X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=ebcb06269d9e10b642f58bf93041520dabce3af8;hb=92d5aeaf6d48b15a8122060f7dd32f16d2f552dc;hp=175adeaef9f78a89741cc0e205de229df98c556a;hpb=d305e02d8b425bb501141ad32142aeb8572adc57;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 175adea..ebcb062 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. * @@ -22,32 +22,39 @@ package jalview.gui; import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; -import jalview.analysis.AnnotationSorter; -import jalview.analysis.AnnotationSorter.SortOrder; +import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; +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.Annotation; +import jalview.datamodel.ColumnSelection; 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.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.JalviewColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; @@ -58,9 +65,9 @@ import jalview.util.MessageManager; import jalview.util.UrlLink; import java.awt.Color; +import java.awt.Component; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Collections; @@ -68,6 +75,7 @@ import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; +import java.util.SortedMap; import java.util.TreeMap; import java.util.Vector; @@ -76,7 +84,6 @@ 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; @@ -88,10 +95,6 @@ import javax.swing.JRadioButtonMenuItem; */ public class PopupMenu extends JPopupMenu { - private static final String ALL_ANNOTATIONS = "All"; - - private static final String COMMA = ","; - JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -120,12 +123,13 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); + JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem(); - // protected JRadioButtonMenuItem covariationColour = new - // JRadioButtonMenuItem(); + // protected JRadioButtonMenuItem RNAInteractionColour; JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); @@ -141,6 +145,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceSelDetails = new JMenuItem(); + JMenuItem makeReferenceSeq = new JMenuItem(); + JMenuItem chooseAnnotations = new JMenuItem(); SequenceI sequence; @@ -151,8 +157,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -177,31 +181,21 @@ public class PopupMenu extends JPopupMenu JMenu pdbMenu = new JMenu(); - JMenuItem pdbFromFile = new JMenuItem(); - - // JBPNote: Commented these out - Should add these services via the web - // services menu system. - // JMenuItem ContraFold = new JMenuItem(); - - // JMenuItem RNAFold = new JMenuItem(); - - JMenuItem enterPDB = new JMenuItem(); - - JMenuItem discoverPDB = new JMenuItem(); - JMenu outputMenu = new JMenu(); JMenu seqShowAnnotationsMenu = new JMenu(); JMenu seqHideAnnotationsMenu = new JMenu(); - JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenu groupShowAnnotationsMenu = new JMenu(); JMenu groupHideAnnotationsMenu = new JMenu(); - JMenuItem groupAddReferenceAnnotations = new JMenuItem(); + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); JMenuItem sequenceFeature = new JMenuItem(); @@ -209,17 +203,16 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenu structureMenu = new JMenu(); + JMenuItem pdbStructureDialog = new JMenuItem(); - JMenu viewStructureMenu = new JMenu(); + JMenu rnaStructureMenu = new JMenu(); - // JMenu colStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); - // JMenuItem annotationMenuItem = new JMenuItem(); - JMenu groupLinksMenu; + JMenuItem hideInsertions = new JMenuItem(); + /** * Creates a new PopupMenu object. * @@ -228,7 +221,7 @@ public class PopupMenu extends JPopupMenu * @param seq * DOCUMENT ME! */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) + public PopupMenu(final AlignmentPanel ap, Sequence seq, List links) { this(ap, seq, links, null); } @@ -241,7 +234,7 @@ public class PopupMenu extends JPopupMenu * @param groupLinks */ public PopupMenu(final AlignmentPanel ap, final SequenceI seq, - Vector links, Vector groupLinks) + List links, List groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -252,30 +245,11 @@ public class PopupMenu extends JPopupMenu this.ap = ap; 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++) + for (String ff : FileFormat.getWritableFormats(true)) { - JMenuItem item = new JMenuItem( - jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); + JMenuItem item = new JMenuItem(ff); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -322,131 +296,93 @@ public class PopupMenu extends JPopupMenu if (seq != null) { sequenceMenu.setText(sequence.getName()); - - if (seq.getDatasetSequence().getPDBId() != null - && seq.getDatasetSequence().getPDBId().size() > 0) + if (seq == ap.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 ActionListener() - { - @Override - 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 (!ap.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 = ap.