X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1c7be464b88154657ea2c65f1fb8c33ec8061cc7;hb=9d139ca8d1af8f0f2d78193d418ae9e9168a3e8a;hp=e256b33145bfea2a12cceada9d37d19a479751f9;hpb=ecfc49bc5a7e416c0f967677651923993f105dd8;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e256b33..1c7be46 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,23 +20,64 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.schemes.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.Conservation; +import jalview.commands.ChangeCaseCommand; +import jalview.commands.EditCommand; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.io.FormatAdapter; +import jalview.io.SequenceAnnotationReport; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.UserColourScheme; +import jalview.schemes.ZappoColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; import jalview.util.UrlLink; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.Collections; +import java.util.Hashtable; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + /** * DOCUMENT ME! * @@ -45,6 +86,10 @@ import jalview.util.UrlLink; */ public class PopupMenu extends JPopupMenu { + private static final String ALL_ANNOTATIONS = "All"; + + private static final String COMMA = ","; + JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -94,6 +139,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceSelDetails = new JMenuItem(); + JMenuItem chooseAnnotations = new JMenuItem(); + SequenceI sequence; JMenuItem createGroupMenuItem = new JMenuItem(); @@ -142,6 +189,18 @@ 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(); @@ -216,6 +275,7 @@ public class PopupMenu extends JPopupMenu item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -225,6 +285,29 @@ 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(); @@ -250,20 +333,20 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO re JAL-860: optionally open dialog or provide a menu entry // allowing user to open just one structure per sequence - //new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] - //{ pdb })[0], null, ap); + // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] + // { pdb })[0], null, ap); new StructureViewer(ap.getStructureSelectionManager()) .viewStructures(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap); } - }); viewStructureMenu.add(menuItem); @@ -300,8 +383,8 @@ 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) { // System.out.println("1:"+structureLine); @@ -342,6 +425,7 @@ public class PopupMenu extends JPopupMenu { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence @@ -362,6 +446,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(false); @@ -377,6 +462,7 @@ public class PopupMenu extends JPopupMenu { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(true); @@ -396,6 +482,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showSequence(index); @@ -417,6 +504,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showAllHiddenSeqs(); @@ -520,9 +608,8 @@ public class PopupMenu extends JPopupMenu SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = (Vector) sq.getDatasetSequence() - .getPDBId(); - if (pes != null && pes.size()>0) + Vector pes = sq.getDatasetSequence().getPDBId(); + if (pes != null && pes.size() > 0) { reppdb.put(pes.get(0).getId(), pes.get(0)); for (PDBEntry pe : pes) @@ -561,7 +648,8 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe)); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(ap, pe, ap.av.collateForPDB(pe)); } }); if (reppdb.size() > 1 && reppdb.size() < pdbe.size()) @@ -579,7 +667,8 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr)); + new StructureViewer(ap.getStructureSelectionManager()) + .viewStructures(ap, pr, ap.av.collateForPDB(pr)); } }); } @@ -733,6 +822,162 @@ 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) { @@ -905,11 +1150,13 @@ public class PopupMenu extends JPopupMenu { url })); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { showLink(url); @@ -945,11 +1192,13 @@ 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 @@ -980,6 +1229,7 @@ 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(); @@ -990,15 +1240,27 @@ 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(); @@ -1009,6 +1271,7 @@ public class PopupMenu extends JPopupMenu sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceSelectionDetails_actionPerformed(); @@ -1019,6 +1282,7 @@ 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(); @@ -1029,6 +1293,7 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createGroupMenuItem_actionPerformed(); @@ -1038,6 +1303,7 @@ 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(); @@ -1047,6 +1313,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideMenuItem_actionPerformed(); @@ -1057,6 +1324,7 @@ public class PopupMenu extends JPopupMenu showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showBoxes_actionPerformed(); @@ -1066,6 +1334,7 @@ public class PopupMenu extends JPopupMenu