*/
package jalview.ext.ensembl;
+ import jalview.bin.Jalview;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
import jalview.util.StringUtils;
import java.io.BufferedReader;
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.3";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "7.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "6.3";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "7.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
protected abstract boolean useGetRequest();
/**
- * Return the desired value for the Content-Type request header
- *
- * @param multipleIds
+ * Returns the desired value for the Content-Type request header. Default is
+ * application/json, override if required to vary this.
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getRequestMimeType(boolean multipleIds);
+ protected String getRequestMimeType()
+ {
+ return "application/json";
+ }
/**
- * Return the desired value for the Accept request header
+ * Return the desired value for the Accept request header. Default is
+ * application/json, override if required to vary this.
*
* @return
* @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
*/
- protected abstract String getResponseMimeType();
+ protected String getResponseMimeType()
+ {
+ return "application/json";
+ }
/**
* Checks Ensembl's REST 'ping' endpoint, and returns true if response
}
/**
- * returns a reader to a Fasta response from the Ensembl sequence endpoint
+ * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
+ * If the request failed the return value may be null.
*
* @param ids
* @return
* @throws IOException
*/
- protected FileParse getSequenceReader(List<String> ids) throws IOException
+ protected BufferedReader getSequenceReader(List<String> ids)
+ throws IOException
{
URL url = getUrl(ids);
BufferedReader reader = getHttpResponse(url, ids);
- if (reader == null)
- {
- // request failed
- return null;
- }
- FileParse fp = new FileParse(reader, url.toString(),
- DataSourceType.URL);
- return fp;
+ return reader;
}
/**
boolean multipleIds = ids != null && ids.size() > 1;
connection.setRequestMethod(
multipleIds ? HttpMethod.POST : HttpMethod.GET);
- connection.setRequestProperty("Content-Type",
- getRequestMimeType(multipleIds));
+ connection.setRequestProperty("Content-Type", getRequestMimeType());
connection.setRequestProperty("Accept", getResponseMimeType());
connection.setDoInput(true);
connection.setDoOutput(multipleIds);
- connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
- connection.setReadTimeout(readTimeout);
+ if (!Jalview.isJS())
+ {
+ connection.setUseCaches(false);
+ connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+ connection.setReadTimeout(readTimeout);
+ }
if (multipleIds)
{
{
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- addDialogThread(new Runnable()
+ new Thread(new Runnable()
{
@Override
public void run()
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
}
- });
+ }).start();
}
public void getIdentifiersOrgData()
{
// Thread off the identifiers fetcher
- addDialogThread(new Runnable()
+ new Thread(new Runnable()
{
@Override
public void run()
+ e.getMessage());
}
}
- });
+ }).start();
+ ;
}
@Override
* Jalview project file
*/
@Override
- public void saveState_actionPerformed()
+ public void saveState_actionPerformed(boolean asCastor)
{
- JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ asCastor ? "jvp" : "jvx",
"Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
- // TODO: JAL-3048 Dialog runner refactoring here
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
{
- final Desktop me = this;
- final java.io.File choice = chooser.getSelectedFile();
+ File choice = chooser.getSelectedFile();
setProjectFile(choice);
new Thread(new Runnable()
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- new Jalview2XML().saveState(choice);
+ if (asCastor)
+ {
+ new Jalview2XML().saveState(choice);
+ }
+ else
+ {
+ new jalview.project.Jalview2XML().saveState(choice);
+ }
} catch (OutOfMemoryError oom)
{
new OOMWarning(
Cache.log.error(
"Problems whilst trying to save to " + choice.getName(),
ex);
- JvOptionPane.showMessageDialog(me,
+ JvOptionPane.showMessageDialog(Desktop.this,
MessageManager.formatMessage(
"label.error_whilst_saving_current_state_to",
new Object[]
setProgressBar(null, choice.hashCode());
}
}).start();
- }
+ }
}
- private void setProjectFile(File choice)
+ void setProjectFile(File choice)
{
this.projectFile = choice;
}
* Prompts the user to choose a file and loads in as a Jalview project file
*/
@Override
- public void loadState_actionPerformed()
+ public void loadState_actionPerformed(boolean asCastor)
{
+ // TODO: GET RID OF .JVX BEFORE RELEASE JIM!
