X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e78eaf2d4d3a48ea4c620676adcee99b8211ca4b;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=7ab60222127c17c8920b5d8cb8e47f54e78e12ea;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 7ab6022..e78eaf2 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -31,56 +31,57 @@ 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.gui.JalviewColourChooser.ColourChooserListener; +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.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; -import jalview.util.DBRefUtils; +import jalview.schemes.ResidueColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.util.UrlLink; +import java.awt.BorderLayout; 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.ButtonGroup; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; +import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; /** * DOCUMENT ME! @@ -88,43 +89,21 @@ import javax.swing.JRadioButtonMenuItem; * @author $author$ * @version $Revision: 1.118 $ */ -public class PopupMenu extends JPopupMenu +public class PopupMenu extends JPopupMenu implements ColourChangeListener { 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 JMenuItem modifyPID = new JMenuItem(); - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem annotationColour; - protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); AlignmentPanel ap; @@ -148,8 +127,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -210,24 +187,31 @@ public class PopupMenu extends JPopupMenu * Creates a new PopupMenu object. * * @param ap - * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * @param features + * non-positional features (for seq not null), or positional features + * at residue (for seq equal to null) */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, List links) + public PopupMenu(final AlignmentPanel ap, SequenceI seq, + List features) { - this(ap, seq, links, null); + this(ap, seq, features, null); } /** + * Constructor * - * @param ap + * @param alignPanel * @param seq - * @param links + * the sequence under the cursor if in the Id panel, null if in the + * sequence panel + * @param features + * non-positional features if in the Id panel, features at the + * clicked residue if in the sequence panel * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, - List links, List groupLinks) + public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, + List features, List groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -235,32 +219,14 @@ public class PopupMenu extends JPopupMenu // // If from the IDPanel, we must display the sequence menu // //////////////////////////////////////////////////////// - this.ap = ap; + this.ap = alignPanel; sequence = seq; - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(purinePyrimidineColour); - colours.add(RNAInteractionColour); - - 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) @@ -277,8 +243,9 @@ 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, @@ -287,9 +254,9 @@ 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 = (alignPanel.av.getSelectionGroup() == null + ? Collections. emptyList() + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -307,18 +274,18 @@ public class PopupMenu extends JPopupMenu if (seq != null) { sequenceMenu.setText(sequence.getName()); - if (seq == ap.av.getAlignment().getSeqrep()) + if (seq == alignPanel.av.getAlignment().getSeqrep()) { - makeReferenceSeq.setText(MessageManager - .getString("action.unmark_as_reference")); + makeReferenceSeq.setText( + MessageManager.getString("action.unmark_as_reference")); } else { - makeReferenceSeq.setText(MessageManager - .getString("action.set_as_reference")); + makeReferenceSeq.setText( + MessageManager.getString("action.set_as_reference")); } - if (!ap.av.getAlignment().isNucleotide()) + if (!alignPanel.av.getAlignment().isNucleotide()) { remove(rnaStructureMenu); } @@ -329,7 +296,7 @@ public class PopupMenu extends JPopupMenu * add menu items to 2D-render any alignment or sequence secondary * structure annotation */ - AlignmentAnnotation[] aas = ap.av.getAlignment() + AlignmentAnnotation[] aas = alignPanel.av.getAlignment() .getAlignmentAnnotation(); if (aas != null) { @@ -342,14 +309,14 @@ public class PopupMenu extends JPopupMenu */ menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", - new Object[] { aa.label })); - menuItem.addActionListener(new java.awt.event.ActionListener() + "label.2d_rna_structure_line", new Object[] + { aa.label })); + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - new AppVarna(seq, aa, ap); + new AppVarna(seq, aa, alignPanel); } }); rnaStructureMenu.add(menuItem); @@ -370,15 +337,15 @@ public class PopupMenu extends JPopupMenu // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", - new Object[] { 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, aa, ap); + new AppVarna(seq, aa, alignPanel); } }); rnaStructureMenu.add(menuItem); @@ -393,7 +360,7 @@ public class PopupMenu extends JPopupMenu 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) @@ -403,13 +370,13 @@ public class PopupMenu extends JPopupMenu }); add(menuItem); - if (ap.av.getSelectionGroup() != null - && ap.av.getSelectionGroup().getSize() > 1) + if (alignPanel.av.getSelectionGroup() != null + && alignPanel.