X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=5f6c55694a49bfc3e481a3aa50ccf67ac99cbe67;hb=8ba93f7655ea7165579539158b6a5eb076135bba;hp=6974d96780ca5238578a775b751c4812d665617a;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 6974d96..5f6c556 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -6,35 +6,77 @@
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.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.renderer.AnnotationRenderer;
+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.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.BitSet;
+import java.util.Collection;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+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!
*
@@ -43,6 +85,10 @@ 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();
@@ -72,6 +118,7 @@ public class PopupMenu extends JPopupMenu
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
@@ -91,8 +138,12 @@ public class PopupMenu extends JPopupMenu
JMenuItem sequenceSelDetails = new JMenuItem();
+ JMenuItem chooseAnnotations = new JMenuItem();
+
SequenceI sequence;
+
JMenuItem createGroupMenuItem = new JMenuItem();
+
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
@@ -124,17 +175,25 @@ public class PopupMenu extends JPopupMenu
JMenu pdbMenu = new JMenu();
JMenuItem pdbFromFile = new JMenuItem();
- // JBPNote: Commented these out - Should add these services via the web services menu system.
- // JMenuItem ContraFold = new JMenuItem();
-
- // JMenuItem RNAFold = new JMenuItem();
-
+
+ // JBPNote: Commented these out - Should add these services via the web
+ // services menu system.
+ // JMenuItem ContraFold = new JMenuItem();
+
+ // JMenuItem RNAFold = new JMenuItem();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
JMenu outputMenu = new JMenu();
+ JMenu showAnnotationsMenu = new JMenu();
+
+ JMenu hideAnnotationsMenu = new JMenu();
+
+ JMenuItem addDatasequenceAnnotations = new JMenuItem();
+
JMenuItem sequenceFeature = new JMenuItem();
JMenuItem textColour = new JMenuItem();
@@ -209,6 +268,7 @@ public class PopupMenu extends JPopupMenu
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
@@ -218,6 +278,11 @@ public class PopupMenu extends JPopupMenu
outputMenu.add(item);
}
+ /*
+ * Build menus for annotation types that may be shown or hidden.
+ */
+ buildAnnotationTypesMenus();
+
try
{
jbInit();
@@ -249,11 +314,13 @@ public class PopupMenu extends JPopupMenu
{
// 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 PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ // 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);
@@ -286,25 +353,29 @@ public class PopupMenu extends JPopupMenu
final String rnastruc = aa[i].getRNAStruc();
final String structureLine = aa[i].label;
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
+ 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);
- new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
- .getName(), ap);
- //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
- System.out.println("end");
+ // 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(),
+ // seq.getName(), ap);
+ System.out.println("end");
}
});
viewStructureMenu.add(menuItem);
@@ -324,13 +395,16 @@ public class PopupMenu extends JPopupMenu
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_sequence_name", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
-
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
@@ -343,9 +417,11 @@ public class PopupMenu extends JPopupMenu
}
- menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(false);
@@ -356,9 +432,12 @@ public class PopupMenu extends JPopupMenu
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
+ menuItem = new JMenuItem(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(true);
@@ -374,9 +453,11 @@ public class PopupMenu extends JPopupMenu
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showSequence(index);
@@ -394,9 +475,11 @@ public class PopupMenu extends JPopupMenu
if (ap.av.hasHiddenRows())
{
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showAllHiddenSeqs();
@@ -413,12 +496,16 @@ public class PopupMenu extends JPopupMenu
}
SequenceGroup sg = ap.av.getSelectionGroup();
- boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
- {
- groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
- groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));
+ {
+ groupName.setText(MessageManager.formatMessage("label.name_param",
+ new String[]
+ { sg.getName() }));
+ groupName.setText(MessageManager
+ .getString("label.edit_name_and_description_current_group"));
if (sg.cs instanceof ZappoColourScheme)
{
@@ -468,8 +555,7 @@ public class PopupMenu extends JPopupMenu
{
purinePyrimidineColour.setSelected(true);
}
-
-
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
@@ -493,15 +579,14 @@ 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())
{
- Vector pes = (Vector) sq.getDatasetSequence()
- .getPDBId();
- if (pes != null)
+ Vector pes = sq.getDatasetSequence().getPDBId();
+ if (pes != null && pes.size() > 0)
{
- reppdb.put(pes.get(0).getId(),pes.get(0));
+ reppdb.put(pes.get(0).getId(), pes.get(0));
for (PDBEntry pe : pes)
{
pdbe.put(pe.getId(), pe);
@@ -515,38 +600,50 @@ public class PopupMenu extends JPopupMenu
if (pdbe.size() > 0)
{
