X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1263b712e6395c2568e7331c63e8b5f0c81e51d6;hb=041905b00ec635c1764f565a22b2ecf762a9a75b;hp=e84a79922034ab829326e8ca4dbf1fd4f88fcbca;hpb=51ed032e5b45fbcb9d011fc93763cc391752d5b0;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e84a799..1263b71 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,14 +20,38 @@ */ package jalview.gui; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.Arrays; +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; + import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; 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.AlignmentView; import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; @@ -56,22 +80,6 @@ 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.Hashtable; -import java.util.List; -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! * @@ -80,6 +88,10 @@ import javax.swing.JRadioButtonMenuItem; */ 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(); @@ -112,9 +124,6 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); - // protected JRadioButtonMenuItem covariationColour = new - // JRadioButtonMenuItem(); - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); @@ -128,6 +137,10 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); + + JMenuItem makeReferenceSeq = new JMenuItem(); + + JMenuItem chooseAnnotations = new JMenuItem(); SequenceI sequence; @@ -165,35 +178,42 @@ public class PopupMenu extends JPopupMenu 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(); - JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); JMenu outputMenu = new JMenu(); + JMenu seqShowAnnotationsMenu = new JMenu(); + + JMenu seqHideAnnotationsMenu = new JMenu(); + + JMenuItem seqAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); + + JMenu groupShowAnnotationsMenu = new JMenu(); + + JMenu groupHideAnnotationsMenu = new JMenu(); + + JMenuItem groupAddReferenceAnnotations = new JMenuItem( + MessageManager.getString("label.add_reference_annotations")); + JMenuItem sequenceFeature = new JMenuItem(); JMenuItem textColour = new JMenuItem(); JMenu jMenu1 = new JMenu(); - JMenu structureMenu = new JMenu(); + JMenuItem structureMenu = new JMenuItem(); JMenu viewStructureMenu = new JMenu(); - // JMenu colStructureMenu = new JMenu(); JMenuItem editSequence = new JMenuItem(); - // JMenuItem annotationMenuItem = new JMenuItem(); - JMenu groupLinksMenu; + JMenuItem hideInsertions = new JMenuItem(); + /** * Creates a new PopupMenu object. * @@ -242,7 +262,6 @@ public class PopupMenu extends JPopupMenu colours.add(BLOSUM62Colour); colours.add(purinePyrimidineColour); colours.add(RNAInteractionColour); - // colours.add(covariationColour); for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) { @@ -251,6 +270,7 @@ public class PopupMenu extends JPopupMenu item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -260,6 +280,29 @@ 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(); @@ -272,6 +315,12 @@ 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) @@ -285,8 +334,9 @@ 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 @@ -298,7 +348,6 @@ public class PopupMenu extends JPopupMenu ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); } - }); viewStructureMenu.add(menuItem); @@ -317,41 +366,28 @@ public class PopupMenu extends JPopupMenu { structureMenu.remove(viewStructureMenu); } - // 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[] + "label.2d_rna_structure_line", new Object[] { 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"); } }); @@ -359,24 +395,24 @@ public class PopupMenu extends JPopupMenu } } - // SequenceFeatures[] test = seq.getSequenceFeatures(); if (seq.getAnnotation() != null) { 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[] + "label.2d_rna_sequence_name", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence @@ -390,13 +426,13 @@ public class PopupMenu extends JPopupMenu } } } - } menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(false); @@ -408,10 +444,11 @@ public class PopupMenu extends JPopupMenu && ap.av.getSelectionGroup().getSize() > 1) { menuItem = new JMenuItem(MessageManager.formatMessage( - "label.represent_group_with", new String[] + "label.represent_group_with", new Object[] { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(true); @@ -431,6 +468,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showSequence(index); @@ -452,6 +490,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showAllHiddenSeqs(); @@ -474,7 +513,7 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { groupName.setText(MessageManager.formatMessage("label.name_param", - new String[] + new Object[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -555,8 +594,7 @@ public class PopupMenu extends JPopupMenu SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = (Vector) sq.getDatasetSequence() - .getPDBId(); + Vector pes = sq.getDatasetSequence().getPDBId(); if (pes != null && pes.size() > 0) { reppdb.put(pes.get(0).getId(), pes.get(0)); @@ -576,50 +614,6 @@ public class PopupMenu extends JPopupMenu 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) }))); - } - else - { - 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.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pe, ap.av.collateForPDB(pe)); - } - }); - if (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")); - rpdbview.