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, ap); + } + }); + 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[] - { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + "label.2d_rna_sequence_name", + new Object[] { seq.getName() })); + 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, ap); } }); - 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) @@ -460,9 +396,9 @@ public class PopupMenu extends JPopupMenu && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] - { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + "label.represent_group_with", + new Object[] { seq.getName() })); + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -528,69 +464,10 @@ public class PopupMenu extends JPopupMenu 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) - { - 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); - } + setColourSelected(sg.cs); if (sg.cs != null && sg.cs.conservationApplied()) { @@ -610,7 +487,7 @@ public class PopupMenu extends JPopupMenu SequenceI sqass = null; for (SequenceI sq : ap.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)); @@ -630,50 +507,6 @@ public class PopupMenu extends JPopupMenu 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 @@ -698,132 +531,73 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - structureMenu.setVisible(false); + pdbStructureDialog.setVisible(false); + rnaStructureMenu.setVisible(false); } if (links != null && links.size() > 0) { + addFeatureLinks(seq, links); + } + } - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - Vector linkset = new Vector(); - for (int i = 0; i < links.size(); i++) - { - 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()) - { - - // 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; - } + /** + * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * + * @param seq + * @param links + */ + void addFeatureLinks(final SequenceI seq, List links) + { + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); + Map> linkset = new LinkedHashMap>(); - 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()); - } - } - } - if (sequence != null) + for (String link : links) + { + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) { - sequenceMenu.add(linkMenu); + Cache.log.error("Exception for URLLink '" + link + "'", foo); + continue; } - else + + if (!urlLink.isValid()) { - add(linkMenu); + Cache.log.error(urlLink.getInvalidMessage()); + continue; } + + urlLink.createLinksFromSeq(seq, linkset); + } + + addshowLinks(linkMenu, linkset.values()); + + // disable link menu if there are no valid entries + if (linkMenu.getItemCount() > 0) + { + linkMenu.setEnabled(true); + } + else + { + linkMenu.setEnabled(false); } + + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } + } + + /** * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. * "All" is added first, followed by a separator. Then add any annotation @@ -845,7 +619,8 @@ public class PopupMenu extends JPopupMenu showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(ALL_ANNOTATIONS); + final List all = Arrays.asList(new String[] { MessageManager + .getString("label.all") }); addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); @@ -863,17 +638,15 @@ public class PopupMenu extends JPopupMenu */ Map>> shownTypes = new LinkedHashMap>>(); Map>> hiddenTypes = new LinkedHashMap>>(); - AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, - hiddenTypes, - AlignmentAnnotationUtils.asList(annotations), - forSequences); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), forSequences); for (String calcId : hiddenTypes.keySet()) { for (List type : hiddenTypes.get(calcId)) { - addAnnotationTypeToShowHide(showMenu, forSequences, - calcId, type, false, true); + addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, + false, true); } } // grey out 'show annotations' if none are hidden @@ -883,8 +656,8 @@ public class PopupMenu extends JPopupMenu { for (List type : shownTypes.get(calcId)) { - addAnnotationTypeToShowHide(hideMenu, forSequences, - calcId, type, false, false); + addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type, + false, false); } } // grey out 'hide annotations' if none are shown @@ -937,50 +710,23 @@ public class PopupMenu extends JPopupMenu 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.setToolTipText(calcId); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showHideAnnotation_actionPerformed(types, forSequences, 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 specified sequences. - * - * @param types - * @param forSequences - * @param anyType - * @param doShow - */ - protected void showHideAnnotation_actionPerformed( - Collection types, List forSequences, - boolean anyType, boolean doShow) - { - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) - { - if (anyType || types.contains(aa.label)) - { - if ((aa.sequenceRef != null) - && forSequences.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 @@ -989,19 +735,15 @@ public class PopupMenu extends JPopupMenu // ID/regex match URLs 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++) { @@ -1015,18 +757,17 @@ 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); @@ -1047,30 +788,28 @@ 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) { @@ -1107,8 +846,6 @@ 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 @@ -1135,6 +872,15 @@ public class PopupMenu extends JPopupMenu } } + private void addshowLinks(JMenu linkMenu, Collection> linkset) + { + for (List linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3)); + } + } + /** * add a show URL menu item to the given linkMenu * @@ -1148,9 +894,8 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new String[] - { url })); - item.addActionListener(new java.awt.event.ActionListener() + "label.open_url_param", new