{
try
{
- String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
+ String viprotocol = jalview.io.AppletFormatAdapter
+ .checkProtocol(vamsasImport);
if (viprotocol == jalview.io.FormatAdapter.FILE)
{
inSession = desktop.vamsasImport(new File(vamsasImport));
}
}
}
- long progress=-1;
+ long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
{
if (!headless)
{
- desktop.setProgressBar("Processing commandline arguments...", progress=System.currentTimeMillis());
+ desktop.setProgressBar("Processing commandline arguments...",
+ progress = System.currentTimeMillis());
}
System.out.println("Opening file: " + file);
if (af == null)
{
System.out.println("error");
- return;
}
-
- data = aparser.getValue("colour", true);
- if (data != null)
+ else
{
- data.replaceAll("%20", " ");
- jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
- .getColour(af.getViewport().getAlignment(), data);
-
- if (cs == null)
+ data = aparser.getValue("colour", true);
+ if (data != null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- "white");
- ucs.parseAppletParameter(data);
- cs = ucs;
- }
+ data.replaceAll("%20", " ");
- System.out.println("colour is " + data);
- af.changeColour(cs);
- }
-
- // Must maintain ability to use the groups flag
- data = aparser.getValue("groups", true);
- if (data != null)
- {
- af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
- }
- data = aparser.getValue("features", true);
- if (data != null)
- {
- af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- System.out.println("Added " + data);
- }
+ jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+ .getColour(af.getViewport().getAlignment(), data);
- data = aparser.getValue("annotations", true);
- if (data != null)
- {
- af.loadJalviewDataFile(data, null, null, null);
- System.out.println("Added " + data);
- }
- // set or clear the sortbytree flag.
- if (aparser.contains("sortbytree"))
- {
- af.getViewport().setSortByTree(true);
- }
- if (aparser.contains("nosortbytree"))
- {
- af.getViewport().setSortByTree(false);
- }
- data = aparser.getValue("tree", true);
- if (data != null)
- {
- jalview.io.NewickFile fin = null;
- try
- {
- fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
- if (fin != null)
+ if (cs == null)
{
- af.getViewport().setCurrentTree(
- af.ShowNewickTree(fin, data).getTree());
- System.out.println("Added tree " + data);
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
}
- } catch (IOException ex)
- {
- System.err.println("Couldn't add tree " + data);
- ex.printStackTrace(System.err);
- }
- }
- // TODO - load PDB structure(s) to alignment JAL-629
- // (associate with identical sequence in alignment, or a specified
- // sequence)
- getFeatures = checkDasArguments(aparser);
- if (af != null && getFeatures != null)
- {
- FeatureFetcher ff = startFeatureFetching(getFeatures);
- if (ff != null)
- while (!ff.allFinished() || af.operationInProgress())
- {
- // wait around until fetching is finished.
- try
- {
- Thread.sleep(100);
- } catch (Exception e)
- {
+ System.out.println("colour is " + data);
+ af.changeColour(cs);
+ }
- }
- }
- getFeatures = null; // have retrieved features - forget them now.
- }
- if (groovyscript != null)
- {
- // Execute the groovy script after we've done all the rendering stuff
- // and before any images or figures are generated.
- if (jalview.bin.Cache.groovyJarsPresent())
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups", true);
+ if (data != null)
{
- System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[] {desktop,af});
+ af.parseFeaturesFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ System.out.println("Added " + data);
}
- else
+ data = aparser.getValue("features", true);
+ if (data != null)
{
- System.err
- .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
- + groovyscript);
+ af.parseFeaturesFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ System.out.println("Added " + data);
}
- groovyscript = null;
- }
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
- {
- format = aparser.nextValue();
- file = aparser.nextValue();
- if (format.equalsIgnoreCase("png"))
+ data = aparser.getValue("annotations", true);
+ if (data != null)
{
- af.createPNG(new java.io.File(file));
- imageName = (new java.io.File(file)).getName();
- System.out.println("Creating PNG image: " + file);
- continue;
+ af.loadJalviewDataFile(data, null, null, null);
+ System.out.println("Added " + data);
}
- else if (format.equalsIgnoreCase("imgMap"))
+ // set or clear the sortbytree flag.
+ if (aparser.contains("sortbytree"))
{
- af.createImageMap(new java.io.File(file), imageName);
- System.out.println("Creating image map: " + file);
- continue;
+ af.getViewport().setSortByTree(true);
}
- else if (format.equalsIgnoreCase("eps"))
+ if (aparser.contains("nosortbytree"))
{
- System.out.println("Creating EPS file: " + file);
- af.createEPS(new java.io.File(file));
- continue;
+ af.getViewport().setSortByTree(false);
}
+ data = aparser.getValue("tree", true);
+ if (data != null)
+ {
+ jalview.io.NewickFile fin = null;
+ try
+ {
+ fin = new jalview.io.NewickFile(data,
+ jalview.io.AppletFormatAdapter.checkProtocol(data));
+ if (fin != null)
+ {
+ af.getViewport().setCurrentTree(
+ af.ShowNewickTree(fin, data).getTree());
+ System.out.println("Added tree " + data);
+ }
+ } catch (IOException ex)
+ {
+ System.err.println("Couldn't add tree " + data);
+ ex.printStackTrace(System.err);
+ }
+ }
+ // TODO - load PDB structure(s) to alignment JAL-629
+ // (associate with identical sequence in alignment, or a specified
+ // sequence)
- if (af.saveAlignment(file, format))
+ getFeatures = checkDasArguments(aparser);
+ if (af != null && getFeatures != null)
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ FeatureFetcher ff = startFeatureFetching(getFeatures);
+ if (ff != null)
+ while (!ff.allFinished() || af.operationInProgress())
+ {
+ // wait around until fetching is finished.
