X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=07b8d168854270c04456f8291fbfe3f1a0930722;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=038477f169aaf831aa05dc39ac9558c431c6c484;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 038477f..07b8d16 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. @@ -20,23 +20,67 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.Conservation; +import jalview.commands.ChangeCaseCommand; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +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.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.Hashtable; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + /** * DOCUMENT ME! * @@ -45,6 +89,10 @@ import jalview.util.UrlLink; */ public class PopupMenu extends JPopupMenu { + private static final String ALL_ANNOTATIONS = "All"; + + private static final String COMMA = ","; + JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -74,6 +122,7 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); + protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); // protected JRadioButtonMenuItem covariationColour = new @@ -92,9 +141,15 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); + + JMenuItem makeReferenceSeq = new JMenuItem(); + + JMenuItem chooseAnnotations = new JMenuItem(); SequenceI sequence; + JMenuItem createGroupMenuItem = new JMenuItem(); + JMenuItem unGroupMenuItem = new JMenuItem(); JMenuItem outline = new JMenuItem(); @@ -126,17 +181,31 @@ public class PopupMenu extends JPopupMenu JMenu pdbMenu = new JMenu(); JMenuItem pdbFromFile = new JMenuItem(); - // JBPNote: Commented these out - Should add these services via the web services menu system. - // JMenuItem ContraFold = new JMenuItem(); - - // JMenuItem RNAFold = new JMenuItem(); - + + // JBPNote: Commented these out - Should add these services via the web + // services menu system. + // JMenuItem ContraFold = new JMenuItem(); + + // JMenuItem RNAFold = new JMenuItem(); + JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); JMenu outputMenu = new JMenu(); + JMenu seqShowAnnotationsMenu = new JMenu(); + + JMenu seqHideAnnotationsMenu = new JMenu(); + + JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + + JMenu groupShowAnnotationsMenu = new JMenu(); + + JMenu groupHideAnnotationsMenu = new JMenu(); + + JMenuItem groupAddReferenceAnnotations = new JMenuItem(); + JMenuItem sequenceFeature = new JMenuItem(); JMenuItem textColour = new JMenuItem(); @@ -154,6 +223,8 @@ public class PopupMenu extends JPopupMenu JMenu groupLinksMenu; + JMenuItem hideInsertions = new JMenuItem(); + /** * Creates a new PopupMenu object. * @@ -211,6 +282,7 @@ public class PopupMenu extends JPopupMenu item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -220,6 +292,29 @@ public class PopupMenu extends JPopupMenu outputMenu.add(item); } + /* + * Build menus for annotation types that may be shown or hidden, and for + * '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)); + buildAnnotationTypesMenus(seqShowAnnotationsMenu, + seqHideAnnotationsMenu, selectedSequence); + configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, + selectedSequence); + + /* + * And repeat for the current selection group (if there is one): + */ + final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections + . emptyList() : ap.av.getSelectionGroup() + .getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); + try { jbInit(); @@ -232,6 +327,12 @@ public class PopupMenu extends JPopupMenu if (seq != null) { sequenceMenu.setText(sequence.getName()); + if (seq == ap.av.getAlignment().getSeqrep()) + { + makeReferenceSeq.setText("Unmark representative"); + } else { + makeReferenceSeq.setText("Mark as representative"); + } if (seq.getDatasetSequence().getPDBId() != null && seq.getDatasetSequence().getPDBId().size() > 0) @@ -245,17 +346,20 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO re JAL-860: optionally open dialog or provide a menu entry // allowing user to open just one structure per sequence - new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] - { pdb })[0], null, ap); - // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); + // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] + // { pdb })[0], null, ap); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(pdb, + ap.av.collateForPDB(new PDBEntry[] + { pdb })[0], null, ap); } - }); viewStructureMenu.add(menuItem); @@ -276,37 +380,39 @@ public class PopupMenu extends JPopupMenu } // structureMenu.remove(colStructureMenu); } - if (ap.av.getAlignment().isNucleotide() == true) { AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - for (int i = 0; i < aa.length; i++) + for (int i = 0; aa != null && i < aa.length; i++) { - if (aa[i].getRNAStruc() != null) + if (aa[i].isValidStruc() && aa[i].sequenceRef == null) { final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label; + final String structureLine = aa[i].label + " (alignment)"; menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine})); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_structure_line", new