/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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 MCview.*;
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentAnnotationUtils;
+import jalview.analysis.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
import jalview.util.GroupUrlLink;
+import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
/**
* DOCUMENT ME!
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.118 $
*/
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();
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem sequenceName = new JMenuItem();
- Sequence sequence;
+ JMenuItem sequenceDetails = new JMenuItem();
+
+ JMenuItem sequenceSelDetails = new JMenuItem();
+
+ JMenuItem chooseAnnotations = new JMenuItem();
+
+ SequenceI sequence;
+
+ JMenuItem createGroupMenuItem = new JMenuItem();
JMenuItem unGroupMenuItem = new JMenuItem();
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();
+
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
JMenu outputMenu = new JMenu();
+ JMenu seqShowAnnotationsMenu = new JMenu();
+
+ JMenu seqHideAnnotationsMenu = new JMenu();
+
+ JMenuItem seqAddReferenceAnnotations = new JMenuItem();
+
+ JMenu groupShowAnnotationsMenu = new JMenu();
+
+ JMenu groupHideAnnotationsMenu = new JMenu();
+
+ JMenuItem groupAddReferenceAnnotations = new JMenuItem();
+
JMenuItem sequenceFeature = new JMenuItem();
JMenuItem textColour = new JMenuItem();
* Creates a new PopupMenu object.
*
* @param ap
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+ public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
{
this(ap, seq, links, null);
}
+
/**
*
* @param ap
* @param links
* @param groupLinks
*/
- public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks)
+ public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
+ Vector links, Vector groupLinks)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
colours.add(userDefinedColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
+ colours.add(purinePyrimidineColour);
+ colours.add(RNAInteractionColour);
+ // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
outputMenu.add(item);
}
+ /*
+ * Build menus for annotation types that may be shown or hidden, and for
+ * 'reference annotations' that may be added to the alignment. First for the
+ * currently selected sequence (if there is one):
+ */
+ final List<SequenceI> selectedSequence = (seq == null ? Collections
+ .<SequenceI> emptyList() : Arrays.asList(seq));
+ buildAnnotationTypesMenus(seqShowAnnotationsMenu,
+ seqHideAnnotationsMenu, selectedSequence);
+ configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
+ selectedSequence);
+
+ /*
+ * And repeat for the current selection group (if there is one):
+ */
+ final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
+ .<SequenceI> emptyList() : ap.av.getSelectionGroup()
+ .getSequences());
+ buildAnnotationTypesMenus(groupShowAnnotationsMenu,
+ groupHideAnnotationsMenu, selectedGroup);
+ configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
+ selectedGroup);
+
try
{
jbInit();
e.printStackTrace();
}
+ JMenuItem menuItem;
if (seq != null)
{
sequenceMenu.setText(sequence.getName());
- JMenuItem menuItem;
if (seq.getDatasetSequence().getPDBId() != null
&& seq.getDatasetSequence().getPDBId().size() > 0)
{
menuItem = new JMenuItem();
menuItem.setText(pdb.getId());
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- Vector seqs = new Vector();
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)
- {
- Vector pdbs = ap.av.alignment.getSequenceAt(i)
- .getDatasetSequence().getPDBId();
- if (pdbs == null)
- continue;
-
- for (int p = 0; p < pdbs.size(); p++)
- {
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
- if (p1.getId().equals(pdb.getId()))
- {
- if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
- seqs.addElement(ap.av.alignment.getSequenceAt(i));
-
- continue;
- }
- }
- }
-
- SequenceI[] seqs2 = new SequenceI[seqs.size()];
- seqs.toArray(seqs2);
-
- new AppJmol(pdb, seqs2, null, ap);
- // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+ // 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 StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(pdb,
+ ap.av.collateForPDB(new PDBEntry[]
+ { pdb })[0], null, ap);
}
});
viewStructureMenu.add(menuItem);
}
else
{
- structureMenu.remove(viewStructureMenu);