final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
- final JMenuItem gpdbview,rpdbview;
+ new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
+ new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
if (pdbe.size() == 1)
{
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_structure_for", new String[]
+ { sqass.getDisplayId(false) })));
}
else
{
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_all_structures", new String[]
+ { new Integer(pdbe.size()).toString() })));
}
- gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
+ gpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
gpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pe, ap.av.collateForPDB(pe));
}
});
- if (reppdb.size()>1 && reppdb.size() 1 && reppdb.size() < pdbe.size())
{
- structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
- rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ .formatMessage(
+ "label.view_all_representative_structures",
+ new String[]
+ { new Integer(reppdb.size()).toString() })));
+ rpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
rpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pr, ap.av.collateForPDB(pr));
}
});
}
@@ -562,11 +659,13 @@ public class PopupMenu extends JPopupMenu
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- jMenu1.setText(MessageManager.getString("action.edit_new_group"));
- } else {
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
- jMenu1.setText(MessageManager.getString("action.edit_group"));
+ jMenu1.setText(MessageManager.getString("action.edit_group"));
}
if (seq == null)
@@ -578,7 +677,7 @@ public class PopupMenu extends JPopupMenu
if (links != null && links.size() > 0)
{
- JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
@@ -698,6 +797,237 @@ public class PopupMenu extends JPopupMenu
}
}
+ /**
+ * Add annotation types to a 'Show annotations' or 'Hide annotations' menu.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection.
+ *
+ * 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)
+ */
+ protected void buildAnnotationTypesMenus()
+ {
+ showAnnotationsMenu.removeAll();
+ hideAnnotationsMenu.removeAll();
+ final List all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showAnnotationsMenu, all, true, true);
+ addAnnotationTypeToShowHide(hideAnnotationsMenu, all, true, false);
+ showAnnotationsMenu.addSeparator();
+ hideAnnotationsMenu.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();
+
+ for (AlignmentAnnotation aa : annotations)
+ {
+
+ if (sequenceGroup == null
+ || (aa.sequenceRef != null && sequenceGroup.getSequences()
+ .contains(aa.sequenceRef)))
+ {
+ /*
+ * 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);
+ }
+ }
+ }
+ }
+ /*
+ * 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())
+ {
+ final List groupLabel = groupLabels.get(group);
+ if (visibleGraphGroups.get(group))
+ {
+ if (!shownTypes.contains(groupLabel))
+ {
+ shownTypes.add(groupLabel);
+ }
+ }
+ else if (!hiddenTypes.contains(groupLabel))
+ {
+ hiddenTypes.add(groupLabel);
+ }
+ }
+ }
+
+ /**
+ * 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.
+ *
+ * @see AnnotationRenderer#drawComponent
+ * @param annotations
+ * @return
+ */
+ public static BitSet getVisibleLineGraphGroups(
+ AlignmentAnnotation[] annotations)
+ {
+ // todo move to a utility class
+ BitSet result = new BitSet();
+ for (AlignmentAnnotation ann : annotations)
+ {
+ if (ann.graph == AlignmentAnnotation.LINE_GRAPH && ann.visible)
+ {
+ int gg = ann.graphGroup;
+ if (gg > -1)
+ {
+ result.set(gg);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @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 Collection 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.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(types, allTypes, actionIsShow);
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ /**
+ * Action on selecting a list of annotation type (or the 'all types' values)
+ * to show or hide for the selection.
+ *
+ * @param types
+ * @param anyType
+ * @param doShow
+ */
+ protected void showHideAnnotation_actionPerformed(
+ Collection types, boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && ap.av.getSelectionGroup().getSequences()
+ .contains(aa.sequenceRef))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ refresh();
+ }
+
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
@@ -705,11 +1035,18 @@ public class PopupMenu extends JPopupMenu
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
JMenu[] linkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
- new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
- // created.
+ { null, new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
+ // types
+ // of url
+ // that
+ // might
+ // be
+ // created.
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
@@ -831,7 +1168,8 @@ public class PopupMenu extends JPopupMenu
}
if (addMenu)
{
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
@@ -857,14 +1195,18 @@ public class PopupMenu extends JPopupMenu
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_param", new String[]
+ { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
showLink(url);
@@ -892,15 +1234,21 @@ public class PopupMenu extends JPopupMenu
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
- // TODO: put in info about what is being sent.
