String getFeatureInput(){
def swingBuilder = new SwingBuilder();
- def response = JOptionPane.showInputDialog(
- null, 'Select columns by feature by type','Enter type of feature', JOptionPane.OK_OPTION)
+ def response = JvOptionPane.showInputDialog(
+ null, 'Select columns by feature by type','Enter type of feature', JvOptionPane.OK_OPTION)
return response
}
\ No newline at end of file
import jalview.datamodel.SequenceI;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
import jalview.gui.UserDefinedColours;
import jalview.io.JalviewFileChooser;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JRadioButtonMenuItem;
public class PDBViewer extends JInternalFrame implements Runnable
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(
+ int option = JvOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop, MessageManager
.getString("label.remove_from_default_list"),
MessageManager
.getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
{
jalview.gui.UserDefinedColours
.removeColourFromDefaults(radioItem.getText());
{
JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop,
MessageManager.getString("label.export_settings"));
dialog.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent e)
{
cancelled = true;
}
}
+ @Override
public void ok_actionPerformed(ActionEvent e)
{
cancelled = false;
dialog.dispose();
}
+ @Override
public void cancel_actionPerformed(ActionEvent e)
{
cancelled = true;
return chkExportGrps.isSelected();
}
+ @Override
public boolean isCancelled()
{
return cancelled;
currentFileFormat = chooser.getSelectedFormat();
while (currentFileFormat == null)
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.select_file_format_before_saving"),
MessageManager
.getString("label.file_format_not_specified"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
value = chooser.showSaveDialog(this);
if (value != JalviewFileChooser.APPROVE_OPTION)
if (!success)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
.formatMessage("label.couldnt_save_file",
new Object[] { fileName }), MessageManager
.getString("label.error_saving_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return success;
}
else
{
- JOptionPane.showInternalMessageDialog(this, warning, title,
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(this, warning, title,
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
- int confirm = JOptionPane.showConfirmDialog(this,
+ int confirm = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
{
return;
}
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(
+ int option = JvOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop, MessageManager
.getString("label.remove_from_default_list"),
MessageManager
.getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
{
jalview.gui.UserDefinedColours
.removeColourFromDefaults(radioItem.getText());
if ((viewport.getSelectionGroup() == null)
|| (viewport.getSelectionGroup().getSize() < 2))
{
- JOptionPane.showInternalMessageDialog(this, MessageManager
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
.getString("label.you_must_select_least_two_sequences"),
MessageManager.getString("label.invalid_selection"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < 4))
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
this,
MessageManager
.getString("label.principal_component_analysis_must_take_least_four_input_sequences"),
MessageManager
.getString("label.sequence_selection_insufficient"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
{
if (viewport.getSelectionGroup().getSize() < 3)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.you_need_more_two_sequences_selected_build_tree"),
MessageManager
.getString("label.not_enough_sequences"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
{
if (_s.getLength() < sg.getEndRes())
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager
.getString("label.sequences_selection_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
// are the visible sequences aligned?
if (!viewport.getAlignment().isAligned(false))
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.sequences_must_be_aligned_before_creating_tree"),
MessageManager
.getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
else if (viewport.getSelectionGroup() != null
&& viewport.getSelectionGroup().getSize() == 1)
{
- int option = JOptionPane.showConfirmDialog(this,
+ int option = JvOptionPane.showConfirmDialog(this,
MessageManager.getString("warn.oneseq_msainput_selection"),
MessageManager.getString("label.invalid_selection"),
- JOptionPane.OK_CANCEL_OPTION);
- if (option == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION);
+ if (option == JvOptionPane.OK_OPTION)
{
msa = viewport.getAlignmentView(false);
}
viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
} catch (Exception ex)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
ex.getMessage(),
MessageManager
.getString("label.problem_reading_tree_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
if (fin != null && fin.hasWarningMessage())
{
- JOptionPane.showMessageDialog(Desktop.desktop, fin
+ JvOptionPane.showMessageDialog(Desktop.desktop, fin
.getWarningMessage(), MessageManager
.getString("label.possible_problem_with_tree_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.ERROR_MESSAGE);
return;
}
if (al == null || al.getHeight() == 0)
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
if (filesmatched.size() > 0)
{
if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
- || JOptionPane
+ || JvOptionPane
.showConfirmDialog(
this,
MessageManager
.toString() }),
MessageManager
.getString("label.automatically_associate_structure_files_by_name"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
{
for (Object[] fm : filesmatched)
{
if (assocfiles > 0
&& (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
+ "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane
.showConfirmDialog(
this,
"<html>"
+ "</html>",
MessageManager
.getString("label.ignore_unmatched_dropped_files"),
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
+ JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
{
return;
}
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
tcf.getWarningMessage() == null ? MessageManager
: tcf.getWarningMessage(),
MessageManager
.getString("label.problem_reading_tcoffee_score_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JOptionPane.showInternalInputDialog(this, msg, msg,
- JOptionPane.QUESTION_MESSAGE);
+ String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
+ JvOptionPane.QUESTION_MESSAGE);
if (reply != null)
{
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.couldnt_run_groovy_script"),
MessageManager
.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
else
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
MessageManager.getString("label.open_split_window"),
- JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
if (response != 1 && response != 2)
else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
- String label = JOptionPane.showInputDialog(this,
+ String label = JvOptionPane.showInputDialog(this,
MessageManager.getString("label.enter_label"), exMesg);
if (label == null)
aa[activeRow].hasIcons = true;
}
- String label = JOptionPane.showInputDialog(MessageManager
+ String label = JvOptionPane.showInputDialog(MessageManager
.getString("label.enter_label_for_the_structure"), symbol);
if (label == null)
}
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new String[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
return files;
}
_sideList.ensureIndexIsVisible(index);
/*
- * TODO Object newName = JOptionPane.showInputDialog( this,
+ * TODO Object newName = JvOptionPane.showInputDialog( this,
* "Specify a new name for this RNA", "Rename RNA",
- * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
+ * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
* (newName!=null) { item.name = newName.toString();
* this._sideList.repaint(); }
*/
if (prompt)
{
- reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
MessageManager
.getString("label.couldnt_find_pdb_id_in_file"),
MessageManager.getString("label.no_pdb_id_in_file"),
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.QUESTION_MESSAGE);
}
if (reply == null)
{
if (!jmb.launchChimera())
{
- JOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.chimera_failed"),
MessageManager.getString("label.error_loading_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
this.dispose();
return;
}
"label.confirm_close_chimera",
new Object[] { jmb.getViewerTitle("Chimera", false) });
prompt = JvSwingUtils.wrapTooltip(true, prompt);
- int confirm = JOptionPane.showConfirmDialog(this, prompt,
+ int confirm = JvOptionPane.showConfirmDialog(this, prompt,
MessageManager.getString("label.close_viewer"),
- JOptionPane.YES_NO_CANCEL_OPTION);
+ JvOptionPane.YES_NO_CANCEL_OPTION);
/*
* abort closure if user hits escape or Cancel
*/
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
