X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1a7235fa1f87f64d66cd81b3869fe78bbbf91af2;hb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;hp=5f6c55694a49bfc3e481a3aa50ccf67ac99cbe67;hpb=fe6b3fb39308b5c045849db2be75ba07824be776;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 5f6c556..1a7235f 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -21,9 +21,11 @@ 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.Annotation; import jalview.datamodel.DBRefEntry; @@ -34,7 +36,6 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; -import jalview.renderer.AnnotationRenderer; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -60,12 +61,13 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.ArrayList; import java.util.Arrays; -import java.util.BitSet; import java.util.Collection; +import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; +import java.util.TreeMap; import java.util.Vector; import javax.swing.ButtonGroup; @@ -188,11 +190,17 @@ public class PopupMenu extends JPopupMenu JMenu outputMenu = new JMenu(); - JMenu showAnnotationsMenu = new JMenu(); + JMenu seqShowAnnotationsMenu = new JMenu(); - JMenu hideAnnotationsMenu = new JMenu(); + JMenu seqHideAnnotationsMenu = new JMenu(); - JMenuItem addDatasequenceAnnotations = new JMenuItem(); + JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + + JMenu groupShowAnnotationsMenu = new JMenu(); + + JMenu groupHideAnnotationsMenu = new JMenu(); + + JMenuItem groupAddReferenceAnnotations = new JMenuItem(); JMenuItem sequenceFeature = new JMenuItem(); @@ -279,9 +287,27 @@ public class PopupMenu extends JPopupMenu } /* - * Build menus for annotation types that may be shown or hidden. + * 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): */ - buildAnnotationTypesMenus(); + final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections + . emptyList() : ap.av.getSelectionGroup() + .getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); try { @@ -308,8 +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 @@ -346,31 +373,30 @@ public class PopupMenu extends JPopupMenu { 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(), @@ -389,7 +415,7 @@ 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(); @@ -798,9 +824,10 @@ public class PopupMenu extends JPopupMenu } /** - * Add annotation types to a 'Show annotations' or 'Hide annotations' menu. + * 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. + * 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 @@ -808,165 +835,82 @@ public class PopupMenu extends JPopupMenu * composite type name, e.g. *

* IUPredWS (Long), IUPredWS (Short) + * + * @param seq */ - protected void buildAnnotationTypesMenus() + protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu, + List forSequences) { - showAnnotationsMenu.removeAll(); - hideAnnotationsMenu.removeAll(); + showMenu.removeAll(); + hideMenu.removeAll(); + final List all = Arrays.asList(ALL_ANNOTATIONS); - addAnnotationTypeToShowHide(showAnnotationsMenu, all, true, true); - addAnnotationTypeToShowHide(hideAnnotationsMenu, all, true, false); - showAnnotationsMenu.addSeparator(); - hideAnnotationsMenu.addSeparator(); + addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); + addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, + false); + showMenu.addSeparator(); + hideMenu.addSeparator(); final AlignmentAnnotation[] annotations = ap.getAlignment() .getAlignmentAnnotation(); - BitSet visibleGraphGroups = PopupMenu - .getVisibleLineGraphGroups(annotations); - - List> shownTypes = new ArrayList>(); - List> hiddenTypes = new ArrayList>(); - PopupMenu.getAnnotationTypesForShowHide(shownTypes, hiddenTypes, - visibleGraphGroups, annotations, ap.av.getSelectionGroup()); - for (List types : hiddenTypes) - { - addAnnotationTypeToShowHide(showAnnotationsMenu, types, false, true); - } - - for (List types : shownTypes) - { - addAnnotationTypeToShowHide(hideAnnotationsMenu, types, false, false); - } - } - - /** - * Helper method to populate lists of annotation types for the Show/Hide - * Annotations menus. If sequenceGroup is not null, this is restricted to - * annotations which are associated with sequences in the selection group. - *

- * If an annotation row is currently visible, its type (label) is added (once - * only per type), to the shownTypes list. If it is currently hidden, it is - * added to the hiddenTypesList. - *

- * For rows that belong to a line graph group, so are always rendered - * together: - *