String[] + { structureLine })); menuItem.addActionListener(new java.awt.event.ActionListener() - { + @Override public void actionPerformed(ActionEvent e) { - //System.out.println("1:"+structureLine); - System.out.println("1:sname"+seq.getName()); - System.out.println("2:seq"+seq); - - //System.out.println("3:"+seq.getSequenceAsString()); - System.out.println("3:strucseq"+rnastruc); - //System.out.println("4:struc"+seq.getRNA()); - System.out.println("5:name"+seq.getName()); - System.out.println("6:ap"+ap); - new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq - .getName(), ap); - //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap); - System.out.println("end"); + // // System.out.println("1:"+structureLine); + // System.out.println("1:sname" + seq.getName()); + // System.out.println("2:seq" + seq); + // + // // System.out.println("3:"+seq.getSequenceAsString()); + // System.out.println("3:strucseq" + rnastruc); + // // System.out.println("4:struc"+seq.getRNA()); + // System.out.println("5:name" + seq.getName()); + // System.out.println("6:ap" + ap); + new AppVarna(structureLine, seq, seq.getSequenceAsString(), + rnastruc, seq.getName(), ap); + // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), + // seq.getName(), ap); + System.out.println("end"); } }); viewStructureMenu.add(menuItem); @@ -320,19 +426,22 @@ public class PopupMenu extends JPopupMenu AlignmentAnnotation seqAnno[] = seq.getAnnotation(); for (int i = 0; i < seqAnno.length; i++) { - if (seqAnno[i].getRNAStruc() != null) + if (seqAnno[i].isValidStruc()) { final String rnastruc = seqAnno[i].getRNAStruc(); // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); - menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()})); + menuItem.setText(MessageManager.formatMessage( + "label.2d_rna_sequence_name", new String[] + { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - + new AppVarna(seq.getName() + " structure", seq, seq .getSequenceAsString(), rnastruc, seq.getName(), ap); @@ -342,12 +451,13 @@ public class PopupMenu extends JPopupMenu } } } - } - menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences")); + menuItem = new JMenuItem( + MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(false); @@ -358,9 +468,12 @@ public class PopupMenu extends JPopupMenu if (ap.av.getSelectionGroup() != null && ap.av.getSelectionGroup().getSize() > 1) { - menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()})); + menuItem = new JMenuItem(MessageManager.formatMessage( + "label.represent_group_with", new String[] + { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(true); @@ -376,9 +489,11 @@ public class PopupMenu extends JPopupMenu if (ap.av.adjustForHiddenSeqs(index) - ap.av.adjustForHiddenSeqs(index - 1) > 1) { - menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences")); + menuItem = new JMenuItem( + MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showSequence(index); @@ -396,9 +511,11 @@ public class PopupMenu extends JPopupMenu if (ap.av.hasHiddenRows()) { { - menuItem = new JMenuItem(MessageManager.getString("action.reveal_all")); + menuItem = new JMenuItem( + MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showAllHiddenSeqs(); @@ -415,12 +532,16 @@ public class PopupMenu extends JPopupMenu } SequenceGroup sg = ap.av.getSelectionGroup(); - boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false; + boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment() + .getGroups().contains(sg) : false; if (sg != null && sg.getSize() > 0) - { - groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()})); - groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group")); + { + groupName.setText(MessageManager.formatMessage("label.name_param", + new String[] + { sg.getName() })); + groupName.setText(MessageManager + .getString("label.edit_name_and_description_current_group")); if (sg.cs instanceof ZappoColourScheme) { @@ -470,8 +591,7 @@ public class PopupMenu extends JPopupMenu { purinePyrimidineColour.setSelected(true); } - - + /* * else if (sg.cs instanceof CovariationColourScheme) { * covariationColour.setSelected(true); } @@ -495,15 +615,14 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(),reppdb=new Hashtable(); + Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = (Vector) sq.getDatasetSequence() - .getPDBId(); - if (pes != null) + Vector pes = sq.getDatasetSequence().getPDBId(); + if (pes != null && pes.size() > 0) { - reppdb.put(pes.get(0).getId(),pes.get(0)); + reppdb.put(pes.get(0).getId(), pes.get(0)); for (PDBEntry pe : pes) { pdbe.put(pe.getId(), pe); @@ -517,38 +636,50 @@ 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 JMenuItem gpdbview,rpdbview; + new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray( + new PDBEntry[reppdb.size()]); + final JMenuItem gpdbview, rpdbview; if (pdbe.size() == 1) { - structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)}))); + structureMenu.add(gpdbview = new JMenuItem(MessageManager + .formatMessage("label.view_structure_for", new String[] + { sqass.getDisplayId(false) }))); } else { - structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()}))); + structureMenu.add(gpdbview = new JMenuItem(MessageManager + .formatMessage("label.view_all_structures", new String[] + { new Integer(pdbe.size()).toString() }))); } - gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); + gpdbview.setToolTipText(MessageManager + .