*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+import jalview.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.Hashtable;
+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!
*
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
JMenuItem sequenceSelDetails = new JMenuItem();
+ JMenuItem chooseAnnotations = new JMenuItem();
+
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();
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
menuItem.setText(pdb.getId());
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO re JAL-860: optionally open dialog or provide a menu entry
// allowing user to open just one structure per sequence
- new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
- { pdb })[0], null, ap);
- // new 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(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_structure_line", new String[]
+ { structureLine }));
menuItem.addActionListener(new java.awt.event.ActionListener()
-
+
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- //System.out.println("1:"+structureLine);
- System.out.println("1:sname"+seq.getName());
- System.out.println("2:seq"+seq);
-
- //System.out.println("3:"+seq.getSequenceAsString());
- System.out.println("3:strucseq"+rnastruc);
- //System.out.println("4:struc"+seq.getRNA());
- System.out.println("5:name"+seq.getName());
- System.out.println("6:ap"+ap);
- new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
- .getName(), ap);
- //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
- System.out.println("end");
+ // System.out.println("1:"+structureLine);
+ System.out.println("1:sname" + seq.getName());
+ System.out.println("2:seq" + seq);
+
+ // System.out.println("3:"+seq.getSequenceAsString());
+ System.out.println("3:strucseq" + rnastruc);
+ // System.out.println("4:struc"+seq.getRNA());
+ System.out.println("5:name" + seq.getName());
+ System.out.println("6:ap" + ap);
+ new AppVarna(structureLine, seq, seq.getSequenceAsString(),
+ rnastruc, seq.getName(), ap);
+ // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
+ // seq.getName(), ap);
+ System.out.println("end");
}
});
viewStructureMenu.add(menuItem);
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
- menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));
+ menuItem.setText(MessageManager.formatMessage(
+ "label.2d_rna_sequence_name", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
// TODO: VARNA does'nt print gaps in the sequence
-
+
new AppVarna(seq.getName() + " structure", seq, seq
.getSequenceAsString(), rnastruc, seq.getName(),
ap);
}
- menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.hide_sequences"));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(false);
if (ap.av.getSelectionGroup() != null
&& ap.av.getSelectionGroup().getSize() > 1)
{
- menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
+ menuItem = new JMenuItem(MessageManager.formatMessage(
+ "label.represent_group_with", new String[]
+ { seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hideSequences(true);
if (ap.av.adjustForHiddenSeqs(index)
- ap.av.adjustForHiddenSeqs(index - 1) > 1)
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_sequences"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showSequence(index);
if (ap.av.hasHiddenRows())
{
{
- menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));
+ menuItem = new JMenuItem(
+ MessageManager.getString("action.reveal_all"));
menuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ap.av.showAllHiddenSeqs();
}
SequenceGroup sg = ap.av.getSelectionGroup();
- boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
+ boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
+ .getGroups().contains(sg) : false;
if (sg != null && sg.getSize() > 0)
- {
- groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
- groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));
+ {
+ groupName.setText(MessageManager.formatMessage("label.name_param",
+ new String[]
+ { sg.getName() }));
+ groupName.setText(MessageManager
+ .getString("label.edit_name_and_description_current_group"));
if (sg.cs instanceof ZappoColourScheme)
{
{
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>(),reppdb=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()
+ Vector<PDBEntry> pes = sq.getDatasetSequence()
.getPDBId();
- if (pes != null)
+ if (pes != null && pes.size() > 0)
{
- reppdb.put(pes.get(0).getId(),pes.get(0));
+ reppdb.put(pes.get(0).getId(), pes.get(0));
for (PDBEntry pe : pes)
{
pdbe.put(pe.getId(), pe);
if (pdbe.size() > 0)
{
final PDBEntry[] pe = pdbe.values().toArray(
- new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
- new PDBEntry[reppdb.size()]);
- final JMenuItem gpdbview,rpdbview;
+ new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
+ new PDBEntry[reppdb.size()]);
+ final JMenuItem gpdbview, rpdbview;
if (pdbe.size() == 1)
{
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_structure_for", new String[]
+ { sqass.getDisplayId(false) })));
}
else
{
- structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));
+ structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ .formatMessage("label.view_all_structures", new String[]
+ { new Integer(pdbe.size()).toString() })));
}
- gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
+ gpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
gpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pe, ap.av.collateForPDB(pe));
}
});
- if (reppdb.size()>1 && reppdb.size()<pdbe.size())
+ 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"));
+ structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ .formatMessage(
+ "label.view_all_representative_structures",
+ new String[]
+ { new Integer(reppdb.size()).toString() })));
+ rpdbview.setToolTipText(MessageManager
+ .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
rpdbview.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pr, ap.av.collateForPDB(pr));
}
});
}
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
jMenu1.setText(MessageManager.getString("action.edit_new_group"));
- } else {
+ }
+ else
+ {
createGroupMenuItem.setVisible(false);
unGroupMenuItem.setVisible(true);
jMenu1.setText(MessageManager.getString("action.edit_group"));
// menu appears asap
// sequence only URLs
// ID/regex match URLs
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
JMenu[] linkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
- new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
- // created.
