X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=bccbf8c80f7ec6f870586fcd36bb773ff50673aa;hb=4663ab6ec8142df859d031bff618d78809e22082;hp=4ff525e1d0cfd00cdea47f6264f41d3d7b26dd4f;hpb=76d3286a73053be49a8cfd6842fffba4db111e08;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4ff525e..bccbf8c 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -21,11 +21,15 @@ package jalview.gui; 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; @@ -57,7 +61,15 @@ 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; @@ -77,6 +89,10 @@ 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(); @@ -125,6 +141,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceDetails = new JMenuItem(); JMenuItem sequenceSelDetails = new JMenuItem(); + + JMenuItem makeReferenceSeq = new JMenuItem(); JMenuItem chooseAnnotations = new JMenuItem(); @@ -176,6 +194,18 @@ public class PopupMenu extends JPopupMenu 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(); @@ -193,6 +223,8 @@ public class PopupMenu extends JPopupMenu JMenu groupLinksMenu; + JMenuItem hideInsertions = new JMenuItem(); + /** * Creates a new PopupMenu object. * @@ -260,6 +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(); @@ -272,6 +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) @@ -285,7 +346,7 @@ 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) @@ -299,7 +360,6 @@ public class PopupMenu extends JPopupMenu ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); } - }); viewStructureMenu.add(menuItem); @@ -320,36 +380,34 @@ 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.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); + // // 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(), @@ -368,7 +426,7 @@ 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(); @@ -393,7 +451,6 @@ public class PopupMenu extends JPopupMenu } } } - } menuItem = new JMenuItem( @@ -562,8 +619,7 @@ public class PopupMenu extends JPopupMenu SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = sq.getDatasetSequence() - .getPDBId(); + Vector pes = sq.getDatasetSequence().getPDBId(); if (pes != null && pes.size() > 0) { reppdb.put(pes.get(0).getId(), pes.get(0)); @@ -777,6 +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) { @@ -1047,8 +1259,7 @@ public class PopupMenu extends JPopupMenu }); chooseAnnotations.setText(MessageManager .getString("label.choose_annotations") + "..."); - chooseAnnotations - .addActionListener(new java.awt.event.ActionListener() + chooseAnnotations.addActionListener(new java.awt.event.ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1263,6 +1474,14 @@ 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() @@ -1297,7 +1516,28 @@ public class PopupMenu extends JPopupMenu 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 @@ -1307,8 +1547,24 @@ public class PopupMenu extends JPopupMenu groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); - this.add(structureMenu); - groupMenu.add(chooseAnnotations); + 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); @@ -1317,6 +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); @@ -1542,6 +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()); @@ -1572,7 +2015,9 @@ 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("

"); } @@ -1745,14 +2190,14 @@ 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(); @@ -1793,6 +2238,7 @@ public class PopupMenu extends JPopupMenu // todo correct way to guard against opening a duplicate panel? new AnnotationChooser(ap); } + /** * DOCUMENT ME! * @@ -2182,7 +2628,8 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), ap.av, true)); + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + ap.av, true)); } public void pdbFromFile_actionPerformed() @@ -2204,7 +2651,8 @@ 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); } } @@ -2286,7 +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); @@ -2329,7 +2777,9 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) + { sequence = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), @@ -2342,7 +2792,7 @@ 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());