df.getContentPane().setLayout(new BorderLayout());
df.getContentPane().add(
(nulserv = !nulserv) ? new RestServiceEditorPane(
- jalview.ws.rest.RestClient
+ jalview.ws.rest.clientdefs.ShmrRestClient
.makeShmmrRestClient()
.getRestDescription())
: new RestServiceEditorPane(),
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
-import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.MessageManager;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.Hashtable;
import java.util.Vector;
import javax.swing.JMenu;
}
}
- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
- .getString("label.multiharmony");
- Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
- jalview.ws.rest.params.JobConstant toolp;
- // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
- // iparams.put(toolp.token, toolp);
- // toolp = new
- // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
- // iparams.put(toolp.token, toolp);
- // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
- // iparams.put(toolp.token, toolp);
-
- jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
- // so we always upload our files.
- aliinput.token = "ali_file";
- aliinput.writeAsFile = true;
- iparams.put(aliinput.token, aliinput);
- jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
- sgroups.setMinsize(2);
- sgroups.min = 2;// need at least two group defined to make a partition
- iparams.put("groups", sgroups);
- sgroups.token = "groups";
- sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(
- action,
- description,
- name,
- "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
- "?tool=jalview", iparams, true, false, '-');
- // a priori knowledge of the data returned from the service
- shmrService.addResultDatatype(JvDataType.ANNOTATION);
- return new RestClient(shmrService);
- }
-
public AlignmentPanel recoverAlignPanelForView()
{
AlignmentPanel[] aps = Desktop
for (RestServiceDescription descr : RestServiceDescription
.parseDescriptions(jalview.bin.Cache.getDefault(
RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ ShmrRestClient.makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
--- /dev/null
+package jalview.ws.rest.clientdefs;
+
+import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.MessageManager;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestClient;
+import jalview.ws.rest.RestServiceDescription;
+import jalview.ws.rest.params.Alignment;
+import jalview.ws.rest.params.JobConstant;
+import jalview.ws.rest.params.SeqGroupIndexVector;
+
+import java.util.Hashtable;
+
+public class ShmrRestClient
+{
+
+ public static RestClient makeShmmrRestClient()
+ {
+ String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
+ .getString("label.multiharmony");
+ Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
+ jalview.ws.rest.params.JobConstant toolp;
+ // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new
+ // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
+ // iparams.put(toolp.token, toolp);
+ // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
+ // iparams.put(toolp.token, toolp);
+
+ jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
+ // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
+ // so we always upload our files.
+ aliinput.token = "ali_file";
+ aliinput.writeAsFile = true;
+ iparams.put(aliinput.token, aliinput);
+ jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
+ sgroups.setMinsize(2);
+ sgroups.min = 2;// need at least two group defined to make a partition
+ iparams.put("groups", sgroups);
+ sgroups.token = "groups";
+ sgroups.sep = " ";
+ RestServiceDescription shmrService = new RestServiceDescription(
+ action,
+ description,
+ name,
+ "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
+ "?tool=jalview", iparams, true, false, '-');
+ // a priori knowledge of the data returned from the service
+ shmrService.addResultDatatype(JvDataType.ANNOTATION);
+ return new RestClient(shmrService);
+ }
+
+}
import static org.testng.AssertJUnit.assertTrue;
import jalview.gui.AlignFrame;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
import java.util.Map;
assertTrue(
"Test Rsd Exchange using using default Shmmr service failed.",
testRsdExchange("Test using default Shmmr service",
- RestClient.makeShmmrRestClient().service));
+ ShmrRestClient.makeShmmrRestClient().service));
}
@Test(groups = { "Functional" })
public void testShmmrServiceDataprep() throws Exception
{
- RestClient _rc = RestClient.makeShmmrRestClient();
+ RestClient _rc = ShmrRestClient.makeShmmrRestClient();
assertNotNull(_rc);
AlignFrame alf = new jalview.io.FileLoader(false)
.LoadFileWaitTillLoaded("examples/testdata/smad.fa",