{
return;
}
- closeChimera = confirm == JOptionPane.YES_OPTION;
+ closeChimera = confirm == JvOptionPane.YES_OPTION;
}
jmb.closeViewer(closeChimera);
}
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new Object[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
if (files.length() > 0)
xrefsAlignment.getSequencesArray());
if (copyAlignment.getHeight() == 0)
{
- JOptionPane.showMessageDialog(alignFrame,
+ JvOptionPane.showMessageDialog(alignFrame,
MessageManager.getString("label.cant_map_cds"),
MessageManager.getString("label.operation_failed"),
- JOptionPane.OK_OPTION);
+ JvOptionPane.OK_OPTION);
System.err.println("Failed to make CDS alignment");
}
import java.awt.event.MouseEvent;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPopupMenu;
import javax.swing.SwingUtilities;
.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
AppletFormatAdapter.SUPPORTED_FORMATS,
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
} catch (java.io.IOException ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.couldnt_read_pasted_text",
new String[] { ex.toString() }), MessageManager
.getString("label.error_parsing_text"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
.getString("label.couldnt_read_data"));
if (!Jalview.isHeadlessMode())
{
- javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
AppletFormatAdapter.SUPPORTED_FORMATS,
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
}
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.SOUTH);
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
panel,
MessageManager.getString("label.enter_local_das_source"),
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (reply != JOptionPane.OK_OPTION)
+ if (reply != JvOptionPane.OK_OPTION)
{
return;
}
if (!sourceRegistry.getSource(nickname).isLocal())
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("label.you_can_only_edit_or_remove_local_das_sources"),
MessageManager.getString("label.public_das_source"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
Object[] options = { "Edit", "Remove", "Cancel" };
- int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
+ int choice = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
"Do you want to edit or remove " + nickname + "?",
"Edit / Remove Local DAS Source",
- JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE,
+ JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.QUESTION_MESSAGE,
null, options, options[2]);
switch (choice)
}
}
- int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+ int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
MessageManager.getString("label.input_alignment_from_url"),
- JOptionPane.OK_CANCEL_OPTION);
+ JvOptionPane.OK_CANCEL_OPTION);
- if (reply != JOptionPane.OK_OPTION)
+ if (reply != JvOptionPane.OK_OPTION)
{
return;
}
if (format.equals("URL NOT FOUND"))
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new Object[] { url }), MessageManager
.getString("label.url_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
// StringBuffer message = getAboutMessage(false);
- // JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
//
- // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+ // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
@Override
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
+ JvOptionPane.showMessageDialog(me, MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
new Object[] { choice.getName() }), MessageManager
.getString("label.couldnt_save_project"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
{
Cache.log.error("Problems whilst loading project from "
+ choice, ex);
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage(
"label.error_whilst_loading_project_from",
new Object[] { choice }), MessageManager
.getString("label.couldnt_load_project"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, choice.hashCode());
}
String fle = chooser.getSelectedFile().toString();
if (!vamsasImport(chooser.getSelectedFile()))
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager.formatMessage(
new Object[] { fle }),
MessageManager
.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
removeProgressPanel(progpanel);
if (warnmsg != null)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+ warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
}
}
}
});
msgPanel.add(jcb);
- JOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+ JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
MessageManager
.getString("label.SEQUENCE_ID_no_longer_used"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
});
} catch (Exception ex)
{
jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
MessageManager.getString("label.groovy_support_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
*
* jd.waitForInput();
*/
- JOptionPane
+ JvOptionPane
.showConfirmDialog(
Desktop.desktop,
new JLabel(
+ "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ " Tools->Preferences dialog box to change them.</p></html>"),
"Web Service Configuration Problem",
- JOptionPane.DEFAULT_OPTION,
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager
.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
bg.add(lineart);
bg.add(text);
- JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");
dialog.setVisible(true);
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
panel2.add(description, BorderLayout.CENTER);
panel.add(panel2, BorderLayout.SOUTH);
}
- int reply = JOptionPane.showInternalConfirmDialog(parent, panel, title,
- JOptionPane.OK_CANCEL_OPTION);
+ int reply = JvOptionPane.showInternalConfirmDialog(parent, panel, title,
+ JvOptionPane.OK_CANCEL_OPTION);
if (!parent.requestFocusInWindow())
{
System.err.println("Bad focus for dialog!");
}
- if (reply == JOptionPane.OK_OPTION)
+ if (reply == JvOptionPane.OK_OPTION)
{
accept = true;
}
: MessageManager.formatMessage("label.amend_delete_features",
new String[] { sequences[0].getName() });
- int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
- bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, options,
+ int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
+ bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.QUESTION_MESSAGE, null, options,
MessageManager.getString("action.ok"));
jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
- if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
{
// This ensures that the last sequence
// is refreshed and new features are rendered
{
SequenceFeature sf = features[featureIndex];
- if (reply == JOptionPane.NO_OPTION)
+ if (reply == JvOptionPane.NO_OPTION)
{
sequences[0].getDatasetSequence().deleteFeature(sf);
}
- else if (reply == JOptionPane.YES_OPTION)
+ else if (reply == JvOptionPane.YES_OPTION)
{
sf.type = lastFeatureAdded;
sf.featureGroup = lastFeatureGroupAdded;
else
// NEW FEATURES ADDED
{
- if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
+ if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
{
for (int i = 0; i < sequences.length; i++)
{
public void noDasSourceActive()
{
complete();
- JOptionPane
+ JvOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
MessageManager
.getString("label.no_das_sources_selected_warn"),
MessageManager
.getString("label.no_das_sources_selected_title"),
- JOptionPane.DEFAULT_OPTION,
- JOptionPane.INFORMATION_MESSAGE);
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.INFORMATION_MESSAGE);
}
// ///////////////////////////////////////////////////////////////////////
// 'SelectRegion' selection
if (!haveResults)
{
- JOptionPane.showInternalMessageDialog(this,
+ JvOptionPane.showInternalMessageDialog(this,
MessageManager.getString("label.finished_searching"), null,
- JOptionPane.INFORMATION_MESSAGE);
+ JvOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
}
message += searchResults.getSize()
+ " subsequence matches found.";
}
- JOptionPane.showInternalMessageDialog(this, message, null,
- JOptionPane.INFORMATION_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(this, message, null,
+ JvOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
}
{
return false;
}
- JOptionPane.showInternalMessageDialog(this, error,
+ JvOptionPane.showInternalMessageDialog(this, error,
MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
return true;
}
String message = iBounds.getHeight() < 1 ? MessageManager
.getString("label.font_doesnt_have_letters_defined")
: MessageManager.getString("label.font_too_small");
- JOptionPane.showInternalMessageDialog(this, message,
+ JvOptionPane.showInternalMessageDialog(this, message,
MessageManager.getString("label.invalid_font"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
/*
* Restore the changed value - note this will reinvoke this method via the
* ActionListener, but now validation should pass
bg.add(lineart);
bg.add(text);
- JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop, "HTML Rendering options");
dialog.setVisible(true);
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
