import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.io.InputStreamReader;
+import java.io.Reader;
+import java.net.UnknownHostException;
import java.util.Hashtable;
import java.util.Vector;
import java.util.jar.JarEntry;
import javax.swing.JOptionPane;
-import org.exolab.castor.xml.IDResolver;
-
/**
* DOCUMENT ME!
*
jarentry = jin.getNextJarEntry();
}
- class NoDescIDResolver implements IDResolver
- {
- public Object resolve(String idref)
- {
- System.out.println(idref + " used");
- return null;
- }
- }
-
if (jarentry != null)
{
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");
- JalviewModel object = new JalviewModel();
+ entryCount++;
+ if (jarentry.getName().endsWith(".xml"))
+ {
+ Reader in = new InputStreamReader(jin, "UTF-8");
+ JalviewModel object = new JalviewModel();
- object = object.unmarshal(in);
+ object = object.unmarshal(in);
- af = LoadFromObject(object, file);
- entryCount++;
+ af = LoadFromObject(object, file);
+ }
}
+ jin.close();
} while (jarentry != null);
- } catch (final java.net.UnknownHostException ex)
+ } catch (final UnknownHostException ex)
{
ex.printStackTrace();
if (raiseGUI)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
+ "\n");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new String[]
- { file }), MessageManager
+ new String[] { file }), MessageManager
.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
}
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
+ MessageManager.formatMessage(
+ "label.error_loading_file_params", new String[]
+ { file }), MessageManager
+ .getString("label.error_loading_jalview_file"),
JOptionPane.WARNING_MESSAGE);
}
});
for (int s = 0; s < ids.length; s++)
{
- seqs.addElement(seqids
- .elementAt(ids[s]));
+ seqs.addElement(seqids.elementAt(ids[s]));
}
jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
- featureColours.put(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ featureColours.put(setting.getType(),
+ new java.awt.Color(setting.getColour()));
renderOrder[fs] = setting.getType();
if (setting.getDisplay())
{
- featuresDisplayed.put(setting.getType(), new Integer(
- setting.getColour()));
+ featuresDisplayed.put(setting.getType(),
+ new Integer(setting.getColour()));
}
}
- FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
+ FeatureRendererSettings frs = new FeatureRendererSettings(
+ renderOrder, new Hashtable(), featureColours, 1.0f, null);
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(frs);
}
af.setMenusFromViewport(af.viewport);