+ { null, new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
+ // types
+ // of url
+ // that
+ // might
+ // be
+ // created.
SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
String[][] idandseqs = GroupUrlLink.formStrings(seqs);
Hashtable commonDbrefs = new Hashtable();
}
if (addMenu)
{
- groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
for (int m = 0; m < linkMenus.length; m++)
{
if (linkMenus[m] != null
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_param", new String[]
+ { url }));
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
showLink(url);
final GroupUrlLink urlgenerator, final Object[] urlstub)
{
JMenuItem item = new JMenuItem(label);
- item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
+ item.setToolTipText(MessageManager.formatMessage(
+ "label.open_url_seqs_param",
+ new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
// TODO: put in info about what is being sent.
item.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
try
groupName.setText(MessageManager.getString("label.name"));
groupName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
groupName_actionPerformed();
}
});
sequenceMenu.setText(MessageManager.getString("label.sequence"));
- sequenceName.setText(MessageManager.getString("label.edit_name_description"));
+ sequenceName.setText(MessageManager
+ .getString("label.edit_name_description"));
sequenceName.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceName_actionPerformed();
}
});
- sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ chooseAnnotations.setText(MessageManager
+ .getString("label.choose_annotations") + "...");
+ chooseAnnotations
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ chooseAnnotations_actionPerformed(e);
+ }
+ });
+ sequenceDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceDetails.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceDetails_actionPerformed();
}
});
- sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
+ sequenceSelDetails.setText(MessageManager
+ .getString("label.sequence_details") + "...");
sequenceSelDetails
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceSelectionDetails_actionPerformed();
}
});
PIDColour.setFocusPainted(false);
- unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
unGroupMenuItem_actionPerformed();
}
});
- createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
- createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ createGroupMenuItem.setText(MessageManager
+ .getString("action.create_group"));
+ createGroupMenuItem
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText(MessageManager.getString("action.border_colour"));
outline.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outline_actionPerformed();
}
});
- nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideMenuItem
+ .setText(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
nucleotideMenuItem_actionPerformed();
showBoxes.setState(true);
showBoxes.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showBoxes_actionPerformed();
showText.setState(true);
showText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showText_actionPerformed();
showColourText.setText(MessageManager.getString("label.colour_text"));
showColourText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showColourText_actionPerformed();
}
});
- displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setText(MessageManager
+ .getString("label.show_non_conversed"));
displayNonconserved.setState(true);
displayNonconserved.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
showNonconserved_actionPerformed();
cut.setText(MessageManager.getString("action.cut"));
cut.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cut_actionPerformed();
upperCase.setText(MessageManager.getString("label.to_upper_case"));
upperCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
copy.setText(MessageManager.getString("action.copy"));
copy.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
copy_actionPerformed();
lowerCase.setText(MessageManager.getString("label.to_lower_case"));
lowerCase.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
toggle.setText(MessageManager.getString("label.toggle_case"));
toggle.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
changeCase(e);
}
});
- pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
+ pdbMenu.setText(MessageManager
+ .getString("label.associate_structure_with_sequence"));
pdbFromFile.setText(MessageManager.getString("label.from_file"));
pdbFromFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pdbFromFile_actionPerformed();
}
});
-// RNAFold.setText("From RNA Fold with predict2D");
-// RNAFold.addActionListener(new ActionListener()
-// {
-// public void actionPerformed(ActionEvent e)
-// {
-// try {
-// RNAFold_actionPerformed();
-// } catch (Exception e1) {
-// // TODO Auto-generated catch block
-// e1.printStackTrace();
-// }
-// }
-// });