finalErrorMessage, "Error "
+ (saving ? "saving" : "loading")
- + " Jalview file", JOptionPane.WARNING_MESSAGE);
+ + " Jalview file", JvOptionPane.WARNING_MESSAGE);
}
});
}
System.err.println("Couldn't locate Jalview XML file : " + ex
+ "\n");
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new String[] { file }), MessageManager
.getString("label.url_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.error_loading_file_params", new String[]
{ file }), MessageManager
.getString("label.error_loading_jalview_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.gui;
+
+import java.awt.Component;
+import java.awt.HeadlessException;
+
+import javax.swing.Icon;
+import javax.swing.JOptionPane;
+
+public class JvOptionPane extends JOptionPane
+{
+ /**
+ *
+ */
+ private static final long serialVersionUID = -3019167117756785229L;
+
+ private static Object mockResponse = JvOptionPane.CANCEL_OPTION;
+
+ private static boolean interactiveMode = true;
+
+ public static int showConfirmDialog(Component parentComponent,
+ Object message) throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showConfirmDialog(
+ parentComponent, message) : (int) getMockResponse();
+ }
+
+ public static int showConfirmDialog(Component parentComponent,
+ Object message, String title, int optionType)
+ throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showConfirmDialog(
+ parentComponent, message, title, optionType)
+ : (int) getMockResponse();
+ }
+
+ public static int showConfirmDialog(Component parentComponent,
+ Object message, String title, int optionType, int messageType)
+ throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showConfirmDialog(
+ parentComponent, message, title, optionType, messageType)
+ : (int) getMockResponse();
+ }
+
+ public static int showConfirmDialog(Component parentComponent,
+ Object message, String title, int optionType, int messageType,
+ Icon icon) throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showConfirmDialog(
+ parentComponent, message, title, optionType, messageType, icon)
+ : (int) getMockResponse();
+ }
+
+ public static int showInternalConfirmDialog(Component parentComponent,
+ Object message)
+ {
+ return isInteractiveMode() ? JOptionPane.showInternalConfirmDialog(
+ parentComponent, message) : (int) getMockResponse();
+ }
+
+ public static int showInternalConfirmDialog(Component parentComponent,
+ Object message, String title, int optionType)
+ {
+ return isInteractiveMode() ? JOptionPane.showConfirmDialog(
+ parentComponent, message, title, optionType)
+ : (int) getMockResponse();
+ }
+
+ public static int showInternalConfirmDialog(Component parentComponent,
+ Object message, String title, int optionType, int messageType)
+ {
+ return isInteractiveMode() ? JOptionPane.showConfirmDialog(
+ parentComponent, message, title, optionType, messageType)
+ : (int) getMockResponse();
+ }
+
+ public static int showInternalConfirmDialog(Component parentComponent,
+ Object message, String title, int optionType, int messageType,
+ Icon icon)
+ {
+ return isInteractiveMode() ? JOptionPane.showInternalConfirmDialog(
+ parentComponent, message, title, optionType, messageType, icon)
+ : (int) getMockResponse();
+ }
+
+ public static int showOptionDialog(Component parentComponent,
+ Object message, String title, int optionType, int messageType,
+ Icon icon, Object[] options, Object initialValue)
+ throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showOptionDialog(
+ parentComponent, message, title, optionType, messageType, icon,
+ options, initialValue) : (int) getMockResponse();
+ }
+
+ public static void showMessageDialog(Component parentComponent,
+ Object message) throws HeadlessException
+ {
+ if (isInteractiveMode())
+ {
+ JOptionPane.showMessageDialog(parentComponent, message);
+ }
+ else
+ {
+ outputMessage(message);
+ }
+ }
+
+ public static void showMessageDialog(Component parentComponent,
+ Object message, String title, int messageType)
+ throws HeadlessException
+ {
+ if (isInteractiveMode())
+ {
+ JOptionPane.showMessageDialog(parentComponent, message, title,
+ messageType);
+ }
+ else
+ {
+ outputMessage(message);
+ }
+ }
+
+ public static void showMessageDialog(Component parentComponent,
+ Object message, String title, int messageType, Icon icon)
+ throws HeadlessException
+ {
+ if (isInteractiveMode())
+ {
+ JOptionPane.showMessageDialog(parentComponent, message, title,
+ messageType, icon);
+ }
+ else
+ {
+ outputMessage(message);
+ }
+ }
+
+ public static void showInternalMessageDialog(Component parentComponent,
+ Object message)
+ {
+ if (isInteractiveMode())
+ {
+ JOptionPane.showMessageDialog(parentComponent, message);
+ }
+ else
+ {
+ outputMessage(message);
+ }
+ }
+
+ public static void showInternalMessageDialog(Component parentComponent,
+ Object message, String title, int messageType)
+ {
+ if (isInteractiveMode())
+ {
+ JOptionPane.showMessageDialog(parentComponent, message, title,
+ messageType);
+ }
+ else
+ {
+ outputMessage(message);
+ }
+ }
+
+ public static void showInternalMessageDialog(Component parentComponent,
+ Object message, String title, int messageType, Icon icon)
+ {
+ if (isInteractiveMode())
+ {
+ JOptionPane.showMessageDialog(parentComponent, message, title,
+ messageType, icon);
+ }
+ else
+ {
+ outputMessage(message);
+ }
+ }
+
+ public static String showInputDialog(Object message)
+ throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showInputDialog(message)
+ : getMockResponse().toString();
+ }
+
+ public static String showInputDialog(Object message,
+ Object initialSelectionValue)
+ {
+ return isInteractiveMode() ? JOptionPane.showInputDialog(message,
+ initialSelectionValue) : getMockResponse().toString();
+ }
+
+ public static String showInputDialog(Component parentComponent,
+ Object message) throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showInputDialog(
+ parentComponent, message) : getMockResponse().toString();
+ }
+
+ public static String showInputDialog(Component parentComponent,
+ Object message, Object initialSelectionValue)
+ {
+ return isInteractiveMode() ? JOptionPane.showInputDialog(
+ parentComponent, message, initialSelectionValue)
+ : getMockResponse().toString();
+ }
+
+ public static String showInputDialog(Component parentComponent,
+ Object message, String title, int messageType)
+ throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showInputDialog(
+ parentComponent, message, title, messageType)
+ : getMockResponse().toString();
+ }
+
+ public static Object showInputDialog(Component parentComponent,
+ Object message, String title, int messageType, Icon icon,
+ Object[] selectionValues, Object initialSelectionValue)
+ throws HeadlessException
+ {
+ return isInteractiveMode() ? JOptionPane.showInputDialog(
+ parentComponent, message, title, messageType, icon,
+ selectionValues, initialSelectionValue) : getMockResponse()
+ .toString();
+ }
+
+ public static String showInternalInputDialog(Component parentComponent,
+ Object message)
+ {
+ return isInteractiveMode() ? JOptionPane.showInternalInputDialog(
+ parentComponent, message) : getMockResponse().toString();
+ }
+
+ public static String showInternalInputDialog(Component parentComponent,
+ Object message, String title, int messageType)
+ {
+ return isInteractiveMode() ? JOptionPane.showInternalInputDialog(
+ parentComponent, message, title, messageType)
+ : getMockResponse().toString();
+ }
+
+ public static Object showInternalInputDialog(Component parentComponent,
+ Object message, String title, int messageType, Icon icon,
+ Object[] selectionValues, Object initialSelectionValue)
+ {
+ return isInteractiveMode() ? JOptionPane.showInternalInputDialog(
+ parentComponent, message, title, messageType, icon,
+ selectionValues, initialSelectionValue) : getMockResponse()
+ .toString();
+ }
+
+ private static void outputMessage(Object message)
+ {
+ System.out.println(">>> JOption Message : " + message.toString());
+ }
+
+ public static Object getMockResponse()
+ {
+ return mockResponse;
+ }
+
+ public static void setMockResponse(Object mockOption)
+ {
+ JvOptionPane.mockResponse = mockOption;
+ }
+
+ public static void resetMock()
+ {
+ setMockResponse(JvOptionPane.CANCEL_OPTION);
+ setInteractiveMode(true);
+ }
+
+ public static boolean isInteractiveMode()
+ {
+ return interactiveMode;
+ }
+
+ public static void setInteractiveMode(boolean interactiveMode)
+ {
+ JvOptionPane.interactiveMode = interactiveMode;
+ }
+
+}
this(string, oomerror, Desktop.desktop);
}
+ @Override
public void run()
{
- javax.swing.JOptionPane.showInternalMessageDialog(desktop,
+ JvOptionPane
+ .showInternalMessageDialog(desktop,
MessageManager.formatMessage("warn.out_of_memory_when_action",
new String[] { action }), MessageManager
.getString("label.out_of_memory"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
// hope that there's enough memory left that no more appear.