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment")); gpdbview.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - new AppJmol(ap, pe, ap.av.collateForPDB(pe)); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(ap, pe, ap.av.collateForPDB(pe)); } }); - if (reppdb.size()>1 && reppdb.size() 1 && reppdb.size() < pdbe.size()) { - structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()}))); - rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); + structureMenu.add(rpdbview = new JMenuItem(MessageManager + .formatMessage( + "label.view_all_representative_structures", + new String[] + { new Integer(reppdb.size()).toString() }))); + rpdbview.setToolTipText(MessageManager + .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment")); rpdbview.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - new AppJmol(ap, pr, ap.av.collateForPDB(pr)); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(ap, pr, ap.av.collateForPDB(pr)); } }); } @@ -565,7 +696,9 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); jMenu1.setText(MessageManager.getString("action.edit_new_group")); - } else { + } + else + { createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); jMenu1.setText(MessageManager.getString("action.edit_group")); @@ -700,6 +833,162 @@ public class PopupMenu extends JPopupMenu } } + /** + * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. + * "All" is added first, followed by a separator. Then add any annotation + * types associated with the current selection. Separate menus are built for + * the selected sequence group (if any), and the selected sequence. + *

+ * Some annotation rows are always rendered together - these can be identified + * by a common graphGroup property > -1. Only one of each group will be marked + * as visible (to avoid duplication of the display). For such groups we add a + * composite type name, e.g. + *

+ * IUPredWS (Long), IUPredWS (Short) + * + * @param seq + */ + protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu, + List forSequences) + { + 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 + * the insertion order, which is the order of the annotations on the + * alignment. + */ + Map>> shownTypes = new LinkedHashMap>>(); + Map>> hiddenTypes = new LinkedHashMap>>(); + AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, + hiddenTypes, + AlignmentAnnotationUtils.asList(annotations), + forSequences); + + for (String calcId : hiddenTypes.keySet()) + { + for (List type : hiddenTypes.get(calcId)) + { + 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); + } + } + // grey out 'hide annotations' if none are shown + hideMenu.setEnabled(!shownTypes.isEmpty()); + } + + /** + * Returns a list of sequences - either the current selection group (if there + * is one), else the specified single sequence. + * + * @param seq + * @return + */ + protected List getSequenceScope(SequenceI seq) + { + List forSequences = null; + final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); + if (selectionGroup != null && selectionGroup.getSize() > 0) + { + forSequences = selectionGroup.getSequences(); + } + else + { + forSequences = seq == null ? Collections. emptyList() + : Arrays.asList(seq); + } + return forSequences; + } + + /** + * Add one annotation type to the 'Show Annotations' or 'Hide Annotations' + * menus. + * + * @param showOrHideMenu + * the menu to add to + * @param forSequences + * the sequences whose annotations may be shown or hidden + * @param calcId + * @param types + * the label to add + * @param allTypes + * if true this is a special label meaning 'All' + * @param actionIsShow + * if true, the select menu item action is to show the annotation + * type, else hide + */ + protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu, + final List forSequences, String calcId, + final List types, final boolean allTypes, + final boolean actionIsShow) + { + String label = types.toString(); // [a, b, c] + label = label.substring(1, label.length() - 1); + final JMenuItem item = new JMenuItem(label); + item.setToolTipText(calcId); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showHideAnnotation_actionPerformed(types, forSequences, allTypes, + actionIsShow); + } + }); + showOrHideMenu.add(item); + } + + /** + * Action on selecting a list of annotation type (or the 'all types' values) + * to show or hide for the specified sequences. + * + * @param types + * @param forSequences + * @param anyType + * @param doShow + */ + protected void showHideAnnotation_actionPerformed( + Collection types, List forSequences, + boolean anyType, boolean doShow) + { + for (AlignmentAnnotation aa : ap.getAlignment() + .getAlignmentAnnotation()) + { + if (anyType || types.contains(aa.label)) + { + if ((aa.sequenceRef != null) + && forSequences.contains(aa.sequenceRef)) + { + aa.visible = doShow; + } + } + } + refresh(); + } + private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { @@ -707,11 +996,18 @@ public class PopupMenu extends JPopupMenu // menu appears asap // sequence only URLs // ID/regex match URLs - groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); + groupLinksMenu = new JMenu( + MessageManager.getString("action.group_link")); JMenu[] linkMenus = new JMenu[] - { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")), - new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be - // created. + { null, new JMenu(MessageManager.getString("action.ids")), + new JMenu(MessageManager.getString("action.sequences")), + new JMenu(MessageManager.getString("action.ids_sequences")) }; // three + // types + // of url + // that + // might + // be + // created. SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); Hashtable commonDbrefs = new Hashtable(); @@ -833,7 +1129,8 @@ public class PopupMenu extends JPopupMenu } if (addMenu) { - groupLinksMenu = new JMenu(MessageManager.getString("action.group_link")); + groupLinksMenu = new JMenu( + MessageManager.getString("action.group_link")); for (int m = 0; m < linkMenus.length; m++) { if (linkMenus[m] != null @@ -859,14 +1156,18 @@ 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 String[]{url})); + item.setToolTipText(MessageManager.formatMessage( + "label.open_url_param", new String[] + { url })); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { showLink(url); @@ -894,15 +1195,21 @@ 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(),urlgenerator.getNumberInvolved(urlstub)})); + item.setToolTipText(MessageManager.formatMessage( + "label.open_url_seqs_param", + new Object[] + { urlgenerator.getUrl_prefix(), + urlgenerator.getNumberInvolved(urlstub) })); // TODO: put in info about what is being sent. item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { try @@ -933,66 +1240,91 @@ public class PopupMenu extends JPopupMenu groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { groupName_actionPerformed(); } }); sequenceMenu.setText(MessageManager.getString("label.sequence")); - sequenceName.setText(MessageManager.getString("label.edit_name_description")); + sequenceName.setText(MessageManager + .getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceName_actionPerformed(); } }); - sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + chooseAnnotations.setText(MessageManager + .getString("label.choose_annotations") + "..."); + chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + chooseAnnotations_actionPerformed(e); + } + }); + sequenceDetails.setText(MessageManager + .getString("label.sequence_details") + "..."); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceDetails_actionPerformed(); } }); - sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "..."); + 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); - unGroupMenuItem.setText(MessageManager.getString("action.remove_group")); + unGroupMenuItem + .setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { unGroupMenuItem_actionPerformed(); } }); - createGroupMenuItem.setText(MessageManager.getString("action.create_group")); - createGroupMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - createGroupMenuItem_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() { + @Override public void actionPerformed(ActionEvent e) { outline_actionPerformed(); } }); - nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide")); + nucleotideMenuItem + .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideMenuItem_actionPerformed(); @@ -1003,6 +1335,7 @@ public class PopupMenu extends JPopupMenu showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showBoxes_actionPerformed(); @@ -1012,6 +1345,7 @@ public class PopupMenu extends JPopupMenu showText.setState(true); showText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showText_actionPerformed(); @@ -1020,15 +1354,18 @@ public class PopupMenu extends JPopupMenu showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showColourText_actionPerformed(); } }); - displayNonconserved.setText(MessageManager.getString("label.show_non_conversed")); + displayNonconserved.setText(MessageManager + .getString("label.show_non_conversed")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showNonconserved_actionPerformed(); @@ -1038,6 +1375,7 @@ public class PopupMenu extends JPopupMenu cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(); @@ -1046,6 +1384,7 @@ public class PopupMenu extends JPopupMenu upperCase.setText(MessageManager.getString("label.to_upper_case")); upperCase.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1054,6 +1393,7 @@ public class PopupMenu extends JPopupMenu copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(); @@ -1062,6 +1402,7 @@ public class PopupMenu extends JPopupMenu lowerCase.setText(MessageManager.getString("label.to_lower_case")); lowerCase.