+ if (ap.av.getAlignment().isNucleotide() == false)
+ {
+ structureMenu.remove(viewStructureMenu);
+ }
// structureMenu.remove(colStructureMenu);
}
- menuItem = new JMenuItem("Hide Sequences");
+ if (ap.av.getAlignment().isNucleotide() == true)
+ {
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ 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.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");
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+
+ // SequenceFeatures[] test = seq.getSequenceFeatures();
+
+ if (seq.getAnnotation() != null)
+ {
+ AlignmentAnnotation seqAnno[] = seq.getAnnotation();
+ for (int i = 0; i < seqAnno.length; i++)
+ {
+ if (seqAnno[i].getRNAStruc() != null)
+ {
+ final String rnastruc = seqAnno[i].getRNAStruc();
+
+ // TODO: make rnastrucF a bit more nice
+ menuItem = new JMenuItem();
+ 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);
+ }
+ });
+ viewStructureMenu.add(menuItem);
+ }
+ }
+ }
+
+ }
+
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(false);
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem("Represent Group with " + 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);
sequenceMenu.add(menuItem);
}
- if (ap.av.hasHiddenRows)
+ if (ap.av.hasHiddenRows())
{
- final int index = ap.av.alignment.findIndex(seq);
+ final int index = ap.av.getAlignment().findIndex(seq);
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem("Reveal Sequences");
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showSequence(index);
});
add(menuItem);
}
-
- menuItem = new JMenuItem("Reveal All");
+ }
+ }
+ // for the case when no sequences are even visible
+ if (ap.av.hasHiddenRows())
+ {
+ {
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showAllHiddenSeqs();
}
SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
- if (sg != null)
+ if (sg != null && sg.getSize() > 0)
{
- groupName.setText(sg.getName());
+ 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)
{
{
clustalColour.setSelected(true);
}
+ else if (sg.cs instanceof PurinePyrimidineColourScheme)
+ {
+ purinePyrimidineColour.setSelected(true);
+ }
+
+ /*
+ * else if (sg.cs instanceof CovariationColourScheme) {
+ * covariationColour.setSelected(true); }
+ */
else
{
noColourmenuItem.setSelected(true);
{
conservationMenuItem.setSelected(true);
}
- displayNonconserved.setSelected(sg.getShowunconserved());
+ displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
showBoxes.setSelected(sg.getDisplayBoxes());
// add any groupURLs to the groupURL submenu and make it visible
- if (groupLinks!=null && groupLinks.size()>0) {
+ if (groupLinks != null && groupLinks.size() > 0)
+ {
buildGroupURLMenu(sg, groupLinks);
}
+ // Add a 'show all structures' for the current selection
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+ SequenceI sqass = null;
+ for (SequenceI sq : ap.av.getSequenceSelection())
+ {
+ Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
+ if (pes != null && pes.size() > 0)
+ {
+ reppdb.put(pes.get(0).getId(), pes.get(0));
+ for (PDBEntry pe : pes)
+ {
+ pdbe.put(pe.getId(), pe);
+ if (sqass == null)
+ {
+ sqass = sq;
+ }
+ }
+ }
+ }
+ 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;
+ if (pdbe.size() == 1)
+ {
+ 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() })));
+ }
+ 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 StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pe, ap.av.collateForPDB(pe));
+ }
+ });
+ if (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"));
+ rpdbview.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ }
+ });
+ }
+ }
}
else
{
editMenu.setVisible(false);
}
- if (!ap.av.alignment.getGroups().contains(sg))
+ if (!isDefinedGroup)
{
+ createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
+ jMenu1.setText(MessageManager.getString("action.edit_new_group"));
+ }
+ else
+ {
+ createGroupMenuItem.setVisible(false);
+ unGroupMenuItem.setVisible(true);
+ jMenu1.setText(MessageManager.getString("action.edit_group"));
}
if (seq == null)
if (links != null && links.size() > 0)
{
-
- JMenu linkMenu = new JMenu("Link");
+
+ JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
Vector linkset = new Vector();
for (int i = 0; i < links.size(); i++)
{
continue;
}
final String label = urlLink.getLabel();
- if (urlLink.isDynamic())
+ if (seq != null && urlLink.isDynamic())
{
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