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_seqs_param",
+ new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // 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
@@ -926,228 +1274,291 @@ public class PopupMenu extends JPopupMenu
*/
private void jbInit() throws Exception
{
- groupMenu.setText(MessageManager.getString("label.group"));
- groupMenu.setText(MessageManager.getString("label.selection"));
- groupName.setText(MessageManager.getString("label.name"));
+ groupMenu.setText(MessageManager.getString("label.group"));
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
}
});
- sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager.getString("label.edit_name_description"));
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+ sequenceName.setText(MessageManager
+ .getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ 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();
}
});
- sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ 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);
- unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ 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.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
}
});
- colourMenu.setText(MessageManager.getString("label.group_colour"));
- showBoxes.setText(MessageManager.getString("action.boxes"));
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ showBoxes.setText(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
}
});
- showText.setText(MessageManager.getString("action.text"));
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
- showColourText.setText(MessageManager.getString("label.colour_text"));
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setText(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText(MessageManager.getString("action.edit"));
- cut.setText(MessageManager.getString("action.cut"));
+ editMenu.setText(MessageManager.getString("action.edit"));
+ cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
}
});
- upperCase.setText(MessageManager.getString("label.to_upper_case"));
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- copy.setText(MessageManager.getString("action.copy"));
+ copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
- lowerCase.setText(MessageManager.getString("label.to_lower_case"));
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- toggle.setText(MessageManager.getString("label.toggle_case"));
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
- pdbFromFile.setText(MessageManager.getString("label.from_file"));
+ pdbMenu.setText(MessageManager
+ .getString("label.associate_structure_with_sequence"));
+ pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pdbFromFile_actionPerformed();
}
});
-// RNAFold.setText("From RNA Fold with predict2D");
-// RNAFold.addActionListener(new ActionListener()
-// {
-// public void actionPerformed(ActionEvent e)
-// {
-// try {
-// RNAFold_actionPerformed();
-// } catch (Exception e1) {
-// // TODO Auto-generated catch block
-// e1.printStackTrace();
-// }
-// }
-// });
-// ContraFold.setText("From Contra Fold with predict2D");
-// ContraFold.addActionListener(new ActionListener()
-// {
-// public void actionPerformed(ActionEvent e)
-// {
-// try {
-// ContraFold_actionPerformed();
-// } catch (Exception e1) {
-// // TODO Auto-generated catch block
-// e1.printStackTrace();
-// }
-// }
-// });
- enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
+ // RNAFold.setText("From RNA Fold with predict2D");
+ // RNAFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // RNAFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // ContraFold.setText("From Contra Fold with predict2D");
+ // ContraFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // ContraFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
enterPDB_actionPerformed();
}
});
- discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
discoverPDB_actionPerformed();
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
- sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
+ showAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ hideAnnotationsMenu.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()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
- textColour.setText(MessageManager.getString("label.text_colour"));
+ 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"));
- structureMenu.setText(MessageManager.getString("label.structure"));
- viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
+ jMenu1.setText(MessageManager.getString("label.group"));
+ structureMenu.setText(MessageManager.getString("label.structure"));
+ viewStructureMenu.setText(MessageManager
+ .getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed(actionEvent);
@@ -1164,6 +1575,10 @@ public class PopupMenu extends JPopupMenu
add(groupMenu);
add(sequenceMenu);
this.add(structureMenu);
+ // groupMenu.add(chooseAnnotations);
+ groupMenu.add(showAnnotationsMenu);
+ groupMenu.add(hideAnnotationsMenu);
+ groupMenu.add(addDatasequenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
@@ -1185,10 +1600,11 @@ public class PopupMenu extends JPopupMenu
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideMenuItem);
- if (ap.getAlignment().isNucleotide()) {
- // JBPNote - commented since the colourscheme isn't functional
- // colourMenu.add(RNAInteractionColour);
- colourMenu.add(purinePyrimidineColour);
+ if (ap.getAlignment().isNucleotide())
+ {
+ // JBPNote - commented since the colourscheme isn't functional
+ // colourMenu.add(RNAInteractionColour);
+ colourMenu.add(purinePyrimidineColour);
}
// colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
@@ -1203,6 +1619,7 @@ 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);
@@ -1223,9 +1640,10 @@ public class PopupMenu extends JPopupMenu
editMenu.add(lowerCase);
editMenu.add(toggle);
pdbMenu.add(pdbFromFile);
- // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
- // pdbMenu.add(RNAFold);
- // pdbMenu.add(ContraFold);
+ // JBPNote: These shouldn't be added here - should appear in a generic
+ // 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
@@ -1238,133 +1656,155 @@ public class PopupMenu extends JPopupMenu
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
- noColourmenuItem.setText(MessageManager.getString("label.none"));
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
}
});
- clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
+ 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.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.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.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.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.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.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.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.setText(MessageManager
+ .getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed();
}
});
- BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ 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(); } });
*/
- conservationMenuItem.setText(MessageManager.getString("label.conservation"));
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
@@ -1372,6 +1812,59 @@ 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.