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1070,49 +1411,53 @@ public class PopupMenu extends JPopupMenu toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); } }); - pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence")); + pdbMenu.setText(MessageManager + .getString("label.associate_structure_with_sequence")); pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pdbFromFile_actionPerformed(); } }); -// RNAFold.setText("From RNA Fold with predict2D"); -// RNAFold.addActionListener(new ActionListener() -// { -// public void actionPerformed(ActionEvent e) -// { -// try { -// RNAFold_actionPerformed(); -// } catch (Exception e1) { -// // TODO Auto-generated catch block -// e1.printStackTrace(); -// } -// } -// }); -// ContraFold.setText("From Contra Fold with predict2D"); -// ContraFold.addActionListener(new ActionListener() -// { -// public void actionPerformed(ActionEvent e) -// { -// try { -// ContraFold_actionPerformed(); -// } catch (Exception e1) { -// // TODO Auto-generated catch block -// e1.printStackTrace(); -// } -// } -// }); + // RNAFold.setText("From RNA Fold with predict2D"); + // RNAFold.addActionListener(new ActionListener() + // { + // public void actionPerformed(ActionEvent e) + // { + // try { + // RNAFold_actionPerformed(); + // } catch (Exception e1) { + // // TODO Auto-generated catch block + // e1.printStackTrace(); + // } + // } + // }); + // ContraFold.setText("From Contra Fold with predict2D"); + // ContraFold.addActionListener(new ActionListener() + // { + // public void actionPerformed(ActionEvent e) + // { + // try { + // ContraFold_actionPerformed(); + // } catch (Exception e1) { + // // TODO Auto-generated catch block + // e1.printStackTrace(); + // } + // } + // }); enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { enterPDB_actionPerformed(); @@ -1121,15 +1466,27 @@ public class PopupMenu extends JPopupMenu discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); discoverPDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { discoverPDB_actionPerformed(); } }); - outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); - 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 public void actionPerformed(ActionEvent e) { sequenceFeature_actionPerformed(); @@ -1138,6 +1495,7 @@ public class PopupMenu extends JPopupMenu textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(); @@ -1145,17 +1503,41 @@ public class PopupMenu extends JPopupMenu }); jMenu1.setText(MessageManager.getString("label.group")); structureMenu.setText(MessageManager.getString("label.structure")); - viewStructureMenu.setText(MessageManager.getString("label.view_structure")); + viewStructureMenu.setText(MessageManager + .getString("label.view_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); } }); + makeReferenceSeq.setText(MessageManager + .getString("label.mark_as_representative")); + makeReferenceSeq.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent actionEvent) + { + makeReferenceSeq_actionPerformed(actionEvent); + + } + }); + hideInsertions.setText(MessageManager.getString("label.hide_insertions")); + hideInsertions.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideInsertions_actionPerformed(e); + } + }); /* * annotationMenuItem.setText("By Annotation"); * annotationMenuItem.addActionListener(new ActionListener() { public void @@ -1165,7 +1547,24 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - this.add(structureMenu); + add(structureMenu); + if (sequence!=null) + { + add(hideInsertions); + } + // annotations configuration panel suppressed for now + // groupMenu.add(chooseAnnotations); + + /* + * Add show/hide annotations to the Sequence menu, and to the Selection menu + * (if a selection group is in force). + */ + sequenceMenu.add(seqShowAnnotationsMenu); + sequenceMenu.add(seqHideAnnotationsMenu); + sequenceMenu.add(seqAddReferenceAnnotations); + groupMenu.add(groupShowAnnotationsMenu); + groupMenu.add(groupHideAnnotationsMenu); + groupMenu.add(groupAddReferenceAnnotations); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); @@ -1174,6 +1573,7 @@ public class PopupMenu extends JPopupMenu groupMenu.add(jMenu1); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); + sequenceMenu.add(makeReferenceSeq); colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); @@ -1187,10 +1587,11 @@ public class PopupMenu extends JPopupMenu colourMenu.add(turnColour); colourMenu.add(buriedColour); colourMenu.add(nucleotideMenuItem); - if (ap.getAlignment().isNucleotide()) { - // JBPNote - commented since the colourscheme isn't functional - // colourMenu.add(RNAInteractionColour); - colourMenu.add(purinePyrimidineColour); + if (ap.getAlignment().isNucleotide()) + { + // JBPNote - commented since the colourscheme isn't functional + // colourMenu.add(RNAInteractionColour); + colourMenu.add(purinePyrimidineColour); } // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); @@ -1205,6 +1606,7 