0) + { + addOption = true; + } + if (addOption) { - menuItem = new JMenuItem( + JMenuItem menuItem = new JMenuItem( MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - ap.av.showAllHiddenSeqs(); - if (ap.overviewPanel != null) + alignPanel.av.showAllHiddenSeqs(); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); - add(menuItem); } - } - SequenceGroup sg = ap.av.getSelectionGroup(); - boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() - .getGroups().contains(sg) : false; + SequenceGroup sg = alignPanel.av.getSelectionGroup(); + boolean isDefinedGroup = (sg != null) + ? alignPanel.av.getAlignment().getGroups().contains(sg) + : false; if (sg != null && sg.getSize() > 0) { - groupName.setText(MessageManager.formatMessage("label.name_param", - new String[] - { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); - if (sg.cs instanceof ZappoColourScheme) - { - zappoColour.setSelected(true); - } - else if (sg.cs instanceof TaylorColourScheme) + ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); + + conservationMenuItem.setEnabled(!sg.isNucleotide()); + + if (sg.cs != null) { - taylorColour.setSelected(true); - } - else if (sg.cs instanceof PIDColourScheme) - { - PIDColour.setSelected(true); - } - else if (sg.cs instanceof Blosum62ColourScheme) - { - BLOSUM62Colour.setSelected(true); - } - else if (sg.cs instanceof UserColourScheme) - { - userDefinedColour.setSelected(true); - } - else if (sg.cs instanceof HydrophobicColourScheme) - { - hydrophobicityColour.setSelected(true); - } - else if (sg.cs instanceof HelixColourScheme) - { - helixColour.setSelected(true); - } - else if (sg.cs instanceof StrandColourScheme) - { - strandColour.setSelected(true); - } - else if (sg.cs instanceof TurnColourScheme) - { - turnColour.setSelected(true); - } - else if (sg.cs instanceof BuriedColourScheme) - { - buriedColour.setSelected(true); - } - else if (sg.cs instanceof ClustalxColourScheme) - { - clustalColour.setSelected(true); - } - else if (sg.cs instanceof PurinePyrimidineColourScheme) - { - purinePyrimidineColour.setSelected(true); - } - - /* - * else if (sg.cs instanceof CovariationColourScheme) { - * covariationColour.setSelected(true); } - */ - else - { - noColourmenuItem.setSelected(true); - } - - if (sg.cs != null && sg.cs.conservationApplied()) - { - conservationMenuItem.setSelected(true); + if (sg.cs.conservationApplied()) + { + conservationMenuItem.setSelected(true); + } + if (sg.cs.getThreshold() > 0) + { + abovePIDColour.setSelected(true); + } } + modifyConservation.setEnabled(conservationMenuItem.isSelected()); + modifyPID.setEnabled(abovePIDColour.isSelected()); displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); @@ -579,11 +663,12 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); + Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + SequenceI sqass = null; - for (SequenceI sq : ap.av.getSequenceSelection()) + for (SequenceI sq : alignPanel.av.getSequenceSelection()) { - Vector pes = sq.getDatasetSequence().getPDBId(); + Vector pes = sq.getDatasetSequence().getAllPDBEntries(); if (pes != null && pes.size() > 0) { reppdb.put(pes.get(0).getId(), pes.get(0)); @@ -599,54 +684,10 @@ public class PopupMenu extends JPopupMenu } if (pdbe.size() > 0) { - final PDBEntry[] pe = pdbe.values().toArray( - new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( - new PDBEntry[reppdb.size()]); + final PDBEntry[] pe = pdbe.values() + .toArray(new PDBEntry[pdbe.size()]), + pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]); final JMenuItem gpdbview, rpdbview; - if (pdbe.size() == 1) - { - structureMenu.add(gpdbview = new JMenuItem(MessageManager - .formatMessage("label.view_structure_for", new String[] - { sqass.getDisplayId(false) }))); - } - else - { - structureMenu.add(gpdbview = new JMenuItem(MessageManager - .formatMessage("label.view_all_structures", new String[] - { new Integer(pdbe.size()).toString() }))); - } - gpdbview.setToolTipText(MessageManager - .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); - gpdbview.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pe, ap.av.collateForPDB(pe)); - } - }); - if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) - { - structureMenu.add(rpdbview = new JMenuItem(MessageManager - .formatMessage( - "label.view_all_representative_structures", - new String[] - { new Integer(reppdb.size()).toString() }))); - rpdbview.setToolTipText(MessageManager - .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); - rpdbview.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pr, ap.av.collateForPDB(pr)); - } - }); - } } } else @@ -659,134 +700,234 @@ public class PopupMenu extends JPopupMenu { createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); - jMenu1.setText(MessageManager.getString("action.edit_new_group")); + editGroupMenu.setText(MessageManager.getString("action.edit_new_group")); } else { createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); - jMenu1.setText(MessageManager.getString("action.edit_group")); + editGroupMenu.setText(MessageManager.getString("action.edit_group")); } - if (seq == null) + if (!forIdPanel) { sequenceMenu.setVisible(false); - structureMenu.setVisible(false); + chooseStructure.setVisible(false); + rnaStructureMenu.setVisible(false); + } + + addLinksAndFeatures(seq, column); + } + + /** + * Adds + *
    + *
  • configured sequence database links (ID panel popup menu)
    • + *
  • non-positional feature links (ID panel popup menu)
    • + *
  • positional feature links (alignment panel popup menu)
    • + *
  • feature details links (alignment panel popup menu)
    • + *