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
+ {
+
+ }
+ }
+ getFeatures = null; // have retrieved features - forget them now.
}
- else
+ if (groovyscript != null)
{
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
+ // Execute the groovy script after we've done all the rendering stuff
+ // and before any images or figures are generated.
+ if (jalview.bin.Cache.groovyJarsPresent())
+ {
+ System.out.println("Executing script " + groovyscript);
+ executeGroovyScript(groovyscript, new Object[]
+ { desktop, af });
+ }
+ else
+ {
+ System.err
+ .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+ + groovyscript);
+ }
+ groovyscript = null;
}
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
- }
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new java.io.File(file));
+ imageName = (new java.io.File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ System.out.println("Creating EPS file: " + file);
+ af.createEPS(new java.io.File(file));
+ continue;
+ }
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ if (af.saveAlignment(file, format))
+ {
+ System.out.println("Written alignment in " + format
+ + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + format + " format!!");
+ }
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
}
}
AlignFrame startUpAlframe = null;
if (!headless && file == null && vamsasImport == null
&& jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) && proteine == true)
{
- file = jalview.bin.Cache.getDefault("STARTUP_FILE",
- jalview.bin.Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/examples/exampleFile_2_7.jar");
+ file = jalview.bin.Cache.getDefault(
+ "STARTUP_FILE",
+ jalview.bin.Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org")
+ + "/examples/exampleFile_2_7.jar");
if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
{
// hardwire upgrade of the startup file
- file.replace("_2_3.jar","_2_7.jar");
- // and remove the stale setting
+ file.replace("_2_3.jar", "_2_7.jar");
+ // and remove the stale setting
jalview.bin.Cache.removeProperty("STARTUP_FILE");
}
-
+
protocol = "File";
if (file.indexOf("http:") > -1)
if (jalview.bin.Cache.groovyJarsPresent())
{
System.out.println("Executing script " + groovyscript);
- executeGroovyScript(groovyscript, new Object[] { desktop, startUpAlframe});
+ executeGroovyScript(groovyscript, new Object[]
+ { desktop, startUpAlframe });
}
else
{
// and finally, turn off batch mode indicator - if the desktop still exists
if (desktop != null)
{
- if (progress!=-1) {
+ if (progress != -1)
+ {
desktop.setProgressBar(null, progress);
}
desktop.setInBatchMode(false);
ex.printStackTrace();
return;
}
- try {
+ try
+ {
sfile = tfile.toURI().toURL();
} catch (Exception x)
{
- System.err.println("Unexpected Malformed URL Exception for temporary file created from STDIN: "+tfile.toURI());
+ System.err
+ .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+ + tfile.toURI());
x.printStackTrace();
return;
}
System.err.println("File '" + groovyscript + "' is empty.");
return;
}
- try {
- sfile = tfile.getAbsoluteFile().toURI().toURL();
+ try
+ {
+ sfile = tfile.getAbsoluteFile().toURI().toURL();
} catch (Exception ex)
{
- System.err.println("Failed to create a file URL for "+tfile.getAbsoluteFile());
+ System.err.println("Failed to create a file URL for "
+ + tfile.getAbsoluteFile());
return;
}
}
--- /dev/null
+package jalview.ws.gui;
+
+import static org.junit.Assert.assertTrue;
+import jalview.gui.WsJobParameters;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
+import java.awt.BorderLayout;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import org.junit.Test;
+
+import compbio.metadata.Option;
+import compbio.metadata.Parameter;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+
+public class Jws2ParamView
+{
+ /**
+ * test servers
+ */
+ public static String[] serviceUrls = new String[]
+ { "http://localhost:8080/jabaws" };
+
+ /**
+ * which services to test
+ */
+ public static List<String> serviceTests = new ArrayList<String>();
+
+ /**
+ * which presets to test for services
+ */
+ public static List<String> presetTests = new ArrayList<String>();
+ static
+ {
+ serviceTests.add("AAConWS".toLowerCase());
+ }
+
+ @Test
+ public void testJws2Gui()
+ {
+ jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
+ .getDiscoverer();
+ int p = 0;
+ String svcurls="";
+ Vector<String> services = new Vector<String>();
+ for (String url : serviceUrls)
+ {
+ svcurls+=url+"; ";
+ services.add(url);
+ }
+ ;
+ Jws2Discoverer.setServiceUrls(services);
+
+ try
+ {
+ disc.run();
+ } catch (Exception e)
+ {
+ System.err.println("Aborting. Problem discovering services. Tried "+svcurls);
+ e.printStackTrace();
+ return;
+ }
+ assertTrue("Failed to discover any services at ",
+ disc.getServices().size() > 0);
+ Jws2Instance lastserv = null;
+ Iterator<String> presetEnum = presetTests.iterator();
+ for (Jws2Instance service : disc.getServices())
+ {
+ lastserv = service;
+ if (serviceTests.size() == 0
+ || serviceTests.contains(service.serviceType.toLowerCase()))
+ {
+ if (lastserv != null)
+ {
+ List<Preset> prl = null;
+ Preset pr = null;
+ if (presetEnum.hasNext())
+ {
+ PresetManager prman = lastserv.getPresets();
+ if (prman != null)
+ {
+ pr = prman.getPresetByName(presetEnum.next());
+ if (pr == null)
+ {
+ // just grab the last preset.