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - new StructureViewer(ap.getStructureSelectionManager()) - .viewStructures(ap, pr, ap.av.collateForPDB(pr)); - } - }); - } } } else @@ -770,6 +764,135 @@ 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); // a, b, c + final JMenuItem item = new JMenuItem(label); + item.setToolTipText(calcId); + item.addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types, + forSequences, allTypes, actionIsShow); + refresh(); + } + }); + showOrHideMenu.add(item); + } + private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks) { @@ -897,8 +1020,6 @@ public class PopupMenu extends JPopupMenu if (urlset != null) { int type = urlLink.getGroupURLType() & 3; - // System.out.println(urlLink.getGroupURLType() - // +" "+((String[])urlset[3])[0]); // first two bits ofurlLink type bitfield are sequenceids and sequences // TODO: FUTURE: ensure the groupURL menu structure can be generalised addshowLink(linkMenus[type], label @@ -938,15 +1059,17 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( - "label.open_url_param", new String[] + "label.open_url_param", new Object[] { url })); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { showLink(url); @@ -982,11 +1105,13 @@ public class PopupMenu extends JPopupMenu // 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 @@ -1017,6 +1142,7 @@ 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(); @@ -1027,15 +1153,27 @@ public class PopupMenu extends JPopupMenu .getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceName_actionPerformed(); } }); + 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(); @@ -1046,6 +1184,7 @@ public class PopupMenu extends JPopupMenu sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceSelectionDetails_actionPerformed(); @@ -1056,6 +1195,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { unGroupMenuItem_actionPerformed(); @@ -1066,6 +1206,7 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createGroupMenuItem_actionPerformed(); @@ -1075,6 +1216,7 @@ public class PopupMenu extends JPopupMenu outline.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outline_actionPerformed(); @@ -1084,6 +1226,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideMenuItem_actionPerformed(); @@ -1094,6 +1237,7 @@ public class PopupMenu extends JPopupMenu showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showBoxes_actionPerformed(); @@ -1103,6 +1247,7 @@ public class PopupMenu extends JPopupMenu showText.setState(true); showText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showText_actionPerformed(); @@ -1111,6 +1256,7 @@ public class PopupMenu extends JPopupMenu showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showColourText_actionPerformed(); @@ -1121,6 +1267,7 @@ public class PopupMenu extends JPopupMenu displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showNonconserved_actionPerformed(); @@ -1130,6 +1277,7 @@ public class PopupMenu extends JPopupMenu cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(); @@ -1138,6 +1286,7 @@ 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); @@ -1146,6 +1295,7 @@ public class PopupMenu extends JPopupMenu copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(); @@ -1154,6 +1304,7 @@ 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); @@ -1162,6 +1313,7 @@ public class PopupMenu extends JPopupMenu toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1172,40 +1324,17 @@ public class PopupMenu extends JPopupMenu 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(); - // } - // } - // }); + enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { enterPDB_actionPerformed(); @@ -1214,6 +1343,7 @@ 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(); @@ -1221,10 +1351,19 @@ public class PopupMenu extends JPopupMenu }); 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(); @@ -1233,13 +1372,29 @@ public class PopupMenu extends JPopupMenu textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(); } }); jMenu1.setText(MessageManager.getString("label.group")); - structureMenu.setText(MessageManager.getString("label.structure")); + structureMenu.setText(MessageManager.getString("label.view_structure")); + structureMenu.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + SequenceI[] selectedSeqs = new SequenceI[] + { sequence }; + if (ap.av.getSelectionGroup() != null) + { + selectedSeqs = ap.av.getSequenceSelection(); + } + new StructureChooser(selectedSeqs, sequence, ap); + } + }); + viewStructureMenu.setText(MessageManager .getString("label.view_structure")); // colStructureMenu.setText("Colour By Structure"); @@ -1247,12 +1402,34 @@ public class PopupMenu extends JPopupMenu + "..."); 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 @@ -1262,7 +1439,24 @@ 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); @@ -1271,6 +1465,7 @@ 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); @@ -1287,10 +1482,8 @@ public class PopupMenu extends JPopupMenu if (ap.getAlignment().isNucleotide()) { // JBPNote - commented since the colourscheme isn't functional - // colourMenu.add(RNAInteractionColour); colourMenu.add(purinePyrimidineColour); } - // colourMenu.add(covariationColour); colourMenu.add(userDefinedColour); if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) @@ -1303,6 +1496,7 @@ 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); @@ -1315,7 +1509,6 @@ public class PopupMenu extends JPopupMenu colourMenu.addSeparator(); colourMenu.add(abovePIDColour); colourMenu.add(conservationMenuItem); - // colourMenu.add(annotationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -1336,12 +1529,10 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); - structureMenu.add(pdbMenu); - structureMenu.add(viewStructureMenu); - // structureMenu.add(colStructureMenu); noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(); @@ -1352,6 +1543,7 @@ public class PopupMenu extends JPopupMenu .getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(); @@ -1360,6 +1552,7 @@ 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(); @@ -1368,6 +1561,7 @@ 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(); @@ -1378,6 +1572,7 @@ public class PopupMenu extends JPopupMenu hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(); @@ -1386,6 +1581,7 @@ 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(); @@ -1395,6 +1591,7 @@ public class PopupMenu extends JPopupMenu .