+ * If this panel is also showed complementary (CDS/protein) features, then links + * to their feature details are also added. + * + * @param seq + * @param column + */ + void addLinksAndFeatures(final SequenceI seq, final int column) + { + List features = null; + if (forIdPanel) + { + features = sequence.getFeatures().getNonPositionalFeatures(); + } + else + { + features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence, + column + 1); + } + + addLinks(seq, features); + + if (!forIdPanel) + { + addFeatureDetails(features, seq, column); + } + } + + /** + * Add a menu item to show feature details for each sequence feature. Any + * linked 'virtual' features (CDS/protein) are also optionally found and + * included. + * + * @param features + * @param seq + * @param column + */ + protected void addFeatureDetails(List features, + final SequenceI seq, final int column) + { + /* + * add features in CDS/protein complement at the corresponding + * position if configured to do so + */ + MappedFeatures mf = null; + if (ap.av.isShowComplementFeatures()) + { + if (!Comparison.isGap(sequence.getCharAt(column))) + { + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + AlignFrame af = Desktop.getAlignFrameFor(complement); + FeatureRendererModel fr2 = af.getFeatureRenderer(); + int seqPos = sequence.findPosition(column); + mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos); + } } - if (links != null && links.size() > 0) + if (features.isEmpty() && mf == null) { + /* + * no features to show at this position + */ + return; + } - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - Vector linkset = new Vector(); - for (int i = 0; i < links.size(); i++) + JMenu details = new JMenu( + MessageManager.getString("label.feature_details")); + add(details); + + String name = seq.getName(); + for (final SequenceFeature sf : features) + { + addFeatureDetailsMenuItem(details, name, sf, null); + } + + if (mf != null) + { + for (final SequenceFeature sf : mf.features) { - 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 (seq != null && urlLink.isDynamic()) - { + addFeatureDetailsMenuItem(details, name, sf, mf); + } + } + } - // 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; - } + /** + * A helper method to add one menu item whose action is to show details for + * one feature. The menu text includes feature description, but this may be + * truncated. + * + * @param details + * @param seqName + * @param sf + * @param mf + */ + void addFeatureDetailsMenuItem(JMenu details, final String seqName, + final SequenceFeature sf, MappedFeatures mf) + { + int start = sf.getBegin(); + int end = sf.getEnd(); + if (mf != null) + { + /* + * show local rather than linked feature coordinates + */ + int[] beginRange = mf.getMappedPositions(start, start); + int[] endRange = mf.getMappedPositions(end, end); + if (beginRange == null || endRange == null) + { + // e.g. variant extending to stop codon so not mappable + return; + } + start = beginRange[0]; + end = endRange[endRange.length - 1]; + int[] localRange = mf.getMappedPositions(start, end); + if (localRange == null) + { + return; + } + start = localRange[0]; + end = localRange[localRange.length - 1]; + } + StringBuilder desc = new StringBuilder(); + desc.append(sf.getType()).append(" ").append(String.valueOf(start)); + if (start != end) + { + desc.append(sf.isContactFeature() ? ":" : "-"); + desc.append(String.valueOf(end)); + } + String description = sf.getDescription(); + if (description != null) + { + desc.append(" "); + description = StringUtils.stripHtmlTags(description); - 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) - { - // 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]); - } - } - } - } - // 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]); - } - } - } - } - } - else - { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) - { - linkset.addElement(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); - } - } + /* + * truncate overlong descriptions unless they contain an href + * (as truncation could leave corrupted html) + */ + boolean hasLink = description.indexOf("a href") > -1; + if (description.length() > FEATURE_DESC_MAX && !hasLink) + { + description = description.substring(0, FEATURE_DESC_MAX) + "..."; + } + desc.append(description); + } + String featureGroup = sf.getFeatureGroup(); + if (featureGroup != null) + { + desc.append(" (").append(featureGroup).append(")"); + } + String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString()); + JMenuItem item = new JMenuItem(htmlText); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showFeatureDetails(sf, seqName, mf); } - if (sequence != null) + }); + details.add(item); + } + + /** + * Opens a panel showing a text report of feature details + * + * @param sf + * @param seqName + * @param mf + */ + protected void showFeatureDetails(SequenceFeature sf, String seqName, + MappedFeatures mf) + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + // it appears Java's CSS does not support border-collapse :-( + cap.addStylesheetRule("table { border-collapse: collapse;}"); + cap.addStylesheetRule("table, td, th {border: 1px solid black;}"); + cap.setText(sf.getDetailsReport(seqName, mf)); + + Desktop.addInternalFrame(cap, + MessageManager.getString("label.feature_details"), 500, 500); + } + + /** + * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * When seq is not null, these are links for the sequence id, which may be to + * external web sites for the sequence accession, and/or links embedded in + * non-positional features. When seq is null, only links embedded in the + * provided features are added. If no links are found, the menu is not added. + * + * @param seq + * @param features + */ + void addLinks(final SequenceI seq, List features) + { + JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features); + + // only add link menu if it has entries + if (linkMenu.getItemCount() > 0) + { + if (forIdPanel) { sequenceMenu.add(linkMenu); } @@ -798,9 +939,10 @@ public class PopupMenu extends JPopupMenu } /** - * Add annotation types to a 'Show annotations' or 'Hide annotations' menu. + * 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. + * 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 @@ -808,165 +950,83 @@ public class PopupMenu extends JPopupMenu * composite type name, e.g. *