oomInprogress = false;
}
if (!sameLength)
{
- JOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.desktop,
MessageManager.getString("label.pca_sequences_not_aligned"),
MessageManager.getString("label.sequences_not_aligned"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
ap,
MessageManager
.getString("label.spaces_converted_to_backslashes"),
MessageManager
.getString("label.no_spaces_allowed_sequence_name"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
boolean valid = false;
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
- JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
while (!valid)
{
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
MessageManager.getString("label.new_sequence_url_link"),
- JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
{
if (link.checkValid())
{
int index = linkNameList.getSelectedIndex();
if (index == -1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.no_link_selected"),
MessageManager.getString("label.no_link_selected"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
nameLinks.removeElementAt(index);
}
} catch (NumberFormatException x)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
}
File f = new File(chimeraPath.getText());
if (!f.canExecute())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.invalid_chimera_path"),
MessageManager.getString("label.invalid_name"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
return false;
}
}
if (!found)
{
String[] options = { "OK", "Help" };
- int showHelp = JOptionPane.showInternalOptionDialog(
+ int showHelp = JvOptionPane.showInternalOptionDialog(
Desktop.desktop,
JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.chimera_missing")),
- "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
- if (showHelp == JOptionPane.NO_OPTION)
+ if (showHelp == JvOptionPane.NO_OPTION)
{
try
{
}
try
{
- int reply = JOptionPane.showConfirmDialog(
+ int reply = JvOptionPane.showConfirmDialog(
Desktop.desktop, // component,
dialogText, dialogTitle,
- (allowCancel) ? JOptionPane.YES_NO_CANCEL_OPTION
- : JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ (allowCancel) ? JvOptionPane.YES_NO_CANCEL_OPTION
+ : JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
// now, ask the desktop to relayer any external windows that might have
// been obsured
if (Desktop.instance != null)
}
// and finish parsing the result
jalview.bin.Cache.log.debug("Got response : " + reply);
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
jalview.bin.Cache.setProperty(property, "true");
}
- else if (reply == JOptionPane.NO_OPTION)
+ else if (reply == JvOptionPane.NO_OPTION)
{
if (removeifunset)
{
@Override
protected void okPressed()
{
- reply = JOptionPane.OK_OPTION;
+ reply = JvOptionPane.OK_OPTION;
}
@Override
protected void cancelPressed()
{
- reply = JOptionPane.CANCEL_OPTION;
+ reply = JvOptionPane.CANCEL_OPTION;
}
};
+ currentservice.getName(), 600, 800);
initTypeLists();
- reply = JOptionPane.CANCEL_OPTION;
+ reply = JvOptionPane.CANCEL_OPTION;
old = toedit;
current = null;
if (old != null)
{
setStateFor(old);
}
- updated = updated && reply == JOptionPane.OK_OPTION;
+ updated = updated && reply == JvOptionPane.OK_OPTION;
frame.validate();
}
bg.add(lineart);
bg.add(text);
- JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION,
- JOptionPane.DEFAULT_OPTION, null, new Object[] { this });
+ JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.DEFAULT_OPTION, null, new Object[] { this });
dialog = pane.createDialog(Desktop.desktop, "SVG Rendering options");
dialog.setVisible(true);
ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed(e);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.cannot_edit_annotations_in_wrapped_view"),
MessageManager.getString("label.wrapped_view_no_edit"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
@Override
public void run()
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
.getString("warn.couldnt_create_sequence_fetcher_client"),
MessageManager
.getString("label.couldnt_create_sequence_fetcher"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
});
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
MessageManager.getString("label.error_retrieving_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ JvOptionPane.showMessageDialog(this, errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
}
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(
+ JvOptionPane.showMessageDialog(
null,
errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
*
* @param pdbId
* @param view
- * @return YES, NO or CANCEL JOptionPane code
+ * @return YES, NO or CANCEL JvOptionPane code
*/
protected int chooseAlignStructureToViewer(String pdbId,
StructureViewerBase view)
{
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
new Object[] { pdbId, view.getTitle() }),
MessageManager
.getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
+ JvOptionPane.YES_NO_CANCEL_OPTION);
return option;
}
continue;
}
int option = chooseAlignStructureToViewer(pdbId, view);
- if (option == JOptionPane.CANCEL_OPTION)
+ if (option == JvOptionPane.CANCEL_OPTION)
{
return true;
}
- else if (option == JOptionPane.YES_OPTION)
+ else if (option == JvOptionPane.YES_OPTION)
{
view.useAlignmentPanelForSuperposition(apanel);
view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
/*
* the PDB file is already loaded
*/
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.pdb_entry_is_already_displayed",
new Object[] { pdbId }), MessageManager
.formatMessage(
"label.map_sequences_to_visible_window",
new Object[] { pdbId }),
- JOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JOptionPane.CANCEL_OPTION)
+ JvOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JvOptionPane.CANCEL_OPTION)
{
finished = true;
}
- else if (option == JOptionPane.YES_OPTION)
+ else if (option == JvOptionPane.YES_OPTION)
{
addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
finished = true;
}
});
- int reply = JOptionPane
+ int reply = JvOptionPane
.showInternalOptionDialog(
ap,
bigpanel,
MessageManager
.getString("label.adjunst_foreground_text_colour_threshold"),
- JOptionPane.OK_CANCEL_OPTION,
- JOptionPane.QUESTION_MESSAGE, null, null, null);
+ JvOptionPane.OK_CANCEL_OPTION,
+ JvOptionPane.QUESTION_MESSAGE, null, null, null);
- if (reply == JOptionPane.CANCEL_OPTION)
+ if (reply == JvOptionPane.CANCEL_OPTION)
{
if (sg == null)
{
{
if (isNoSelectionMade())
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.getString("label.no_colour_selection_in_scheme"),
MessageManager.getString("label.no_colour_selection_warn"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
else
{
{
if (isNoSelectionMade())
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.getString("label.no_colour_selection_in_scheme"),
MessageManager.getString("label.no_colour_selection_warn"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
UserColourScheme ucs = getSchemeFromButtons();
{
if (schemeName.getText().trim().length() < 1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.user_colour_scheme_must_have_name"),
MessageManager.getString("label.no_name_colour_scheme"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
if (userColourSchemes != null
&& userColourSchemes.containsKey(schemeName.getText()))
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.colour_scheme_exists_overwrite", new Object[] {
schemeName.getText(), schemeName.getText() }),
MessageManager.getString("label.duplicate_scheme_name"),
- JOptionPane.YES_NO_OPTION);
- if (reply != JOptionPane.YES_OPTION)
+ JvOptionPane.YES_NO_OPTION);
+ if (reply != JvOptionPane.YES_OPTION)
{
return;
}
+ qid + "&rid=" + rid;
jalview.bin.Cache.log.info("Prompting user for questionnaire at "
+ qurl);
- int reply = JOptionPane
+ int reply = JvOptionPane
.showInternalConfirmDialog(Desktop.desktop, MessageManager
.getString("label.jalview_new_questionnaire"),
MessageManager
.getString("label.jalview_user_survey"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
jalview.bin.Cache.log.debug("Opening " + qurl);
jalview.util.BrowserLauncher.openURL(qurl);
}
} catch (InvalidSessionDocumentException e)
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
MessageManager
.getString("label.vamsas_document_import_failed"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
}
{
Cache.log
.debug("Asking user if the vamsas session should be stored.");
- int reply = JOptionPane
+ int reply = JvOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
"The current VAMSAS session has unsaved data - do you want to save it ?",
"VAMSAS Session Shutdown",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
Cache.log.debug("Prompting for vamsas store filename.");
Desktop.instance.vamsasSave_actionPerformed(null);
{
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, message,
- title, JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
+ title, JvOptionPane.WARNING_MESSAGE);
}
});
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
frame.validate();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
// jobPanel.setDividerLocation(0.25);
new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
update_actionPerformed(e);
new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
delete_actionPerformed(e);
new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
create_actionPerformed(e);
new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
revert_actionPerformed(e);
MessageManager.getString("label.start_job_current_settings"),
new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
startjob_actionPerformed(e);
MessageManager.getString("label.cancel_job_close_dialog"),
new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
canceljob_actionPerformed(e);
validate();
}
+ @Override
public void argSetModified(Object modifiedElement, boolean b)
{
if (settingDialog)
settingDialog = stn;
}
+ @Override
public void refreshParamLayout()
{
// optsAndparams.setPreferredSize(null);
jf.addWindowListener(new WindowListener()
{
+ @Override
public void windowActivated(WindowEvent e)
{
// TODO Auto-generated method stub
}
+ @Override
public void windowClosed(WindowEvent e)
{
}
+ @Override
public void windowClosing(WindowEvent e)
{
thr.interrupt();
}
+ @Override
public void windowDeactivated(WindowEvent e)
{
// TODO Auto-generated method stub
}
+ @Override
public void windowDeiconified(WindowEvent e)
{
// TODO Auto-generated method stub
}
+ @Override
public void windowIconified(WindowEvent e)
{
// TODO Auto-generated method stub
}
+ @Override
public void windowOpened(WindowEvent e)
{
// TODO Auto-generated method stub
String curSetName = null;
+ @Override
public void itemStateChanged(ItemEvent e)
{
if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
}
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
doPreferenceComboStateChange(setname);
}
settingDialog = true;
System.out.println("Prompting to save " + lsetname);
- if (javax.swing.JOptionPane
+ if (JvOptionPane
.showConfirmDialog(
this,
"Parameter set '"
+ lsetname
+ "' is modifed, and your changes will be lost.\nReally change preset ?",
"Warning: Unsaved Changes",
- javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION) != JvOptionPane.OK_OPTION)
{
// revert the combobox to the current item
settingDialog = true;
*/
String lastDescrText = null;
+ @Override
public void actionPerformed(ActionEvent e)
{
if (e.getSource() instanceof Component)
settingDialog = false;
