X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d6e370f465bdb640db000ea699a5ddb1c9bbdadc;hb=eaf9092bfa74b5162589c8775f68a19dd79dbb1d;hp=cd60e4724b29feb717741fbdb5bf662a67097b9b;hpb=abdc3a7c9a4b7dbf7a3bb6dd26ba9d76881933d6;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index cd60e47..d6e370f 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.Conservation; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; @@ -58,8 +59,14 @@ 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; @@ -79,6 +86,10 @@ 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(); @@ -178,9 +189,17 @@ public class PopupMenu extends JPopupMenu JMenu outputMenu = new JMenu(); - JMenu showAnnotationsMenu = new JMenu(); + JMenu seqShowAnnotationsMenu = new JMenu(); + + JMenu seqHideAnnotationsMenu = new JMenu(); + + JMenuItem seqAddReferenceAnnotations = new JMenuItem(); + + JMenu groupShowAnnotationsMenu = new JMenu(); - JMenu hideAnnotationsMenu = new JMenu(); + JMenu groupHideAnnotationsMenu = new JMenu(); + + JMenuItem groupAddReferenceAnnotations = new JMenuItem(); JMenuItem sequenceFeature = new JMenuItem(); @@ -266,7 +285,28 @@ public class PopupMenu extends JPopupMenu outputMenu.add(item); } - buildAnnotationTypesMenu(); + /* + * 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 { @@ -293,7 +333,7 @@ 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) @@ -307,7 +347,6 @@ public class PopupMenu extends JPopupMenu ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); } - }); viewStructureMenu.add(menuItem); @@ -344,7 +383,6 @@ public class PopupMenu extends JPopupMenu "label.2d_rna_structure_line", new String[] { structureLine })); menuItem.addActionListener(new java.awt.event.ActionListener() - { @Override public void actionPerformed(ActionEvent e) @@ -570,8 +608,7 @@ 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)); @@ -786,67 +823,153 @@ public class PopupMenu extends JPopupMenu } /** - * Find which sequence-specific annotation types are associated with the - * current selection, and add these as menu items (for show / hide annotation - * types). + * 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 buildAnnotationTypesMenu() + protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu, + List forSequences) { - List found = new ArrayList(); - for (AlignmentAnnotation aa : ap.getAlignment() - .getAlignmentAnnotation()) + 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()) { - if (aa.sequenceRef != null) + for (List type : hiddenTypes.get(calcId)) { - if (ap.av.getSelectionGroup().getSequences() - .contains(aa.sequenceRef)) - { - final String label = aa.label; - if (!found.contains(label)) - { - found.add(label); - final JMenuItem showitem = new JMenuItem(label); - showitem.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - showHideAnnotation_actionPerformed(label, true); - } - }); - showAnnotationsMenu.add(showitem); - final JMenuItem hideitem = new JMenuItem(label); - hideitem.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - showHideAnnotation_actionPerformed(label, false); - } - }); - hideAnnotationsMenu.add(hideitem); - } - } + 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 an annotation type to show or hide for the selection. + * Action on selecting a list of annotation type (or the 'all types' values) + * to show or hide for the specified sequences. * - * @param type + * @param types + * @param forSequences + * @param anyType * @param doShow */ - protected void showHideAnnotation_actionPerformed(String type, - boolean doShow) + protected void showHideAnnotation_actionPerformed( + Collection types, List forSequences, + boolean anyType, boolean doShow) { for (AlignmentAnnotation aa : ap.getAlignment() .getAlignmentAnnotation()) { - if (aa.sequenceRef != null && type.equals(aa.label)) + if (anyType || types.contains(aa.label)) { - if (ap.av.getSelectionGroup().getSequences() - .contains(aa.sequenceRef)) + if ((aa.sequenceRef != null) + && forSequences.contains(aa.sequenceRef)) { aa.visible = doShow; } @@ -1125,8 +1248,7 @@ 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) @@ -1341,9 +1463,13 @@ 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")); sequenceFeature.setText(MessageManager .getString("label.create_sequence_feature")); @@ -1390,9 +1516,19 @@ public class PopupMenu extends JPopupMenu add(groupMenu); add(sequenceMenu); this.add(structureMenu); - groupMenu.add(chooseAnnotations); - groupMenu.add(showAnnotationsMenu); - groupMenu.add(hideAnnotationsMenu); + // 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); @@ -1626,6 +1762,146 @@ 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 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. + * + * @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 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) + { + continue; + } + final List result = new ArrayList(); + 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()) + { + 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) + 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() { createSequenceDetailsReport(ap.av.getSequenceSelection()); @@ -1877,6 +2153,7 @@ public class PopupMenu extends JPopupMenu // todo correct way to guard against opening a duplicate panel? new AnnotationChooser(ap); } + /** * DOCUMENT ME! * @@ -2266,7 +2543,8 @@ 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() @@ -2413,7 +2691,9 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) + { sequence = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(),