* IUPredWS (Long), IUPredWS (Short) + * + * @param seq */ - protected void buildAnnotationTypesMenus() + protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu, + List forSequences) { - showAnnotationsMenu.removeAll(); - hideAnnotationsMenu.removeAll(); - final List all = Arrays.asList(ALL_ANNOTATIONS); - addAnnotationTypeToShowHide(showAnnotationsMenu, all, true, true); - addAnnotationTypeToShowHide(hideAnnotationsMenu, all, true, false); - showAnnotationsMenu.addSeparator(); - hideAnnotationsMenu.addSeparator(); + 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(); - BitSet visibleGraphGroups = PopupMenu - .getVisibleLineGraphGroups(annotations); - - List> shownTypes = new ArrayList>(); - List> hiddenTypes = new ArrayList>(); - PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes, - visibleGraphGroups, annotations, ap.av.getSelectionGroup()); - - for (List types : hiddenTypes) - { - addAnnotationTypeToShowHide(showAnnotationsMenu, types, false, true); - } - - for (List types : shownTypes) - { - addAnnotationTypeToShowHide(hideAnnotationsMenu, types, false, false); - } - } - - /** - * Helper method to populate lists of annotation types for the Show/Hide - * Annotations menus. If sequenceGroup is not null, this is restricted to - * annotations which are associated with sequences in the selection group. - *

- * If an annotation row is currently visible, its type (label) is added (once - * only per type), to the shownTypes list. If it is currently hidden, it is - * added to the hiddenTypesList. - *

- * For rows that belong to a line graph group, so are always rendered - * together: - *

    - *
  • Treat all rows in the group as visible, if at least one of them is
    • - *
  • Build a comma-separated label with all the types that belong to the - * group
    • - *
- * - * @param shownTypes - * @param hiddenTypes - * @param visibleGraphGroups - * @param annotations - * @param sequenceGroup - */ - public static void getAnnotationTypesForShowHide( - List> shownTypes, List> hiddenTypes, - BitSet visibleGraphGroups, AlignmentAnnotation[] annotations, - SequenceGroup sequenceGroup) - { - // lookup table, key = graph group, value = list of types in the group - Map> groupLabels = new LinkedHashMap>(); - List addedToShown = new ArrayList(); - List addedToHidden = new ArrayList(); + /* + * Find shown/hidden annotations types, distinguished by source (calcId), + * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in + * the insertion order, which is the order of the annotations on the + * alignment. + */ + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), forSequences); - for (AlignmentAnnotation aa : annotations) + for (String calcId : hiddenTypes.keySet()) { - - if (sequenceGroup == null - || (aa.sequenceRef != null && sequenceGroup.getSequences() - .contains(aa.sequenceRef))) + for (List type : hiddenTypes.get(calcId)) { - /* - * Build a 'composite label' for types in line graph groups. - */ - final List labelAsList = new ArrayList(); - labelAsList.add(aa.label); - if (aa.graph == AlignmentAnnotation.LINE_GRAPH - && aa.graphGroup > -1) - { - if (groupLabels.containsKey(aa.graphGroup)) - { - if (!groupLabels.get(aa.graphGroup).contains(aa.label)) - { - groupLabels.get(aa.graphGroup).add(aa.label); - } - } - else - { - groupLabels.put(aa.graphGroup, labelAsList); - } - } - else if (aa.visible && !addedToShown.contains(aa.label)) - { - shownTypes.add(labelAsList); - addedToShown.add(aa.label); - } - else - { - if (!aa.visible && !addedToHidden.contains(aa.label)) - { - hiddenTypes.add(labelAsList); - addedToHidden.add(aa.label); - } - } + addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, + false, true); } } - /* - * finally add the 'composite group labels' to the appropriate lists, - * depending on whether the group is identified as visible or hidden - */ - for (int group : groupLabels.keySet()) + // grey out 'show annotations' if none are hidden + showMenu.setEnabled(!hiddenTypes.isEmpty()); + + for (String calcId : shownTypes.keySet()) { - final List groupLabel = groupLabels.get(group); - if (visibleGraphGroups.get(group)) + for (List type : shownTypes.get(calcId)) { - if (!shownTypes.contains(groupLabel)) - { - shownTypes.add(groupLabel); - } - } - else if (!hiddenTypes.contains(groupLabel)) - { - hiddenTypes.add(groupLabel); + addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type, + false, false); } } + // grey out 'hide annotations' if none are shown + hideMenu.setEnabled(!shownTypes.isEmpty()); } /** - * Returns a BitSet (possibly empty) of those graphGroups for line graph - * annotations, which have at least one member annotation row marked visible. - * The logic is that only one row in the group is marked visible, but when it - * is drawn, so are all the other rows in the same group. - *

- * This lookup set allows us to check whether rows marked not visible are in - * fact shown. + * Returns a list of sequences - either the current selection group (if there + * is one), else the specified single sequence. * - * @see AnnotationRenderer#drawComponent - * @param annotations + * @param seq * @return */ - public static BitSet getVisibleLineGraphGroups( - AlignmentAnnotation[] annotations) + protected List getSequenceScope(SequenceI seq) { - // todo move to a utility class - BitSet result = new BitSet(); - for (AlignmentAnnotation ann : annotations) + List forSequences = null; + final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); + if (selectionGroup != null && selectionGroup.getSize() > 0) { - if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible) - { - int gg = ann.graphGroup; - if (gg > -1) - { - result.set(gg); - } - } + forSequences = selectionGroup.getSequences(); + } + else + { + forSequences = seq == null ? Collections. emptyList() + : Arrays.asList(seq); } - return result; + return forSequences; } /** @@ -975,6 +1035,9 @@ public class PopupMenu extends JPopupMenu * * @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 @@ -984,77 +1047,50 @@ public class PopupMenu extends JPopupMenu * type, else hide */ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu, - final Collection types, final boolean allTypes, + 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); + label = label.substring(1, label.length() - 1); // a, b, c final JMenuItem item = new JMenuItem(label); - item.addActionListener(new java.awt.event.ActionListener() + item.setToolTipText(calcId); + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, allTypes, actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); + refresh(); } }); showOrHideMenu.add(item); } - /** - * Action on selecting a list of annotation type (or the 'all