X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=2c4eb7aceb922e904ef1fa2f1825af2558a776a7;hb=58962a97c9819d186ce347072e8750dbcae16f0f;hp=3b79fdcb41560d2b5f2c1ed327ae9ef6f456ac20;hpb=a86ad83f39c98c9a06d08a1ba1fa8b529d30a63c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 3b79fdc..2c4eb7a 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -31,30 +31,22 @@ 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.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.gui.ColourMenuHelper.ColourChangeListener; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; 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.ColourSchemeI; +import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.UserColourScheme; -import jalview.schemes.ZappoColourScheme; -import jalview.util.DBRefUtils; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; @@ -65,22 +57,22 @@ 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.SortedMap; 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! @@ -88,44 +80,20 @@ import javax.swing.JRadioButtonMenuItem; * @author $author$ * @version $Revision: 1.118 $ */ -public class PopupMenu extends JPopupMenu +public class PopupMenu extends JPopupMenu implements ColourChangeListener { JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); - protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem(); - - protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem(); - - JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JMenuItem modifyPID = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); + AlignmentPanel ap; JMenu sequenceMenu = new JMenu(); @@ -148,8 +116,6 @@ public class PopupMenu extends JPopupMenu JMenuItem outline = new JMenuItem(); - JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -238,29 +204,11 @@ public class PopupMenu extends JPopupMenu this.ap = ap; sequence = seq; - ButtonGroup colours = new ButtonGroup(); - colours.add(noColourmenuItem); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - colours.add(purinePyrimidineColour); - colours.add(RNAInteractionColour); - - for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++) - { - JMenuItem item = new JMenuItem( - jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]); - - item.addActionListener(new java.awt.event.ActionListener() + for (String ff : FileFormats.getInstance().getWritableFormats(true)) + { + JMenuItem item = new JMenuItem(ff); + + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -344,7 +292,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(MessageManager.formatMessage( "label.2d_rna_structure_line", new Object[] { aa.label })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -372,7 +320,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(MessageManager.formatMessage( "label.2d_rna_sequence_name", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -393,7 +341,7 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -409,7 +357,7 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem(MessageManager.formatMessage( "label.represent_group_with", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -466,7 +414,6 @@ public class PopupMenu extends JPopupMenu add(menuItem); } - } SequenceGroup sg = ap.av.getSelectionGroup(); @@ -478,68 +425,23 @@ public class PopupMenu extends JPopupMenu groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); - if (sg.cs instanceof ZappoColourScheme) - { - zappoColour.setSelected(true); - } - else if (sg.cs instanceof TaylorColourScheme) - { - taylorColour.setSelected(true); - } - else if (sg.cs instanceof PIDColourScheme) - { - PIDColour.setSelected(true); - } - else if (sg.cs instanceof Blosum62ColourScheme) - { - BLOSUM62Colour.setSelected(true); - } - else if (sg.cs instanceof UserColourScheme) - { - userDefinedColour.setSelected(true); - } - else if (sg.cs instanceof HydrophobicColourScheme) - { - hydrophobicityColour.setSelected(true); - } - else if (sg.cs instanceof HelixColourScheme) - { - helixColour.setSelected(true); - } - else if (sg.cs instanceof StrandColourScheme) - { - strandColour.setSelected(true); - } - else if (sg.cs instanceof TurnColourScheme) - { - turnColour.setSelected(true); - } - else if (sg.cs instanceof BuriedColourScheme) - { - buriedColour.setSelected(true); - } - else if (sg.cs instanceof ClustalxColourScheme) - { - clustalColour.setSelected(true); - } - else if (sg.cs instanceof PurinePyrimidineColourScheme) - { - purinePyrimidineColour.setSelected(true); - } + ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); - /* - * else if (sg.cs instanceof CovariationColourScheme) { - * covariationColour.setSelected(true); } - */ - else - { - noColourmenuItem.setSelected(true); - } + conservationMenuItem.setEnabled(!sg.isNucleotide()); - if (sg.cs != null && sg.cs.conservationApplied()) + if (sg.cs != null) { - conservationMenuItem.setSelected(true); + if (sg.cs.conservationApplied()) + { + conservationMenuItem.setSelected(true); + } + if (sg.cs.getThreshold() > 0) + { + abovePIDColour.setSelected(true); + } } + modifyConservation.setEnabled(conservationMenuItem.isSelected()); + modifyPID.setEnabled(abovePIDColour.isSelected()); displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); @@ -550,7 +452,7 @@ public class PopupMenu extends JPopupMenu buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(), reppdb = new Hashtable(); + Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { @@ -617,7 +519,8 @@ public class PopupMenu extends JPopupMenu void addFeatureLinks(final SequenceI seq, List links) { JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - List linkset = new ArrayList(); + Map> linkset = new LinkedHashMap<>(); + for (String link : links) { UrlLink urlLink = null; @@ -629,80 +532,28 @@ public class PopupMenu extends JPopupMenu Cache.log.error("Exception for URLLink '" + link + "'", foo); continue; } - ; + if (!urlLink.isValid()) { Cache.log.error(urlLink.getInvalidMessage()); continue; } - final String label = urlLink.getLabel(); - - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } - - if (seq != null && urlLink.usesSeqId()) // link is ID - { - // collect matching db-refs - DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(), - new String[] { urlLink.getTarget() }); - // if there are any dbrefs which match up with the link - if (dbr != null) - { - for (int r = 0; r < dbr.length; r++) - { - if (id != null && dbr[r].getAccessionId().equals(id)) - { - // suppress duplicate link creation for the bare sequence ID - // string with this link - id = null; - } - // create Bare ID link for this URL - createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset, - linkMenu, label, true); - } - } + urlLink.createLinksFromSeq(seq, linkset); + } - // Create urls from description but only for URL links which are regex - // links - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description where regex matches - createBareURLLink(urlLink, descr, linkset, linkMenu, label, false); - } - - } - else if (seq != null && !urlLink.usesSeqId()) // link is name - { - if (id != null) - { - // create Bare ID link for this URL - createBareURLLink(urlLink, id, linkset, linkMenu, label, false); - } - // Create urls from description but only for URL links which are regex - // links - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description where regex matches - createBareURLLink(urlLink, descr, linkset, linkMenu, label, false); - } - } - else - { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) - { - linkset.add(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); - } - } + addshowLinks(linkMenu, linkset.values()); + // disable link menu if there are no valid entries + if (linkMenu.getItemCount() > 0) + { + linkMenu.setEnabled(true); + } + else + { + linkMenu.setEnabled(false); } + if (sequence != null) { sequenceMenu.add(linkMenu); @@ -711,34 +562,7 @@ public class PopupMenu extends JPopupMenu { add(linkMenu); } - } - /* - * Create a bare URL Link - */ - private void createBareURLLink(UrlLink urlLink, String id, - List linkset, JMenu linkMenu, String label, - Boolean addSepToLabel) - { - String[] urls = urlLink.makeUrls(id, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.add(urls[u] + "|" + urls[u + 1]); - if (addSepToLabel) - { - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); - } - else - { - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } } /** @@ -779,8 +603,8 @@ public class PopupMenu extends JPopupMenu * the insertion order, which is the order of the annotations on the * alignment. */ - Map>> shownTypes = new LinkedHashMap>>(); - Map>> hiddenTypes = new LinkedHashMap>>(); + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, AlignmentAnnotationUtils.asList(annotations), forSequences); @@ -856,7 +680,7 @@ public class PopupMenu extends JPopupMenu label = label.substring(1, label.length() - 1); // a, b, c final JMenuItem item = new JMenuItem(label); item.setToolTipText(calcId); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -886,7 +710,7 @@ public class PopupMenu extends JPopupMenu SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); - Hashtable commonDbrefs = new Hashtable(); + Hashtable commonDbrefs = new Hashtable<>(); for (int sq = 0; sq < seqs.length; sq++) { @@ -1015,6 +839,15 @@ public class PopupMenu extends JPopupMenu } } + private void addshowLinks(JMenu linkMenu, Collection> linkset) + { + for (List linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3)); + } + } + /** * add a show URL menu item to the given linkMenu * @@ -1029,7 +862,7 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_param", new Object[] { url })); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1106,7 +939,7 @@ public class PopupMenu extends JPopupMenu { groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); - groupName.addActionListener(new java.awt.event.ActionListener() + groupName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1117,7 +950,7 @@ public class PopupMenu extends JPopupMenu sequenceMenu.setText(MessageManager.getString("label.sequence")); sequenceName.setText(MessageManager .getString("label.edit_name_description")); - sequenceName.addActionListener(new java.awt.event.ActionListener() + sequenceName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1127,7 +960,7 @@ public class PopupMenu extends JPopupMenu }); chooseAnnotations.setText(MessageManager .getString("action.choose_annotations")); - chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + chooseAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1137,7 +970,7 @@ public class PopupMenu extends JPopupMenu }); sequenceDetails.setText(MessageManager .getString("label.sequence_details")); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1147,19 +980,18 @@ public class PopupMenu extends JPopupMenu }); sequenceSelDetails.setText(MessageManager .getString("label.sequence_details")); - sequenceSelDetails - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sequenceSelectionDetails_actionPerformed(); - } - }); - PIDColour.setFocusPainted(false); + sequenceSelDetails.