    - *
  • Treat all rows in the group as visible, if at least one of them is
    • - *
  • Build a comma-separated label with all the types that belong to the - * group
    • - *
- * - * @param shownTypes - * @param hiddenTypes - * @param visibleGraphGroups - * @param annotations - * @param sequenceGroup - */ - public static void getAnnotationTypesForShowHide( - List> shownTypes, List> hiddenTypes, - BitSet visibleGraphGroups, AlignmentAnnotation[] annotations, - SequenceGroup sequenceGroup) - { - // lookup table, key = graph group, value = list of types in the group - Map> groupLabels = new LinkedHashMap>(); - - List addedToShown = new ArrayList(); - List addedToHidden = new ArrayList(); + /* + * 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 (AlignmentAnnotation aa : annotations) + for (String calcId : hiddenTypes.keySet()) { - - if (sequenceGroup == null - || (aa.sequenceRef != null && sequenceGroup.getSequences() - .contains(aa.sequenceRef))) + for (List type : hiddenTypes.get(calcId)) { - /* - * Build a 'composite label' for types in line graph groups. - */ - final List labelAsList = new ArrayList(); - labelAsList.add(aa.label); - if (aa.graph == AlignmentAnnotation.LINE_GRAPH - && aa.graphGroup > -1) - { - if (groupLabels.containsKey(aa.graphGroup)) - { - if (!groupLabels.get(aa.graphGroup).contains(aa.label)) - { - groupLabels.get(aa.graphGroup).add(aa.label); - } - } - else - { - groupLabels.put(aa.graphGroup, labelAsList); - } - } - else if (aa.visible && !addedToShown.contains(aa.label)) - { - shownTypes.add(labelAsList); - addedToShown.add(aa.label); - } - else - { - if (!aa.visible && !addedToHidden.contains(aa.label)) - { - hiddenTypes.add(labelAsList); - addedToHidden.add(aa.label); - } - } + addAnnotationTypeToShowHide(showMenu, forSequences, + calcId, type, false, true); } } - /* - * finally add the 'composite group labels' to the appropriate lists, - * depending on whether the group is identified as visible or hidden - */ - for (int group : groupLabels.keySet()) + // grey out 'show annotations' if none are hidden + showMenu.setEnabled(!hiddenTypes.isEmpty()); + + for (String calcId : shownTypes.keySet()) { - final List groupLabel = groupLabels.get(group); - if (visibleGraphGroups.get(group)) - { - if (!shownTypes.contains(groupLabel)) - { - shownTypes.add(groupLabel); - } - } - else if (!hiddenTypes.contains(groupLabel)) + for (List type : shownTypes.get(calcId)) { - hiddenTypes.add(groupLabel); + addAnnotationTypeToShowHide(hideMenu, forSequences, + calcId, type, false, false); } } + // grey out 'hide annotations' if none are shown + hideMenu.setEnabled(!shownTypes.isEmpty()); } /** - * Returns a BitSet (possibly empty) of those graphGroups for line graph - * annotations, which have at least one member annotation row marked visible. - * The logic is that only one row in the group is marked visible, but when it - * is drawn, so are all the other rows in the same group. - *