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- JOptionPane.showMessageDialog(ourframe, MessageManager
+ JvOptionPane.showMessageDialog(ourframe, MessageManager
.getString("label.invalid_name_preset_exists"),
MessageManager.getString("label.invalid_name"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
}
+ @Override
public void insertUpdate(DocumentEvent e)
{
checkDescrModified();
}
+ @Override
public void removeUpdate(DocumentEvent e)
{
checkDescrModified();
}
+ @Override
public void changedUpdate(DocumentEvent e)
{
checkDescrModified();
File pfile = new File(filename);
if (pfile.exists() && pfile.canWrite())
{
- if (JOptionPane.showConfirmDialog(Desktop.instance,
+ if (JvOptionPane.showConfirmDialog(Desktop.instance,
"Delete the preset's file, too ?", "Delete User Preset ?",
- JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION)
{
pfile.delete();
}
pane12.add(urltf, BorderLayout.EAST);
panel.add(pane12, BorderLayout.NORTH);
boolean valid = false;
- int resp = JOptionPane.CANCEL_OPTION;
+ int resp = JvOptionPane.CANCEL_OPTION;
while (!valid
- && (resp = JOptionPane.showInternalConfirmDialog(
+ && (resp = JvOptionPane.showInternalConfirmDialog(
Desktop.desktop, panel, title,
- JOptionPane.OK_CANCEL_OPTION)) == JOptionPane.OK_OPTION)
+ JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION)
{
try
{
} catch (Exception e)
{
valid = false;
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.invalid_url"));
}
}
- if (valid && resp == JOptionPane.OK_OPTION)
+ if (valid && resp == JvOptionPane.OK_OPTION)
{
- int validate = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int validate = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.getString("info.validate_jabaws_server"),
MessageManager.getString("label.test_server"),
- JOptionPane.YES_NO_OPTION);
+ JvOptionPane.YES_NO_OPTION);
- if (validate == JOptionPane.OK_OPTION)
+ if (validate == JvOptionPane.OK_OPTION)
{
if (Jws2Discoverer.testServiceUrl(foo))
{
}
else
{
- int opt = JOptionPane
+ int opt = JvOptionPane
.showInternalOptionDialog(
Desktop.desktop,
"The Server '"
+ foo.toString()
+ "' failed validation,\ndo you want to add it anyway? ",
"Server Validation Failed",
- JOptionPane.YES_NO_OPTION,
- JOptionPane.INFORMATION_MESSAGE, null, null, null);
- if (opt == JOptionPane.YES_OPTION)
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.INFORMATION_MESSAGE, null, null, null);
+ if (opt == JvOptionPane.YES_OPTION)
{
return foo.toString();
}
else
{
- JOptionPane
+ JvOptionPane
.showInternalMessageDialog(
Desktop.desktop,
MessageManager
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- javax.swing.JOptionPane.showInternalMessageDialog(
+ JvOptionPane.showInternalMessageDialog(
Desktop.desktop,
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.SUPPORTED_FORMATS,
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
errorMessage, MessageManager
.getString("label.error_loading_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
@Override
public void run()
{
- javax.swing.JOptionPane.showInternalMessageDialog(
+ JvOptionPane.showInternalMessageDialog(
Desktop.desktop, MessageManager.formatMessage(
"label.problems_opening_file",
new String[] { file }), MessageManager
.getString("label.file_open_error"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
@Override
public void run()
{
- javax.swing.JOptionPane.showInternalMessageDialog(
+ JvOptionPane.showInternalMessageDialog(
Desktop.desktop, MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }), MessageManager
.getString("label.out_of_memory"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
//////////////////////////////////////////////////////////////////
package jalview.io;
+import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import jalview.util.Platform;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JFileChooser;
import javax.swing.JList;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SpringLayout;
if ((ret == JalviewFileChooser.APPROVE_OPTION)
&& getSelectedFile().exists())
{
- int confirm = JOptionPane.showConfirmDialog(parent,
+ int confirm = JvOptionPane.showConfirmDialog(parent,
MessageManager.getString("label.overwrite_existing_file"),
MessageManager.getString("label.file_already_exists"),
- JOptionPane.YES_NO_OPTION);
+ JvOptionPane.YES_NO_OPTION);
- if (confirm != JOptionPane.YES_OPTION)
+ if (confirm != JvOptionPane.YES_OPTION)
{
ret = JalviewFileChooser.CANCEL_OPTION;
}
import jalview.gui.AlignmentPanel;
import jalview.gui.CutAndPasteTransfer;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Vector;
import javax.swing.ImageIcon;
-import javax.swing.JOptionPane;
import uk.ac.ebi.www.Data;
import uk.ac.ebi.www.InputParams;
{
// This must be outside the run() body as java 1.5
// will not return any value from the OptionPane to the expired thread.
- int reply = JOptionPane.showConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showConfirmDialog(Desktop.desktop,
"Automatically update suggested ids?",
- "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
+ "Auto replace sequence ids", JvOptionPane.YES_NO_OPTION);
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
Enumeration keys = suggestedIds.elements();
while (keys.hasMoreElements())
}
}
+ @Override
public void run()
{
while (jobsRunning > 0)
this.sequence = sequence;
}
+ @Override
public void run()
{
StartJob();
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.schemes.ColourSchemeProperty;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JTabbedPane;
{
radioItem.removeActionListener(radioItem.getActionListeners()[0]);
- int option = JOptionPane.showInternalConfirmDialog(
+ int option = JvOptionPane.showInternalConfirmDialog(
jalview.gui.Desktop.desktop, MessageManager
.getString("label.remove_from_default_list"),
MessageManager
.getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
+ JvOptionPane.YES_NO_OPTION);
+ if (option == JvOptionPane.YES_OPTION)
{
jalview.gui.UserDefinedColours
.removeColourFromDefaults(radioItem.getText());
*/
package jalview.jbgui;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
import javax.swing.BorderFactory;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTextField;
import javax.swing.SwingConstants;
return true;
}
- JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop,
MessageManager.getString("warn.url_must_contain"),
MessageManager.getString("label.invalid_url"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return false;
}
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
+import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.util.UrlLink;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.JOptionPane;
-
import org.biodas.jdas.client.FeaturesClient;
import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
{
- int reply = JOptionPane.YES_OPTION;
+ int reply = JvOptionPane.YES_OPTION;
if (promptFetchDbrefs)
{
- reply = JOptionPane
+ reply = JvOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
MessageManager
.getString("info.you_want_jalview_to_find_uniprot_accessions"),
MessageManager
.getString("label.find_uniprot_accession_ids"),
- JOptionPane.YES_NO_OPTION,
- JOptionPane.QUESTION_MESSAGE);
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.QUESTION_MESSAGE);
}
- if (reply == JOptionPane.YES_OPTION)
+ if (reply == JvOptionPane.YES_OPTION)
{
Thread thread = new Thread(new FetchDBRefs());
thread.start();
*/
package jalview.ws.jws1;
+import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.JOptionPane;
-
import ext.vamsas.IRegistry;
import ext.vamsas.IRegistryServiceLocator;
import ext.vamsas.RegistryServiceSoapBindingStub;
{
if (jalview.gui.Desktop.desktop != null)
{
- JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
+ JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop,
MessageManager.getString("label.set_proxy_settings"),
MessageManager
.getString("label.proxy_authorization_failed"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
else
/**
* creates a new thread to call discoverServices()
*/
+ @Override
public void run()
{
final Discoverer discoverer = this;
Thread discoverThread = new Thread()
{
+ @Override
public void run()
{
discoverer.doDiscovery();
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import ext.vamsas.Jpred;
import ext.vamsas.JpredServiceLocator;
} catch (Exception ex)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
MessageManager
new String[] { WebServiceName, WsURL }),
MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
wsInfo.setProgressText(MessageManager
.formatMessage(
"label.secondary_structure_prediction_service_couldnt_be_located",
return server;
}
+ @Override
public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
final AlignFrame af)
{
method.setToolTipText(sh.getEndpointURL());
method.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import ext.vamsas.MuscleWSServiceLocator;
import ext.vamsas.MuscleWSSoapBindingStub;
alignFrame = _alignFrame;
if (!sh.getAbstractName().equals("MsaWS"))
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.service_called_is_not_msa_service",
new String[] { sh.getName() }), MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.msa_service_is_unknown",
new String[] { sh.getName() }), MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import ext.vamsas.SeqSearchServiceLocator;
import ext.vamsas.SeqSearchServiceSoapBindingStub;
// name to service client name
if (!sh.getAbstractName().equals(this.getServiceActionKey()))
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage(
"label.service_called_is_not_seq_search_service",
new String[] { sh.getName() }), MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
if ((wsInfo = setWebService(sh)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.seq_search_service_is_unknown",
new String[] { sh.getName() }), MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
import jalview.datamodel.AlignmentView;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.util.MessageManager;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.ToolTipManager;
import compbio.data.msa.MsaWS;
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.service_called_is_not_msa_service",
new String[] { sh.serviceType }), MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
server = (MsaWS) sh.service;
if ((wsInfo = setWebService(sh, false)) == null)
{
- JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.msa_service_is_unknown",
new String[] { sh.serviceType }), MessageManager
.getString("label.internal_jalview_error"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
}
else
{
- JOptionPane.showMessageDialog(alignFrame,
+ JvOptionPane.showMessageDialog(alignFrame,
MessageManager.getString("info.invalid_msa_input_mininfo"),
MessageManager.getString("info.invalid_msa_notenough"),
- JOptionPane.INFORMATION_MESSAGE);
+ JvOptionPane.INFORMATION_MESSAGE);
wsInfo.setVisible(false);
}
}
// dan changed! dan test. comment out if conditional
// if (alignFrame.getViewport().getAlignment().isNucleotide())
// {
- // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
+ // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType
// + " can only be used\nfor amino acid alignments.",
- // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE);
+ // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE);
// return;
//
// }
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
else
{
// TODO: try to tell the user why the job couldn't be started.
