*/
public static String getProperty(String key)
{
- return applicationProperties.getProperty(key);
+ String prop = applicationProperties.getProperty(key);
+ if (prop == null && Platform.isJS())
+ {
+ prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
+ + "_" + JS_PROPERTY_PREFIX + key);
+ }
+ return prop;
}
/**
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
+import ext.vamsas.ServiceHandle;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
+ Hashtable<String, String> scoreSorts = new Hashtable<>();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
}
}
}
- Enumeration labels = scoreSorts.keys();
+ Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
+ labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
+ Vector<ServiceHandle> secstrpr = Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ final ext.vamsas.ServiceHandle sh = secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu webService = new JMenu();
+ public JMenu webService = new JMenu();// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
- protected JMenuItem webServiceNoServices;
+ public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
- protected JLabel statusBar = new JLabel();
+ public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+ // sufficient for
+ // AlignFrame.printWriter
protected JMenu outputTextboxMenu = new JMenu();
protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
- protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
+ protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop
+ .createTabbedPane();
protected JMenuItem reload = new JMenuItem();
protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
-
+
protected JMenuItem openFeatureSettings;
private SequenceAnnotationOrder annotationSortOrder;
{
// for Web-page embedding using id=align-frame-div
- setName("align-frame");
+ setName("jalview-alignment");
jbInit();
setJMenuBar(alignFrameMenuBar);
/*
* Translate as cDNA with sub-menu of translation tables
*/
- showTranslation.setText(MessageManager
- .getString("label.translate_cDNA"));
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
boolean first = true;
for (final GeneticCodeI table : GeneticCodes.getInstance()
.getCodeTables())
associatedData_actionPerformed(e);
}
});
- loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
+ loadVcf = new JMenuItem(
+ MessageManager.getString("label.load_vcf_file"));
loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
loadVcf.addActionListener(new ActionListener()
{
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class GDesktop extends JFrame
{
*/
private void jbInit() throws Exception
{
-
+ setName("jalview-desktop");
FileMenu.setText(MessageManager.getString("action.file"));
HelpMenu.setText(MessageManager.getString("action.help"));
VamsasMenu.setText("Vamsas");
import javax.swing.JInternalFrame;
+@SuppressWarnings("serial")
public class GRnaStructureViewer extends JInternalFrame
{
public GRnaStructureViewer()
private void jbInit() throws Exception
{
+
+ setName("jalview-rnastructureviewer");
}
*/
public GSplitFrame(GAlignFrame top, GAlignFrame bottom)
{
+ setName("jalview-splitframe");
this.topFrame = top;
this.bottomFrame = bottom;
import javax.swing.JPanel;
import javax.swing.JRadioButtonMenuItem;
+@SuppressWarnings("serial")
public abstract class GStructureViewer extends JInternalFrame
implements JalviewStructureDisplayI, ColourChangeListener
{
private void jbInit() throws Exception
{
+
+ setName("jalview-structureviewer");
+
JMenuBar menuBar = new JMenuBar();
this.setJMenuBar(menuBar);
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+@SuppressWarnings("serial")
public class GTreePanel extends JInternalFrame
{
BorderLayout borderLayout1 = new BorderLayout();
private void jbInit() throws Exception
{
+ setName("jalview-tree");
this.getContentPane().setLayout(borderLayout1);
this.setBackground(Color.white);
this.setFont(new java.awt.Font("Verdana", 0, 12));
saveAsNewick.setText(MessageManager.getString("label.newick_format"));
saveAsNewick.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
saveAsNewick_actionPerformed(e);
printMenu.setText(MessageManager.getString("action.print"));
printMenu.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
printMenu_actionPerformed(e);
viewMenu.setText(MessageManager.getString("action.view"));
viewMenu.addMenuListener(new MenuListener()
{
+ @Override
public void menuSelected(MenuEvent e)
{
viewMenu_menuSelected();
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuCanceled(MenuEvent e)
{
}
MessageManager.getString("label.sort_alignment_by_tree"));
sortAssocViews.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortByTree_actionPerformed();
font.setText(MessageManager.getString("action.font"));
font.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
font_actionPerformed(e);
MessageManager.getString("label.show_bootstrap_values"));
bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
bootstrapMenu_actionPerformed(e);
distanceMenu.setText(MessageManager.getString("label.show_distances"));