+ prl = prman.getPresets();
+ }
+ }
+ }
+ else
+ {
+ PresetManager prman = lastserv.getPresets();
+ if (prman != null)
+ {
+ prl = prman.getPresets();
+ }
+ }
+ Iterator<Preset> en = (prl == null) ? null : prl.iterator();
+ while (en != null && en.hasNext())
+ {
+ if (en != null)
+ {
+ if (!en.hasNext())
+ {
+ en = prl.iterator();
+ }
+ pr = en.next();
+ }
+ {
+ System.out.println("Testing opts dupes for "
+ + lastserv.getUri() + " : "
+ + lastserv.getActionText() + ":" + pr.getName());
+ List<Option> rg = lastserv.getRunnerConfig().getOptions();
+ for (Option o : rg)
+ {
+ try
+ {
+ Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
+ } catch (Exception e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ }
+ }
+ }
+ {
+ System.out.println("Testing param dupes:");
+ List<Parameter> rg = lastserv.getRunnerConfig()
+ .getParameters();
+ for (Parameter o : rg)
+ {
+ try
+ {
+ Parameter cpy = jalview.ws.jws2.ParameterUtils
+ .copyParameter(o);
+ } catch (Exception e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ System.err.println("Failed to copy " + o.getName());
+ e.printStackTrace();
+ }
+ }
+ }
+ {
+ System.out.println("Testing param write:");
+ List<String> writeparam = null, readparam = null;
+ try
+ {
+ writeparam = jalview.ws.jws2.ParameterUtils
+ .writeParameterSet(
+ pr.getArguments(lastserv.getRunnerConfig()),
+ " ");
+ System.out.println("Testing param read :");
+ List<Option> pset = jalview.ws.jws2.ParameterUtils
+ .processParameters(writeparam,
+ lastserv.getRunnerConfig(), " ");
+ readparam = jalview.ws.jws2.ParameterUtils
+ .writeParameterSet(pset, " ");
+ Iterator<String> o = pr.getOptions().iterator(), s = writeparam
+ .iterator(), t = readparam.iterator();
+ boolean failed = false;
+ while (s.hasNext() && t.hasNext())
+ {
+ String on = o.next(), sn = s.next(), st = t.next();
+ if (!sn.equals(st))
+ {
+ System.out.println("Original was " + on
+ + " Phase 1 wrote " + sn + "\tPhase 2 wrote "
+ + st);
+ failed = true;
+ }
+ }
+ if (failed)
+ {
+ System.out.println("Original parameters:\n"
+ + pr.getOptions());
+ System.out.println("Wrote parameters in first set:\n"
+ + writeparam);
+ System.out.println("Wrote parameters in second set:\n"
+ + readparam);
+
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ WsJobParameters pgui = new WsJobParameters(lastserv,
+ new JabaPreset(lastserv, pr));
+ JFrame jf = new JFrame("Parameters for "
+ + lastserv.getActionText());
+ JPanel cont = new JPanel(new BorderLayout());
+ pgui.validate();
+ cont.setPreferredSize(pgui.getPreferredSize());
+ cont.add(pgui, BorderLayout.CENTER);
+ jf.setLayout(new BorderLayout());
+ jf.add(cont, BorderLayout.CENTER);
+ jf.validate();
+ final Thread thr = Thread.currentThread();
+ jf.addWindowListener(new WindowListener()
+ {
+
+ public void windowActivated(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void windowClosed(WindowEvent e)
+ {
+ }
+
+ public void windowClosing(WindowEvent e)
+ {
+ thr.interrupt();
+
+ }
+
+ public void windowDeactivated(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void windowDeiconified(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void windowIconified(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void windowOpened(WindowEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ });
+ jf.setVisible(true);
+ boolean inter = false;
+ while (!inter)
+ {
+ try
+ {
+ Thread.sleep(10000);
+ } catch (Exception e)
+ {
+ inter = true;
+ }
+ ;
+ }
+ jf.dispose();
+ }
+ }
+ }
+ }
+ }
+}