- .getDBRef(), new String[]
- { urlLink.getTarget() });
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { urlLink.getTarget() });
// collect id string too
String id = seq.getName();
String descr = seq.getDescription();
- if (descr!=null && descr.length()<1)
+ if (descr != null && descr.length() < 1)
{
descr = null;
}
{
for (int u = 0; u < urls.length; u += 2)
{
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
- linkset.addElement(urls[u]+"|"+urls[u+1]);
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
+ addshowLink(linkMenu, label + "|" + urls[u],
+ urls[u + 1]);
}
}
}
{
for (int u = 0; u < urls.length; u += 2)
{
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
- linkset.addElement(urls[u]+"|"+urls[u+1]);
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label, urls[u + 1]);
}
}
}
}
- // Create urls from description but only for URL links which are regex links
- if (descr != null && urlLink.getRegexReplace()!=null)
+ // 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
String[] urls = urlLink.makeUrls(descr, true);
{
for (int u = 0; u < urls.length; u += 2)
{
- if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+ if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
{
- linkset.addElement(urls[u]+"|"+urls[u+1]);
+ linkset.addElement(urls[u] + "|" + urls[u + 1]);
addshowLink(linkMenu, label, urls[u + 1]);
}
}
}
else
{
- if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
+ if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
{
- linkset.addElement(label+"|"+urlLink.getUrl_prefix());
+ linkset.addElement(label + "|" + urlLink.getUrl_prefix());
// Add a non-dynamic link
addshowLink(linkMenu, label, urlLink.getUrl_prefix());
}
}
}
}
-
+
+ /**
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
+ * <p>
+ * 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.
+ * <p>
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
+ List<SequenceI> forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
+ */
+ Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
+ Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
+ hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations),
+ forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List<String> type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences,
+ calcId, type, false, true);
+ }
+ }
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List<String> type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences,
+ calcId, type, false, false);
+ }
+ }
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
+
+ /**
+ * Returns a list of sequences - either the current selection group (if there
+ * is one), else the specified single sequence.
+ *
+ * @param seq
+ * @return
+ */
+ protected List<SequenceI> getSequenceScope(SequenceI seq)
+ {
+ List<SequenceI> forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
+ {
+ forSequences = selectionGroup.getSequences();
+ }
+ else
+ {
+ forSequences = seq == null ? Collections.<SequenceI> emptyList()
+ : Arrays.asList(seq);
+ }
+ return forSequences;
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
+ final List<SequenceI> forSequences, String calcId,
+ final List<String> types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showHideAnnotation_actionPerformed(types, forSequences, allTypes,
+ actionIsShow);
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ /**
+ * Action on selecting a list of annotation type (or the 'all types' values)
+ * to show or hide for the specified sequences.
+ *
+ * @param types
+ * @param forSequences
+ * @param anyType
+ * @param doShow
+ */
+ protected void showHideAnnotation_actionPerformed(
+ Collection<String> types, List<SequenceI> forSequences,
+ boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : ap.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && forSequences.contains(aa.sequenceRef))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ refresh();
+ }
+
private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
{
-
- // TODO: usability: thread off the generation of group url content so root menu appears asap
+
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu("Group Link");
- JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
- SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
+ 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.