distanceMenu.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
distanceMenu_actionPerformed(e);
fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
fitToWindow.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
fitToWindow_actionPerformed(e);
epsTree.setText("EPS");
epsTree.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
writeTreeImage(TYPE.EPS);
pngTree.setText("PNG");
pngTree.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
writeTreeImage(TYPE.PNG);
MessageManager.getString("label.mark_unlinked_leaves"));
placeholdersMenu.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
placeholdersMenu_actionPerformed(e);
textbox.setText(MessageManager.getString("label.out_to_textbox"));
textbox.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
textbox_actionPerformed(e);
originalSeqData.setText(MessageManager.getString("label.input_data"));
originalSeqData.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
originalSeqData_actionPerformed(e);
* if (key.indexOf(prefix) == 0) { value = "" + info[key];
*/
+ System.out.println(
+ "Platform id=" + id + " reading Info." + key + " = " + value);
p.put(id + "_" + key, value);
/**
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
+import java.net.URL;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.util.Vector;
static private java.net.URL RootServiceURL = null;
- static public Vector ServiceURLList = null;
+ static public Vector<URL> ServiceURLList = null;
static private boolean reallyDiscoverServices = true;
- public static java.util.Hashtable services = null; // vectors of services
-
+ public static java.util.Hashtable<String, Vector<ServiceHandle>> services = null;
// stored by
// abstractServiceType
// string
- public static java.util.Vector serviceList = null; // flat list of services
+ public static java.util.Vector<ServiceHandle> serviceList = null;
- static private Vector getDiscoveryURLS()
+ static private Vector<URL> getDiscoveryURLS()
{
- Vector urls = new Vector();
+ Vector<URL> urls = new Vector<>();
String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
else
{
jalview.bin.Cache.log.debug("Setting default services");
- services = new Hashtable();
+ services = new Hashtable<>();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
"Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ "\ndoi://10.1093/nar/gkv332",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
"JPred Secondary Structure Prediction") };
- services = new Hashtable();
- serviceList = new Vector();
+ services = new Hashtable<>();
+ serviceList = new Vector<>();
buildServiceLists(defServices, serviceList, services);
}
* Hashtable
* @return boolean
*/
- static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
- Hashtable sscat)
+ static private boolean buildServiceLists(ServiceHandle[] sh,
+ Vector<ServiceHandle> cat,
+ Hashtable<String, Vector<ServiceHandle>> sscat)
{
boolean seenNewDiscovery = false;
for (int i = 0, j = sh.length; i < j; i++)
+ sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
{
- sscat.put(sh[i].getAbstractName(), cat = new Vector());
+ sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
}
else
{
- cat = (Vector) sscat.get(sh[i].getAbstractName());
+ cat = sscat.get(sh[i].getAbstractName());
}
cat.add(sh[i]);
if (sh[i].getAbstractName().equals("Registry"))
public void discoverServices()
{
- Hashtable sscat = new Hashtable();
- Vector cat = new Vector();
+ Hashtable<String, Vector<ServiceHandle>> sscat = new Hashtable<>();
+ Vector<ServiceHandle> cat = new Vector<>();
ServiceHandle sh[] = null;
int s_url = 0;
if (ServiceURLList == null)
while (s_url < ServiceURLList.size())
{
if ((sh = getServices(
- (java.net.URL) ServiceURLList.get(s_url))) != null)
+ ServiceURLList.get(s_url))) != null)
{
buildServiceLists(sh, cat, sscat);
// so no need to access original discovery thread.
// Curent decision is to change properties then notify listeners with old
// and new values.
- Hashtable oldServices = services;
+ Hashtable<String, Vector<ServiceHandle>> oldServices = services;
// Vector oldServicelist = serviceList;
services = sscat;
serviceList = cat;
@Override
public void run()
{
- discoverer.doDiscovery();
+ Discoverer.doDiscovery();
discoverer.discoverServices();
}
};
/**
* binding service abstract name to handler class
*/
- private static Hashtable serviceClientBindings;
+ private static Hashtable<String, WS1Client> serviceClientBindings;
public static WS1Client getServiceClient(ServiceHandle sh)
{
if (serviceClientBindings == null)
{
// get a list from Config or create below
- serviceClientBindings = new Hashtable();
+ serviceClientBindings = new Hashtable<>();
serviceClientBindings.put("MsaWS", new MsaWSClient());
serviceClientBindings.put("SecStrPred", new JPredClient());
serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
}
- WS1Client instance = (WS1Client) serviceClientBindings
+ WS1Client instance = serviceClientBindings
.get(sh.getAbstractName());
if (instance == null)
{
git://source.jalview.org / jalview.git / commitdiff