-// ContraFold.setText("From Contra Fold with predict2D");
-// ContraFold.addActionListener(new ActionListener()
-// {
-// public void actionPerformed(ActionEvent e)
-// {
-// try {
-// ContraFold_actionPerformed();
-// } catch (Exception e1) {
-// // TODO Auto-generated catch block
-// e1.printStackTrace();
-// }
-// }
-// });
+ // RNAFold.setText("From RNA Fold with predict2D");
+ // RNAFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // RNAFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // ContraFold.setText("From Contra Fold with predict2D");
+ // ContraFold.addActionListener(new ActionListener()
+ // {
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // try {
+ // ContraFold_actionPerformed();
+ // } catch (Exception e1) {
+ // // TODO Auto-generated catch block
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
enterPDB_actionPerformed();
discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
discoverPDB.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
discoverPDB_actionPerformed();
}
});
- outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
- sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
+ outputMenu.setText(MessageManager.getString("label.out_to_textbox")
+ + "...");
+ sequenceFeature.setText(MessageManager
+ .getString("label.create_sequence_feature"));
sequenceFeature.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sequenceFeature_actionPerformed();
textColour.setText(MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textColour_actionPerformed();
});
jMenu1.setText(MessageManager.getString("label.group"));
structureMenu.setText(MessageManager.getString("label.structure"));
- viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
+ viewStructureMenu.setText(MessageManager
+ .getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
- editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
+ editSequence.setText(MessageManager.getString("label.edit_sequence")
+ + "...");
editSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
editSequence_actionPerformed(actionEvent);
add(groupMenu);
add(sequenceMenu);
this.add(structureMenu);
+ groupMenu.add(chooseAnnotations);
groupMenu.add(editMenu);
groupMenu.add(outputMenu);
groupMenu.add(sequenceFeature);
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);
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);
+ // 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);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
noColourmenuItem_actionPerformed();
}
});
- clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
+ clustalColour.setText(MessageManager
+ .getString("label.clustalx_colours"));
clustalColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clustalColour_actionPerformed();
zappoColour.setText(MessageManager.getString("label.zappo"));
zappoColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed();
taylorColour.setText(MessageManager.getString("label.taylor"));
taylorColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed();
}
});
- hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
hydrophobicityColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed();
helixColour.setText(MessageManager.getString("label.helix_propensity"));
helixColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed();
}
});
- strandColour.setText(MessageManager.getString("label.strand_propensity"));
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
strandColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed();
turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed();
buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
+ abovePIDColour.setText(MessageManager
+ .getString("label.above_identity_percentage"));
abovePIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
abovePIDColour_actionPerformed();
}
});
- userDefinedColour.setText(MessageManager.getString("action.user_defined"));
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
userDefinedColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
PIDColour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed();
BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed();
}
});
- purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
purinePyrimidineColour
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
purinePyrimidineColour_actionPerformed();
}
});
-
-
+
/*
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
- conservationMenuItem.setText(MessageManager.getString("label.conservation"));
+ conservationMenuItem.setText(MessageManager
+ .getString("label.conservation"));
conservationMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
conservationMenuItem_actionPerformed();
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>");
+ 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, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))
- ,500, 400);
+ Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequece_details_for",
+ (sequences.length == 1 ? new String[]