types' values) - * to show or hide for the selection. - * - * @param types - * @param anyType - * @param doShow - */ - protected void showHideAnnotation_actionPerformed( - Collection types, boolean anyType, boolean doShow) - { - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) - { - if (anyType || types.contains(aa.label)) - { - if ((aa.sequenceRef != null) - && ap.av.getSelectionGroup().getSequences() - .contains(aa.sequenceRef)) - { - aa.visible = doShow; - } - } - } - refresh(); - } - - private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) + private void buildGroupURLMenu(SequenceGroup sg, List groupLinks) { // TODO: usability: thread off the generation of group url content so root // menu appears asap // sequence only URLs // ID/regex match URLs - groupLinksMenu = new JMenu( + JMenu groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); - JMenu[] linkMenus = new JMenu[] - { null, new JMenu(MessageManager.getString("action.ids")), + // 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")) }; // three - // types - // of url - // that - // might - // be - // created. + new JMenu(MessageManager.getString("action.ids_sequences")) }; + SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); - Hashtable commonDbrefs = new Hashtable(); + 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()); + 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 @@ -1063,18 +1099,17 @@ public class PopupMenu extends JPopupMenu { sqi = sqi.getDatasetSequence(); } - DBRefEntry[] dbr = sqi.getDBRef(); + DBRefEntry[] dbr = sqi.getDBRefs(); if (dbr != null && dbr.length > 0) { for (int d = 0; d < dbr.length; d++) { String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); - Object[] sarray = (Object[]) commonDbrefs.get(src); + Object[] sarray = commonDbrefs.get(src); if (sarray == null) { sarray = new Object[2]; - sarray[0] = new int[] - { 0 }; + sarray[0] = new int[] { 0 }; sarray[1] = new String[seqs.length]; commonDbrefs.put(src, sarray); @@ -1082,8 +1117,8 @@ public class PopupMenu extends JPopupMenu if (((String[]) sarray[1])[sq] == null) { - if (!dbr[d].hasMap() - || (dbr[d].getMap().locateMappedRange(start, end) != null)) + if (!dbr[d].hasMap() || (dbr[d].getMap() + .locateMappedRange(start, end) != null)) { ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); ((int[]) sarray[0])[0]++; @@ -1095,30 +1130,28 @@ public class PopupMenu extends JPopupMenu // 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 (int i = 0; i < groupLinks.size(); i++) + for (String link : groupLinks) { - String link = groupLinks.elementAt(i).toString(); GroupUrlLink urlLink = null; try { urlLink = new GroupUrlLink(link); } catch (Exception foo) { - jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link - + "'", foo); + Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); continue; } ; if (!urlLink.isValid()) { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + Cache.log.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 = (Object[]) commonDbrefs.get(ltarget.toUpperCase()); + Object[] idset = commonDbrefs.get(ltarget.toUpperCase()); String[] seqstr, ids; // input to makeUrl if (idset != null) { @@ -1155,13 +1188,12 @@ public class PopupMenu extends JPopupMenu if (urlset != null) { int type = urlLink.getGroupURLType() & 3; - // System.out.println(urlLink.getGroupURLType() - // +" "+((String[])urlset[3])[0]); // 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) + ")") : ""), + addshowLink(linkMenus[type], + label + (((type & 1) == 1) + ? ("(" + (usingNames ? "Names" : ltarget) + ")") + : ""), urlLink, urlset); addMenu = true; } @@ -1170,100 +1202,17 @@ public class PopupMenu extends JPopupMenu { groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); - for (int m = 0; m < linkMenus.length; m++) - { - if (linkMenus[m] != null - && linkMenus[m].getMenuComponentCount() > 0) - { - groupLinksMenu.add(linkMenus[m]); - } - } - - groupMenu.add(groupLinksMenu); - } - } - - /** - * 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(MessageManager.formatMessage( - "label.open_url_param", new String[] - { url })); - item.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - new Thread(new Runnable() - { - - @Override - public void run() - { - showLink(url); - } - - }).start(); - } - }); - - linkMenu.add(item); - } - - /** - * add a late bound groupURL item to the given linkMenu - * - * @param linkMenu - * @param label - * - menu label string - * @param urlgenerator - * GroupURLLink used to generate URL - * @param urlstub - * Object array returned from the makeUrlStubs function. - */ - private void addshowLink(JMenu linkMenu, String label, - final GroupUrlLink urlgenerator, final Object[] urlstub) - { - JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage( - "label.open_url_seqs_param", - new Object[] - { urlgenerator.getUrl_prefix(), - urlgenerator.getNumberInvolved(urlstub) })); - // TODO: put in info about what is being sent. - item.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) + for (int m = 0; m < linkMenus.length; m++) { - new Thread(new Runnable() + if (linkMenus[m] != null + && linkMenus[m].getMenuComponentCount() > 0) { - - @Override - public void run() - { - try - { - showLink(urlgenerator.constructFrom(urlstub)); - } catch (UrlStringTooLongException e) - { - } - } - - }).start(); + groupLinksMenu.add(linkMenus[m]); + } } - }); - linkMenu.add(item); + groupMenu.add(groupLinksMenu); + } } /** @@ -1274,10 +1223,9 @@ public class PopupMenu extends JPopupMenu */ private void jbInit() throws Exception { - groupMenu.setText(MessageManager.getString("label.group")); groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); - groupName.addActionListener(new java.awt.event.ActionListener() + groupName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1286,9 +1234,10 @@ public class PopupMenu extends JPopupMenu } }); sequenceMenu.setText(MessageManager.getString("label.sequence")); - sequenceName.setText(MessageManager - .getString("label.edit_name_description")); - sequenceName.addActionListener(new java.awt.event.ActionListener() + + JMenuItem sequenceName = new JMenuItem( + MessageManager.getString("label.edit_name_description")); + sequenceName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1296,9 +1245,9 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); - chooseAnnotations.setText(MessageManager - .getString("label.choose_annotations") + "..."); - chooseAnnotations.