X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=2ef71cce5d6fff162391756b1425434754dcce56;hb=6d06be2714c9cba8c69148d5e2d26b50b7051840;hp=ad3d6af347997305f9483e80c07b1b5dbf1e490d;hpb=e373651097c72eb6c9ca6009fb70d47341e8f405;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index ad3d6af..2ef71cc 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,114 +20,80 @@ */ package jalview.gui; -import java.awt.Color; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.util.Arrays; -import java.util.Collections; -import java.util.Hashtable; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeMap; -import java.util.Vector; - -import javax.swing.ButtonGroup; -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.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.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; 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.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.ColourSchemeI; +import jalview.schemes.ColourSchemes; 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; +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.SortedMap; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; + /** * DOCUMENT ME! * * @author $author$ * @version $Revision: 1.118 $ */ -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(); - - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - 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(); - - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); + AlignmentPanel ap; JMenu sequenceMenu = new JMenu(); @@ -137,7 +103,7 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); - + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -150,8 +116,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -176,12 +140,6 @@ public class PopupMenu extends JPopupMenu JMenu pdbMenu = new JMenu(); - JMenuItem pdbFromFile = new JMenuItem(); - - JMenuItem enterPDB = new JMenuItem(); - - JMenuItem discoverPDB = new JMenuItem(); - JMenu outputMenu = new JMenu(); JMenu seqShowAnnotationsMenu = new JMenu(); @@ -204,7 +162,7 @@ public class PopupMenu extends JPopupMenu JMenu jMenu1 = new JMenu(); - JMenuItem proteinStructureMenu = new JMenuItem(); + JMenuItem pdbStructureDialog = new JMenuItem(); JMenu rnaStructureMenu = new JMenu(); @@ -222,7 +180,8 @@ 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); } @@ -235,7 +194,7 @@ 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 @@ -246,29 +205,11 @@ 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); - - 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) @@ -285,8 +226,9 @@ public class PopupMenu extends JPopupMenu * 'reference annotations' that may be added to the alignment. First for the * currently selected sequence (if there is one): */ - final List selectedSequence = (seq == null ? Collections - . emptyList() : Arrays.asList(seq)); + final List selectedSequence = (seq == null + ? Collections. emptyList() + : Arrays.asList(seq)); buildAnnotationTypesMenus(seqShowAnnotationsMenu, seqHideAnnotationsMenu, selectedSequence); configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, @@ -295,9 +237,9 @@ public class PopupMenu extends JPopupMenu /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections - . emptyList() : ap.av.getSelectionGroup() - .getSequences()); + final List selectedGroup = (ap.av.getSelectionGroup() == null + ? Collections. emptyList() + : ap.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -317,9 +259,13 @@ public class PopupMenu extends JPopupMenu sequenceMenu.setText(sequence.getName()); if (seq == ap.av.getAlignment().getSeqrep()) { - makeReferenceSeq.setText("Unmark representative"); - } else { - makeReferenceSeq.setText("Mark as representative"); + makeReferenceSeq.setText( + MessageManager.getString("action.unmark_as_reference")); + } + else + { + makeReferenceSeq.setText( + MessageManager.getString("action.set_as_reference")); } if (!ap.av.getAlignment().isNucleotide()) @@ -328,6 +274,7 @@ public class PopupMenu extends JPopupMenu } else { + int origCount = rnaStructureMenu.getItemCount(); /* * add menu items to 2D-render any alignment or sequence secondary * structure annotation @@ -347,7 +294,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(MessageManager.formatMessage( "label.2d_rna_structure_line", new Object[] { aa.label })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -375,7 +322,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(MessageManager.formatMessage( "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) @@ -388,11 +335,15 @@ public class PopupMenu extends JPopupMenu } } } + 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) @@ -405,10 +356,10 @@ public class PopupMenu extends JPopupMenu if (ap.av.getSelectionGroup() != null && ap.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new Object[] + 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) @@ -465,83 +416,35 @@ public class PopupMenu extends JPopupMenu add(menuItem); } - } SequenceGroup sg = ap.av.getSelectionGroup(); - boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() - .getGroups().contains(sg) : false; + boolean isDefinedGroup = (sg != null) + ? ap.av.getAlignment().getGroups().contains(sg) + : false; if (sg != null && sg.getSize() > 0) { - groupName.setText(MessageManager.formatMessage("label.name_param", - new Object[] - { 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); - } + ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); - /* - * else if (sg.cs instanceof CovariationColourScheme) { - * covariationColour.setSelected(true); } - */ - else - { - noColourmenuItem.setSelected(true); - } + conservationMenuItem.setEnabled(!sg.isNucleotide()); - if (sg.cs != null && sg.cs.conservationApplied()) + if (sg.cs != null) { - 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()); @@ -552,11 +455,12 @@ 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()) { - 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)); @@ -572,9 +476,9 @@ 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; } } @@ -600,131 +504,69 @@ public class PopupMenu extends JPopupMenu if (seq == null) { sequenceMenu.setVisible(false); - proteinStructureMenu.