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
- for (int sq = 0; sq<seqs.length;sq++) {
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
- int start = seqs[sq].findPosition(sg.getStartRes()),end=seqs[sq].findPosition(sg.getEndRes());
+ int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
+ .findPosition(sg.getEndRes());
// just collect ids from dataset sequence
- // TODO: check if IDs collected from selecton group intersects with the current selection, too
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
SequenceI sqi = seqs[sq];
- while (sqi.getDatasetSequence()!=null) {
- sqi = sqi.getDatasetSequence(); }
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
DBRefEntry[] dbr = sqi.getDBRef();
- if (dbr!=null && dbr.length>0)
+ if (dbr != null && dbr.length > 0)
{
- for (int d=0;d<dbr.length;d++)
+ for (int d = 0; d < dbr.length; d++)
{
- String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
Object[] sarray = (Object[]) commonDbrefs.get(src);
- if (sarray==null)
+ if (sarray == null)
{
sarray = new Object[2];
- sarray[0] = new int[] { 0 };
+ sarray[0] = new int[]
+ { 0 };
sarray[1] = new String[seqs.length];
-
- commonDbrefs.put(src,sarray);
+
+ commonDbrefs.put(src, sarray);
}
-
- if (((String[])sarray[1])[sq]==null) {
- if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
- ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
- ((int[])sarray[0])[0]++;
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!dbr[d].hasMap()
+ || (dbr[d].getMap().locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+ ((int[]) sarray[0])[0]++;
}
}
}
}
}
// now create group links for all distinct ID/sequence sets.
- boolean addMenu = false; // indicates if there are any group links to give to user
- for (int i = 0; i < groupLinks.size(); i++) {
- String link = groupLinks.elementAt(i).toString();
- GroupUrlLink urlLink = null;
- try
- {
- urlLink = new GroupUrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- boolean usingNames = false;
- // Now see which parts of the group apply for this URL
- String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
- String[] seqstr,ids; // input to makeUrl
- if (idset!=null)
+ boolean addMenu = false; // indicates if there are any group links to give
+ // to user
+ for (int i = 0; i < groupLinks.size(); i++)
+ {
+ String link = groupLinks.elementAt(i).toString();
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+ + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+ String[] seqstr, ids; // input to makeUrl
+ if (idset != null)
+ {
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
{
- int numinput = ((int[])idset[0])[0];
- String[] allids = ((String[])idset[1]);
- seqstr = new String[numinput];
- ids = new String[numinput];
- for (int sq=0,idcount=0;sq<seqs.length;sq++)
+ if (allids[sq] != null)
{
- if (allids[sq]!=null) {
- ids[idcount] = allids[sq];
- seqstr[idcount++] = idandseqs[1][sq];
- }
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
}
- } else {
- // just use the id/seq set
- seqstr = idandseqs[1];
- ids = idandseqs[0];
- usingNames=true;
- }
- // and try and make the groupURL!
-
- Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
- if (urlset!=null)
- {
- int type = urlLink.getGroupURLType() & 3;
- //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
- // first two bits ofurlLink type bitfield are sequenceids and sequences
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), urlLink, urlset);
- addMenu = true;
}
}
+ else
+ {
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames = true;
+ }
+ // and try and make the groupURL!
+
+ Object[] urlset = null;
+ try
+ {
+ urlset = urlLink.makeUrlStubs(ids, seqstr,
+ "FromJalview" + System.currentTimeMillis(), false);
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // System.out.println(urlLink.getGroupURLType()
+ // +" "+((String[])urlset[3])[0]);
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(linkMenus[type], label
+ + (((type & 1) == 1) ? ("("
+ + (usingNames ? "Names" : ltarget) + ")") : ""),
+ urlLink, urlset);
+ addMenu = true;
+ }
+ }
if (addMenu)
{
- groupLinksMenu = new JMenu("Group Links");
- for (int m=0;m<linkMenus.length; m++)
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ for (int m = 0; m < linkMenus.length; m++)
{
- if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+ if (linkMenus[m] != null
+ && linkMenus[m].getMenuComponentCount() > 0)
{
groupLinksMenu.add(linkMenus[m]);
}
}
-
+
groupMenu.add(groupLinksMenu);
}
}
* add a show URL menu item to the given linkMenu
*
* @param linkMenu
- * @param label -
- * menu label string
- * @param url -
- * url to open
+ * @param label
+ * - menu label string
+ * @param url
+ * - url to open
*/
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL: " + 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);
linkMenu.add(item);
}
+
/**
* add a late bound groupURL item to the given linkMenu
*
* @param linkMenu
- * @param label -
- * menu label string
- * @param urlgenerator GroupURLLink used to generate URL
- * @param urlstub Object array returned from the makeUrlStubs function.