+ final String[] suffix = asCastor ? new String[] { "jvp", "jar" }
+ : new String[]
+ { "jvx" };
+ final String[] desc = asCastor
+ ? new String[]
+ { "Jalview Project", "Jalview Project (old)" }
+ : new String[]
+ { "Jalview Project" };
JalviewFileChooser chooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "jvp", "jar" },
- new String[]
- { "Jalview Project", "Jalview Project (old)" },
+ Cache.getProperty("LAST_DIRECTORY"), suffix,
+ desc,
"Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
{
- final File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ final String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
- try
+ @Override
+ public void run()
{
- if (asCastor)
- {
- new Jalview2XML().loadJalviewAlign(choice);
- }
- else
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
- try
- {
- new Jalview2XML().loadJalviewAlign(choice);
++ try {
++ if (asCastor)
++ {
++ new Jalview2XML().loadJalviewAlign(choice);
++ }
++ else
++ {
++ new jalview.project.Jalview2XML().loadJalviewAlign(choice);
++ }
+ } catch (OutOfMemoryError oom)
{
- new jalview.project.Jalview2XML().loadJalviewAlign(choice);
- }
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
+ new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
+ } catch (Exception ex)
+ {
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
- setProgressBar(null, choice.hashCode());
}
- setProgressBar(null, choice.hashCode());
- }
- }).start();
- }
+ }).start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
- import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcher;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import jalview.util.Platform;
+ import jalview.util.dialogrunner.RunResponse;
import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.JalviewUserColours.Filter;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
- import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
*/
void load()
{
- // TODO: JAL-3048 relies on Castor XML parsing: not needed for JS-jalview core
- // functionalty
-
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- File file = chooser.getSelectedFile();
- load(file);
- }
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION){
+
+ @Override
+ public void run() {
+ File file = chooser.getSelectedFile();
+ load(file);
+ }});
+ chooser.showOpenDialog(this);
}
/**
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
- JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(in);
+ JAXBElement<JalviewUserColours> jbe = um.unmarshal(streamReader,
+ JalviewUserColours.class);
+ JalviewUserColours jucs = jbe.getValue();
+
+ // JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
/*
* load feature colours
*/
- for (int i = jucs.getColourCount() - 1; i >= 0; i--)
+ for (int i = jucs.getColour().size() - 1; i >= 0; i--)
{
- jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
- FeatureColourI colour = Jalview2XML.unmarshalColour(newcol);
+ Colour newcol = jucs.getColour().get(i);
+ FeatureColourI colour = jalview.project.Jalview2XML
+ .parseColour(newcol);
fr.setColour(newcol.getName(), colour);
- fr.setOrder(newcol.getName(), i / (float) jucs.getColourCount());
+ fr.setOrder(newcol.getName(), i / (float) jucs.getColour().size());
}
/*
* load feature filters; loaded filters will replace any that are
* currently defined, other defined filters are left unchanged
*/
- for (int i = 0; i < jucs.getFilterCount(); i++)
+ for (int i = 0; i < jucs.getFilter().size(); i++)
{
- jalview.schemabinding.version2.Filter filterModel = jucs
- .getFilter(i);
+ Filter filterModel = jucs.getFilter().get(i);
String featureType = filterModel.getFeatureType();
- FeatureMatcherSetI filter = Jalview2XML.unmarshalFilter(featureType,
- filterModel.getMatcherSet());
+ FeatureMatcherSetI filter = jalview.project.Jalview2XML
+ .parseFilter(featureType, filterModel.getMatcherSet());
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
*/
void save()
{
- // TODO: JAL-3048 not needed for Jalview-JS - save colours
JalviewFileChooser chooser = new JalviewFileChooser("fc",
SEQUENCE_FEATURE_COLOURS);
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- save(chooser.getSelectedFile());
- }
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ save(file);
+ }
}
/**
for (String featureType : sortedTypes)
{
FeatureColourI fcol = fr.getFeatureStyle(featureType);
- jalview.schemabinding.version2.Colour col = Jalview2XML.marshalColour(
- featureType, fcol);
- ucs.addColour(col);
+ Colour col = jalview.project.Jalview2XML.marshalColour(featureType,
+ fcol);