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); } + } /** @@ -748,8 +590,11 @@ public class PopupMenu extends JPopupMenu showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(ALL_ANNOTATIONS); - addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + 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(); @@ -764,19 +609,17 @@ public class PopupMenu extends JPopupMenu * 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); + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); + 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 @@ -786,8 +629,8 @@ 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 @@ -843,20 +686,20 @@ public class PopupMenu extends JPopupMenu 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) { - AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, - forSequences, allTypes, actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); refresh(); } }); showOrHideMenu.add(item); } - 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 @@ -865,24 +708,20 @@ 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++) { - 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 @@ -891,18 +730,17 @@ 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); @@ -910,8 +748,8 @@ 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]++; @@ -923,30 +761,28 @@ 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) { @@ -985,9 +821,10 @@ public class PopupMenu extends JPopupMenu int type = urlLink.getGroupURLType() & 3; // first two bits ofurlLink type bitfield are sequenceids and sequences // TODO: FUTURE: ensure the groupURL menu structure can be generalised - addshowLink(linkMenus[type], label - + (((type & 1) == 1) ? ("(" - + (usingNames ? "Names" : ltarget) + ")") : ""), + addshowLink(linkMenus[type], + label + (((type & 1) == 1) + ? ("(" + (usingNames ? "Names" : ltarget) + ")") + : ""), urlLink, urlset); addMenu = true; } @@ -1009,6 +846,16 @@ 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 * @@ -1021,10 +868,10 @@ public class PopupMenu extends JPopupMenu private void addshowLink(JMenu linkMenu, String label, final String url) { JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new Object[] + item.setToolTipText(MessageManager.formatMessage("label.open_url_param", + new Object[] { url })); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1060,13 +907,12 @@ public class PopupMenu extends JPopupMenu final GroupUrlLink urlgenerator, final Object[] urlstub) { JMenuItem item = new JMenuItem(label); - item.setToolTipText(MessageManager.formatMessage( - "label.open_url_seqs_param", - new Object[] + 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() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1080,7 +926,7 @@ public class PopupMenu extends JPopupMenu try { showLink(urlgenerator.constructFrom(urlstub)); - } catch (UrlStringTooLongException e) + } catch (UrlStringTooLongException e2) { } } @@ -1100,10 +946,9 @@ 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) @@ -1112,9 +957,9 @@ 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.setText( + MessageManager.getString("label.edit_name_description")); + sequenceName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1122,9 +967,9 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); - chooseAnnotations.setText(MessageManager - .getString("label.choose_annotations") + "..."); - chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + chooseAnnotations + .setText(MessageManager.getString("action.choose_annotations")); + chooseAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1132,9 +977,9 @@ public class PopupMenu extends JPopupMenu chooseAnnotations_actionPerformed(e); } }); - sequenceDetails.setText(MessageManager - .getString("label.sequence_details") + "..."); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + sequenceDetails + .setText(MessageManager.getString("label.sequence_details")); + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1142,21 +987,20 @@ public class PopupMenu extends JPopupMenu sequenceDetails_actionPerformed(); } }); - 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); + .setText(MessageManager.getString("label.sequence_details")); + sequenceSelDetails.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); + unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1164,38 +1008,26 @@ 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() + + outline.setText(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() @@ -1225,8 +1057,8 @@ 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() { @@ -1282,48 +1114,18 @@ 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(); - } - }); - - 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 - .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")); - 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")); + sequenceFeature.setText( + MessageManager.getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() { @Override @@ -1332,25 +1134,15 @@ public class PopupMenu extends JPopupMenu sequenceFeature_actionPerformed(); } }); - textColour.setText(MessageManager.getString("label.text_colour")); - textColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - textColour_actionPerformed(); - } - }); jMenu1.setText(MessageManager.getString("label.group")); - proteinStructureMenu.setText(MessageManager - .getString("label.view_protein_structure")); - proteinStructureMenu.addActionListener(new ActionListener() + pdbStructureDialog.setText( + MessageManager.getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { - SequenceI[] selectedSeqs = new SequenceI[] - { sequence }; + SequenceI[] selectedSeqs = new SequenceI[] { sequence }; if (ap.av.getSelectionGroup() != null) { selectedSeqs = ap.av.getSequenceSelection(); @@ -1359,12 +1151,12 @@ public class PopupMenu extends JPopupMenu } }); - rnaStructureMenu.setText(MessageManager - .getString("label.view_rna_structure")); + rnaStructureMenu + .setText(MessageManager.getString("label.view_rna_structure")); // colStructureMenu.setText("Colour By Structure"); - editSequence.setText(MessageManager.getString("label.edit_sequence") - + "..."); + editSequence.setText( + MessageManager.getString("label.edit_sequence") + "..."); editSequence.addActionListener(new ActionListener() { @Override @@ -1373,19 +1165,20 @@ public class PopupMenu extends JPopupMenu editSequence_actionPerformed(actionEvent); } }); - makeReferenceSeq.setText(MessageManager - .getString("label.mark_as_representative")); + makeReferenceSeq.setText( + MessageManager.getString("label.mark_as_representative")); makeReferenceSeq.