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(userColours.nextElement().toString()); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -1225,9 +1627,10 @@ public class PopupMenu extends JPopupMenu editMenu.add(lowerCase); editMenu.add(toggle); pdbMenu.add(pdbFromFile); - // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu' - // pdbMenu.add(RNAFold); - // pdbMenu.add(ContraFold); + // JBPNote: These shouldn't be added here - should appear in a generic + // 'apply web service to this sequence menu' + // pdbMenu.add(RNAFold); + // pdbMenu.add(ContraFold); pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); jMenu1.add(groupName); @@ -1243,15 +1646,18 @@ public class PopupMenu extends JPopupMenu noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(); } }); - clustalColour.setText(MessageManager.getString("label.clustalx_colours")); + clustalColour.setText(MessageManager + .getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(); @@ -1260,6 +1666,7 @@ public class PopupMenu extends JPopupMenu zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { zappoColour_actionPerformed(); @@ -1268,15 +1675,18 @@ public class PopupMenu extends JPopupMenu taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { taylorColour_actionPerformed(); } }); - hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity")); + hydrophobicityColour.setText(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(); @@ -1285,14 +1695,17 @@ public class PopupMenu extends JPopupMenu helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { helixColour_actionPerformed(); } }); - strandColour.setText(MessageManager.getString("label.strand_propensity")); + strandColour.setText(MessageManager + .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(); @@ -1301,6 +1714,7 @@ public class PopupMenu extends JPopupMenu turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { turnColour_actionPerformed(); @@ -1309,30 +1723,37 @@ public class PopupMenu extends JPopupMenu 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.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.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 + .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(); @@ -1341,32 +1762,36 @@ public class PopupMenu extends JPopupMenu 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.setText(MessageManager + .getString("label.purine_pyrimidine")); purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(); } }); - - + /* * covariationColour.addActionListener(new java.awt.event.ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(); } }); */ - conservationMenuItem.setText(MessageManager.getString("label.conservation")); + conservationMenuItem.setText(MessageManager + .getString("label.conservation")); conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(); @@ -1374,6 +1799,192 @@ public class PopupMenu extends JPopupMenu }); } + /** + * Check for any annotations on the underlying dataset sequences (for the + * current selection group) which are not 'on the alignment'.If any are found, + * enable the option to add them to the alignment. The criteria for 'on the + * alignment' is finding an alignment annotation on the alignment, matched on + * calcId, label and sequenceRef. + * + * A tooltip is also constructed that displays the source (calcId) and type + * (label) of the annotations that can be added. + * + * @param menuItem + * @param forSequences + */ + protected void configureReferenceAnnotationsMenu( + JMenuItem menuItem, List forSequences) + { + menuItem.setText(MessageManager + .getString("label.add_reference_annotations")); + menuItem.setEnabled(false); + if (forSequences == null) + { + return; + } + + /* + * Temporary store to hold distinct calcId / type pairs for the tooltip. + * Using TreeMap means calcIds are shown in alphabetical order. + */ + Map tipEntries = new TreeMap(); + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + + /* + * For each sequence selected in the alignment, make a list of any + * annotations on the underlying dataset sequence which are not already on + * the alignment. + * + * Build a map of { alignmentSequence, } + */ + AlignmentI al = this.ap.av.getAlignment(); + final Map> candidates = new LinkedHashMap>(); + for (SequenceI seq : forSequences) + { + SequenceI dataset = seq.getDatasetSequence(); + if (dataset == null) + { + continue; + } + AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); + if (datasetAnnotations == null) + { + continue; + } + final List result = new ArrayList(); + for (AlignmentAnnotation dsann : datasetAnnotations) + { + /* + * Find matching annotations on the alignment. + */ + final Iterable matchedAlignmentAnnotations = al + .findAnnotations(seq, dsann.getCalcId(), + dsann.label); + if (!matchedAlignmentAnnotations.iterator().hasNext()) + { + result.add(dsann); + tipEntries.put(dsann.getCalcId(), dsann.label); + } + } + /* + * Save any addable annotations for this sequence + */ + if (!result.isEmpty()) + { + candidates.put(seq, result); + } + } + if (!candidates.isEmpty()) + { + /* + * Found annotations that could be added. Enable the menu item, and + * configure its tooltip and action. + */ + menuItem.setEnabled(true); + for (String calcId : tipEntries.keySet()) + { + tooltip.append("