- JOptionPane
+ JvOptionPane
.showMessageDialog(
Desktop.desktop,
(jobsthread.hasWarnings() ? jobsthread.getWarnings()
.getString("label.job_couldnt_be_started_check_input")),
MessageManager
.getString("label.unable_start_web_service_analysis"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
}
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AtomTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the constructor that parses a PDB file format ATOM line. Fields are in
* fixed column positions
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class BondTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testTranslate()
{
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.TaylorColourScheme;
import jalview.structure.StructureImportSettings;
import java.awt.Color;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBChainTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
PDBChain c;
final Atom a1 = new Atom(1f, 2f, 3f);
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.structure.StructureImportSettings;
import java.io.IOException;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBfileTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testIsRna()
{
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
+import jalview.gui.JvOptionPane;
+
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ResidueTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testFindAtom()
{
import jalview.datamodel.ProfilesI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AAFrequencyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testCalculate_noProfile()
{
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignSeqTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testExtractGaps()
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import java.io.IOException;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AlignmentAnnotationUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// 4 sequences x 13 positions
final static String EOL = "\n";
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import java.util.Map;
import java.util.TreeMap;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignmentUtilsTests
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AnnotationSorterTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final int NUM_SEQS = 6;
private static final int NUM_ANNS = 7;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class CodingUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testDecodeCodon()
{
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ConservationTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testRecordConservation()
{
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
import java.util.List;
import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class CrossRefTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testFindXDbRefs()
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.FastaFile;
import java.util.Arrays;
import java.util.Random;
+import org.testng.annotations.BeforeClass;
+
/**
* Generates, and outputs in Fasta format, a random DNA alignment for given
* sequence length and count. Will regenerate the same alignment each time if
*/
public class DnaAlignmentGenerator
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final char GAP = '-';
private static final char ZERO = '0';
private Random random;
+
/**
* Outputs a DNA 'alignment' where each position is a random choice from
* 'GTCA-'.
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
import jalview.io.FormatAdapter;
import java.io.IOException;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DnaTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// @formatter:off
// AA encoding codons as ordered on the Jalview help page Amino Acid Table
private static String fasta = ">B\n" + "GCT" + "GCC" + "GCA" + "GCG"
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
public class FinderTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private AlignFrame af;
private AlignmentI al;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.Arrays;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class GroupingTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Sequence s1 = new Sequence("s1", "AAAADDDDEEEE");
Sequence s2 = new Sequence("s2", "AAAADDDDEEEE");
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class ParsePropertiesTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private Alignment al;
private ParseProperties pp;
import static org.testng.AssertJUnit.fail;
import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.gui.JvOptionPane;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class RnaTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testGetSimpleBPs() throws WUSSParseException
{
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.Hashtable;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class SeqsetUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+
/**
* test for JAL-2046 bug - duplication of sequence features on reconstructed
* alignment
import jalview.analysis.SequenceIdMatcher.SeqIdName;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SequenceIdMatcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+
/**
* Test the method that checks for one sequence id starting with the other,
* followed by an 'allowed' separator character
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.PrintStream;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class TestAlignSeq
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
SequenceI s1, s2, s3;
/**
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import java.util.Arrays;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FeatureScoreModelTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ArgsParserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetValue()
{
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.Locale;
public class CacheTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private Locale locale;
@BeforeClass(alwaysRun = true)
*/
package jalview.bin;
+import jalview.gui.JvOptionPane;
+
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import org.testng.Assert;
import org.testng.FileAssert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class CommandLineOperations
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on
// full test run than on
// individual tests
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class JalviewLiteTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testSeparatorListToArray()
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class EditCommandTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private EditCommand testee;
private SequenceI[] seqs;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class TrimRegionCommandTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private AlignmentI al;
@BeforeMethod(alwaysRun = true)
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import java.util.Arrays;
import java.util.BitSet;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignViewControllerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testFindColumnsWithFeature()
{
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignedCodonFrameTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the method that locates the first aligned sequence that has a mapping.
*/
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.Iterator;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class AlignedCodonIteratorTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test normal case for iterating over aligned codons.
*/
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignedCodonTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testEquals()
{
import static org.testng.AssertJUnit.assertNull;
import jalview.analysis.AlignSeq;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignmentAnnotationTests
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testCopyConstructor()
{
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class AlignmentTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// @formatter:off
private static final String TEST_DATA =
"# STOCKHOLM 1.0\n" +
import static org.testng.Assert.assertEquals;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignmentViewTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testGetVisibleAlignmentGapChar()
{
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
import java.util.BitSet;
import java.util.Collections;
import java.util.ConcurrentModificationException;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ColumnSelectionTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testAddElement()
{
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DBRefEntryTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Tests for the method that compares equality of reference (but not mapping)
*/
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class HiddenSequencesTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static int SEQ_COUNT = 10;
SequenceI[] seqs;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.Arrays;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class MappingTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* trite test of the intersectVisContigs method for a simple DNA -> Protein
* exon map and a range of visContigs
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;
-import jalview.datamodel.MappingType;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class MappingTypeTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetInverse()
{
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class MatchTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testToString()
{
import static org.testng.Assert.fail;
import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
//import org.testng.Assert;
import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBEntryTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
import static org.testng.Assert.assertTrue;
import jalview.datamodel.ResidueCount.SymbolCounts;
+import jalview.gui.JvOptionPane;
import org.junit.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ResidueCountTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test a mix of add and put for nucleotide counting
*/
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.BitSet;
import org.junit.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SearchResultsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testToString()
{
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import jalview.gui.JvOptionPane;
import jalview.util.Comparison;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class SeqCigarTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testFindPosition()
{
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test
public class SequenceDummyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* test for become method
*/
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SequenceFeatureTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testCopyConstructor()
{
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.io.File;
import java.util.Vector;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class SequenceTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Sequence seq;
@BeforeMethod(alwaysRun = true)
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class EmblEntryTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetCdsRanges()
{
import static org.testng.AssertJUnit.assertNull;
import jalview.datamodel.DBRefEntry;
+import jalview.gui.JvOptionPane;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class EmblFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testGetEmblFile()
{
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.fail;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/*
*/
public class SparseIntArrayTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testPut()
{
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.fail;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SparseShortArrayTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testPut()
{
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
public class EnsemblCdnaTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeClass(alwaysRun = true)
public void setUp()
{
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
public class EnsemblCdsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeClass(alwaysRun = true)
public void setUp()
{
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
public class EnsemblGeneTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeClass(alwaysRun = true)
public void setUp()
{
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
public class EnsemblGenomeTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeClass(alwaysRun = true)
public void setUp()
{
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class EnsemblProteinTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testIsValidReference() throws Exception
{
import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FastaFile;
import jalview.io.FileParse;
public class EnsemblSeqProxyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final Object[][] allSeqs = new Object[][] {
{
new EnsemblProtein(),
import static org.testng.AssertJUnit.assertFalse;
import jalview.datamodel.DBRefEntry;
+import jalview.gui.JvOptionPane;
import java.io.BufferedReader;
import java.io.IOException;
