/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
+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;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.Conservation;
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!
*
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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 jMenu1 = new JMenu();
- JMenu structureMenu = new JMenu();
+ JMenuItem structureMenu = new JMenuItem();
JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
-
JMenu groupLinksMenu;
JMenuItem hideInsertions = new JMenuItem();
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
colours.add(RNAInteractionColour);
- // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
{
structureMenu.remove(viewStructureMenu);
}
- // structureMenu.remove(colStructureMenu);
}
if (ap.av.getAlignment().isNucleotide() == true)
{
final String structureLine = aa[i].label + " (alignment)";
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_structure_line", new String[]
+ "label.2d_rna_structure_line", new Object[]
{ 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");
}
});
}
}
- // SequenceFeatures[] test = seq.getSequenceFeatures();
if (seq.getAnnotation() != null)
{
// TODO: make rnastrucF a bit more nice
menuItem = new JMenuItem();
menuItem.setText(MessageManager.formatMessage(
- "label.2d_rna_sequence_name", new String[]
+ "label.2d_rna_sequence_name", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
&& ap.av.getSelectionGroup().getSize() > 1)
{
menuItem = new JMenuItem(MessageManager.formatMessage(
- "label.represent_group_with", new String[]
+ "label.represent_group_with", new Object[]
{ seq.getName() }));
menuItem.addActionListener(new java.awt.event.ActionListener()
{
if (sg != null && sg.getSize() > 0)
{
groupName.setText(MessageManager.formatMessage("label.name_param",
- new String[]
+ new Object[]
{ sg.getName() }));
groupName.setText(MessageManager
.getString("label.edit_name_and_description_current_group"));
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
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
{
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
- "label.open_url_param", new String[]
+ "label.open_url_param", new Object[]
{ url }));
item.addActionListener(new java.awt.event.ActionListener()
{
pdbFromFile_actionPerformed();
}
});
- // RNAFold.setText("From RNA Fold with predict2D");
- // RNAFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // RNAFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
- // ContraFold.setText("From Contra Fold with predict2D");
- // ContraFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // ContraFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
+
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
+ structureMenu.setText(MessageManager.getString("label.view_structure"));
+ structureMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
viewStructureMenu.setText(MessageManager
.getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
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)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
+ MessageManager
.formatMessage(
"label.create_sequence_details_report_annotation_for",
- new String[]
+ new Object[]
{ seq.getDisplayId(true) }) + "</h2></p><p>");
new SequenceAnnotationReport(null)
.createSequenceAnnotationReport(
}
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[]
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) } : new Object[]
{ MessageManager.getString("label.selection") })), 500, 400);
}
if (sg != null)
{
- int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+ List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(),
sg.getEndRes() + 1);
String description;
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(null);
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new String[]
+ "label.alignment_output_command", new Object[]
{ e.getActionCommand() }), 600, 500);
String[] omitHidden = null;
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager.formatMessage(
- "label.select_pdb_file_for", new String[]
+ "label.select_pdb_file_for", new Object[]
{ sequence.getDisplayId(false) }));
chooser.setToolTipText(MessageManager.formatMessage(
- "label.load_pdb_file_associate_with_sequence", new String[]
+ "label.load_pdb_file_associate_with_sequence", new Object[]
{ 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");
- // }
+
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
git://source.jalview.org / jalview.git / blobdiff