" + calcId + "/" + tipEntries.get(calcId)); + } + String tooltipText = JvSwingUtils.wrapTooltip(true, + tooltip.toString()); + menuItem.setToolTipText(tooltipText); + + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + addReferenceAnnotations_actionPerformed(candidates); + } + }); + } + } + + /** + * Add annotations to the sequences and to the alignment. + * + * @param candidates + * a map whose keys are sequences on the alignment, and values a list + * of annotations to add to each sequence + */ + protected void addReferenceAnnotations_actionPerformed( + Map> candidates) + { + /* + * Add annotations at the top of the annotation, in the same order as their + * related sequences. + */ + for (SequenceI seq : candidates.keySet()) + { + for (AlignmentAnnotation ann : candidates.get(seq)) + { + AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); + int startRes = 0; + int endRes = ann.annotations.length; + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + if (selectionGroup != null) + { + startRes = selectionGroup.getStartRes(); + endRes = selectionGroup.getEndRes(); + } + copyAnn.restrict(startRes, endRes); + + /* + * Add to the sequence (sets copyAnn.datasetSequence), unless the + * original annotation is already on the sequence. + */ + if (!seq.hasAnnotation(ann)) + { + seq.addAlignmentAnnotation(copyAnn); + } + // adjust for gaps + copyAnn.adjustForAlignment(); + // add to the alignment and set visible + this.ap.getAlignment().addAnnotation(copyAnn); + copyAnn.visible = true; + } + } + refresh(); + } + + protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent) + { + if (!ap.av.getAlignment().hasSeqrep()) + { + // initialise the display flags so the user sees something happen + ap.av.setDisplayReferenceSeq(true); + ap.av.setColourByReferenceSeq(true); + ap.av.getAlignment().setSeqrep(sequence); + } + else + { + if (ap.av.getAlignment().getSeqrep() == sequence) + { + ap.av.getAlignment().setSeqrep(null); + } + else + { + ap.av.getAlignment().setSeqrep(sequence); + } + } + refresh(); + } + + protected void hideInsertions_actionPerformed(ActionEvent actionEvent) + { + if (sequence != null) + { + ColumnSelection cs = ap.av.getColumnSelection(); + if (cs == null) + { + cs = new ColumnSelection(); + } + cs.hideInsertionsFor(sequence); + ap.av.setColumnSelection(cs); + } + refresh(); + } protected void sequenceSelectionDetails_actionPerformed() { createSequenceDetailsReport(ap.av.getSequenceSelection()); @@ -1391,8 +2002,12 @@ public class PopupMenu extends JPopupMenu StringBuffer contents = new StringBuffer(); for (SequenceI seq : sequences) { - contents.append("

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

"); + contents.append("

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

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( contents, @@ -1400,14 +2015,19 @@ public class PopupMenu extends JPopupMenu true, true, false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + (ap.getSeqPanel().seqCanvas.fr != null) ? ap + .getSeqPanel().seqCanvas.fr + .getMinMax() : null); contents.append("

"); } cap.setText("" + contents.toString() + ""); - Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")})) - ,500, 400); + Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage( + "label.sequece_details_for", + (sequences.length == 1 ? new String[] + { sequences[0].getDisplayId(true) } : new String[] + { MessageManager.getString("label.selection") })), 500, 400); } @@ -1543,7 +2163,6 @@ public class PopupMenu extends JPopupMenu refresh(); } - /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1609,6 +2228,18 @@ public class PopupMenu extends JPopupMenu } /** + * Open a panel where the user can choose which types of sequence annotation + * to show or hide. + * + * @param e + */ + protected void chooseAnnotations_actionPerformed(ActionEvent e) + { + // todo correct way to guard against opening a duplicate panel? + new AnnotationChooser(ap); + } + + /** * DOCUMENT ME! * * @param e @@ -1671,7 +2302,7 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { - // JBPNote: Conservation name shouldn't be i18n translated + // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, sg.getSequences(ap.av .getHiddenRepSequences()), sg.getStartRes(), @@ -1723,8 +2354,10 @@ public class PopupMenu extends JPopupMenu SequenceGroup sg = getGroup(); EditNameDialog dialog = new EditNameDialog(sg.getName(), - sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ", - MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"), + sg.getDescription(), " " + + MessageManager.getString("label.group_name") + " ", + MessageManager.getString("label.group_description") + " ", + MessageManager.getString("label.edit_group_name_description"), ap.alignFrame); if (!dialog.accept) @@ -1763,8 +2396,12 @@ public class PopupMenu extends JPopupMenu 