+ *
+ * @return
+ */
+ protected List getDatasequenceAnnotationsNotOnAlignment(
+ SequenceGroup sg)
+ {
+ List result = new ArrayList();
+
+ for (SequenceI seq : sg.getSequences())
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations != null)
+ {
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * 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);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Add any annotations on the sequence dataset to the alignment (that are not
+ * already copied to it).
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ List anns)
+ {
+ for (AlignmentAnnotation ann : anns)
+ {
+ // todo: copy, add, adjust...
+ }
+ }
+
protected void sequenceSelectionDetails_actionPerformed()
{
createSequenceDetailsReport(ap.av.getSequenceSelection());
@@ -1389,8 +1882,12 @@ public class PopupMenu extends JPopupMenu
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
- + "
");
+ contents.append("
"
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new String[]
+ { seq.getDisplayId(true) }) + "
");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
contents,
@@ -1404,8 +1901,11 @@ public class PopupMenu extends JPopupMenu
}
cap.setText("" + contents.toString() + "");
- Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))
- ,500, 400);
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequece_details_for",
+ (sequences.length == 1 ? new String[]
+ { sequences[0].getDisplayId(true) } : new String[]
+ { MessageManager.getString("label.selection") })), 500, 400);
}
@@ -1541,7 +2041,6 @@ public class PopupMenu extends JPopupMenu
refresh();
}
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@ -1592,7 +2091,7 @@ public class PopupMenu extends JPopupMenu
{
SequenceGroup sg = getGroup();
- if (e.getSource().equals(userDefinedColour))
+ if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
@@ -1607,6 +2106,18 @@ 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
@@ -1669,7 +2180,7 @@ public class PopupMenu extends JPopupMenu
if (conservationMenuItem.isSelected())
{
- // JBPNote: Conservation name shouldn't be i18n translated
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
@@ -1721,8 +2232,10 @@ public class PopupMenu extends JPopupMenu
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",
- MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
+ sg.getDescription(), " "
+ + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -1761,8 +2274,12 @@ public class PopupMenu extends JPopupMenu
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",
- MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
+ sequence.getDescription(),
+ " " + MessageManager.getString("label.sequence_name")
+ + " ",
+ MessageManager.getString("label.sequence_description") + " ",
+ MessageManager
+ .getString("label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
@@ -1774,10 +2291,14 @@ public class PopupMenu extends JPopupMenu
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- MessageManager.getString("label.spaces_converted_to_backslashes"),
- MessageManager.getString("label.no_spaces_allowed_sequence_name"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
@@ -1804,9 +2325,11 @@ public class PopupMenu extends JPopupMenu
ap.av.setSelectionGroup(null);
refresh();
}
+
void createGroupMenuItem_actionPerformed()
{
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
refresh();
}
@@ -1819,7 +2342,8 @@ public class PopupMenu extends JPopupMenu
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
@@ -1873,11 +2397,10 @@ public class PopupMenu extends JPopupMenu
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
@@ -1943,17 +2466,17 @@ public class PopupMenu extends JPopupMenu
if (source == toggle)
{
- description = MessageManager.getString("label.toggle_case");
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = MessageManager.getString("label.to_upper_case");
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = MessageManager.getString("label.to_lower_case");
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
@@ -1973,31 +2496,18 @@ public class PopupMenu extends JPopupMenu
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
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()
@@ -2005,8 +2515,12 @@ public class PopupMenu extends JPopupMenu
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
- chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
@@ -2019,22 +2533,25 @@ public class PopupMenu extends JPopupMenu
}
}
- // JBNote: commented out - these won't be instantiated here...!
-// public void RNAFold_actionPerformed() throws Exception
-// {
-// Predict2D P2D = new Predict2D();
-// P2D.getStructure2DFromRNAFold("toto");
-// }
-//
-// public void ContraFold_actionPerformed() throws Exception
-// {
-// Predict2D P2D = new Predict2D();
-// P2D.getStructure2DFromContraFold("toto");
-// }
+
+ // JBNote: commented out - these won't be instantiated here...!
+ // public void RNAFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromRNAFold("toto");
+ // }
+ //
+ // public void ContraFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromContraFold("toto");
+ // }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
@@ -2052,6 +2569,7 @@ public class PopupMenu extends JPopupMenu
: ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
+ @Override
public void run()
{
@@ -2136,16 +2654,19 @@ 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(),
- sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
- MessageManager.getString("label.edit_sequence"), ap.alignFrame);
+ sg.getEndRes() + 1), null,
+ MessageManager.getString("label.edit_sequence"), null,
+ MessageManager.getString("label.edit_sequence"),
+ ap.alignFrame);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),