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(); @@ -1403,6 +1600,7 @@ 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(); @@ -1411,6 +1609,7 @@ 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(); @@ -1420,6 +1619,7 @@ public class PopupMenu extends JPopupMenu .getString("label.above_identity_percentage")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { abovePIDColour_actionPerformed(); @@ -1429,6 +1629,7 @@ public class PopupMenu extends JPopupMenu .getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { userDefinedColour_actionPerformed(e); @@ -1438,6 +1639,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(); @@ -1446,6 +1648,7 @@ 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(); @@ -1456,6 +1659,7 @@ public class PopupMenu extends JPopupMenu purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(); @@ -1473,6 +1677,7 @@ public class PopupMenu extends JPopupMenu conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(); @@ -1480,6 +1685,116 @@ 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.setEnabled(false); + + /* + * Temporary store to hold distinct calcId / type pairs for the tooltip. + * Using TreeMap means calcIds are shown in alphabetical order. + */ + Map tipEntries = new TreeMap(); + final Map> candidates = new LinkedHashMap>(); + AlignmentI al = this.ap.av.getAlignment(); + AlignmentUtils.findAddableReferenceAnnotations(forSequences, + tipEntries, candidates, al); + if (!candidates.isEmpty()) + { + StringBuilder tooltip = new StringBuilder(64); + tooltip.append(MessageManager.getString("label.add_annotations_for")); + + /* + * 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) + { + final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); + final AlignmentI alignment = this.ap.getAlignment(); + AlignmentUtils.addReferenceAnnotations(candidates, alignment, + selectionGroup); + 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()); @@ -1501,7 +1816,7 @@ public class PopupMenu extends JPopupMenu + MessageManager .formatMessage( "label.create_sequence_details_report_annotation_for", - new String[] + new Object[] { seq.getDisplayId(true) }) + "

"); new SequenceAnnotationReport(null) .createSequenceAnnotationReport( @@ -1510,16 +1825,18 @@ 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[] + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.sequence_details_for", + (sequences.length == 1 ? new Object[] + { sequences[0].getDisplayId(true) } : new Object[] { MessageManager.getString("label.selection") })), 500, 400); } @@ -1683,14 +2000,14 @@ public class PopupMenu extends JPopupMenu int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); } else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } refresh(); @@ -1721,6 +2038,18 @@ 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 @@ -2029,15 +2358,7 @@ public class PopupMenu extends JPopupMenu } int gsize = sg.getSize(); - SequenceI[] hseqs; - - hseqs = new SequenceI[gsize]; - - int index = 0; - for (int i = 0; i < gsize; i++) - { - hseqs[index++] = sg.getSequenceAt(i); - } + SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]); ap.av.hideSequence(hseqs); // refresh(); TODO: ? needed ? @@ -2061,7 +2382,8 @@ public class PopupMenu extends JPopupMenu if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + List startEnd = ap.av.getVisibleRegionBoundaries( + sg.getStartRes(), sg.getEndRes() + 1); String description; @@ -2100,7 +2422,7 @@ public class PopupMenu extends JPopupMenu CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new String[] + "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -2109,20 +2431,8 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - AlignmentView selvew = ap.av.getAlignmentView(true, false); - AlignmentI aselview = selvew.getVisibleAlignment(ap.av - .getGapCharacter()); - List ala = (ap.av - .getVisibleAlignmentAnnotation(true)); - if (ala != null) - { - for (AlignmentAnnotation aa : ala) - { - aselview.addAnnotation(aa); - } - } cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - aselview, null, null, null)); + ap.av, true)); } public void pdbFromFile_actionPerformed() @@ -2131,10 +2441,10 @@ public class PopupMenu extends JPopupMenu jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new jalview.io.JalviewFileView()); chooser.setDialogTitle(MessageManager.formatMessage( - "label.select_pdb_file_for", new String[] + "label.select_pdb_file_for", new Object[] { sequence.getDisplayId(false) })); chooser.setToolTipText(MessageManager.formatMessage( - "label.load_pdb_file_associate_with_sequence", new String[] + "label.load_pdb_file_associate_with_sequence", new Object[] { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -2144,23 +2454,13 @@ 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"); - // } + public void enterPDB_actionPerformed() { String id = JOptionPane.showInternalInputDialog(Desktop.desktop, @@ -2184,6 +2484,7 @@ public class PopupMenu extends JPopupMenu : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { + @Override public void run() { @@ -2225,7 +2526,7 @@ 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); @@ -2268,7 +2569,9 @@ 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(), @@ -2281,7 +2584,7 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', + Action.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());