Object[] { url })); + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1188,11 +933,10 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_seqs_param", - new Object[] - { urlgenerator.getUrl_prefix(), + new Object[] { urlgenerator.getUrl_prefix(), urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1206,7 +950,7 @@ public class PopupMenu extends JPopupMenu try { showLink(urlgenerator.constructFrom(urlstub)); - } catch (UrlStringTooLongException e) + } catch (UrlStringTooLongException e2) { } } @@ -1226,10 +970,9 @@ 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) @@ -1240,7 +983,7 @@ 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() + sequenceName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1249,8 +992,8 @@ public class PopupMenu extends JPopupMenu } }); chooseAnnotations.setText(MessageManager - .getString("label.choose_annotations") + "..."); - chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + .getString("action.choose_annotations")); + chooseAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1259,8 +1002,8 @@ public class PopupMenu extends JPopupMenu } }); sequenceDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + .getString("label.sequence_details")); + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1269,9 +1012,9 @@ public class PopupMenu extends JPopupMenu } }); sequenceSelDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); + .getString("label.sequence_details")); sequenceSelDetails - .addActionListener(new java.awt.event.ActionListener() +.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1282,7 +1025,7 @@ public class PopupMenu extends JPopupMenu PIDColour.setFocusPainted(false); unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1293,7 +1036,7 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem.setText(MessageManager .getString("action.create_group")); createGroupMenuItem - .addActionListener(new java.awt.event.ActionListener() +.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1303,7 +1046,7 @@ public class PopupMenu extends JPopupMenu }); outline.setText(MessageManager.getString("action.border_colour")); - outline.addActionListener(new java.awt.event.ActionListener() + outline.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1311,17 +1054,6 @@ public class PopupMenu extends JPopupMenu outline_actionPerformed(); } }); - nucleotideMenuItem - .setText(MessageManager.getString("label.nucleotide")); - nucleotideMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - nucleotideMenuItem_actionPerformed(); - } - }); - colourMenu.setText(MessageManager.getString("label.group_colour")); showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() @@ -1352,7 +1084,7 @@ public class PopupMenu extends JPopupMenu } }); displayNonconserved.setText(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1408,61 +1140,6 @@ 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") + "..."); seqShowAnnotationsMenu.setText(MessageManager @@ -1483,19 +1160,26 @@ public class PopupMenu extends JPopupMenu sequenceFeature_actionPerformed(); } }); - textColour.setText(MessageManager.getString("label.text_colour")); - textColour.addActionListener(new ActionListener() + jMenu1.setText(MessageManager.getString("label.group")); + pdbStructureDialog.setText(MessageManager + .getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.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") + "..."); @@ -1507,17 +1191,44 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); + makeReferenceSeq.setText(MessageManager + .getString("label.mark_as_representative")); + makeReferenceSeq.addActionListener(new ActionListener() + { - /* - * annotationMenuItem.setText("By Annotation"); - * annotationMenuItem.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent actionEvent) { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + makeReferenceSeq_actionPerformed(actionEvent); + + } + }); + hideInsertions.setText(MessageManager + .getString("label.hide_insertions")); + hideInsertions.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + hideInsertions_actionPerformed(e); + } + }); + /* + * 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(pdbStructureDialog); + if (sequence != null) + { + add(hideInsertions); + } // annotations configuration panel suppressed for now // groupMenu.add(chooseAnnotations); @@ -1539,65 +1250,20 @@ public class PopupMenu extends JPopupMenu groupMenu.add(jMenu1); 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); + sequenceMenu.add(makeReferenceSeq); - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); + buildColourMenu(); - 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); - } - } - - 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); @@ -1605,11 +1271,27 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); - structureMenu.add(pdbMenu); - structureMenu.add(viewStructureMenu); - // structureMenu.add(colStructureMenu); + + initColourMenu(); + } + + /** + * 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) + { + textColour_actionPerformed(); + } + }); noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + noColourmenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1618,9 +1300,9 