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", - new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem = new JMenuItem(MessageManager + .formatMessage("label.represent_group_with", new Object[] + { seq.getName() })); + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -420,12 +387,12 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows()) + if (alignPanel.av.hasHiddenRows()) { - final int index = ap.av.getAlignment().findIndex(seq); + final int index = alignPanel.av.getAlignment().findIndex(seq); - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) + if (alignPanel.av.adjustForHiddenSeqs(index) + - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_sequences")); @@ -434,10 +401,10 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - ap.av.showSequence(index); - if (ap.overviewPanel != null) + alignPanel.av.showSequence(index); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); @@ -445,9 +412,20 @@ public class PopupMenu extends JPopupMenu } } } - // for the case when no sequences are even visible - if (ap.av.hasHiddenRows()) + + /* + * offer 'Reveal All' + * - in the IdPanel (seq not null) if any sequence is hidden + * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null) + */ + if (alignPanel.av.hasHiddenRows()) { + boolean addOption = seq != null; + if (!addOption && alignPanel.av.getAlignment().getHeight() == 0) + { + addOption = true; + } + if (addOption) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_all")); @@ -456,90 +434,44 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - ap.av.showAllHiddenSeqs(); - if (ap.overviewPanel != null) + alignPanel.av.showAllHiddenSeqs(); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); - add(menuItem); } - } - SequenceGroup sg = ap.av.getSelectionGroup(); - boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() - .getGroups().contains(sg) : false; + SequenceGroup sg = alignPanel.av.getSelectionGroup(); + boolean isDefinedGroup = (sg != null) + ? alignPanel.av.getAlignment().getGroups().contains(sg) + : false; if (sg != null && sg.getSize() > 0) { groupName.setText(MessageManager .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()); @@ -550,9 +482,10 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); + Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + SequenceI sqass = null; - for (SequenceI sq : ap.av.getSequenceSelection()) + for (SequenceI sq : alignPanel.av.getSequenceSelection()) { Vector pes = sq.getDatasetSequence().getAllPDBEntries(); if (pes != null && pes.size() > 0) @@ -570,9 +503,9 @@ 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; } } @@ -602,23 +535,153 @@ public class PopupMenu extends JPopupMenu rnaStructureMenu.setVisible(false); } - if (links != null && links.size() > 0) + addLinks(seq, features); + + if (seq == null) + { + addFeatureDetails(features); + } + } + + /** + * Add a link to show feature details for each sequence feature + * + * @param features + */ + protected void addFeatureDetails(List features) + { + if (features == null || features.isEmpty()) + { + return; + } + JMenu details = new JMenu( + MessageManager.getString("label.feature_details")); + add(details); + + for (final SequenceFeature sf : features) + { + int start = sf.getBegin(); + int end = sf.getEnd(); + String desc = null; + if (start == end) + { + desc = String.format("%s %d", sf.getType(), start); + } + else + { + desc = String.format("%s %d-%d", sf.getType(), start, end); + } + String tooltip = desc; + String description = sf.getDescription(); + if (description != null) + { + description = StringUtils.stripHtmlTags(description); + if (description.length() > 12) + { + desc = desc + " " + description.substring(0, 12) + ".."; + } + else + { + desc = desc + " " + description; + } + tooltip = tooltip + " " + description; + } + if (sf.getFeatureGroup() != null) + { + tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")"); + } + JMenuItem item = new JMenuItem(desc); + item.setToolTipText(tooltip); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showFeatureDetails(sf); + } + }); + details.add(item); + } + } + + /** + * Opens a panel showing a text report of feature dteails + * + * @param sf + */ + protected void showFeatureDetails(SequenceFeature sf) + { + JInternalFrame details; + if (/** @j2sNative true || */ false) + { + details = new JInternalFrame(); + JPanel panel = new JPanel(new BorderLayout()); + panel.setOpaque(true); + panel.setBackground(Color.white); + // TODO JAL-3026 set style of table correctly