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
*/
- private void addshowLink(JMenu linkMenu, String label, final GroupUrlLink urlgenerator, final Object[] urlstub)
+ private void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText("open URL ("+urlgenerator.getUrl_prefix()+"..) ("+urlgenerator.getNumberInvolved(urlstub)+" seqs)"); // 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()
{
- showLink(urlgenerator.constructFrom(urlstub));
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e)
+ {
+ }
}
}).start();
linkMenu.add(item);
}
+
/**
* DOCUMENT ME!
*
* @throws Exception
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private void jbInit() throws Exception
{
- groupMenu.setText("Group");
- groupMenu.setText("Selection");
- groupName.setText("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("Sequence");
- sequenceName.setText("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();
}
});
+ 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
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
- outline.setText("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("Nucleotide");
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
}
});
- colourMenu.setText("Group Colour");
- showBoxes.setText("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("Text");
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
}
});
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
- displayNonconserved.setText("Show Nonconserved");
+ 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("Edit");
- cut.setText("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("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("Copy");
+ copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
}
});
- lowerCase.setText("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("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- pdbMenu.setText("Associate Structure with Sequence");
- pdbFromFile.setText("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();
}
});
- enterPDB.setText("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("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("Output to Textbox...");
- sequenceFeature.setText("Create Sequence Feature");
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
+ seqShowAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ seqHideAnnotationsMenu.setText(MessageManager
+ .getString("label.hide_annotations"));
+ groupShowAnnotationsMenu.setText(MessageManager
+ .getString("label.show_annotations"));
+ groupHideAnnotationsMenu.setText(MessageManager
+ .getString("label.hide_annotations"));
+ sequenceFeature.setText(MessageManager
+ .getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
}
});
- textColour.setText("Text Colour");
+ textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
}
});
- jMenu1.setText("Group");
- structureMenu.setText("Structure");
- viewStructureMenu.setText("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("Edit Sequence...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed(actionEvent);
}
});
+
/*
* annotationMenuItem.setText("By Annotation");
* annotationMenuItem.addActionListener(new ActionListener() { public void
* actionPerformed(ActionEvent actionEvent) {
* annotationMenuItem_actionPerformed(actionEvent); } });
*/
-
+ groupMenu.add(sequenceSelDetails);
add(groupMenu);
-
add(sequenceMenu);
this.add(structureMenu);
+ // annotations configuration panel suppressed for now
+ // groupMenu.add(chooseAnnotations);
+
+ /*
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
+ */
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(jMenu1);
sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
colourMenu.add(textColour);
colourMenu.add(noColourmenuItem);
colourMenu.add(clustalColour);
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);
+ }
+ // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
JMenuItem item = new JMenuItem(userColours.nextElement().toString());
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
userDefinedColour_actionPerformed(evt);
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);
pdbMenu.add(enterPDB);
pdbMenu.add(discoverPDB);
jMenu1.add(groupName);
- jMenu1.add(unGroupMenuItem);
jMenu1.add(colourMenu);
jMenu1.add(showBoxes);
jMenu1.add(showText);
structureMenu.add(pdbMenu);
structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
- noColourmenuItem.setText("None");
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
}
});
- clustalColour.setText("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("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed();
}
});
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed();
}
});
- helixColour.setText("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("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("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("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("Above % Identity");
+ 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("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("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("BLOSUM62");
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
}
});
- conservationMenuItem.setText("Conservation");
+ 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
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
});
}
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not on the alignment annotations for the
+ * sequence. If any are found, enable the option to add them to the alignment.
+ * The criteria for 'on the alignment' is finding an alignment annotation on
+ * the sequence, that matches on calcId and label. A tooltip is also
+ * constructed that displays the source (calcId) and type (label) of the
+ * annotations that can be added.