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent actionEvent) { makeReferenceSeq_actionPerformed(actionEvent); - + } }); - hideInsertions.setText(MessageManager.getString("label.hide_insertions")); + hideInsertions + .setText(MessageManager.getString("label.hide_insertions")); hideInsertions.addActionListener(new ActionListener() { @@ -1395,18 +1188,13 @@ public class PopupMenu extends JPopupMenu 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); add(rnaStructureMenu); - add(proteinStructureMenu); - if (sequence!=null) + add(pdbStructureDialog); + if (sequence != null) { add(hideInsertions); } @@ -1432,62 +1220,20 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); sequenceMenu.add(makeReferenceSeq); - 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(purinePyrimidineColour); - } - colourMenu.add(userDefinedColour); - - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); - while (userColours.hasMoreElements()) - { - JMenuItem item = new JMenuItem(userColours.nextElement().toString()); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.add(item); - } - } + initColourMenu(); + buildColourMenu(); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); 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); @@ -1495,160 +1241,118 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); - noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(); - } - }); + } - clustalColour.setText(MessageManager - .getString("label.clustalx_colours")); - clustalColour.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() + /** + * 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) { - turnColour_actionPerformed(); + textColour_actionPerformed(); } }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() + + abovePIDColour.setText( + MessageManager.getString("label.above_identity_threshold")); + abovePIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(); + abovePIDColour_actionPerformed(abovePIDColour.isSelected()); } }); - abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() + + modifyPID.setText( + MessageManager.getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(); + modifyPID_actionPerformed(); } }); - userDefinedColour.setText(MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + + conservationMenuItem + .setText(MessageManager.getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); + conservationMenuItem_actionPerformed( + conservationMenuItem.isSelected()); } }); - PIDColour - .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() + + modifyConservation.setText(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(); + modifyConservation_actionPerformed(); } }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + } + + /** + * Builds the group colour sub-menu, including any user-defined colours which + * were loaded at startup or during the Jalview session + */ + protected void buildColourMenu() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) { - @Override - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(); - } - }); - purinePyrimidineColour.setText(MessageManager - .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); + /* + * popup menu with no sequence group scope + */ + return; + } + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.addSeparator(); - /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * covariationColour_actionPerformed(); } }); - */ + ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); - conservationMenuItem.setText(MessageManager - .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDColour); + colourMenu.add(modifyPID); + } + + protected void modifyConservation_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + } + + protected void modifyPID_actionPerformed() + { + 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(); + } } /** @@ -1664,8 +1368,8 @@ public class PopupMenu extends JPopupMenu * @param menuItem * @param forSequences */ - protected void configureReferenceAnnotationsMenu( - JMenuItem menuItem, List forSequences) + protected void configureReferenceAnnotationsMenu(JMenuItem menuItem, + List forSequences) { menuItem.setEnabled(false); @@ -1673,11 +1377,11 @@ public class PopupMenu extends JPopupMenu * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ - Map tipEntries = new TreeMap(); - final Map> candidates = new LinkedHashMap>(); + SortedMap tipEntries = new TreeMap<>(); + final Map> candidates = new LinkedHashMap<>(); AlignmentI al = this.ap.av.getAlignment(); - AlignmentUtils.findAddableReferenceAnnotations(forSequences, - tipEntries, candidates, al); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries, + candidates, al); if (!candidates.isEmpty()) { StringBuilder tooltip = new StringBuilder(64); @@ -1749,18 +1453,62 @@ public class PopupMenu extends JPopupMenu protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - if (sequence != null) + + HiddenColumns hidden = new HiddenColumns(); + BitSet inserts = new BitSet(), mask = new BitSet(); + + // set mask to preserve existing hidden columns outside selected group + if (ap.av.hasHiddenColumns()) + { + ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask); + } + + boolean markedPopup = false; + // mark inserts in current selection + if (ap.av.getSelectionGroup() != null) { - ColumnSelection cs = ap.av.getColumnSelection(); - if (cs == null) + // mark just the columns in the selection group to be hidden + inserts.set(ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes() + 1); + + // and clear that part of the mask + mask.andNot(inserts); + + // now clear columns without gaps + for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) { - cs = new ColumnSelection(); + if (sq == sequence) + { + markedPopup = true; + } + inserts.and(sq.getInsertionsAsBits()); } - cs.hideInsertionsFor(sequence); - ap.av.setColumnSelection(cs); } + else + { + // initially, mark all columns to be hidden + inserts.set(0, ap.av.getAlignment().getWidth()); + + // and clear out old hidden regions completely + mask.clear(); + } + + // now mark for sequence under popup if we haven't already done it + if (!markedPopup && sequence != null) + { + inserts.and(sequence.getInsertionsAsBits()); + } + + // finally, preserve hidden regions outside selection + inserts.or(mask); + + // and set hidden columns accordingly + hidden.hideMarkedBits(inserts); + + ap.av.getAlignment().setHiddenColumns(hidden); refresh(); } + protected void sequenceSelectionDetails_actionPerformed() { createSequenceDetailsReport(ap.av.getSequenceSelection()); @@ -1768,42 +1516,36 @@ 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 Object[] - { seq.getDisplayId(true) }) + "