showText.setState(true); showText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showText_actionPerformed(); @@ -1074,6 +1343,7 @@ public class PopupMenu extends JPopupMenu showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showColourText_actionPerformed(); @@ -1084,6 +1354,7 @@ public class PopupMenu extends JPopupMenu displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showNonconserved_actionPerformed(); @@ -1093,6 +1364,7 @@ public class PopupMenu extends JPopupMenu cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(); @@ -1101,6 +1373,7 @@ 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); @@ -1109,6 +1382,7 @@ public class PopupMenu extends JPopupMenu copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(); @@ -1117,6 +1391,7 @@ 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); @@ -1125,6 +1400,7 @@ public class PopupMenu extends JPopupMenu toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1135,6 +1411,7 @@ public class PopupMenu extends JPopupMenu pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pdbFromFile_actionPerformed(); @@ -1169,6 +1446,7 @@ public class PopupMenu extends JPopupMenu enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { enterPDB_actionPerformed(); @@ -1177,6 +1455,7 @@ 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(); @@ -1184,10 +1463,19 @@ 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(); @@ -1196,6 +1484,7 @@ public class PopupMenu extends JPopupMenu textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(); @@ -1210,6 +1499,7 @@ public class PopupMenu extends JPopupMenu + "..."); editSequence.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { editSequence_actionPerformed(actionEvent); @@ -1226,6 +1516,19 @@ public class PopupMenu extends JPopupMenu add(groupMenu); add(sequenceMenu); this.add(structureMenu); + // 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); @@ -1266,6 +1569,7 @@ 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); @@ -1305,6 +1609,7 @@ public class PopupMenu extends JPopupMenu noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(); @@ -1315,6 +1620,7 @@ public class PopupMenu extends JPopupMenu .getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(); @@ -1323,6 +1629,7 @@ 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(); @@ -1331,6 +1638,7 @@ 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(); @@ -1341,6 +1649,7 @@ public class PopupMenu extends JPopupMenu hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(); @@ -1349,6 +1658,7 @@ 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(); @@ -1358,6 +1668,7 @@ public class PopupMenu extends JPopupMenu .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(); @@ -1366,6 +1677,7 @@ 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(); @@ -1374,6 +1686,7 @@ 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(); @@ -1383,6 +1696,7 @@ 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(); @@ -1392,6 +1706,7 @@ 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); @@ -1401,6 +1716,7 @@ 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(); @@ -1409,6 +1725,7 @@ 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(); @@ -1419,6 +1736,7 @@ public class PopupMenu extends JPopupMenu purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(); @@ -1436,6 +1754,7 @@ public class PopupMenu extends JPopupMenu conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(); @@ -1443,6 +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()); @@ -1684,6 +2143,18 @@ 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 @@ -2071,23 +2542,9 @@ public class PopupMenu extends JPopupMenu System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens // or we simply trust the user wants // wysiwig behaviour - SequenceGroup sg = ap.av.getSelectionGroup(); - ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); - omitHidden = ap.av.getViewAsString(true); - Alignment oal = new Alignment(ap.av.getSequenceSelection()); - AlignmentAnnotation[] nala = ap.av.getAlignment() - .getAlignmentAnnotation(); - if (nala != null) - { - for (int i = 0; i < nala.length; i++) - { - AlignmentAnnotation na = nala[i]; - oal.addAnnotation(na); - } - } + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), - oal, omitHidden, csel, sg)); - oal = null; + ap.av, true)); } public void pdbFromFile_actionPerformed() @@ -2100,7 +2557,7 @@ public class PopupMenu extends JPopupMenu { sequence.getDisplayId(false) })); chooser.setToolTipText(MessageManager.formatMessage( "label.load_pdb_file_associate_with_sequence", new String[] - { new Integer(sequence.getDisplayId(false)).toString() })); + { sequence.getDisplayId(false) })); int value = chooser.showOpenDialog(null); @@ -2109,7 +2566,8 @@ 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); } } @@ -2149,6 +2607,7 @@ public class PopupMenu extends JPopupMenu : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { + @Override public void run() { @@ -2233,7 +2692,9 @@ 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(),