/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.schemes.*;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
+import jalview.util.MessageManager;
import jalview.util.UrlLink;
/**
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
SequenceI sequence;
+ JMenuItem createGroupMenuItem = new JMenuItem();
+
JMenuItem unGroupMenuItem = new JMenuItem();
JMenuItem outline = new JMenuItem();
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();
{
// 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);
}
});
final String rnastruc = aa[i].getRNAStruc();
final String structureLine = aa[i].label;
menuItem = new JMenuItem();
- menuItem.setText("2D RNA " + structureLine);
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new String[]
+ { structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
-
+
{
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);
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText("2D RNA - " + seq.getName());
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_sequence_name", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
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);
}
- menuItem = new JMenuItem("Hide Sequences");
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
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()
{
public void actionPerformed(ActionEvent e)
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()
{
public void actionPerformed(ActionEvent e)
if (ap.av.hasHiddenRows())
{
{
- menuItem = new JMenuItem("Reveal All");
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
}
SequenceGroup sg = ap.av.getSelectionGroup();
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
{
- groupName.setText("Name: " + sg.getName());
- groupName.setText("Edit name and description of 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)
{
{
purinePyrimidineColour.setSelected(true);
}
-
-
+
/*
* else if (sg.cs instanceof CovariationColourScheme) {
* covariationColour.setSelected(true); }
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
+ 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 = (Vector<PDBEntry>) sq.getDatasetSequence()
.getPDBId();
- if (pes != null)
+ 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 (pdbe.size() > 0)
{
final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]);
- final JMenuItem gpdbview;
+ 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("View structure for "
- + 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("View all "
- + pdbe.size() + " structures."));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_all_structures", new String[]
+ { new Integer(pdbe.size()).toString() })));
}
- gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the 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() < 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.getAlignment().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++)
{
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu("Group Link");
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.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.
+ { 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();
}
if (addMenu)
{
- groupLinksMenu = new JMenu("Group Links");
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
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()
{
public void actionPerformed(ActionEvent e)
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()
{
public void actionPerformed(ActionEvent e)
*/
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()
{
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()
{
public void actionPerformed(ActionEvent e)
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText("Sequence Details ...");
+ sequenceDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText("Sequence Details ...");
+ sequenceSelDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
}
});
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText("Remove Group");
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
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();
+ }
+ });
- outline.setText("Border colour");
+ outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText("Nucleotide");
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
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()
{
showBoxes_actionPerformed();
}
});
- showText.setText("Text");
+ showText.setText(MessageManager.getString("action.text"));
showText.setState(true);
showText.addActionListener(new ActionListener()
{
showText_actionPerformed();
}
});
- showColourText.setText("Colour Text");
+ showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
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()
{
showNonconserved_actionPerformed();
}
});
- editMenu.setText("Edit");
- cut.setText("Cut");
+ editMenu.setText(MessageManager.getString("action.edit"));
+ cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
cut_actionPerformed();
}
});
- upperCase.setText("To Upper Case");
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- copy.setText("Copy");
+ copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
copy_actionPerformed();
}
});
- lowerCase.setText("To Lower Case");
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
changeCase(e);
}
});
- toggle.setText("Toggle Case");
+ toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
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()
{
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("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()
{
public void actionPerformed(ActionEvent e)
enterPDB_actionPerformed();
}
});
- discoverPDB.setText("Discover PDB ids");
+ discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
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")
+ + "...");
+ sequenceFeature.setText(MessageManager
+ .getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
sequenceFeature_actionPerformed();
}
});
- textColour.setText("Text Colour");
+ textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
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()
{
public void actionPerformed(ActionEvent actionEvent)
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(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);
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);
- 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()
{
public void actionPerformed(ActionEvent e)
}
});
- clustalColour.setText("Clustalx colours");
+ clustalColour.setText(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
clustalColour_actionPerformed();
}
});
- zappoColour.setText("Zappo");
+ zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
zappoColour_actionPerformed();
}
});
- taylorColour.setText("Taylor");
+ taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText("Hydrophobicity");
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
hydrophobicityColour_actionPerformed();
}
});
- helixColour.setText("Helix propensity");
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
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()
{
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()
{
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()
{
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()
{
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()
{
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()
{
public void actionPerformed(ActionEvent e)
PIDColour_actionPerformed();
}
});
- BLOSUM62Colour.setText("BLOSUM62");
+ BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
purinePyrimidineColour_actionPerformed();
}
});
-
-
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
- conservationMenuItem.setText("Conservation");
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
StringBuffer contents = new StringBuffer();
for (SequenceI seq : sequences)
{
- contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
- + "</h2></p><p>");
+ 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,
}
cap.setText("<html>" + contents.toString() + "</html>");
- Desktop.instance.addInternalFrame(cap, "Sequence Details for "
- + (sequences.length == 1 ? sequences[0].getDisplayId(true)
- : "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);
}
refresh();
}
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
{
SequenceGroup sg = getGroup();
- if (e.getActionCommand().equals("User Defined..."))
+ if (e.getSource().equals(userDefinedColour))
{
new UserDefinedColours(ap, sg);
}
if (conservationMenuItem.isSelected())
{
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " Group Name ",
- "Group Description ", "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)
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " Sequence Name ",
- "Sequence Description ", "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)
{
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(' ', '_'));
refresh();
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
+ refresh();
+ }
+
/**
* 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)
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;
}
{
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.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
+
+ AlignmentView selvew = ap.av.getAlignmentView(true, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.av
+ .getGapCharacter());
+ List<AlignmentAnnotation> ala = (ap.av
+ .getVisibleAlignmentAnnotation(true));
+ if (ala != null)
{
- for (int i = 0; i < nala.length; i++)
+ for (AlignmentAnnotation aa : ala)
{
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
+ aselview.addAnnotation(aa);
}
}
cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
+ aselview, null, null, null));
}
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 for "
- + sequence.getDisplayId(false));
- chooser.setToolTipText("Load a PDB file and associate it with sequence '"
- + sequence.getDisplayId(false) + "'");
+ 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);
}
}
- // 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,
- "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)
{
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, "Edit Sequence ", null,
- "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("Edit Sequences",
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
git://source.jalview.org / jalview.git / blobdiff