import java.net.URL;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class EnsemblXrefTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
//@formatter:off
private static final String JSON =
"[{\"primary_id\":\"CCDS5863\",\"dbname\":\"CCDS\"}," +
package jalview.ext.htsjdk;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.File;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class TestHtsContigDb
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public final void testHTSReferenceSequence() throws Exception
{
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.gui.SequenceRenderer;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class JmolCommandsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testGetColourBySequenceCommand_noFeatures()
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileLoader;
import jalview.structure.StructureImportSettings;
import java.util.Vector;
import org.jmol.c.STR;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class JmolParserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/*
* 1GAQ has been reduced to alpha carbons only
* 1QCF is the full PDB file including headers, HETATM etc
import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
public class JmolViewerTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
package jalview.ext.jmol;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import java.io.File;
import java.util.Set;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
+
import MCview.PDBfile;
/**
public class JmolVsJalviewPDBParserEndToEndTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static void main(String[] args)
{
if (args == null || args[0] == null)
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.FastaFile;
import jalview.io.FormatAdapter;
import org.testng.Assert;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import MCview.PDBfile;
public class TestAnnotate3D
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Network" }, enabled = true)
public void test1GIDbyId() throws Exception
{
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.awt.Color;
import java.util.Arrays;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testAddColourRange()
{
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
public class ChimeraConnect
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testLaunchAndExit()
{
import jalview.bin.Cache;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.gui.Preferences;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
public class JalviewChimeraView
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
import jalview.io.gff.SequenceOntologyI;
import org.testng.annotations.BeforeClass;
public class SequenceOntologyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private SequenceOntologyI so;
@BeforeClass(alwaysRun = true)
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.gui.JvOptionPane;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class FTSRestClientTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private FTSRestClient ftsRestClient;
@BeforeMethod(alwaysRun = true)
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import javax.swing.JInternalFrame;
import javax.swing.JTextField;
import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBFTSPanelTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.gui.JvOptionPane;
import java.io.BufferedReader;
import java.io.FileReader;
import org.json.simple.parser.ParseException;
import org.testng.Assert;
import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBFTSRestClientTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AlignFrameTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testHideFeatureColumns()
{
public class AlignViewportTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
AlignmentI al;
AlignViewport testee;
import javax.swing.JButton;
import javax.swing.JPanel;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class AnnotationChooserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// 4 sequences x 13 positions
final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ "TIETHKEAELVG-\n"
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AppVarnaTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testReplaceOddGaps()
{
import java.awt.Font;
import java.awt.FontMetrics;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FontChooserTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Not a real test as it runs no methods on FontChooser and makes no
* assertions, but this method writes to sysout the names of any (currently
import javax.help.HelpSetException;
import javax.help.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class HelpTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void checkHelpTargets() throws HelpSetException
{
{
@BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.gui;
+
+import java.awt.Component;
+import java.awt.Dimension;
+
+import javax.swing.Icon;
+import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class JvOptionPaneTest
+{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ Component parentComponent = null;
+
+ String message = "Hello World!";
+
+ String title = "Title";
+
+ int optionType = JvOptionPane.OK_CANCEL_OPTION;
+
+ int messageType = JvOptionPane.INFORMATION_MESSAGE;
+
+ Icon icon = null;
+
+ Object initialSelectionValue = null;
+
+ Object[] selectionValues = null;
+
+
+ @Test(groups = { "Functional" })
+ public void showConfirmDialogFamilyTest()
+ {
+ JvOptionPane.showConfirmDialog(parentComponent, message);
+ JvOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType);
+ JvOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType, messageType);
+ JvOptionPane.showConfirmDialog(parentComponent, message, title,
+ optionType, messageType, icon);
+ Assert.assertTrue(true);
+ }
+
+ @Test(groups = { "Functional" })
+ public void showInputDialogFamilyTest()
+ {
+ JvOptionPane.showInputDialog(message);
+ JvOptionPane.showInputDialog(parentComponent, message);
+ JvOptionPane.showInputDialog(message, initialSelectionValue);
+ JvOptionPane.showInputDialog(parentComponent, message,
+ initialSelectionValue);
+ JvOptionPane.showInputDialog(parentComponent, message, title,
+ messageType);
+ JvOptionPane.showInputDialog(parentComponent, message, title,
+ messageType, icon, selectionValues, initialSelectionValue);
+ Assert.assertTrue(true);
+ }
+
+ @Test(groups = { "Functional" })
+ public void showMessageDialogFamilyTest()
+ {
+ JvOptionPane.showMessageDialog(parentComponent, message);
+ JvOptionPane.showMessageDialog(parentComponent, message, title,
+ messageType);
+ JvOptionPane.showMessageDialog(parentComponent, message, title,
+ messageType, icon);
+ Assert.assertTrue(true);
+ }
+
+ @Test(groups = { "Functional" })
+ public void showInternalMessageDialogFamilyTest()
+ {
+ JvOptionPane.showInternalMessageDialog(parentComponent, message);
+ JvOptionPane.showInternalMessageDialog(parentComponent, message, title,
+ messageType);
+ JvOptionPane.showInternalMessageDialog(parentComponent, message, title,
+ messageType, icon);
+ Assert.assertTrue(true);
+ }
+
+ @Test(groups = { "Functional" })
+ public void showInternalConfirmDialogFamilyTest()
+ {
+ JvOptionPane.showInternalConfirmDialog(parentComponent, message, title,
+ optionType);
+ JvOptionPane.showInternalConfirmDialog(parentComponent, message, title,
+ optionType, messageType);
+
+ JvOptionPane.showInternalConfirmDialog(getDummyDesktopPane(), message);
+
+ JvOptionPane.showInternalConfirmDialog(getDummyDesktopPane(), message,
+ title, optionType, messageType, icon);
+ JvOptionPane.showInternalInputDialog(getDummyDesktopPane(), message);
+ JvOptionPane.showInternalInputDialog(getDummyDesktopPane(), message,
+ title, messageType);
+ JvOptionPane.showInternalInputDialog(getDummyDesktopPane(), message,
+ title, messageType, icon, selectionValues,
+ initialSelectionValue);
+ Assert.assertTrue(true);
+
+ }
+
+ private JDesktopPane getDummyDesktopPane()
+ {
+ JFrame frame = new JFrame("Dummy JDesktopPane");
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ @SuppressWarnings("serial")
+ JDesktopPane jdpDesktop = new JDesktopPane()
+ {
+ @Override
+ public Dimension getPreferredSize()
+ {
+ return new Dimension(400, 300);
+ }
+ };
+ frame.setContentPane(jdpDesktop);
+ JPanel panel = new JPanel();
+ panel.setBounds(0, 0, 400, 300);
+ jdpDesktop.add(panel);
+ frame.pack();
+ frame.setVisible(true);
+ panel.setVisible(true);
+ return jdpDesktop;
+ }
+}
import javax.swing.JScrollBar;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class JvSwingUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testGetScrollBarProportion()
{
import javax.swing.JPanel;
import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PaintRefresherTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// TODO would prefer PaintRefresher to be a single rather than static
@BeforeMethod(alwaysRun = true)
public void setUp()
import javax.swing.JPopupMenu;
import javax.swing.JSeparator;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PopupMenuTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// 4 sequences x 13 positions
final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+ "TIETHKEAELVG-\n"
import javax.swing.JPanel;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ProgressBarTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private JPanel statusPanel;
private JLabel statusBar;
import java.awt.Color;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SequenceRendererTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testGetResidueBoxColour_zappo()
{
import java.util.Vector;
import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class StructureChooserTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Sequence seq;
@BeforeMethod(alwaysRun = true)
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class StructureViewerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetUniquePdbFiles()
{
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
public class AnnotatedPDBFileInputTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
AlignmentI al;
String pdbId;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile.ViewDef;
import java.io.File;
import java.util.Hashtable;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class AnnotationFileIOTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static String TestFiles[][] = {
{ "Test example annotation import/export", "examples/uniref50.fa",
"examples/testdata/example_annot_file.jva" },
*/
package jalview.io;
+import jalview.gui.JvOptionPane;
import jalview.json.binding.biojs.BioJSReleasePojo;
import jalview.json.binding.biojs.BioJSRepositoryPojo;
import org.testng.Assert;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class BioJsHTMLOutputTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void getJalviewAlignmentAsJsonString()
{
import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.io.IOException;
import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FeaturesFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
@Test(groups = { "Functional" })
*/
package jalview.io;
+import jalview.gui.JvOptionPane;
+
import java.io.File;
import java.io.IOException;
public class FileIOTester
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class FormatAdapterTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test saving and re-reading in a specified format
*
*/
package jalview.io;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class HtmlFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" }, enabled = false)
public void test()
{
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class IdentifyFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" }, dataProvider = "identifyFiles")
public void testIdentify(String data, String expectedFileType)
{
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
public class JSONFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private int TEST_SEQ_HEIGHT = 0;
private int TEST_GRP_HEIGHT = 0;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import java.util.Date;
public class Jalview2xmlBase
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import org.testng.Assert;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class Jalview2xmlTests extends Jalview2xmlBase
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testRNAStructureRecovery() throws Exception
{
import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
public class JalviewExportPropertiesTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.gui.JvOptionPane;
import java.util.Arrays;
import java.util.Collection;
public class NewickFileTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Factory
public static Object[] factoryData()
{
package jalview.io;
import jalview.datamodel.AlignmentI;
+import jalview.gui.JvOptionPane;
import java.io.IOException;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class PfamFormatInputTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testPfamFormatNoLimits() throws IOException
{
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
public class PhylipFileTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// interleaved file from
// http://www.molecularevolution.org/molevolfiles/fileformats/dna.phy.dat
// sequential file is the interleave file converted into sequential format
*/
package jalview.io;
+import jalview.gui.JvOptionPane;
+
import java.io.File;