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setText(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() + clustalColour.setText(MessageManager.getString("label.clustalx")); + clustalColour.setName(JalviewColourScheme.Clustal.toString()); + clustalColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1629,7 +1311,8 @@ public class PopupMenu extends JPopupMenu } }); zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() + zappoColour.setName(JalviewColourScheme.Zappo.toString()); + zappoColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1638,7 +1321,8 @@ public class PopupMenu extends JPopupMenu } }); taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() + taylorColour.setName(JalviewColourScheme.Taylor.toString()); + taylorColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1649,16 +1333,18 @@ public class PopupMenu extends JPopupMenu hydrophobicityColour.setText(MessageManager .getString("label.hydrophobicity")); hydrophobicityColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); + .setName(JalviewColourScheme.Hydrophobic.toString()); + hydrophobicityColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new java.awt.event.ActionListener() + helixColour.setName(JalviewColourScheme.Helix.toString()); + helixColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1668,7 +1354,8 @@ public class PopupMenu extends JPopupMenu }); strandColour.setText(MessageManager .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() + strandColour.setName(JalviewColourScheme.Strand.toString()); + strandColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1677,7 +1364,8 @@ public class PopupMenu extends JPopupMenu } }); turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() + turnColour.setName(JalviewColourScheme.Turn.toString()); + turnColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1686,7 +1374,8 @@ public class PopupMenu extends JPopupMenu } }); buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() + buriedColour.setName(JalviewColourScheme.Buried.toString()); + buriedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1695,8 +1384,8 @@ public class PopupMenu extends JPopupMenu } }); abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() + .getString("label.above_identity_threshold")); + abovePIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1706,7 +1395,8 @@ public class PopupMenu extends JPopupMenu }); userDefinedColour.setText(MessageManager .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + userDefinedColour.setName(JalviewColourScheme.UserDefined.toString()); + userDefinedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1716,7 +1406,8 @@ public class PopupMenu extends JPopupMenu }); PIDColour .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() + PIDColour.setName(JalviewColourScheme.PID.toString()); + PIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1724,8 +1415,10 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(); } }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + BLOSUM62Colour + .setText(MessageManager.getString("label.blosum62_score")); + BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString()); + BLOSUM62Colour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1733,112 +1426,191 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(); } }); + nucleotideColour.setText(MessageManager.getString("label.nucleotide")); + nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString()); + nucleotideColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + nucleotideMenuItem_actionPerformed(); + } + }); purinePyrimidineColour.setText(MessageManager .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); + purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine + .toString()); + purinePyrimidineColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); + + tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString()); + tcoffeeColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + tcoffeeColorScheme_actionPerformed(); + } + }); /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * covariationColour.addActionListener(new 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(); + .getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); } }); } /** - * Check for any annotations on the underlying dataset sequences (for the - * current selection group) which are not on the alignment annotations for the - * sequence. 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 sequence, that matches on calcId and label. A tooltip is also - * constructed that displays the source (calcId) and type (label) of the - * annotations that can be added. - * - * @param menuItem - * @param forSequences + * Builds the group colour sub-menu, including any user-defined colours which + * were loaded at startup or during the Jalview session */ - protected void configureReferenceAnnotationsMenu( - JMenuItem menuItem, List forSequences) + protected void buildColourMenu() { - menuItem.setText(MessageManager - .getString("label.add_reference_annotations")); - menuItem.setEnabled(false); - if (forSequences == null) - { - return; - } + SequenceGroup sg = getGroup(); + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + // in Java 8, isApplicableTo can be a static method on the interface + clustalColour.setEnabled(new ClustalxColourScheme(sg, null) + .isApplicableTo(sg)); + colourMenu.add(BLOSUM62Colour); + BLOSUM62Colour + .setEnabled(new