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); + unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1169,36 +1001,24 @@ public class PopupMenu extends JPopupMenu }); createGroupMenuItem.setText(MessageManager .getString("action.create_group")); - createGroupMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - createGroupMenuItem_actionPerformed(); - } - }); - - outline.setText(MessageManager.getString("action.border_colour")); - outline.addActionListener(new java.awt.event.ActionListener() + createGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - outline_actionPerformed(); + createGroupMenuItem_actionPerformed(); } }); - nucleotideMenuItem - .setText(MessageManager.getString("label.nucleotide")); - nucleotideMenuItem.addActionListener(new ActionListener() + + outline.setText(MessageManager.getString("action.border_colour")); + outline.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - nucleotideMenuItem_actionPerformed(); + outline_actionPerformed(); } }); - colourMenu.setText(MessageManager.getString("label.group_colour")); showBoxes.setText(MessageManager.getString("action.boxes")); showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() @@ -1229,7 +1049,7 @@ public class PopupMenu extends JPopupMenu } }); displayNonconserved.setText(MessageManager - .getString("label.show_non_conversed")); + .getString("label.show_non_conserved")); displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { @@ -1305,15 +1125,6 @@ public class PopupMenu extends JPopupMenu sequenceFeature_actionPerformed(); } }); - textColour.setText(MessageManager.getString("label.text_colour")); - textColour.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - textColour_actionPerformed(); - } - }); jMenu1.setText(MessageManager.getString("label.group")); pdbStructureDialog.setText(MessageManager .getString("label.show_pdbstruct_dialog")); @@ -1368,12 +1179,7 @@ public class PopupMenu extends JPopupMenu hideInsertions_actionPerformed(e); } }); - /* - * annotationMenuItem.setText("By Annotation"); - * annotationMenuItem.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent actionEvent) { - * annotationMenuItem_actionPerformed(actionEvent); } }); - */ + groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); @@ -1405,49 +1211,10 @@ public class PopupMenu extends JPopupMenu sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); sequenceMenu.add(makeReferenceSeq); - colourMenu.add(textColour); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideMenuItem); - if (ap.getAlignment().isNucleotide()) - { - // JBPNote - commented since the colourscheme isn't functional - colourMenu.add(purinePyrimidineColour); - } - colourMenu.add(userDefinedColour); - - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); - while (userColours.hasMoreElements()) - { - JMenuItem item = new JMenuItem(userColours.nextElement().toString()); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - colourMenu.add(item); - } - } + initColourMenu(); + buildColourMenu(); - colourMenu.addSeparator(); - colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -1465,160 +1232,119 @@ public class PopupMenu extends JPopupMenu jMenu1.add(showColourText); jMenu1.add(outline); jMenu1.add(displayNonconserved); - noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + } + + /** + * Constructs the entries for the colour menu + */ + protected void initColourMenu() + { + colourMenu.setText(MessageManager.getString("label.group_colour")); + textColour.setText(MessageManager.getString("label.text_colour")); + textColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(); + textColour_actionPerformed(); } }); - clustalColour.setText(MessageManager - .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(); - } - }); - zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(); - } - }); - taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(); - } - }); - hydrophobicityColour.setText(MessageManager - .getString("label.hydrophobicity")); - hydrophobicityColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); - helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(); - } - }); - strandColour.setText(MessageManager - .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(); - } - }); - turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(); - } - }); - buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(); - } - }); abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() + .getString("label.above_identity_threshold")); + abovePIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(); + abovePIDColour_actionPerformed(abovePIDColour.isSelected()); } }); - userDefinedColour.setText(MessageManager - .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + + modifyPID.setText(MessageManager + .getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); + modifyPID_actionPerformed(); } }); - PIDColour - .