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

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

"); + new SequenceAnnotationReport(null).createSequenceAnnotationReport( + contents, seq, true, true, + (ap.getSeqPanel().seqCanvas.fr != null) + ? ap.getSeqPanel().seqCanvas.fr.getMinMax() + : null); 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); + 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); } @@ -1819,126 +1561,13 @@ public class PopupMenu extends JPopupMenu void refresh() { ap.updateAnnotation(); - ap.paintAlignment(true); + // removed paintAlignment(true) here: + // updateAnnotation calls paintAlignment already, so don't need to call + // again PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void clustalColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void zappoColour_actionPerformed() - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void taylorColour_actionPerformed() - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed() - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void helixColour_actionPerformed() - { - getGroup().cs = new HelixColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void strandColour_actionPerformed() - { - getGroup().cs = new StrandColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void turnColour_actionPerformed() - { - getGroup().cs = new TurnColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void buriedColour_actionPerformed() - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - public void nucleotideMenuItem_actionPerformed() - { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } - - protected void purinePyrimidineColour_actionPerformed() - { - getGroup().cs = new PurinePyrimidineColourScheme(); - refresh(); - } - /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1946,10 +1575,12 @@ 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) @@ -1957,14 +1588,14 @@ 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.isIgnoreGapsConsensus()); @@ -1974,36 +1605,14 @@ public class PopupMenu extends JPopupMenu // remove PIDColouring { sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); + SliderPanel.hidePIDSlider(); } + modifyPID.setEnabled(selected); 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); - } - else - { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); - - sg.cs = udc; - } - refresh(); - } - - /** * Open a panel where the user can choose which types of sequence annotation * to show or hide. * @@ -2021,54 +1630,7 @@ 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) @@ -2076,45 +1638,28 @@ 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(); } @@ -2130,8 +1675,8 @@ 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); @@ -2176,8 +1721,8 @@ 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) @@ -2189,14 +1734,12 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane - .showMessageDialog( - ap, - MessageManager - .getString("label.spaces_converted_to_backslashes"), - MessageManager - .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(ap, + MessageManager + .getString("label.spaces_converted_to_backslashes"), + MessageManager + .getString("label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -2205,8 +1748,8 @@ public class PopupMenu extends JPopupMenu sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); } @@ -2295,10 +1838,10 @@ 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(); } @@ -2306,29 +1849,7 @@ 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 = sg.getSequences().toArray(new SequenceI[gsize]); - - ap.av.hideSequence(hseqs); - // refresh(); TODO: ? needed ? - ap.av.sendSelection(); + ap.av.hideSequences(sequence, representGroup); } public void copy_actionPerformed() @@ -2349,8 +1870,7 @@ public class PopupMenu extends JPopupMenu if (sg != null) { List startEnd = ap.av.getVisibleRegionBoundaries( - sg.getStartRes(), - sg.getEndRes() + 1); + sg.getStartRes(), sg.getEndRes() + 1); String description; int caseChange; @@ -2377,8 +1897,8 @@ 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()); } } @@ -2387,8 +1907,8 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2397,69 +1917,10 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(), - ap, 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 Object[] - { sequence.getDisplayId(false) })); - chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new Object[] - { 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, - Desktop.instance); - } - - } - - - 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() @@ -2470,33 +1931,37 @@ 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, 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.getSeqPanel().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.highlightSearchResults(null); + } } } @@ -2541,8 +2006,8 @@ public class PopupMenu extends JPopupMenu EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, - MessageManager.getString("label.edit_sequence"), null, + sg.getEndRes() + 1), + null, MessageManager.getString("label.edit_sequence"), null, MessageManager.getString("label.edit_sequence"), ap.alignFrame); @@ -2550,17 +2015,45 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - Action.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, 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(); + } + }