import compbio.metadata.Option;
import compbio.metadata.Preset;
import compbio.metadata.PresetManager;
-import jalview.ws.jws2.Jws2Discoverer.Jws2Instance;
import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
/**
*/
MsaWS server;
- AlignFrame alignFrame;
-
- private WsParamSetI preset;
-
- private List<Argument> paramset;
-
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, String altitle,
+ public MsaWSClient(Jws2Instance sh, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
// TODO Auto-generated constructor stub
}
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+ public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
String altitle, jalview.datamodel.AlignmentView msa,
boolean submitGaps, boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
* DOCUMENT ME!
*/
- public MsaWSClient(Jws2Discoverer.Jws2Instance sh, WsParamSetI preset,
+ public MsaWSClient(Jws2Instance sh, WsParamSetI preset,
List<Argument> arguments, boolean editParams, String altitle,
jalview.datamodel.AlignmentView msa, boolean submitGaps,
boolean preserveOrder, Alignment seqdataset,
AlignFrame _alignFrame)
{
- super();
- alignFrame = _alignFrame;
+ super(_alignFrame, preset, arguments);
+ if (!processParams(sh, editParams))
+ {
+ return;
+ }
+
if (!(sh.service instanceof MsaWS))
{
// redundant at mo - but may change
return;
}
- server = sh.service;
- this.preset=preset;
- if (preset != null)
- {
- if (!((preset instanceof JabaPreset) || preset instanceof JabaWsParamSet)) {
- /*{
- this.preset = ((JabaPreset) preset).p;
- }
- else if (preset instanceof JabaWsParamSet)
- {
- List<Argument> newargs = new ArrayList<Argument>();
- JabaWsParamSet pset = ((JabaWsParamSet) preset);
- for (Option opt : pset.getjabaArguments())
- {
- newargs.add(opt);
- }
- if (arguments != null && arguments.size() > 0)
- {
- // merge arguments with preset's own arguments.
- for (Argument opt : arguments)
- {
- newargs.add(opt);
- }
- }
- paramset = newargs;
- }
- else
- {*/
- throw new Error(
- "Implementation error: Can only instantiate Jaba parameter sets.");
- }
- }
- else
- {
- // just provided with a bunch of arguments
- this.paramset = arguments;
- }
- if (editParams)
- {
- if (sh.paramStore == null)
- {
- sh.paramStore = new JabaParamStore(sh,
- Desktop.getUserParameterStore());
- }
- WsJobParameters jobParams = new WsJobParameters(sh, preset);
- if (!jobParams.showRunDialog())
- {
- return;
- }
- WsParamSetI prset = jobParams.getPreset();
- if (prset == null)
- {
- paramset = JabaParamStore.getJabafromJwsArgs(jobParams
- .getJobParams());
- }
- else
- {
- this.preset = prset; // ((JabaPreset) prset).p;
- paramset = null; // no user supplied parameters.
- }
- }
-
+ server = (MsaWS) sh.service;
if ((wsInfo = setWebService(sh, false)) == null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
return (WebServiceName.indexOf("lustal") > -1); // cheat!
}
+
public void attachWSMenuEntry(JMenu rmsawsmenu,
final Jws2Instance service, final AlignFrame alignFrame)
{