+ ucs.getColour().add(col);
}
/*
{
Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
FeatureMatcherI firstMatcher = iterator.next();
- MatcherSet ms = Jalview2XML.marshalFilter(firstMatcher, iterator,
+ jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
+ .marshalFilter(firstMatcher, iterator,
filter.isAnded());
Filter filterModel = new Filter();
filterModel.setFeatureType(featureType);
filterModel.setMatcherSet(ms);
- ucs.addFilter(filterModel);
+ ucs.getFilter().add(filterModel);
}
}
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ out.flush();
- ucs.marshal(out);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
JPanel buttonPanel = new JPanel();
buttonPanel.add(ok);
buttonPanel.add(cancel);
- if (!Jalview.isJS())
- {
- /*
- * no save/load XML in JalviewJS for now
- */
- buttonPanel.add(loadColours);
- buttonPanel.add(saveColours);
- }
+ buttonPanel.add(loadColours);
+ buttonPanel.add(saveColours);
bigPanel.add(scrollPane, BorderLayout.CENTER);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.GUserDefinedColours;
-import jalview.schemabinding.version2.Colour;
-import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeLoader;
import jalview.schemes.ColourSchemes;
import jalview.util.ColorUtils;
import jalview.util.Format;
import jalview.util.MessageManager;
+ import jalview.util.dialogrunner.RunResponse;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.ObjectFactory;
import java.awt.Color;
import java.awt.Font;
import javax.swing.JInternalFrame;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
/**
* This panel allows the user to assign colours to Amino Acid residue codes, and
* flag is true if the colour scheme has been changed since the
* dialog was opened, or the changes last saved to file
*/
- boolean changed;
+ boolean changedButNotSaved;
JInternalFrame frame;
button.setForeground(ColorUtils.brighterThan(newColour));
}
- changed = true;
+ changedButNotSaved = true;
}
/**
{
// BH 2018 no warning in JavaScript TODO
- if (/** @j2sNative true || */ !changed)
+ if (/** @j2sNative true || */ !changedButNotSaved)
{
return;
}
question, title, JvOptionPane.DEFAULT_OPTION,
JvOptionPane.PLAIN_MESSAGE, null, options, options[0]);
if (response == 0)
{
/*
- * prompt to save changes to file
+ * prompt to save changes to file; if done,
+ * resets 'changed' flag to false
*/
- saved = savebutton_actionPerformed();
+ savebutton_actionPerformed();
}
/*
* if user chooses not to save (either in this dialog or in the
* save as dialogs), treat this as a new user defined colour scheme
*/
- if (!saved)
+ if (changedButNotSaved)
{
/*
* clear scheme name and re-apply as an anonymous scheme
{
upperCaseButtons = new ArrayList<>();
lowerCaseButtons = new ArrayList<>();
- // TODO: JAL-3048 requires Castor dependency for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.load_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.load"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value != JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
- File choice = chooser.getSelectedFile();
- Cache.setProperty(LAST_DIRECTORY, choice.getParent());
-
- UserColourScheme ucs = ColourSchemeLoader
- .loadColourScheme(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getSchemeName());
-
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = lowerCaseButtons.get(i);
- button.setBackground(ucs.getLowerCaseColours()[i]);
- }
- }
- else
- {
- caseSensitive.setSelected(false);
- lcaseColour.setEnabled(false);
- resetButtonPanel(false);
- }
-
- for (int i = 0; i < upperCaseButtons.size(); i++)
- {
- JButton button = upperCaseButtons.get(i);
- button.setBackground(colors[i]);
- }
-
- addNewColourScheme(choice.getPath());
+ chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) {
+ @Override
+ public void run() {
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
+
+ UserColourScheme ucs = ColourSchemeLoader
+ .loadColourScheme(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
+
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
+ }
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
+
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
+ }
+
+ addNewColourScheme(choice.getPath());
+ }});
+
+ chooser.showOpenDialog(this);
}
/**
* <li>Don't apply the changes if the currently selected scheme is different,
* to allow a new scheme to be configured and saved but not applied</li>
* </ul>
- * Returns true if the scheme is saved to file, false if it is not
- *
- * @return
+ * If the scheme is saved to file, the 'changed' flag field is reset to false.