- * This lookup set allows us to check whether rows marked not visible are in - * fact shown. + * Returns a list of sequences - either the current selection group (if there + * is one), else the specified single sequence. * - * @see AnnotationRenderer#drawComponent - * @param annotations + * @param seq * @return */ - public static BitSet getVisibleLineGraphGroups( - AlignmentAnnotation[] annotations) + protected List getSequenceScope(SequenceI seq) { - // todo move to a utility class - BitSet result = new BitSet(); - for (AlignmentAnnotation ann : annotations) + List forSequences = null; + final SequenceGroup selectionGroup = ap.av.getSelectionGroup(); + if (selectionGroup != null && selectionGroup.getSize() > 0) { - if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible) - { - int gg = ann.graphGroup; - if (gg > -1) - { - result.set(gg); - } - } + forSequences = selectionGroup.getSequences(); } - return result; + else + { + forSequences = seq == null ? Collections. emptyList() + : Arrays.asList(seq); + } + return forSequences; } /** @@ -975,6 +919,9 @@ public class PopupMenu extends JPopupMenu * * @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 @@ -984,18 +931,21 @@ public class PopupMenu extends JPopupMenu * type, else hide */ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu, - final Collection types, final boolean allTypes, + 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, allTypes, actionIsShow); + showHideAnnotation_actionPerformed(types, forSequences, allTypes, + actionIsShow); } }); showOrHideMenu.add(item); @@ -1003,14 +953,16 @@ public class PopupMenu extends JPopupMenu /** * Action on selecting a list of annotation type (or the 'all types' values) - * to show or hide for the selection. + * to show or hide for the specified sequences. * * @param types + * @param forSequences * @param anyType * @param doShow */ protected void showHideAnnotation_actionPerformed( - Collection types, boolean anyType, boolean doShow) + Collection types, List forSequences, + boolean anyType, boolean doShow) { for (AlignmentAnnotation aa : ap.getAlignment() .getAlignmentAnnotation()) @@ -1018,8 +970,7 @@ public class PopupMenu extends JPopupMenu if (anyType || types.contains(aa.label)) { if ((aa.sequenceRef != null) - && ap.av.getSelectionGroup().getSequences() - .contains(aa.sequenceRef)) + && forSequences.contains(aa.sequenceRef)) { aa.visible = doShow; } @@ -1513,23 +1464,14 @@ public class PopupMenu extends JPopupMenu }); outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "..."); - showAnnotationsMenu.setText(MessageManager + seqShowAnnotationsMenu.setText(MessageManager .getString("label.show_annotations")); - hideAnnotationsMenu.setText(MessageManager + seqHideAnnotationsMenu.setText(MessageManager + .getString("label.hide_annotations")); + groupShowAnnotationsMenu.setText(MessageManager + .getString("label.show_annotations")); + groupHideAnnotationsMenu.setText(MessageManager .getString("label.hide_annotations")); - final List referenceAnns = getDatasequenceAnnotationsNotOnAlignment(ap.av - .getSelectionGroup()); - addDatasequenceAnnotations.setText(MessageManager - .getString("label.add_reference_annotations")); - addDatasequenceAnnotations.setEnabled(!referenceAnns.isEmpty()); - addDatasequenceAnnotations.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - addReferenceAnnotations_actionPerformed(referenceAnns); - } - }); sequenceFeature.setText(MessageManager .getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() @@ -1575,10 +1517,19 @@ public class PopupMenu extends JPopupMenu add(groupMenu); add(sequenceMenu); this.add(structureMenu); + // annotations configuration panel suppressed for now // groupMenu.add(chooseAnnotations); - groupMenu.add(showAnnotationsMenu); - groupMenu.add(hideAnnotationsMenu); - groupMenu.add(addDatasequenceAnnotations); + + /* + * 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); @@ -1813,56 +1764,143 @@ public class PopupMenu extends JPopupMenu } /** - * Get a list of any annotations on the dataset sequences in the current - * selection group that are not also on the alignment. - *

- * The criteria for 'on the alignment' is finding an annotation that matches - * on sequenceRef.datasetSequence, calcId and label. + * Check for any annotations on the underlying dataset sequences (for the + * current selection group) which are not on the alignment annotations for the + * sequence. 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 sequence, that matches on calcId and label. A tooltip is also + * constructed that displays the source (calcId) and type (label) of the + * annotations that can be added. * - * @return + * @param menuItem + * @param forSequences */ - protected List getDatasequenceAnnotationsNotOnAlignment( - SequenceGroup sg) + protected void configureReferenceAnnotationsMenu( + JMenuItem menuItem, List forSequences) { - List result = new ArrayList(); - - for (SequenceI seq : sg.getSequences()) + 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 sequence in the alignment. + * + * Build a map of { alignmentSequence, } + */ + final Map> candidates = new LinkedHashMap>(); + for (SequenceI seq : forSequences) { SequenceI dataset = seq.getDatasetSequence(); + if (dataset == null) + { + continue; + } AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation(); - if (datasetAnnotations != null) + if (datasetAnnotations == null) + { + continue; + } + final List result = new ArrayList(); + for (AlignmentAnnotation dsann : datasetAnnotations) { - for (AlignmentAnnotation dsann : datasetAnnotations) + /* + * If the sequence has no annotation that matches this one, then add + * this one to the results list. + */ + if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label) + .isEmpty()) { - /* - * If the alignment has no annotation that matches this one... - */ - if (!ap.getAlignment() - .findAnnotation(dataset, dsann.getCalcId(), dsann.label) - .iterator().hasNext()) - { - /* - * ...then add it to the result list - */ - result.add(dsann); - } + 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); + } + }); } - return result; } /** - * Add any annotations on the sequence dataset to the alignment (that are not - * already copied to it). + * 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( - List anns) + Map> candidates) { - for (AlignmentAnnotation ann : anns) + /* + * Add annotations at the top of the annotation, in the same order as their + * related sequences. + */ + for (SequenceI seq : candidates.keySet()) { - // todo: copy, add, adjust... + 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) + 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 sequenceSelectionDetails_actionPerformed() @@ -1895,7 +1933,7 @@ 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.minmax : null); contents.append("

"); } @@ -2529,7 +2567,8 @@ 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); } } @@ -2611,7 +2650,7 @@ 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); @@ -2654,7 +2693,9 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) + { sequence = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), @@ -2667,7 +2708,7 @@ 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());