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() + + conservationMenuItem.setText(MessageManager + .getString("action.by_conservation")); + conservationMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(); + conservationMenuItem_actionPerformed(conservationMenuItem + .isSelected()); } }); - BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + + modifyConservation.setText(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(); + modifyConservation_actionPerformed(); } }); - purinePyrimidineColour.setText(MessageManager - .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); + } - /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { - * public void actionPerformed(ActionEvent e) { - * covariationColour_actionPerformed(); } }); - */ + /** + * Builds the group colour sub-menu, including any user-defined colours which + * were loaded at startup or during the Jalview session + */ + protected void buildColourMenu() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) + { + /* + * popup menu with no sequence group scope + */ + return; + } + colourMenu.removeAll(); + colourMenu.add(textColour); + colourMenu.addSeparator(); - conservationMenuItem.setText(MessageManager - .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); + ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); + + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDColour); + colourMenu.add(modifyPID); + } + + protected void modifyConservation_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + } + + protected void modifyPID_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + // .getName()); + // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); + SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + .getName()); + SliderPanel.showPIDSlider(); + } } /** @@ -1643,8 +1369,8 @@ public class PopupMenu extends JPopupMenu * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ - Map tipEntries = new TreeMap(); - final Map> candidates = new LinkedHashMap>(); + SortedMap tipEntries = new TreeMap<>(); + final Map> candidates = new LinkedHashMap<>(); AlignmentI al = this.ap.av.getAlignment(); AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries, candidates, al); @@ -1719,16 +1445,59 @@ public class PopupMenu extends JPopupMenu protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - if (sequence != null) + + HiddenColumns hidden = new HiddenColumns(); + BitSet inserts = new BitSet(), mask = new BitSet(); + + // set mask to preserve existing hidden columns outside selected group + if (ap.av.hasHiddenColumns()) + { + ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask); + } + + boolean markedPopup = false; + // mark inserts in current selection + if (ap.av.getSelectionGroup() != null) { - ColumnSelection cs = ap.av.getColumnSelection(); - if (cs == null) + // mark just the columns in the selection group to be hidden + inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av + .getSelectionGroup().getEndRes() + 1); + + // and clear that part of the mask + mask.andNot(inserts); + + // now clear columns without gaps + for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) { - cs = new ColumnSelection(); + if (sq == sequence) + { + markedPopup = true; + } + inserts.and(sq.getInsertionsAsBits()); } - cs.hideInsertionsFor(sequence); - ap.av.setColumnSelection(cs); } + else + { + // initially, mark all columns to be hidden + inserts.set(0, ap.av.getAlignment().getWidth()); + + // and clear out old hidden regions completely + mask.clear(); + } + + // now mark for sequence under popup if we haven't already done it + if (!markedPopup && sequence != null) + { + inserts.and(sequence.getInsertionsAsBits()); + } + + // finally, preserve hidden regions outside selection + inserts.or(mask); + + // and set hidden columns accordingly + hidden.hideMarkedBits(inserts); + + ap.av.getAlignment().setHiddenColumns(hidden); refresh(); } @@ -1787,126 +1556,13 @@ public class PopupMenu extends JPopupMenu void refresh() { ap.updateAnnotation(); - ap.paintAlignment(true); + // removed paintAlignment(true) here: + // updateAnnotation calls paintAlignment already, so don't need to call + // again PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void clustalColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void zappoColour_actionPerformed() - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void taylorColour_actionPerformed() - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void hydrophobicityColour_actionPerformed() - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void helixColour_actionPerformed() - { - getGroup().cs = new HelixColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void strandColour_actionPerformed() - { - getGroup().cs = new StrandColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void turnColour_actionPerformed() - { - getGroup().cs = new TurnColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void buriedColour_actionPerformed() - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - public void nucleotideMenuItem_actionPerformed() - { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } - - protected void purinePyrimidineColour_actionPerformed() - { - getGroup().cs = new PurinePyrimidineColourScheme(); - refresh(); - } - /* * protected void