for feature details + JLabel reprt = new JLabel(MessageManager.formatMessage("label.html_content", + new Object[] + { sf.getDetailsReport()})); + reprt.setBackground(Color.WHITE); + reprt.setOpaque(true); + panel.add(reprt,BorderLayout.CENTER); + details.setContentPane(panel); + details.pack(); + } + else { - addFeatureLinks(seq, links); + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + // it appears Java's CSS does not support border-collaps :-( + cap.addStylesheetRule("table { border-collapse: collapse;}"); + cap.addStylesheetRule("table, td, th {border: 1px solid black;}"); + cap.setText(sf.getDetailsReport()); + details = cap; } + Desktop.addInternalFrame(details, + MessageManager.getString("label.feature_details"), 500, 500); } /** * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * When seq is not null, these are links for the sequence id, which may be to + * external web sites for the sequence accession, and/or links embedded in + * non-positional features. When seq is null, only links embedded in the + * provided features are added. * * @param seq - * @param links + * @param features */ - void addFeatureLinks(final SequenceI seq, List links) + void addLinks(final SequenceI seq, List features) { JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - List linkset = new ArrayList(); - for (String link : links) + + List nlinks = null; + if (seq != null) + { + nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + } + else + { + nlinks = new ArrayList<>(); + } + + if (features != null) + { + for (SequenceFeature sf : features) + { + if (sf.links != null) + { + for (String link : sf.links) + { + nlinks.add(link); + } + } + } + } + + Map> linkset = new LinkedHashMap<>(); + + for (String link : nlinks) { UrlLink urlLink = null; try @@ -629,105 +692,30 @@ public class PopupMenu extends JPopupMenu Cache.log.error("Exception for URLLink '" + link + "'", foo); continue; } - ; + if (!urlLink.isValid()) { Cache.log.error(urlLink.getInvalidMessage()); continue; } - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { - // collect matching db-refs - DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(), - new String[] { urlLink.getTarget() }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } + urlLink.createLinksFromSeq(seq, linkset); + } - 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 URL - 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.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); - } - } - } - } - } - if (id != null) - { - // create Bare ID link for this URL - 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.add(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.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } + addshowLinks(linkMenu, linkset.values()); + + // only add link menu if it has entries + if (linkMenu.getItemCount() > 0) + { + if (sequence != null) + { + sequenceMenu.add(linkMenu); } else { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) - { - linkset.add(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); - } + add(linkMenu); } } - if (sequence != null) - { - sequenceMenu.add(linkMenu); - } - else - { - add(linkMenu); - } } /** @@ -751,9 +739,11 @@ public class PopupMenu extends JPopupMenu showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(new String[] { MessageManager - .getString("label.all") }); - 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(); @@ -768,8 +758,8 @@ 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>>(); + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, AlignmentAnnotationUtils.asList(annotations), forSequences); @@ -845,7 +835,7 @@ 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) @@ -875,12 +865,12 @@ public class PopupMenu extends JPopupMenu 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 @@ -889,12 +879,14 @@ public class PopupMenu extends JPopupMenu { sqi = sqi.getDatasetSequence(); } - DBRefEntry[] dbr = sqi.getDBRefs(); - if (dbr != null && dbr.length > 0) + List dbr = sqi.getDBRefs(); + int nd; + if (dbr != null && (nd = dbr.size()) > 0) { - for (int d = 0; d < dbr.length; d++) + for (int d = 0; d < nd; d++) { - String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); + DBRefEntry e = dbr.get(d); + String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); Object[] sarray = commonDbrefs.get(src); if (sarray == null) { @@ -907,10 +899,10 @@ public class PopupMenu extends JPopupMenu if (((String[]) sarray[1])[sq] == null) { - if (!dbr[d].hasMap() - || (dbr[d].getMap().locateMappedRange(start, end) != null)) + if (!e.hasMap() || (e.getMap() + .locateMappedRange(start, end) != null)) { - ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); + ((String[]) sarray[1])[sq] = e.getAccessionId(); ((int[]) sarray[0])[0]++; } } @@ -980,9 +972,10 @@ 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; } @@ -1004,6 +997,16 @@ 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 * @@ -1016,9 +1019,10 @@ 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[] { url })); - item.addActionListener(new java.awt.event.ActionListener() + item.setToolTipText(MessageManager.formatMessage("label.open_url_param", + new Object[] + { url })); + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1054,9 +1058,9 @@ 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[] { urlgenerator.getUrl_prefix(), + item.setToolTipText(MessageManager + .formatMessage("label.open_url_seqs_param", new Object[] + { urlgenerator.getUrl_prefix(), urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. item.addActionListener(new ActionListener() @@ -1095,7 +1099,7 @@ public class PopupMenu extends JPopupMenu { 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) @@ -1104,9 +1108,9 @@ 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) @@ -1114,9 +1118,9 @@ public class PopupMenu extends JPopupMenu sequenceName_actionPerformed(); } }); - chooseAnnotations.setText(MessageManager - .getString("action.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) @@ -1124,9 +1128,9 @@ 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) @@ -1134,21 +1138,20 @@ 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) @@ -1156,38 +1159,26 @@ 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() @@ -1217,8 +1208,8 @@ 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() { @@ -1274,18 +1265,18 @@ public class PopupMenu extends JPopupMenu changeCase(e); } }); - 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 @@ -1294,18 +1285,9 @@ 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")); - pdbStructureDialog.setText(MessageManager - .getString("label.show_pdbstruct_dialog")); + pdbStructureDialog.setText( + MessageManager.getString("label.show_pdbstruct_dialog")); pdbStructureDialog.addActionListener(new ActionListener() { @Override @@ -1320,22 +1302,22 @@ 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 public void actionPerformed(ActionEvent actionEvent) { - editSequence_actionPerformed(actionEvent); + editSequence_actionPerformed(); } }); - makeReferenceSeq.setText(MessageManager - .getString("label.mark_as_representative")); + makeReferenceSeq.setText( + MessageManager.getString("label.mark_as_representative")); makeReferenceSeq.addActionListener(new ActionListener() { @@ -1346,8 +1328,8 @@ public class PopupMenu extends JPopupMenu } }); - hideInsertions.setText(MessageManager - .getString("label.hide_insertions")); + hideInsertions + .setText(MessageManager.getString("label.hide_insertions")); hideInsertions.addActionListener(new ActionListener() { @@ -1357,12 +1339,7 @@ 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); @@ -1394,49 +1371,10 @@ 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); @@ -1454,160 +1392,128 @@ 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() + } + + /** + * 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) { - noColourmenuItem_actionPerformed(); + textColour_actionPerformed(); } }); - clustalColour.setText(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() + abovePIDColour.setText( + MessageManager.getString("label.above_identity_threshold")); + abovePIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(); + abovePIDColour_actionPerformed(abovePIDColour.isSelected()); } }); - zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() + + modifyPID.setText( + MessageManager.getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(); + modifyPID_actionPerformed(); } }); - taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() + + conservationMenuItem + .setText(MessageManager.getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(); + conservationMenuItem_actionPerformed( + conservationMenuItem.isSelected()); } }); - 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() + + annotationColour = new JRadioButtonMenuItem( + MessageManager.getString("action.by_annotation")); + annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); + annotationColour.setEnabled(false); + annotationColour.setToolTipText( + MessageManager.getString("label.by_annotation_tooltip")); + + modifyConservation.setText(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(); + modifyConservation_actionPerformed(); } }); - strandColour.setText(MessageManager - .getString("label.strand_propensity")); - strandColour.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) - { - strandColour_actionPerformed(); - } - }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(); - } - }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(); - } - }); - abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(); - } - }); - userDefinedColour.setText(MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour - .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(); - } - }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - @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(); } }); - */ + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg, + false); + bg.add(annotationColour); + colourMenu.add(annotationColour); - 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(); + } } /** @@ -1632,11 +1538,11 @@ 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); @@ -1708,15 +1614,37 @@ public class PopupMenu extends JPopupMenu protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - if (sequence != null) + HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); + BitSet inserts = new BitSet(); + + 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); // TODO why +1? + + // 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); + hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes()); + } + + // now mark for sequence under popup if we haven't already done it + else if (!markedPopup && sequence != null) + { + inserts.or(sequence.getInsertionsAsBits()); + + // and set hidden columns accordingly + hidden.hideColumns(inserts); } refresh(); } @@ -1733,36 +1661,49 @@ public class PopupMenu extends JPopupMenu public void createSequenceDetailsReport(SequenceI[] sequences) { - CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - StringBuffer contents = new StringBuffer(); + StringBuilder contents = new StringBuilder(128); + contents.append(""); for (SequenceI seq : sequences) { - contents.append("

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

"); - 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); 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); + contents.append(""); + String report = contents.toString(); + + JInternalFrame frame; + if (Platform.isJS()) + { + JLabel textLabel = new JLabel(); + textLabel.setText(report); + textLabel.setBackground(Color.WHITE); + JPanel pane = new JPanel(new BorderLayout()); + ((JPanel) pane).setOpaque(true); + pane.setBackground(Color.WHITE); + ((JPanel) pane).add(textLabel, BorderLayout.NORTH); + frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(pane)); + } + else + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + cap.setText(report); + frame = cap; + } + Desktop.addInternalFrame(frame, + MessageManager.formatMessage("label.sequence_details_for", + (sequences.length == 1 ? new Object[] + { sequences[0].getDisplayId(true) } + : new Object[] + { MessageManager + .getString("label.selection") })), + 500, 400); } protected void showNonconserved_actionPerformed() @@ -1777,126 +1718,13 @@ 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(); } @@ -1904,10 +1732,12 @@ 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) @@ -1915,14 +1745,14 @@ 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()); @@ -1932,36 +1762,14 @@ 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. * @@ -1979,54 +1787,7 @@ 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) @@ -2034,73 +1795,54 @@ public class PopupMenu extends JPopupMenu return; } - if (conservationMenuItem.isSelected()) + if (selected) { // JBPNote: Conservation name shouldn't be i18n translated - Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av - .getHiddenRepSequences()), sg.getStartRes(), - sg.getEndRes() + 1); + Conservation c = new Conservation("Group", + 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(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a dialog where group name and description may be edited */ protected void groupName_actionPerformed() { - SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " " - + MessageManager.getString("label.group_name") + " ", - MessageManager.getString("label.group_description") + " ", + sg.getDescription(), + MessageManager.getString("label.group_name"), + MessageManager.getString("label.group_description")); + dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - ap.alignFrame); - - if (!dialog.accept) - { - return; - } - - sg.setName(dialog.getName()); - sg.setDescription(dialog.getDescription()); - refresh(); + new Runnable() + { + @Override + public void run() + { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + }); } /** @@ -2121,50 +1863,41 @@ public class PopupMenu extends JPopupMenu } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a dialog where sequence name and description may be edited */ void sequenceName_actionPerformed() { EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence.getDescription(), - " " + MessageManager.getString("label.sequence_name") - + " ", - MessageManager.getString("label.sequence_description") + " ", - MessageManager - .getString("label.edit_sequence_name_description"), - ap.alignFrame); - - if (!dialog.accept) - { - return; - } - - if (dialog.getName() != null) - { - 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); - } - - sequence.setName(dialog.getName().replace(' ', '_')); - ap.paintAlignment(false); - } - - sequence.setDescription(dialog.getDescription()); - - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); - + MessageManager.getString("label.sequence_name"), + MessageManager.getString("label.sequence_description")); + dialog.showDialog(ap.alignFrame, + MessageManager.getString( + "label.edit_sequence_name_description"), + new