+ *
+ * @param menuItem
+ * @param forSequences
+ */
+ protected void configureReferenceAnnotationsMenu(
+ JMenuItem menuItem, List<SequenceI> forSequences)
+ {
+ menuItem.setText(MessageManager
+ .getString("label.add_reference_annotations"));
+ menuItem.setEnabled(false);
+ if (forSequences == null)
+ {
+ return;
+ }
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ Map<String, String> tipEntries = new TreeMap<String, String>();
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * For each sequence selected in the alignment, make a list of any
+ * annotations on the underlying dataset sequence which are not already on
+ * the sequence in the alignment.
+ *
+ * Build a map of { alignmentSequence, <List of annotations to add> }
+ */
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+ for (SequenceI seq : forSequences)
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * If the sequence has no annotation that matches this one, then add
+ * this one to the results list.
+ */
+ if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label)
+ .isEmpty())
+ {
+ result.add(dsann);
+ tipEntries.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ if (!candidates.isEmpty())
+ {
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its tooltip and action.
+ */
+ menuItem.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ menuItem.setToolTipText(tooltipText);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map<SequenceI, List<AlignmentAnnotation>> candidates)
+ {
+ /*
+ * Add annotations at the top of the annotation, in the same order as their
+ * related sequences.
+ */
+ for (SequenceI seq : candidates.keySet())
+ {
+ for (AlignmentAnnotation ann : candidates.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ // add to the sequence (sets copyAnn.datasetSequence)
+ seq.addAlignmentAnnotation(copyAnn);
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ this.ap.getAlignment().addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ refresh();
+ }
+
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void sequenceDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { sequence });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append("<p><h2>"
+ + MessageManager
+ .formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new String[]
+ { seq.getDisplayId(true) }) + "</h2></p><p>");
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ : null);
+ contents.append("</p>");
+ }
+ cap.setText("<html>" + contents.toString() + "</html>");
+
+ 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);
+
+ }
+
protected void showNonconserved_actionPerformed()
{
- getGroup().setShowunconserved(displayNonconserved.isSelected());
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg
- .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
- .getWidth());
+ sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void zappoColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void taylorColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void hydrophobicityColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void helixColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void strandColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void turnColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void buriedColour_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void nucleotideMenuItem_actionPerformed()
{
refresh();
}
+ protected void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new PurinePyrimidineColourScheme();
+ refresh();
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void abovePIDColour_actionPerformed()
{
if (abovePIDColour.isSelected())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
.getName());
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void userDefinedColour_actionPerformed(ActionEvent e)
{
SequenceGroup sg = getGroup();
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
}
/**
+ * 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
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void BLOSUM62Colour_actionPerformed()
{
sg.cs = new Blosum62ColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg
- .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
- .getEndRes() + 1));
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
refresh();
}
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void noColourmenuItem_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void conservationMenuItem_actionPerformed()
{
if (conservationMenuItem.isSelected())
{
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg
- .getSequences(ap.av.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1);
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), sg.getStartRes(),
+ sg.getEndRes() + 1);
c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
+ c.verdict(false, ap.av.getConsPercGaps());
sg.cs.setConservation(c);
return;
}
- AnnotationColourGradient acg = new AnnotationColourGradient(sequence
- .getAnnotation()[0], null,
+ AnnotationColourGradient acg = new AnnotationColourGradient(
+ sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void groupName_actionPerformed()
{
SequenceGroup sg = getGroup();
- EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
- .getDescription(), " Group Name ", "Group Description ",
- "Edit Group Name/Description");
+ 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"),
+ ap.alignFrame);
if (!dialog.accept)
{
}
/**
- * Get selection group - adding it to the alignment if necessary.
+ * Get selection group - adding it to the alignment if necessary.
*
* @return sequence group to operate on
*/
// this method won't add a new group if it already exists
if (sg != null)
{
- ap.av.alignment.addGroup(sg);
+ ap.av.getAlignment().addGroup(sg);
}
return sg;
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void sequenceName_actionPerformed()
{
- EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
- .getDescription(), " Sequence Name ",
- "Sequence Description ", "Edit Sequence Name/Description");
+ 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"),
+ ap.alignFrame);
if (!dialog.accept)
{
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- "Spaces have been converted to \"_\"",
- "No spaces allowed in 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(' ', '_'));
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
refresh();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
+ refresh();
+ }
+
/**
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, "Select Outline Colour",
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showBoxes_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showText_actionPerformed()
{
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void showColourText_actionPerformed()
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Unixers: Couldn't find default web browser."