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) @@ -1306,31 +1255,30 @@ public class PopupMenu extends JPopupMenu chooseAnnotations_actionPerformed(e); } }); - sequenceDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + JMenuItem sequenceDetails = new JMenuItem( + MessageManager.getString("label.sequence_details")); + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - sequenceDetails_actionPerformed(); + createSequenceDetailsReport(new SequenceI[] { sequence }); } }); - sequenceSelDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); - sequenceSelDetails - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sequenceSelectionDetails_actionPerformed(); - } - }); - PIDColour.setFocusPainted(false); + JMenuItem sequenceSelDetails = new JMenuItem( + MessageManager.getString("label.sequence_details")); + sequenceSelDetails.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createSequenceDetailsReport(ap.av.getSequenceSelection()); + } + }); + unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1338,38 +1286,27 @@ public class PopupMenu extends JPopupMenu unGroupMenuItem_actionPerformed(); } }); - createGroupMenuItem.setText(MessageManager - .getString("action.create_group")); createGroupMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - createGroupMenuItem_actionPerformed(); - } - }); - - outline.setText(MessageManager.getString("action.border_colour")); - outline.addActionListener(new java.awt.event.ActionListener() + .setText(MessageManager.getString("action.create_group")); + createGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - outline_actionPerformed(); + createGroupMenuItem_actionPerformed(); } }); - nucleotideMenuItem - .setText(MessageManager.getString("label.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(MessageManager.getString("label.group_colour")); showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() @@ -1399,8 +1336,8 @@ public class PopupMenu extends JPopupMenu showColourText_actionPerformed(); } }); - displayNonconserved.setText(MessageManager - .getString("label.show_non_conversed")); + displayNonconserved + .setText(MessageManager.getString("label.show_non_conserved")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1411,7 +1348,7 @@ public class PopupMenu extends JPopupMenu } }); editMenu.setText(MessageManager.getString("action.edit")); - cut.setText(MessageManager.getString("action.cut")); + JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { @Override @@ -1429,7 +1366,7 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - copy.setText(MessageManager.getString("action.copy")); + JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { @Override @@ -1456,82 +1393,18 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - pdbMenu.setText(MessageManager - .getString("label.associate_structure_with_sequence")); - pdbFromFile.setText(MessageManager.getString("label.from_file")); - pdbFromFile.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - pdbFromFile_actionPerformed(); - } - }); - // RNAFold.setText("From RNA Fold with predict2D"); - // RNAFold.addActionListener(new ActionListener() - // { - // public void actionPerformed(ActionEvent e) - // { - // try { - // RNAFold_actionPerformed(); - // } catch (Exception e1) { - // // TODO Auto-generated catch block - // e1.printStackTrace(); - // } - // } - // }); - // ContraFold.setText("From Contra Fold with predict2D"); - // ContraFold.addActionListener(new ActionListener() - // { - // public void actionPerformed(ActionEvent e) - // { - // try { - // ContraFold_actionPerformed(); - // } catch (Exception e1) { - // // TODO Auto-generated catch block - // e1.printStackTrace(); - // } - // } - // }); - enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); - enterPDB.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - enterPDB_actionPerformed(); - } - }); - discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); - discoverPDB.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - discoverPDB_actionPerformed(); - } - }); - outputMenu.setText(MessageManager.getString("label.out_to_textbox") - + "..."); - showAnnotationsMenu.setText(MessageManager - .getString("label.show_annotations")); - hideAnnotationsMenu.setText(MessageManager - .getString("label.hide_annotations")); - final List referenceAnns = getDatasequenceAnnotationsNotOnAlignment(ap.av - .getSelectionGroup()); - addDatasequenceAnnotations.setText(MessageManager - .getString("label.add_reference_annotations")); - addDatasequenceAnnotations.setEnabled(!referenceAnns.isEmpty()); - addDatasequenceAnnotations.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - addReferenceAnnotations_actionPerformed(referenceAnns); - } - }); - sequenceFeature.setText(MessageManager - .getString("label.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 @@ -1540,22 +1413,29 @@ public class PopupMenu extends JPopupMenu sequenceFeature_actionPerformed(); } }); - textColour.setText(MessageManager.getString("label.text_colour")); - textColour.addActionListener(new ActionListener() + editGroupMenu.setText(MessageManager.getString("label.group")); + chooseStructure.setText( + MessageManager.getString("label.show_pdbstruct_dialog")); + chooseStructure.addActionListener(new ActionListener() { @Override - public void actionPerformed(ActionEvent e) + 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(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.structure")); - viewStructureMenu.setText(MessageManager - .getString("label.view_structure")); + + rnaStructureMenu + .setText(MessageManager.getString("label.view_rna_structure")); + // colStructureMenu.setText("Colour By Structure"); - editSequence.setText(MessageManager.getString("label.edit_sequence") - + "..."); + JMenuItem editSequence = new JMenuItem( + MessageManager.getString("label.edit_sequence") + "..."); editSequence.addActionListener(new ActionListener() { @Override @@ -1564,481 +1444,384 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + makeReferenceSeq.setText( + MessageManager.getString("label.mark_as_representative")); + makeReferenceSeq.