X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=86febed3100cf399ada7722a76b9f72a226d3ce0;hb=16d109024847af92482237e43f99b82fd997451a;hp=9bc2ca1d4c337920d5054034d71162022f7d7a18;hpb=b3cd7fa160c1323a80af9dd69d13e1a45e7c189c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 9bc2ca1..86febed 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -34,7 +34,6 @@ import jalview.datamodel.Annotation; 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; @@ -47,9 +46,11 @@ import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; +import jalview.util.StringUtils; import jalview.util.UrlLink; import java.awt.Color; @@ -68,11 +69,13 @@ 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.JMenu; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; /** * DOCUMENT ME! @@ -92,6 +95,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem annotationColour; + protected JMenuItem modifyConservation = new JMenuItem(); AlignmentPanel ap; @@ -176,25 +181,31 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * 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 @@ -202,7 +213,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener // // If from the IDPanel, we must display the sequence menu // //////////////////////////////////////////////////////// - this.ap = ap; + this.ap = alignPanel; sequence = seq; for (String ff : FileFormats.getInstance().getWritableFormats(true)) @@ -237,9 +248,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (ap.av.getSelectionGroup() == null + final List selectedGroup = (alignPanel.av.getSelectionGroup() == null ? Collections. emptyList() - : ap.av.getSelectionGroup().getSequences()); + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -257,7 +268,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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")); @@ -268,7 +279,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager.getString("action.set_as_reference")); } - if (!ap.av.getAlignment().isNucleotide()) + if (!alignPanel.av.getAlignment().isNucleotide()) { remove(rnaStructureMenu); } @@ -279,7 +290,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * 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) { @@ -299,7 +310,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @Override public void actionPerformed(ActionEvent e) { - new AppVarna(seq, aa, ap); + new AppVarna(seq, aa, alignPanel); } }); rnaStructureMenu.add(menuItem); @@ -328,7 +339,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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); @@ -353,8 +364,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener }); 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[] @@ -370,12 +381,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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")); @@ -384,10 +395,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @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(); } } }); @@ -395,9 +406,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } } - // 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")); @@ -406,21 +428,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @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(); + SequenceGroup sg = alignPanel.av.getSelectionGroup(); boolean isDefinedGroup = (sg != null) - ? ap.av.getAlignment().getGroups().contains(sg) + ? alignPanel.av.getAlignment().getGroups().contains(sg) : false; if (sg != null && sg.getSize() > 0) @@ -458,7 +479,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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) @@ -508,24 +529,133 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener rnaStructureMenu.setVisible(false); } - if (links != null && links.size() > 0) + addLinks(seq, features); + + if (seq == null) { - addFeatureLinks(seq, links); + 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) + { + 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()); + + Desktop.addInternalFrame(cap, + MessageManager.getString("label.feature_details"), 500, 500); + } + + /** * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * When seq is not null, these are links for the sequence id, which may be to + * external web sites for the sequence accession, and/or links embedded in + * non-positional features. When seq is null, only links embedded in the + * provided features are added. * * @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 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 : links) + for (String link : nlinks) { UrlLink urlLink = null; try @@ -548,25 +678,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener addshowLinks(linkMenu, linkset.values()); - // disable link menu if there are no valid entries + // only add link menu if it has entries if (linkMenu.getItemCount() > 0) { - linkMenu.setEnabled(true); - } - else - { - linkMenu.setEnabled(false); - } - - if (sequence != null) - { - sequenceMenu.add(linkMenu); - } - else - { - add(linkMenu); + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } } - } /** @@ -1293,6 +1416,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); + 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() @@ -1323,7 +1453,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg, + false); + bg.add(annotationColour); + colourMenu.add(annotationColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1473,7 +1606,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } inserts.and(sq.getInsertionsAsBits()); } - hidden.hideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), + hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), ap.av.getSelectionGroup().getEndRes()); } @@ -1509,10 +1642,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); } cap.setText("" + contents.toString() + ""); @@ -2021,7 +2151,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * switch to the chosen colour scheme (or null for None) */ ColourSchemeI colourScheme = ColourSchemes.getInstance() - .getColourScheme(colourSchemeName, sg, + .getColourScheme(colourSchemeName, ap.av, sg, ap.av.getHiddenRepSequences()); sg.setColourScheme(colourScheme); if (colourScheme instanceof Blosum62ColourScheme