- + "\nAdd the full path to your browser in Preferences.",
- "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();
}
if (source == toggle)
{
- description = "Toggle Case";
+ description = MessageManager.getString("label.toggle_case");
caseChange = ChangeCaseCommand.TOGGLE_CASE;
}
else if (source == upperCase)
{
- description = "To Upper Case";
+ description = MessageManager.getString("label.to_upper_case");
caseChange = ChangeCaseCommand.TO_UPPER;
}
else
{
- description = "To Lower Case";
+ description = MessageManager.getString("label.to_lower_case");
caseChange = ChangeCaseCommand.TO_LOWER;
}
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
- .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
- caseChange);
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ startEnd, caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap, "Alignment output - "
- + 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.alignment.getAlignmentAnnotation();
- for (int i = 0; i < nala.length; i++)
- {
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
- }
+ // or we simply trust the user wants
+ // wysiwig behaviour
+
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
+ ap.av, true));
}
public void pdbFromFile_actionPerformed()
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Select a PDB file");
- chooser.setToolTipText("Load a PDB file");
+ 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);
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
- PDBEntry entry = new PDBEntry();
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- try
- {
- MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
- jalview.io.AppletFormatAdapter.FILE);
-
- if (pdbfile.id == null)
- {
- String reply = JOptionPane
- .showInternalInputDialog(
- Desktop.desktop,
- "Couldn't find a PDB id in the file supplied."
- + "Please enter an Id to identify this structure.",
- "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
- if (reply == null)
- {
- return;
- }
-
- entry.setId(reply);
- }
- else
- {
- entry.setId(pdbfile.id);
- }
- } catch (java.io.IOException ex)
- {
- ex.printStackTrace();
- }
-
- entry.setFile(choice);
- sequence.getDatasetSequence().addPDBId(entry);
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
+ jalview.io.AppletFormatAdapter.FILE, sequence, true,
+ Desktop.instance);
}
}
+ // 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,
- "Enter PDB Id", "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)
{
public void discoverPDB_actionPerformed()
{
- final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
{ sequence }
- : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+ : ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
+ @Override
public void run()
{
return;
}
- int rsize=0,gSize = sg.getSize();
- SequenceI[] rseqs,seqs = new SequenceI[gSize];
- SequenceFeature[] tfeatures,features = new SequenceFeature[gSize];
-
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+
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)
+ if (start <= end)
{
seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
features[rsize] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
+ "Jalview");
rsize++;
}
}
rseqs = new SequenceI[rsize];
tfeatures = new SequenceFeature[rsize];
- System.arraycopy(seqs,0,rseqs, 0, rsize);
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
System.arraycopy(features, 0, tfeatures, 0, rsize);
features = tfeatures;
seqs = rseqs;
public void colourByStructure(String pdbid)
{
- Annotation[] anots = jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().colourSequenceFromStructure(
- sequence, pdbid);
+ Annotation[] anots = ap.av.getStructureSelectionManager()
+ .colourSequenceFromStructure(sequence, pdbid);
AlignmentAnnotation an = new AlignmentAnnotation("Structure",
"Coloured by " + pdbid, anots);
- ap.av.alignment.addAnnotation(an);
+ ap.av.getAlignment().addAnnotation(an);
an.createSequenceMapping(sequence, 0, true);
// an.adjustForAlignment();
- ap.av.alignment.setAnnotationIndex(an, 0);
+ ap.av.getAlignment().setAnnotationIndex(an, 0);
ap.adjustAnnotationHeight();
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, "Edit Sequence ", null, "Edit Sequence");
+ 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);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
- ap.av.getGapCharacter()), sg
- .getSequencesAsArray(ap.av.hiddenRepSequences), sg
- .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);