covariationColour_actionPerformed() { getGroup().cs = new * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); } @@ -1914,10 +1570,12 @@ public class PopupMenu extends JPopupMenu /** * DOCUMENT ME! * + * @param selected + * * @param e * DOCUMENT ME! */ - protected void abovePIDColour_actionPerformed() + public void abovePIDColour_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -1925,13 +1583,14 @@ public class PopupMenu extends JPopupMenu return; } - if (abovePIDColour.isSelected()) + if (selected) { sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1)); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + int threshold = SliderPanel.setPIDSliderSource(ap, + sg.getGroupColourScheme(), getGroup() .getName()); sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); @@ -1942,36 +1601,14 @@ public class PopupMenu extends JPopupMenu // remove PIDColouring { sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); + SliderPanel.hidePIDSlider(); } + modifyPID.setEnabled(selected); refresh(); } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void userDefinedColour_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - if (e.getSource().equals(userDefinedColour)) - { - new UserDefinedColours(ap, sg); - } - else - { - UserColourScheme udc = (UserColourScheme) UserDefinedColours - .getUserColourSchemes().get(e.getActionCommand()); - - sg.cs = udc; - } - refresh(); - } - - /** * Open a panel where the user can choose which types of sequence annotation * to show or hide. * @@ -1989,54 +1626,7 @@ public class PopupMenu extends JPopupMenu * @param e * DOCUMENT ME! */ - protected void PIDColour_actionPerformed() - { - SequenceGroup sg = getGroup(); - sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void BLOSUM62Colour_actionPerformed() - { - SequenceGroup sg = getGroup(); - - sg.cs = new Blosum62ColourScheme(); - - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void noColourmenuItem_actionPerformed() - { - getGroup().cs = null; - refresh(); - } - - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ - protected void conservationMenuItem_actionPerformed() + public void conservationMenuItem_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -2044,44 +1634,28 @@ public class PopupMenu extends JPopupMenu return; } - if (conservationMenuItem.isSelected()) + if (selected) { // JBPNote: Conservation name shouldn't be i18n translated - Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av + Conservation c = new Conservation("Group", sg.getSequences(ap.av .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.getConsPercGaps()); - sg.cs.setConservation(c); - SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(), + sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { sg.cs.setConservation(null); + SliderPanel.hideConservationSlider(); } - - refresh(); - } - - public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) - { - SequenceGroup sg = getGroup(); - if (sg == null) - { - return; - } - - AnnotationColourGradient acg = new AnnotationColourGradient( - sequence.getAnnotation()[0], null, - AnnotationColourGradient.NO_THRESHOLD); - - acg.setPredefinedColours(true); - sg.cs = acg; + modifyConservation.setEnabled(selected); refresh(); } @@ -2156,14 +1730,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane + JvOptionPane .showMessageDialog( ap, MessageManager .getString("label.spaces_converted_to_backslashes"), MessageManager .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -2262,10 +1836,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } @@ -2341,8 +1915,8 @@ public class PopupMenu extends JPopupMenu // or we simply trust the user wants // wysiwig behaviour - cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(), - ap, true)); + FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand()); + cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true)); } public void sequenceFeature_actionPerformed() @@ -2353,33 +1927,36 @@ public class PopupMenu extends JPopupMenu return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + int gSize = sg.getSize(); for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, null, start, end, null)); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) - { - ap.alignFrame.setShowSeqFeatures(true); - ap.highlightSearchResults(null); + + /* + * an entirely gapped region will generate empty lists of sequence / features + */ + if (!seqs.isEmpty()) + { + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures( + seqs, features, true, ap)) + { + ap.alignFrame.setShowSeqFeatures(true); + ap.highlightSearchResults(null); + } } } @@ -2446,4 +2023,32 @@ public class PopupMenu extends JPopupMenu } } + /** + * Action on user selecting an item from the colour menu (that does not have + * its bespoke action handler) + * + * @return + */ + @Override + public void changeColour_actionPerformed(String colourSchemeName) + { + SequenceGroup sg = getGroup(); + /* + * switch to the chosen colour scheme (or null for None) + */ + ColourSchemeI colourScheme = ColourSchemes.getInstance() + .getColourScheme(colourSchemeName, sg, + ap.av.getHiddenRepSequences()); + sg.setColourScheme(colourScheme); + if (colourScheme instanceof Blosum62ColourScheme + || colourScheme instanceof PIDColourScheme) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); + } + + refresh(); + } + }