Runnable() + { + @Override + public void run() + { + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JvOptionPane.showMessageDialog(ap, + MessageManager.getString( + "label.spaces_converted_to_underscores"), + MessageManager.getString( + "label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); + } + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false, false); + } + sequence.setDescription(dialog.getDescription()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + }); } /** @@ -2189,24 +1922,23 @@ public class PopupMenu extends JPopupMenu } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Offers a colour chooser and sets the selected colour as the group outline */ protected void outline_actionPerformed() { - SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_outline_colour"), - Color.BLUE); - - if (col != null) + String title = MessageManager + .getString("label.select_outline_colour"); + ColourChooserListener listener = new ColourChooserListener() { - sg.setOutlineColour(col); - } - - refresh(); + @Override + public void colourSelected(Color c) + { + getGroup().setOutlineColour(c); + refresh(); + }; + }; + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), + title, Color.BLUE, listener); } /** @@ -2252,10 +1984,10 @@ 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(); } @@ -2268,12 +2000,12 @@ public class PopupMenu extends JPopupMenu public void copy_actionPerformed() { - ap.alignFrame.copy_actionPerformed(null); + ap.alignFrame.copy_actionPerformed(); } public void cut_actionPerformed() { - ap.alignFrame.cut_actionPerformed(null); + ap.alignFrame.cut_actionPerformed(); } void changeCase(ActionEvent e) @@ -2311,8 +2043,8 @@ 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()); } } @@ -2321,9 +2053,9 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", - new Object[] { e.getActionCommand() }), 600, 500); + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] + { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2331,8 +2063,10 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(), - ap, true)); + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); + cap.setText( + new FormatAdapter(ap).formatSequences(fileFormat, ap, true)); } public void sequenceFeature_actionPerformed() @@ -2343,33 +2077,31 @@ public class PopupMenu extends JPopupMenu return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + int gSize = sg.getSize(); for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, start, end, null)); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; - if (ap.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()) + { + new FeatureEditor(ap, seqs, features, true).showDialog(); } } @@ -2401,7 +2133,12 @@ public class PopupMenu extends JPopupMenu } - public void editSequence_actionPerformed(ActionEvent actionEvent) + /** + * Shows a dialog where sequence characters may be edited. Any changes are + * applied, and added as an available 'Undo' item in the edit commands + * history. + */ + public void editSequence_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); @@ -2414,26 +2151,58 @@ 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); + dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_sequence"), - ap.alignFrame); - - if (dialog.accept) - { - EditCommand editCommand = new EditCommand( - MessageManager.getString("label.edit_sequences"), - Action.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), - sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); - - ap.alignFrame.addHistoryItem(editCommand); + new Runnable() + { + @Override + public void run() + { + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), + Action.REPLACE, + dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray( + ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, + ap.av.getAlignment()); + ap.alignFrame.addHistoryItem(editCommand); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + }); + } + } - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); - } + /** + * Action on user selecting an item from the colour menu (that does not have + * its bespoke action handler) + * + * @return + */ + @Override + public void changeColour_actionPerformed(String colourSchemeName) + { + SequenceGroup sg = getGroup(); + /* + * switch to the chosen colour scheme (or null for None) + */ + ColourSchemeI colourScheme = ColourSchemes.getInstance() + .getColourScheme(colourSchemeName, ap.av, sg, + ap.av.getHiddenRepSequences()); + sg.setColourScheme(colourScheme); + if (colourScheme instanceof Blosum62ColourScheme + || colourScheme instanceof PIDColourScheme) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); } + + refresh(); } }