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"), + sequence.getDescription(), + " " + MessageManager.getString("label.sequence_name") + + " ", + MessageManager.getString("label.sequence_description") + " ", + MessageManager + .getString("label.edit_sequence_name_description"), ap.alignFrame); if (!dialog.accept) @@ -1776,10 +2413,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane.showMessageDialog(ap, - MessageManager.getString("label.spaces_converted_to_backslashes"), - MessageManager.getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + 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(' ', '_')); @@ -1806,9 +2447,11 @@ public class PopupMenu extends JPopupMenu ap.av.setSelectionGroup(null); refresh(); } + void createGroupMenuItem_actionPerformed() { - getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this + getGroup(); // implicitly creates group - note - should apply defaults / use + // standard alignment window logic for this refresh(); } @@ -1821,7 +2464,8 @@ public class PopupMenu extends JPopupMenu protected void outline_actionPerformed() { SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"), + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_outline_colour"), Color.BLUE); if (col != null) @@ -1875,11 +2519,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - MessageManager.getString("label.web_browser_not_found_unix"), - MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.web_browser_not_found_unix"), + MessageManager.getString("label.web_browser_not_found"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -1975,31 +2618,18 @@ public class PopupMenu extends JPopupMenu { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new String[] + { e.getActionCommand() }), 600, 500); String[] omitHidden = null; System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens // or we simply trust the user wants // wysiwig behaviour - SequenceGroup sg = ap.av.getSelectionGroup(); - ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); - omitHidden = ap.av.getViewAsString(true); - Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.getAlignment() - .getAlignmentAnnotation(); - if (nala != null) - { - for (int i = 0; i < nala.length; i++) - { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); - } - } + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - oal, omitHidden, csel, sg)); - oal = null; + ap.av, true)); } public void pdbFromFile_actionPerformed() @@ -2007,8 +2637,12 @@ public class PopupMenu extends JPopupMenu jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)})); - chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()})); + chooser.setDialogTitle(MessageManager.formatMessage( + "label.select_pdb_file_for", new String[] + { sequence.getDisplayId(false) })); + chooser.setToolTipText(MessageManager.formatMessage( + "label.load_pdb_file_associate_with_sequence", new String[] + { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -2017,26 +2651,30 @@ public class PopupMenu extends JPopupMenu String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, sequence, true); + jalview.io.AppletFormatAdapter.FILE, sequence, true, + Desktop.instance); } } - // JBNote: commented out - these won't be instantiated here...! -// public void RNAFold_actionPerformed() throws Exception -// { -// Predict2D P2D = new Predict2D(); -// P2D.getStructure2DFromRNAFold("toto"); -// } -// -// public void ContraFold_actionPerformed() throws Exception -// { -// Predict2D P2D = new Predict2D(); -// P2D.getStructure2DFromContraFold("toto"); -// } + + // JBNote: commented out - these won't be instantiated here...! + // public void RNAFold_actionPerformed() throws Exception + // { + // Predict2D P2D = new Predict2D(); + // P2D.getStructure2DFromRNAFold("toto"); + // } + // + // public void ContraFold_actionPerformed() throws Exception + // { + // Predict2D P2D = new Predict2D(); + // P2D.getStructure2DFromContraFold("toto"); + // } public void enterPDB_actionPerformed() { String id = JOptionPane.showInternalInputDialog(Desktop.desktop, - MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE); + MessageManager.getString("label.enter_pdb_id"), + MessageManager.getString("label.enter_pdb_id"), + JOptionPane.QUESTION_MESSAGE); if (id != null && id.length() > 0) { @@ -2054,6 +2692,7 @@ public class PopupMenu extends JPopupMenu : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { + @Override public void run() { @@ -2095,7 +2734,7 @@ public class PopupMenu extends JPopupMenu System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.setShowSeqFeatures(true); @@ -2138,17 +2777,22 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) - sequence = (Sequence) sg.getSequenceAt(0); + { + sequence = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, - MessageManager.getString("label.edit_sequence"), ap.alignFrame); + sg.getEndRes() + 1), null, + MessageManager.getString("label.edit_sequence"), null, + MessageManager.getString("label.edit_sequence"), + ap.alignFrame); if (dialog.accept) { - EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', + 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());