X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3c32180ed65672a53b5ca215ae77487d7b7fdb9f;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=8a37952d68e363dea01d81db84cf8b9f2574d854;hpb=0b573ed90b14079f7326281f50c0c9cffdace586;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 8a37952..3c32180 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,12 +20,43 @@ */ package jalview.gui; +import java.util.Locale; + +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.Objects; +import java.util.SortedMap; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; + import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; import jalview.api.AlignViewportI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; @@ -35,11 +66,13 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; import jalview.datamodel.PDBEntry; +import jalview.datamodel.ResidueCount; 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.CountReader; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FormatAdapter; @@ -58,35 +91,8 @@ import jalview.util.StringUtils; import jalview.util.UrlLink; import jalview.viewmodel.seqfeatures.FeatureRendererModel; -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.Objects; -import java.util.SortedMap; -import java.util.TreeMap; -import java.util.Vector; - -import javax.swing.ButtonGroup; -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JInternalFrame; -import javax.swing.JLabel; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JPanel; -import javax.swing.JPopupMenu; -import javax.swing.JRadioButtonMenuItem; -import javax.swing.JScrollPane; - +import java.io.IOException; +import java.net.MalformedURLException; /** * The popup menu that is displayed on right-click on a sequence id, or in the * sequence alignment. @@ -94,6 +100,11 @@ import javax.swing.JScrollPane; public class PopupMenu extends JPopupMenu implements ColourChangeListener { /* + * maximum length of feature description to include in popup menu item text + */ + private static final int FEATURE_DESC_MAX = 40; + + /* * true for ID Panel menu, false for alignment panel menu */ private final boolean forIdPanel; @@ -223,13 +234,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener urlLink = new UrlLink(link); } catch (Exception foo) { - Cache.log.error("Exception for URLLink '" + link + "'", foo); + Console.error("Exception for URLLink '" + link + "'", foo); continue; } if (!urlLink.isValid()) { - Cache.log.error(urlLink.getInvalidMessage()); + Console.error(urlLink.getInvalidMessage()); continue; } @@ -296,7 +307,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE); @@ -540,6 +551,35 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } + if (seq.hasHMMProfile()) + { + menuItem = new JMenuItem(MessageManager + .getString("action.add_background_frequencies")); + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + ResidueCount counts = CountReader.getBackgroundFrequencies(ap, + seq); + if (counts != null) + { + seq.getHMM().setBackgroundFrequencies(counts); + ap.alignFrame.buildColourMenu(); + } + } catch (MalformedURLException e1) + { + e1.printStackTrace(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + add(menuItem); + } menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new ActionListener() @@ -663,8 +703,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { buildGroupURLMenu(sg, groupLinks); } + // TODO REMOVE FOR 2.12 ? // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + Hashtable pdbe = new Hashtable<>(); + Hashtable reppdb = new Hashtable<>(); SequenceI sqass = null; for (SequenceI sq : alignPanel.av.getSequenceSelection()) @@ -756,14 +798,16 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * Add a link to show feature details for each sequence feature + * Add a menu item to show feature details for each sequence feature. Any + * linked 'virtual' features (CDS/protein) are also optionally found and + * included. * * @param features - * @param column * @param seq + * @param column */ protected void addFeatureDetails(List features, - SequenceI seq, int column) + final SequenceI seq, final int column) { /* * add features in CDS/protein complement at the corresponding @@ -798,82 +842,98 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener String name = seq.getName(); for (final SequenceFeature sf : features) { - addFeatureDetailsMenuItem(details, name, sf); + addFeatureDetailsMenuItem(details, name, sf, null); } if (mf != null) { - name = mf.fromSeq == seq ? mf.mapping.getTo().getName() - : mf.fromSeq.getName(); for (final SequenceFeature sf : mf.features) { - addFeatureDetailsMenuItem(details, name, sf); + addFeatureDetailsMenuItem(details, name, sf, mf); } } } /** - * A helper method to add one menu item whose action is to show details for one - * feature + * A helper method to add one menu item whose action is to show details for + * one feature. The menu text includes feature description, but this may be + * truncated. * * @param details * @param seqName * @param sf + * @param mf */ void addFeatureDetailsMenuItem(JMenu details, final String seqName, - final SequenceFeature sf) + final SequenceFeature sf, MappedFeatures mf) { int start = sf.getBegin(); int end = sf.getEnd(); - String desc = null; - if (start == end) + if (mf != null) { - desc = String.format("%s %d", sf.getType(), start); + /* + * show local rather than linked feature coordinates + */ + int[] localRange = mf.getMappedPositions(start, end); + if (localRange == null) + { + // e.g. variant extending to stop codon so not mappable + return; + } + start = localRange[0]; + end = localRange[localRange.length - 1]; } - else + StringBuilder desc = new StringBuilder(); + desc.append(sf.getType()).append(" ").append(String.valueOf(start)); + if (start != end) { - desc = String.format("%s %d-%d", sf.getType(), start, end); + desc.append(sf.isContactFeature() ? ":" : "-"); + desc.append(String.valueOf(end)); } - String tooltip = desc; String description = sf.getDescription(); if (description != null) { + desc.append(" "); description = StringUtils.stripHtmlTags(description); - if (description.length() > 12) - { - desc = desc + " " + description.substring(0, 12) + ".."; - } - else + + /* + * truncate overlong descriptions unless they contain an href + * (as truncation could leave corrupted html) + */ + boolean hasLink = description.indexOf("a href") > -1; + if (description.length() > FEATURE_DESC_MAX && !hasLink) { - desc = desc + " " + description; + description = description.substring(0, FEATURE_DESC_MAX) + "..."; } - tooltip = tooltip + " " + description; + desc.append(description); } - if (sf.getFeatureGroup() != null) + String featureGroup = sf.getFeatureGroup(); + if (featureGroup != null) { - tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")"); + desc.append(" (").append(featureGroup).append(")"); } - JMenuItem item = new JMenuItem(desc); - item.setToolTipText(tooltip); + String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString()); + JMenuItem item = new JMenuItem(htmlText); item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - showFeatureDetails(seqName, sf); + showFeatureDetails(sf, seqName, mf); } }); details.add(item); } /** - * Opens a panel showing a text report of feature dteails - * - * @param seqName + * Opens a panel showing a text report of feature details * * @param sf + * @param seqName + * @param mf */ - protected void showFeatureDetails(String seqName, SequenceFeature sf) + protected void showFeatureDetails(SequenceFeature sf, String seqName, + MappedFeatures mf) { JInternalFrame details; if (Platform.isJS()) @@ -885,7 +945,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener // TODO JAL-3026 set style of table correctly for feature details JLabel reprt = new JLabel(MessageManager .formatMessage("label.html_content", new Object[] - { sf.getDetailsReport(seqName) })); + { sf.getDetailsReport(seqName, mf) })); reprt.setBackground(Color.WHITE); reprt.setOpaque(true); panel.add(reprt, BorderLayout.CENTER); @@ -900,10 +960,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - // it appears Java's CSS does not support border-collaps :-( + // it appears Java's CSS does not support border-collapse :-( cap.addStylesheetRule("table { border-collapse: collapse;}"); cap.addStylesheetRule("table, td, th {border: 1px solid black;}"); - cap.setText(sf.getDetailsReport(seqName)); + cap.setText(sf.getDetailsReport(seqName, mf)); details = cap; } Desktop.addInternalFrame(details, @@ -1106,7 +1166,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener for (int d = 0; d < nd; d++) { DBRefEntry e = dbr.get(d); - String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); + String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT); Object[] sarray = commonDbrefs.get(src); if (sarray == null) { @@ -1140,19 +1200,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener urlLink = new GroupUrlLink(link); } catch (Exception foo) { - Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); + Console.error("Exception for GroupURLLink '" + link + "'", foo); continue; } if (!urlLink.isValid()) { - Cache.log.error(urlLink.getInvalidMessage()); + Console.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 = commonDbrefs.get(ltarget.toUpperCase()); + Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT)); String[] seqstr, ids; // input to makeUrl if (idset != null) { @@ -1788,8 +1848,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener contents.append("

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

"); - new SequenceAnnotationReport(null).createSequenceAnnotationReport( + { seq.getDisplayId(true) }) + "

\n

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

"); } @@ -2021,8 +2081,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener ap.paintAlignment(false, false); } sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.notifyAlignment(); } }); } @@ -2064,7 +2123,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } }; - JalviewColourChooser.showColourChooser(Desktop.getDesktop(), + JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), title, Color.BLUE, listener); } @@ -2153,9 +2212,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener startEnd, caseChange); ap.alignFrame.addHistoryItem(caseCommand); + ap.av.notifyAlignment(); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); } } @@ -2262,8 +2320,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment()); ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + ap.av.notifyAlignment(); } }); }