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent actionEvent) + { + makeReferenceSeq_actionPerformed(actionEvent); + + } + }); - /* - * annotationMenuItem.setText("By Annotation"); - * annotationMenuItem.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent actionEvent) { - * annotationMenuItem_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); - groupMenu.add(showAnnotationsMenu); - groupMenu.add(hideAnnotationsMenu); - groupMenu.add(addDatasequenceAnnotations); + + /* + * 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(createGroupMenuItem); groupMenu.add(unGroupMenuItem); - groupMenu.add(jMenu1); + groupMenu.add(editGroupMenu); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); - 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); - if (ap.getAlignment().isNucleotide()) - { - // JBPNote - commented since the colourscheme isn't functional - // colourMenu.add(RNAInteractionColour); - colourMenu.add(purinePyrimidineColour); - } - // colourMenu.add(covariationColour); - colourMenu.add(userDefinedColour); - - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); + sequenceMenu.add(makeReferenceSeq); - while (userColours.hasMoreElements()) - { - JMenuItem item = new JMenuItem(userColours.nextElement().toString()); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.add(item); - } - } + 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); - // JBPNote: These shouldn't be added here - should appear in a generic - // 'apply web service to this sequence menu' - // pdbMenu.add(RNAFold); - // pdbMenu.add(ContraFold); - pdbMenu.add(enterPDB); - pdbMenu.add(discoverPDB); - jMenu1.add(groupName); - 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(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - @Override - 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(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(); - } - }); - zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(); - } - }); - taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(); - } - }); - hydrophobicityColour.setText(MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); - helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(); - } - }); - strandColour.setText(MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(); - } - }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(); - } - }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.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(MessageManager - .getString("label.above_identity_percentage")); - 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(MessageManager - .getString("action.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(MessageManager.getString("label.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(MessageManager.getString("label.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(); } }); - purinePyrimidineColour.setText(MessageManager - .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); - - /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * covariationColour_actionPerformed(); } }); - */ - - conservationMenuItem.setText(MessageManager - .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); - } - - /** - * Get a list of any annotations on the dataset sequences in the current - * selection group that are not also on the alignment. - *

- * The criteria for 'on the alignment' is finding an annotation that matches - * on sequenceRef.datasetSequence, calcId and label. - * - * @return - */ - protected List getDatasequenceAnnotationsNotOnAlignment( - SequenceGroup sg) - { - List result = new ArrayList(); - - for (SequenceI seq : sg.getSequences()) - { - SequenceI dataset = seq.getDatasetSequence(); - AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); - if (datasetAnnotations != null) - { - for (AlignmentAnnotation dsann : datasetAnnotations) - { - /* - * If the alignment has no annotation that matches this one... - */ - if (!ap.getAlignment() - .findAnnotation(dataset, dsann.getCalcId(), dsann.label) - .iterator().hasNext()) - { - /* - * ...then add it to the result list - */ - result.add(dsann); - } - } - } - } - return result; } /** - * Add any annotations on the sequence dataset to the alignment (that are not - * already copied to it). + * Builds the group colour sub-menu, including any user-defined colours which + * were loaded at startup or during the Jalview session */ - protected void addReferenceAnnotations_actionPerformed( - List anns) + protected void buildColourMenu() { - for (AlignmentAnnotation ann : anns) + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) { - // todo: copy, add, adjust... + /* + * popup menu with no sequence group scope + */ + return; } - } + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.addSeparator(); - protected void sequenceSelectionDetails_actionPerformed() - { - createSequenceDetailsReport(ap.av.getSequenceSelection()); - } + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg, + false); + bg.add(annotationColour); + colourMenu.add(annotationColour); - protected void sequenceDetails_actionPerformed() - { - createSequenceDetailsReport(new SequenceI[] - { sequence }); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDColour); + colourMenu.add(modifyPID); } - public void createSequenceDetailsReport(SequenceI[] sequences) + protected void modifyConservation_actionPerformed() { - CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - StringBuffer contents = new StringBuffer(); - for (SequenceI seq : sequences) + SequenceGroup sg = getGroup(); + if (sg.cs != null) { - contents.append("

" - + MessageManager - .formatMessage( - "label.create_sequence_details_report_annotation_for", - new String[] - { seq.getDisplayId(true) }) + "

"); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport( - contents, - seq, - true, - true, - false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax - : null); - contents.append("

"); + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); } - cap.setText("" + contents.toString() + ""); - - Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( - "label.sequece_details_for", - (sequences.length == 1 ? new String[] - { sequences[0].getDisplayId(true) } : new String[] - { MessageManager.getString("label.selection") })), 500, 400); - } - protected void showNonconserved_actionPerformed() + protected void modifyPID_actionPerformed() { - getGroup().setShowNonconserved(displayNonconserved.isSelected()); - 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(); + } } /** - * call to refresh view after settings change + * 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. + * + * A tooltip is also constructed that displays the source (calcId) and type + * (label) of the annotations that can be added. + * + * @param menuItem + * @param forSequences */ - void refresh() + protected void configureReferenceAnnotationsMenu(JMenuItem menuItem, + List forSequences) { - ap.updateAnnotation(); - ap.paintAlignment(true); + menuItem.setEnabled(false); - PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); - } + /* + * 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")); - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void clustalColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); - refresh(); + /* + * 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 */ - protected void zappoColour_actionPerformed() + protected void addReferenceAnnotations_actionPerformed( + Map> candidates) { - getGroup().cs = new ZappoColourScheme(); + 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 taylorColour_actionPerformed() + protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent) { - getGroup().cs = new TaylorColourScheme(); + 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(sequence); + } + else + { + if (ap.av.getAlignment().getSeqrep() == sequence) + { + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(sequence); + } + } refresh(); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed() + protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } + HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); + BitSet inserts = new BitSet(); - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void helixColour_actionPerformed() - { - getGroup().cs = new HelixColourScheme(); + 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? + + // 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()); + } + + // now mark for sequence under popup if we haven't already done it + else if (!markedPopup && sequence != null) + { + inserts.or(sequence.getInsertionsAsBits()); + + // and set hidden columns accordingly + hidden.hideColumns(inserts); + } refresh(); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void strandColour_actionPerformed() + protected void sequenceSelectionDetails_actionPerformed() { - getGroup().cs = new StrandColourScheme(); - refresh(); + createSequenceDetailsReport(ap.av.getSequenceSelection()); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void turnColour_actionPerformed() + public void createSequenceDetailsReport(SequenceI[] sequences) { - getGroup().cs = new TurnColourScheme(); - refresh(); + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + StringBuilder contents = new StringBuilder(128); + for (SequenceI seq : sequences) + { + contents.append("

" + MessageManager.formatMessage( + "label.create_sequence_details_report_annotation_for", + new Object[] + { seq.getDisplayId(true) }) + "

"); + new SequenceAnnotationReport(false).createSequenceAnnotationReport( + contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); + contents.append("

"); + } + cap.setText("" + contents.toString() + ""); + + Desktop.addInternalFrame(cap, + MessageManager.formatMessage("label.sequence_details_for", + (sequences.length == 1 ? new Object[] + { sequences[0].getDisplayId(true) } + : new Object[] + { MessageManager + .getString("label.selection") })), + 500, 400); + } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void buriedColour_actionPerformed() + protected void showNonconserved_actionPerformed() { - getGroup().cs = new BuriedColourScheme(); + getGroup().setShowNonconserved(displayNonconserved.isSelected()); refresh(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * call to refresh view after settings change */ - public void nucleotideMenuItem_actionPerformed() + void refresh() { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } + ap.updateAnnotation(); + // removed paintAlignment(true) here: + // updateAnnotation calls paintAlignment already, so don't need to call + // again - protected void purinePyrimidineColour_actionPerformed() - { - getGroup().cs = new PurinePyrimidineColourScheme(); - refresh(); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } /* @@ -2048,10 +1831,12 @@ public class PopupMenu extends JPopupMenu /** * DOCUMENT ME! * + * @param selected + * * @param e * DOCUMENT ME! */ - protected void abovePIDColour_actionPerformed() + public void abovePIDColour_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -2059,49 +1844,27 @@ public class PopupMenu extends JPopupMenu return; } - if (abovePIDColour.isSelected()) + if (selected) { sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() - .getName()); + int threshold = SliderPanel.setPIDSliderSource(ap, + sg.getGroupColourScheme(), getGroup().getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); - } - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - if (e.getSource().equals(userDefinedColour)) - { - new UserDefinedColours(ap, sg); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); + SliderPanel.hidePIDSlider(); } - else - { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); + modifyPID.setEnabled(selected); - sg.cs = udc; - } refresh(); } @@ -2123,54 +1886,7 @@ public class PopupMenu extends JPopupMenu * @param e * DOCUMENT ME! */ - protected void PIDColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void BLOSUM62Colour_actionPerformed() - { - SequenceGroup sg = getGroup(); - - sg.cs = new Blosum62ColourScheme(); - - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed() - { - getGroup().cs = null; - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void conservationMenuItem_actionPerformed() + public void conservationMenuItem_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -2178,45 +1894,28 @@ 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 - .getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1); + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); 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.setPredefinedColours(true); - sg.cs = acg; + modifyConservation.setEnabled(selected); refresh(); } @@ -2232,8 +1931,8 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " " - + MessageManager.getString("label.group_name") + " ", + sg.getDescription(), + " " + MessageManager.getString("label.group_name") + " ", MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), ap.alignFrame); @@ -2266,10 +1965,9 @@ public class PopupMenu extends JPopupMenu } /** - * 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() { @@ -2278,8 +1976,8 @@ public class PopupMenu extends JPopupMenu " " + MessageManager.getString("label.sequence_name") + " ", MessageManager.getString("label.sequence_description") + " ", - MessageManager - .getString("label.edit_sequence_name_description"), + MessageManager.getString( + "label.edit_sequence_name_description"), ap.alignFrame); if (!dialog.accept) @@ -2287,28 +1985,28 @@ public class PopupMenu extends JPopupMenu return; } - if (dialog.getName() != null) + String name = dialog.getName(); + if (name != null) { - if (dialog.getName().indexOf(" ") > -1) + if (name.indexOf(" ") > -1) { - JOptionPane - .showMessageDialog( - ap, - MessageManager - .getString("label.spaces_converted_to_backslashes"), - MessageManager - .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(ap, + MessageManager + .getString("label.spaces_converted_to_backslashes"), + MessageManager + .getString("label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); + name = name.replace(' ', '_'); } - sequence.setName(dialog.getName().replace(' ', '_')); - ap.paintAlignment(false); + sequence.setName(name); + ap.paintAlignment(false, false); } sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } @@ -2390,55 +2088,9 @@ public class PopupMenu extends JPopupMenu refresh(); } - public void showLink(String url) - { - try - { - jalview.util.BrowserLauncher.openURL(url); - } catch (Exception ex) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); - - 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); - // refresh(); TODO: ? needed ? - ap.av.sendSelection(); + ap.av.hideSequences(sequence, representGroup); } public void copy_actionPerformed() @@ -2458,8 +2110,8 @@ 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; @@ -2486,8 +2138,8 @@ public class PopupMenu extends JPopupMenu ap.alignFrame.addHistoryItem(caseCommand); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } } @@ -2496,8 +2148,8 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2506,79 +2158,10 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - ap.av, true)); - } - - 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(MessageManager.formatMessage( - "label.select_pdb_file_for", new String[] - { sequence.getDisplayId(false) })); - chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] - { sequence.getDisplayId(false) })); - - int value = chooser.showOpenDialog(null); - - if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); - new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, sequence, true); - } - - } - - // JBNote: commented out - these won't be instantiated here...! - // public void RNAFold_actionPerformed() throws Exception - // { - // Predict2D P2D = new Predict2D(); - // P2D.getStructure2DFromRNAFold("toto"); - // } - // - // public void ContraFold_actionPerformed() throws Exception - // { - // Predict2D P2D = new Predict2D(); - // P2D.getStructure2DFromContraFold("toto"); - // } - public void enterPDB_actionPerformed() - { - String id = JOptionPane.showInternalInputDialog(Desktop.desktop, - MessageManager.getString("label.enter_pdb_id"), - MessageManager.getString("label.enter_pdb_id"), - JOptionPane.QUESTION_MESSAGE); - - 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.getSelectionGroup() == null) ? new SequenceI[] - { sequence } - : ap.av.getSequenceSelection()); - Thread discpdb = new Thread(new Runnable() - { - @Override - 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() @@ -2589,33 +2172,37 @@ public class PopupMenu extends JPopupMenu return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, 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++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, start, end, null)); } } - 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.setShowSeqFeatures(true); - ap.highlightSearchResults(null); + + /* + * an entirely gapped region will generate empty lists of sequence / features + */ + if (!seqs.isEmpty()) + { + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer() + .amendFeatures(seqs, features, true, ap)) + { + ap.alignFrame.setShowSeqFeatures(true); + ap.av.setSearchResults(null); // clear highlighting + ap.repaint(); // draw new/amended features + } } } @@ -2628,38 +2215,22 @@ public class PopupMenu extends JPopupMenu } } - public void colourByStructure(String pdbid) - { - Annotation[] anots = ap.av.getStructureSelectionManager() - .colourSequenceFromStructure(sequence, pdbid); - - AlignmentAnnotation an = new AlignmentAnnotation("Structure", - "Coloured by " + pdbid, anots); - - ap.av.getAlignment().addAnnotation(an); - an.createSequenceMapping(sequence, 0, true); - // an.adjustForAlignment(); - ap.av.getAlignment().setAnnotationIndex(an, 0); - - ap.adjustAnnotationHeight(); - - sequence.addAlignmentAnnotation(an); - - } - public void editSequence_actionPerformed(ActionEvent actionEvent) { SequenceGroup sg = ap.av.getSelectionGroup(); + SequenceI seq = sequence; if (sg != null) { - if (sequence == null) - sequence = sg.getSequenceAt(0); + if (seq == null) + { + seq = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( - sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, - MessageManager.getString("label.edit_sequence"), null, + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1), + null, MessageManager.getString("label.edit_sequence"), null, MessageManager.getString("label.edit_sequence"), ap.alignFrame); @@ -2667,17 +2238,45 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), + 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(); + } + }