X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=8c758b3a8ab5c2a1aa64db8ef3fa3cfc1c5fd32d;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=d71fdd4318d6c918b7f93a6f6aed0ca9d2b476a6;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index d71fdd4..8c758b3 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,22 +20,6 @@ */ package jalview.appletgui; -import java.awt.CheckboxMenuItem; -import java.awt.Frame; -import java.awt.Menu; -import java.awt.MenuItem; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.util.Arrays; -import java.util.Collections; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.TreeMap; -import java.util.Vector; - import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; @@ -67,6 +51,22 @@ import jalview.schemes.ZappoColourScheme; import jalview.util.MessageManager; import jalview.util.UrlLink; +import java.awt.CheckboxMenuItem; +import java.awt.Frame; +import java.awt.Menu; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.util.Arrays; +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; + public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener { @@ -175,13 +175,13 @@ public class APopupMenu extends java.awt.PopupMenu implements MessageManager.getString("label.edit_sequence")); MenuItem sequenceDetails = new MenuItem( - MessageManager.getString("label.sequence_details") + "..."); + MessageManager.getString("label.sequence_details")); MenuItem selSeqDetails = new MenuItem( - MessageManager.getString("label.sequence_details") + "..."); + MessageManager.getString("label.sequence_details")); MenuItem makeReferenceSeq = new MenuItem(); - + SequenceI seq; MenuItem revealAll = new MenuItem(); @@ -231,8 +231,7 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null && sg.getSize() > 0) { editGroupName.setLabel(MessageManager.formatMessage( - "label.name_param", new Object[] - { sg.getName() })); + "label.name_param", new Object[] { sg.getName() })); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); @@ -275,8 +274,7 @@ public class APopupMenu extends java.awt.PopupMenu implements // collect matching db-refs DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( - seq.getDBRef(), new String[] - { target }); + seq.getDBRef(), new String[] { target }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); @@ -390,8 +388,7 @@ public class APopupMenu extends java.awt.PopupMenu implements .getString("action.set_as_reference")); // ); } repGroup.setLabel(MessageManager.formatMessage( - "label.represent_group_with", new Object[] - { seq.getName() })); + "label.represent_group_with", new Object[] { seq.getName() })); } else { @@ -720,7 +717,8 @@ public class APopupMenu extends java.awt.PopupMenu implements if (dialog.accept) { - EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), Action.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), @@ -807,7 +805,8 @@ public class APopupMenu extends java.awt.PopupMenu implements features, true, ap)) { ap.alignFrame.sequenceFeatures.setState(true); - ap.av.setShowSequenceFeatures(true);; + ap.av.setShowSequenceFeatures(true); + ; ap.highlightSearchResults(null); } } @@ -825,14 +824,14 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.selection_output_command", new Object[] - { e.getActionCommand() }), 600, 500); + "label.selection_output_command", + new Object[] { e.getActionCommand() }), 600, 500); // JBPNote: getSelectionAsNewSequence behaviour has changed - this method // now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( - e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true)); + e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true)); } @@ -843,8 +842,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void showSequenceDetails() { - createSequenceDetailsReport(new SequenceI[] - { seq }); + createSequenceDetailsReport(new SequenceI[] { seq }); } public void createSequenceDetailsReport(SequenceI[] sequences) @@ -856,17 +854,16 @@ public class APopupMenu extends java.awt.PopupMenu implements for (SequenceI seq : sequences) { contents.append(MessageManager.formatMessage( - "label.annotation_for_displayid", new Object[] - { seq.getDisplayId(true) })); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport( - contents, - seq, - true, - true, - false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() - : null); + "label.annotation_for_displayid", + new Object[] { seq.getDisplayId(true) })); + new SequenceAnnotationReport(null).createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr + .getMinMax() : null); contents.append("

"); } Frame frame = new Frame(); @@ -875,8 +872,7 @@ public class APopupMenu extends java.awt.PopupMenu implements + (sequences.length == 1 ? sequences[0].getDisplayId(true) : "Selection"), 600, 500); cap.setText(MessageManager.formatMessage("label.html_content", - new Object[] - { contents.toString() })); + new Object[] { contents.toString() })); } void editName() @@ -896,19 +892,19 @@ public class APopupMenu extends java.awt.PopupMenu implements void addPDB() { - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement(); + PDBEntry entry = seq.getAllPDBEntries().firstElement(); if (ap.av.applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(entry, new SequenceI[] - { seq }, null, ap, AppletFormatAdapter.URL); + new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq }, + null, ap, AppletFormatAdapter.URL); } else { - new MCview.AppletPDBViewer(entry, new SequenceI[] - { seq }, null, ap, AppletFormatAdapter.URL); + new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, + ap, AppletFormatAdapter.URL); } } @@ -920,8 +916,8 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.paste_pdb_file_for_sequence", new Object[] - { seq.getName() }), 400, 300); + "label.paste_pdb_file_for_sequence", + new Object[] { seq.getName() }), 400, 300); } } @@ -964,8 +960,7 @@ public class APopupMenu extends java.awt.PopupMenu implements pdb.setLabel(MessageManager.getString("label.view_pdb_structure")); hideSeqs.setLabel(MessageManager.getString("action.hide_sequences")); repGroup.setLabel(MessageManager.formatMessage( - "label.represent_group_with", new Object[] - { "" })); + "label.represent_group_with", new Object[] { "" })); revealAll.setLabel(MessageManager.getString("action.reveal_all")); revealSeq.setLabel(MessageManager.getString("action.reveal_sequences")); menu1.setLabel(MessageManager.getString("label.group") + ":"); @@ -1005,31 +1000,39 @@ public class APopupMenu extends java.awt.PopupMenu implements noColourmenuItem.setLabel(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(this); - clustalColour.setLabel(MessageManager.getString("label.clustalx_colours")); + clustalColour.setLabel(MessageManager + .getString("label.clustalx_colours")); clustalColour.addActionListener(this); zappoColour.setLabel(MessageManager.getString("label.zappo")); zappoColour.addActionListener(this); taylorColour.setLabel(MessageManager.getString("label.taylor")); taylorColour.addActionListener(this); - hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity")); + hydrophobicityColour.setLabel(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour.addActionListener(this); - helixColour.setLabel(MessageManager.getString("label.helix_propensity")); + helixColour + .setLabel(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(this); - strandColour.setLabel(MessageManager.getString("label.strand_propensity")); + strandColour.setLabel(MessageManager + .getString("label.strand_propensity")); strandColour.addActionListener(this); turnColour.setLabel(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(this); buriedColour.setLabel(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(this); - abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage")); + abovePIDColour.setLabel(MessageManager + .getString("label.above_identity_percentage")); - userDefinedColour.setLabel(MessageManager.getString("action.user_defined")); + userDefinedColour.setLabel(MessageManager + .getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel(MessageManager.getString("action.percentage_identity")); + PIDColour.setLabel(MessageManager + .getString("label.percentage_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62"); BLOSUM62Colour.addActionListener(this); - conservationMenuItem.setLabel(MessageManager.getString("label.conservation")); + conservationMenuItem.setLabel(MessageManager + .getString("label.conservation")); editMenu.add(copy); copy.addActionListener(this); @@ -1258,6 +1261,7 @@ public class APopupMenu extends java.awt.PopupMenu implements getGroup().setDisplayText(showText.getState()); refresh(); } + public void makeReferenceSeq_actionPerformed() { if (!ap.av.getAlignment().hasSeqrep()) @@ -1298,8 +1302,7 @@ public class APopupMenu extends java.awt.PopupMenu implements SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg.getSize() < 1) { - ap.av.hideSequence(new SequenceI[] - { seq }); + ap.av.hideSequence(new SequenceI[] { seq }); return; } @@ -1347,17 +1350,17 @@ public class APopupMenu extends java.awt.PopupMenu implements { showMenu.removeAll(); hideMenu.removeAll(); - + final List all = Arrays.asList(ALL_ANNOTATIONS); addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); showMenu.addSeparator(); hideMenu.addSeparator(); - + final AlignmentAnnotation[] annotations = ap.getAlignment() .getAlignmentAnnotation(); - + /* * Find shown/hidden annotations types, distinguished by source (calcId), * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in @@ -1366,28 +1369,26 @@ public class APopupMenu extends java.awt.PopupMenu implements */ Map>> shownTypes = new LinkedHashMap>>(); Map>> hiddenTypes = new LinkedHashMap>>(); - AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, - hiddenTypes, - AlignmentAnnotationUtils.asList(annotations), - forSequences); - + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), forSequences); + for (String calcId : hiddenTypes.keySet()) { for (List type : hiddenTypes.get(calcId)) { - addAnnotationTypeToShowHide(showMenu, forSequences, - calcId, type, false, true); + addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type, + false, true); } } // grey out 'show annotations' if none are hidden showMenu.setEnabled(!hiddenTypes.isEmpty()); - + for (String calcId : shownTypes.keySet()) { for (List type : shownTypes.get(calcId)) { - addAnnotationTypeToShowHide(hideMenu, forSequences, - calcId, type, false, false); + addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type, + false, false); } } // grey out 'hide annotations' if none are shown @@ -1424,8 +1425,8 @@ public class APopupMenu extends java.awt.PopupMenu implements @Override public void actionPerformed(ActionEvent e) { - AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, - forSequences, allTypes, actionIsShow); + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), + types, forSequences, allTypes, actionIsShow); refresh(); } });