Blosum62ColourScheme().isApplicableTo(sg)); + colourMenu.add(PIDColour); + PIDColour.setEnabled(new PIDColourScheme().isApplicableTo(sg)); + colourMenu.add(zappoColour); + zappoColour.setEnabled(new ZappoColourScheme().isApplicableTo(sg)); + colourMenu.add(taylorColour); + taylorColour.setEnabled(new TaylorColourScheme().isApplicableTo(sg)); + colourMenu.add(hydrophobicityColour); + hydrophobicityColour.setEnabled(new HydrophobicColourScheme() + .isApplicableTo(sg)); + colourMenu.add(helixColour); + helixColour.setEnabled(new HelixColourScheme().isApplicableTo(sg)); + colourMenu.add(strandColour); + strandColour.setEnabled(new StrandColourScheme().isApplicableTo(sg)); + colourMenu.add(turnColour); + turnColour.setEnabled(new TurnColourScheme().isApplicableTo(sg)); + colourMenu.add(buriedColour); + buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(sg)); + colourMenu.add(nucleotideColour); + nucleotideColour.setEnabled(new NucleotideColourScheme() + .isApplicableTo(sg)); + colourMenu.add(purinePyrimidineColour); + purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme() + .isApplicableTo(sg)); + colourMenu.add(tcoffeeColour); + tcoffeeColour + .setEnabled(new TCoffeeColourScheme(sg).isApplicableTo(sg)); /* - * Temporary store to hold distinct calcId / type pairs for the tooltip. - * Using TreeMap means calcIds are shown in alphabetical order. + * add some of these items to a ButtonGroup so their + * selection is mutually exclusive */ - Map tipEntries = new TreeMap(); - StringBuilder tooltip = new StringBuilder(64); - tooltip.append(MessageManager.getString("label.add_annotations_for")); + ButtonGroup colours = new ButtonGroup(); /* - * For each sequence selected in the alignment, make a list of any - * annotations on the underlying dataset sequence which are not already on - * the sequence in the alignment. - * - * Build a map of { alignmentSequence, } + * add any user-defined colours loaded on startup or + * during the application session */ - final Map> candidates = new LinkedHashMap>(); - for (SequenceI seq : forSequences) + SortedMap userColourSchemes = UserDefinedColours + .getUserColourSchemes(); + if (userColourSchemes != null) { - SequenceI dataset = seq.getDatasetSequence(); - if (dataset == null) - { - continue; - } - AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); - if (datasetAnnotations == null) + for (String userColour : userColourSchemes.keySet()) { - continue; - } - final List result = new ArrayList(); - for (AlignmentAnnotation dsann : datasetAnnotations) - { - /* - * If the sequence has no annotation that matches this one, then add - * this one to the results list. - */ - if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label) - .isEmpty()) + JRadioButtonMenuItem item = new JRadioButtonMenuItem(userColour); + item.setName(userColour); // button name identifies selected colour + item.addActionListener(new ActionListener() { - result.add(dsann); - tipEntries.put(dsann.getCalcId(), dsann.label); - } - } - /* - * Save any addable annotations for this sequence - */ - if (!result.isEmpty()) - { - candidates.put(seq, result); + @Override + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + colours.add(item); } } + colourMenu.add(userDefinedColour); + + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(abovePIDColour); + + colours.add(noColourmenuItem); + colours.add(clustalColour); + colours.add(BLOSUM62Colour); + colours.add(PIDColour); + colours.add(zappoColour); + colours.add(taylorColour); + colours.add(hydrophobicityColour); + colours.add(helixColour); + colours.add(strandColour); + colours.add(turnColour); + colours.add(buriedColour); + colours.add(purinePyrimidineColour); + colours.add(tcoffeeColour); + colours.add(nucleotideColour); + colours.add(userDefinedColour); + colours.add(abovePIDColour); + // colours.add(RNAInteractionColour); + + } + + /** + * 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 + */ + protected void configureReferenceAnnotationsMenu(JMenuItem menuItem, + List forSequences) + { + menuItem.setEnabled(false); + + /* + * Temporary store to hold distinct calcId / type pairs for the tooltip. + * Using TreeMap means calcIds are shown in alphabetical order. + */ + SortedMap tipEntries = new TreeMap(); + final Map> candidates = new LinkedHashMap>(); + AlignmentI al = this.ap.av.getAlignment(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, + tipEntries, candidates, al); if (!candidates.isEmpty()) { + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + /* * Found annotations that could be added. Enable the menu item, and * configure its tooltip and action. @@ -1873,39 +1645,48 @@ public class PopupMenu extends JPopupMenu protected void addReferenceAnnotations_actionPerformed( Map> candidates) { - /* - * Add annotations at the top of the annotation, in the same order as their - * related sequences. - */ - for (SequenceI seq : candidates.keySet()) + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + final AlignmentI alignment = this.ap.getAlignment(); + AlignmentUtils.addReferenceAnnotations(candidates, alignment, + selectionGroup); + refresh(); + } + + protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent) + { + 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 { - for (AlignmentAnnotation ann : candidates.get(seq)) + if (ap.av.getAlignment().getSeqrep() == sequence) { - AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); - int startRes = 0; - int endRes = ann.annotations.length; - final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); - if (selectionGroup != null) - { - startRes = selectionGroup.getStartRes(); - endRes = selectionGroup.getEndRes(); - } - copyAnn.restrict(startRes, endRes); + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(sequence); + } + } + refresh(); + } - // add to the sequence (sets copyAnn.datasetSequence) - seq.addAlignmentAnnotation(copyAnn); - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - this.ap.getAlignment().addAnnotation(copyAnn); - copyAnn.visible = true; + protected void hideInsertions_actionPerformed(ActionEvent actionEvent) + { + if (sequence != null) + { + ColumnSelection cs = ap.av.getColumnSelection(); + if (cs == null) + { + cs = new ColumnSelection(); } + cs.hideInsertionsFor(sequence); + ap.av.setColumnSelection(cs); } - // TODO: save annotation sort order on AlignViewport - // do sorting from AlignmentPanel.updateAnnotation() - new AnnotationSorter(this.ap.getAlignment()).sort(this.ap - .getAlignment().getAlignmentAnnotation(), - SortOrder.SEQUENCE_AND_TYPE); refresh(); } @@ -1916,40 +1697,39 @@ public class PopupMenu extends JPopupMenu protected void sequenceDetails_actionPerformed() { - createSequenceDetailsReport(new SequenceI[] - { sequence }); + createSequenceDetailsReport(new SequenceI[] { sequence }); } public void createSequenceDetailsReport(SequenceI[] sequences) { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - StringBuffer contents = new StringBuffer(); + StringBuilder contents = new StringBuilder(128); for (SequenceI seq : sequences) { contents.append("

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

"); + new Object[] { seq.getDisplayId(true) }) + + "

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

"); } cap.setText("" + contents.toString() + ""); - Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( - "label.sequece_details_for", - (sequences.length == 1 ? new String[] - { sequences[0].getDisplayId(true) } : new String[] - { MessageManager.getString("label.selection") })), 500, 400); + Desktop.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); } @@ -2085,6 +1865,12 @@ public class PopupMenu extends JPopupMenu refresh(); } + protected void tcoffeeColorScheme_actionPerformed() + { + getGroup().cs = new TCoffeeColourScheme(getGroup()); + refresh(); + } + /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -2112,14 +1898,14 @@ public class PopupMenu extends JPopupMenu int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } refresh(); @@ -2141,7 +1927,7 @@ public class PopupMenu extends JPopupMenu } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours + UserColourScheme udc = UserDefinedColours .getUserColourSchemes().get(e.getActionCommand()); sg.cs = udc; @@ -2225,9 +2011,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { // JBPNote: Conservation name shouldn't be i18n translated - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(ap.av - .getHiddenRepSequences()), sg.getStartRes(), + Conservation c = new Conservation("Group", sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -2335,14 +2120,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane + JvOptionPane .showMessageDialog( ap, MessageManager .getString("label.spaces_converted_to_backslashes"), MessageManager .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -2441,10 +2226,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -2452,37 +2237,7 @@ public class PopupMenu extends JPopupMenu 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() @@ -2502,8 +2257,8 @@ 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; @@ -2541,8 +2296,8 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] - { e.getActionCommand() }), 600, 500); + "label.alignment_output_command", + new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2550,79 +2305,8 @@ 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 = FileFormat.forName(e.getActionCommand()); + cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true)); } public void sequenceFeature_actionPerformed() @@ -2655,7 +2339,7 @@ public class PopupMenu extends JPopupMenu System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.setShowSeqFeatures(true); @@ -2713,7 +2397,7 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', + Action.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); @@ -2726,4 +2410,36 @@ public class PopupMenu extends JPopupMenu } } + /** + * Marks as selected the colour menu item matching the given name, or the + * first item ('None') if no match is found + * + * @param cs + */ + protected void setColourSelected(ColourSchemeI cs) + { + noColourmenuItem.setSelected(true); + if (cs == null) + { + return; + } + + String schemeName = cs.getSchemeName(); + /* + * look for a radio button with a name that matches the colour name + * (note the button text may not as it may be internationalised) + */ + for (Component menuItem : colourMenu.getMenuComponents()) + { + if (menuItem instanceof JRadioButtonMenuItem) + { + if (schemeName.equals(((JRadioButtonMenuItem) menuItem).getName())) + { + ((JRadioButtonMenuItem) menuItem).setSelected(true); + return; + } + } + } + } + }