+ { sequences[0].getDisplayId(true) } : new String[]
+ { MessageManager.getString("label.selection") })), 500, 400);
}
refresh();
}
-
/*
* protected void covariationColour_actionPerformed() { getGroup().cs = new
* CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
}
/**
+ * 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
if (conservationMenuItem.isSelected())
{
- // JBPNote: Conservation name shouldn't be i18n translated
+ // JBPNote: Conservation name shouldn't be i18n translated
Conservation c = new Conservation("Group",
ResidueProperties.propHash, 3, sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
SequenceGroup sg = getGroup();
EditNameDialog dialog = new EditNameDialog(sg.getName(),
- sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",
- MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
+ sg.getDescription(), " "
+ + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
ap.alignFrame);
if (!dialog.accept)
void sequenceName_actionPerformed()
{
EditNameDialog dialog = new EditNameDialog(sequence.getName(),
- sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",
- MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
+ sequence.getDescription(),
+ " " + MessageManager.getString("label.sequence_name")
+ + " ",
+ MessageManager.getString("label.sequence_description") + " ",
+ MessageManager
+ .getString("label.edit_sequence_name_description"),
ap.alignFrame);
if (!dialog.accept)
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane.showMessageDialog(ap,
- MessageManager.getString("label.spaces_converted_to_backslashes"),
- MessageManager.getString("label.no_spaces_allowed_sequence_name"),
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane
+ .showMessageDialog(
+ ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
ap.av.setSelectionGroup(null);
refresh();
}
+
void createGroupMenuItem_actionPerformed()
{
- getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
refresh();
}
protected void outline_actionPerformed()
{
SequenceGroup sg = getGroup();
- Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_outline_colour"),
Color.BLUE);
if (col != null)
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
- Desktop.addInternalFrame(cap,
- MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new String[]
+ { e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
// or we simply trust the user wants
// wysiwig behaviour
- SequenceGroup sg = ap.av.getSelectionGroup();
- ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
- omitHidden = ap.av.getViewAsString(true);
- Alignment oal = new Alignment(ap.av.getSequenceSelection());
- AlignmentAnnotation[] nala = ap.av.getAlignment()
- .getAlignmentAnnotation();
- if (nala != null)
- {
- for (int i = 0; i < nala.length; i++)
- {
- AlignmentAnnotation na = nala[i];
- oal.addAnnotation(na);
- }
- }
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
- oal, omitHidden, csel, sg));
- oal = null;
+
+ cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), 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(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
- chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { sequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
}
}
- // JBNote: commented out - these won't be instantiated here...!
-// public void RNAFold_actionPerformed() throws Exception
-// {
-// Predict2D P2D = new Predict2D();
-// P2D.getStructure2DFromRNAFold("toto");
-// }
-//
-// public void ContraFold_actionPerformed() throws Exception
-// {
-// Predict2D P2D = new Predict2D();
-// P2D.getStructure2DFromContraFold("toto");
-// }
+
+ // JBNote: commented out - these won't be instantiated here...!
+ // public void RNAFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromRNAFold("toto");
+ // }
+ //
+ // public void ContraFold_actionPerformed() throws Exception
+ // {
+ // Predict2D P2D = new Predict2D();
+ // P2D.getStructure2DFromContraFold("toto");
+ // }
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
- MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
if (id != null && id.length() > 0)
{
: ap.av.getSequenceSelection());
Thread discpdb = new Thread(new Runnable()
{
+ @Override
public void run()
{
if (sg != null)
{
if (sequence == null)
- sequence = (Sequence) sg.getSequenceAt(0);
+ sequence = sg.getSequenceAt(0);
EditNameDialog dialog = new EditNameDialog(
sequence.getSequenceAsString(sg.getStartRes(),
- sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
- MessageManager.getString("label.edit_sequence"), ap.alignFrame);
+ sg.getEndRes() + 1), null,
+ MessageManager.getString("label.edit_sequence"), null,
+ MessageManager.getString("label.edit_sequence"),
+ ap.alignFrame);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
EditCommand.REPLACE, dialog.getName().replace(' ',
ap.av.getGapCharacter()),
sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
git://source.jalview.org / jalview.git / blobdiff