import org.testng.annotations.AfterClass;
{
@BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
}
import static org.testng.AssertJUnit.assertEquals;
import jalview.datamodel.SequenceFeature;
+import jalview.gui.JvOptionPane;
import java.util.Hashtable;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SequenceAnnotationReportTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testAppendFeature_disulfideBond()
{
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class StockholmFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
static String PfamFile = "examples/PF00111_seed.stk",
RfamFile = "examples/RF00031_folded.stk";
*/
package jalview.io;
+import jalview.gui.JvOptionPane;
import jalview.io.TCoffeeScoreFile.Block;
import jalview.io.TCoffeeScoreFile.Header;
import java.util.List;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class TCoffeeScoreFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
final static File SCORE_FILE = new File(
"test/jalview/io/tcoffee.score_ascii");
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ExonerateHelperTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetMappingType()
{
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class Gff3HelperTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test processing one PASA GFF line giving a match from forward strand to
* forward strand
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class GffHelperBaseTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the method that parses lines like <br>
* ID=2345;Name=Something,Another thing;Notes=Hello;Notes=World
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class GffHelperFactoryTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetHelper()
{
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
*/
public class GffTests
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the case where we load a protein ('query') sequence, then exonerateGff
* describing its mapping to cDNA, and then a DNA sequence including the
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class InterProScanHelperTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test processing one InterProScan GFF line
*
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DnaCodonTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testAmbiguityCodeGeneration()
{
import static org.testng.AssertJUnit.fail;
import jalview.datamodel.SequenceFeature;
+import jalview.gui.JvOptionPane;
import jalview.util.Format;
import java.awt.Color;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FeatureColourTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testCopyConstructor()
{
import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
import jalview.datamodel.Profiles;
+import jalview.gui.JvOptionPane;
import java.awt.Color;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ResidueColourSchemeTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testAboveThreshold()
{
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
+import jalview.gui.JvOptionPane;
+
import java.util.Collections;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ResiduePropertiesTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test 'standard' codon translations (no ambiguity codes)
*/
package jalview.schemes;
import jalview.api.analysis.ScoreModelI;
+import jalview.gui.JvOptionPane;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ScoreMatrixPrinter
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void printAllMatrices()
{
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
+import jalview.gui.JvOptionPane;
+
import java.awt.Color;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class UserColourSchemeTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testGetColourFromString()
{
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.StructureFile;
import org.testng.Assert;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class Mapping
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/*
* more test data
*
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.FormatAdapter;
import jalview.io.StructureFile;
import jalview.util.MapList;
import java.util.ArrayList;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class StructureSelectionManagerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private StructureSelectionManager ssm;
@BeforeMethod(alwaysRun = true)
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.structure.AtomSpec;
import jalview.structure.StructureSelectionManager;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
*/
public class AAStructureBindingModelTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/*
* Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
*/
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ArrayUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testReverseIntArray()
{
import static org.testng.Assert.assertNotEquals;
import static org.testng.Assert.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class CaseInsensitiveStringTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testEquals()
{
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
+import jalview.gui.JvOptionPane;
+
import java.awt.Color;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ColorUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Color paleColour = new Color(97, 203, 111); // pale green
Color midColour = new Color(135, 57, 41); // mid red
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ComparisonTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testIsGap()
{
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DBRefUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test the method that selects DBRefEntry items whose source is in a supplied
* list
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.fail;
+import jalview.gui.JvOptionPane;
+
import java.text.ParseException;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DnaUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Tests for parsing an ENA/GenBank location specifier
*
import static org.testng.Assert.assertEquals;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class FormatTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testAppendPercentage()
{
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import jalview.gui.JvOptionPane;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class MapListTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testSomething()
{
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class MappingUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private AlignViewportI dnaView;
private AlignViewportI proteinView;
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ParseHtmlBodyAndLinksTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testParseHtml_noLinks()
{
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.awt.Button;
import java.awt.Event;
import java.awt.event.MouseEvent;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class PlatformTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Button b = new Button();
/**
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
import java.util.Random;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class QuickSortTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final String c1 = "Blue";
private static final String c2 = "Yellow";
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
+import jalview.gui.JvOptionPane;
+
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ShiftListTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testParseMap()
{
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class SparseCountTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = "Functional")
public void testAdd()
{
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class StringUtilsTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testInsertCharAt()
{
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
+import jalview.gui.JvOptionPane;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class UrlLinkTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
final static String DB = "Test";
final static String URL_PREFIX = "http://www.jalview.org/";
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.gui.JvOptionPane;
+
import java.awt.Color;
import java.lang.reflect.Field;
import java.util.Random;
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ViewStyleTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
Random r = new Random();
/**
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import java.util.Collections;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class AlignCalcManagerTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private AlignFrame alignFrame;
/**
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.StructureParser;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
public class PDBSequenceFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
SequenceFetcher sf;
@BeforeMethod(alwaysRun = true)
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.ws.seqfetcher.ASequenceFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.List;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
+
public class SequenceFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* simple run method to test dbsources.
*
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.UniprotEntry;
+import jalview.gui.JvOptionPane;
import java.io.Reader;
import java.io.StringReader;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class UniprotTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
// adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
+ "<uniprot>"
package jalview.ws.dbsources;
import jalview.datamodel.AlignmentI;
+import jalview.gui.JvOptionPane;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class XfamFetcherTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "External" })
public void testRfamSeed() throws Exception
{
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class EBIFetchClientTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Test method that constructs URL to fetch from
*/
package jalview.ws.gui;
import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
import jalview.gui.WsJobParameters;
import jalview.util.MessageManager;
import jalview.ws.jabaws.JalviewJabawsTestUtils;
public class Jws2ParamView
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* which services to test
*/
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
@Test(groups = { "External" })
public class DisorderAnnotExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static String testseqs = "examples/uniref50.fa";
public static Jws2Discoverer disc;
*/
package jalview.ws.jabaws;
+import jalview.gui.JvOptionPane;
import jalview.ws.jws2.Jws2Discoverer;
import java.util.Vector;
{
@BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
}
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
public class JpredJabaStructExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static String testseqs = "examples/uniref50.fa";
public static Jws2Discoverer disc;
import static org.testng.AssertJUnit.assertEquals;
+import jalview.gui.JvOptionPane;
+
import java.util.ArrayList;
import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import compbio.data.msa.MsaWS;
public class MinJabawsClientTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* simple test for the benefit of JAL-1338
*
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
public class RNAStructExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final String JAR_FILE_NAME = "testRnalifold_param.jar";
public static String testseqs = "examples/RF00031_folded.stk";
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
import jalview.ws.jabaws.JalviewJabawsTestUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
public class ParameterUtilsTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/*
* To limit tests to specify services, add them to this list; leave list empty
* to test all
import static org.testng.AssertJUnit.assertEquals;
import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
import java.util.Vector;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class RestClientTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* Refactored 'as is' from main method
*/
import static org.testng.AssertJUnit.assertTrue;
import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
import java.util.Map;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
public class ShmmrRSBSService
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testShmmrService()
{
*/
package jalview.ws.seqfetcher;
+import jalview.gui.JvOptionPane;
+
import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class DasSequenceFetcher
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testDasRegistryContact()
{
import jalview.datamodel.FeatureProperties;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
import jalview.ws.SequenceFetcher;
import jalview.ws.dbsources.Pdb;
public class DbRefFetcherTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.structure.StructureMapping;
import jalview.xml.binding.sifts.Entry.Entity;
import org.testng.Assert;
import org.testng.FileAssert;
import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
public class SiftsClientTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
.getProperty("user.home")
+ File.separatorChar
git://source.jalview.org / jalview.git / commitdiff