*/
@Override
- protected boolean savebutton_actionPerformed()
+ protected void savebutton_actionPerformed()
{
String name = schemeName.getText().trim();
if (name.length() < 1)
.getString("label.user_colour_scheme_must_have_name"),
MessageManager.getString("label.no_name_colour_scheme"),
JvOptionPane.WARNING_MESSAGE);
- return false;
}
if (ColourSchemes.getInstance().nameExists(name))
JvOptionPane.YES_NO_OPTION);
if (reply != JvOptionPane.YES_OPTION)
{
- return false;
}
}
- // TODO: JAL-3048 saveas, also requires Castor dependency for Jalview-JS
JalviewFileChooser chooser = new JalviewFileChooser("jc",
"Jalview User Colours");
chooser.setDialogTitle(
MessageManager.getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value != JalviewFileChooser.APPROVE_OPTION)
- {
- return false;
- }
-
- File file = chooser.getSelectedFile();
- UserColourScheme updatedScheme = addNewColourScheme(file.getPath());
- saveToFile(file);
- changed = false;
-
- /*
- * changes saved - apply to alignment if we are changing
- * the currently selected colour scheme; also make the updated
- * colours the 'backout' scheme on Cancel
- */
- if (oldColourScheme != null
- && name.equals(oldColourScheme.getSchemeName()))
- {
- oldColourScheme = updatedScheme;
- applyButton_actionPerformed();
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ UserColourScheme updatedScheme = addNewColourScheme(file.getPath());
+ saveToFile(file);
+ changedButNotSaved = false;
+
+ /*
+ * changes saved - apply to alignment if we are changing
+ * the currently selected colour scheme; also make the updated
+ * colours the 'backout' scheme on Cancel
+ */
+ if (oldColourScheme != null
+ && name.equals(oldColourScheme.getSchemeName()))
+ {
+ oldColourScheme = updatedScheme;
+ applyButton_actionPerformed();
+ }
}
- return true;
}
/**
Colour col = new Colour();
col.setName(button.getText());
col.setRGB(Format.getHexString(button.getBackground()));
- ucs.addColour(col);
+ ucs.getColour().add(col);
}
- ucs.marshal(out);
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+ // ucs.marshal(out);
out.close();
} catch (Exception ex)
{
@Override
public void actionPerformed(ActionEvent e)
{
- saveState_actionPerformed();
+ saveState_actionPerformed(true);
+ }
+ });
+ JMenuItem saveAsJaxb = new JMenuItem("Save Project as JAXB");
+ saveAsJaxb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ saveState_actionPerformed(false);
}
});
loadState.setText(MessageManager.getString("action.load_project"));
@Override
public void actionPerformed(ActionEvent e)
{
- loadState_actionPerformed();
+ loadState_actionPerformed(true);
+ }
+ });
+ JMenuItem loadAsJaxb = new JMenuItem("Load Project as JAXB");
+ loadAsJaxb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadState_actionPerformed(false);
}
});
inputMenu.setText(MessageManager.getString("label.input_alignment"));
desktopMenubar.add(windowMenu);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
- if (!Jalview.isJS())
- FileMenu.addSeparator();
- FileMenu.add(saveState);
- FileMenu.add(loadState);
- FileMenu.addSeparator();
++ FileMenu.addSeparator();
++ FileMenu.add(saveAsJaxb);
++ FileMenu.add(loadAsJaxb);
++ if (!Jalview.isJS())
+ {
- FileMenu.addSeparator();
+ FileMenu.add(saveState);
+ FileMenu.add(loadState);
+ }
-
- FileMenu.add(saveAsJaxb);
- FileMenu.add(loadAsJaxb);
+ FileMenu.addSeparator();
FileMenu.add(quit);
HelpMenu.add(aboutMenuItem);
HelpMenu.add(documentationMenuItem);
{
}
- public void saveState_actionPerformed()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void saveState_actionPerformed(boolean asCastor)
{
}
- public void loadState_actionPerformed()
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void loadState_actionPerformed(boolean asCastor)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void loadJalviewAlign_actionPerformed(ActionEvent e)
{
}
git://source.jalview.org / jalview.git / commitdiff