X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FMinJabawsClientTests.java;h=145cddfb65141598205594004d7cc7e8e3567f0d;hb=refs%2Fheads%2FJAL-1562_help-documentation-system-refactoring;hp=5c9a192a10d2b58d7c4b568f778dee9292f60239;hpb=971ca3752d1e1139b8fa1c9bd80698e4d83dcab7;p=jalview.git

diff --git a/test/jalview/ws/jabaws/MinJabawsClientTests.java b/test/jalview/ws/jabaws/MinJabawsClientTests.java
index 5c9a192..145cddf 100644
--- a/test/jalview/ws/jabaws/MinJabawsClientTests.java
+++ b/test/jalview/ws/jabaws/MinJabawsClientTests.java
@@ -1,18 +1,13 @@
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.function.Consumer;
-
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
 
 import org.junit.Test;
 
-import compbio.data.msa.Category;
-import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;
 import compbio.data.msa.RegistryWS;
 import compbio.data.sequence.FastaSequence;
@@ -22,63 +17,87 @@ import compbio.ws.client.Services;
 
 public class MinJabawsClientTests {
 
-	@SuppressWarnings("rawtypes")
-	@Test
-	public void msaTest() throws Exception {
-		String url;
-		RegistryWS registry = Jws2Client
-				.connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
-		if (registry != null) {
+  /**
+   * simple test for the benefit of JAL-1338
+   * @throws Exception
+   */
+  @SuppressWarnings("rawtypes")
+  @Test
+  public void msaTest() throws Exception {
+    String url;
+    RegistryWS registry = Jws2Client
+            .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
+    if (registry != null)
+    {
+
+      MsaWS msaservice = null;
+      for (Services service : registry.getSupportedServices())
+      {
+        if (service.equals(Services.ClustalOWS))
+        {
+          msaservice = (MsaWS) Jws2Client.connect(url, service);
+          if (msaservice != null)
+          {
+            break;
+          }
+        }
+      }
+      if (msaservice == null)
+      {
+        fail("couldn't find a clustalO service on the public registry");
+      }
+      FastaSequence fsq = new FastaSequence("seqA",
+              "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
+      List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
+      for (int i = 0; i < 9; i++)
+      {
+        iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
+                + fsq.getSequence().substring(i + 3, i + 3 + i)));
+      }
 
-			MsaWS msaservice = null;
-			for (Services service : registry.getSupportedServices()) {
-				if (service.equals(Services.ClustalOWS)) {
-					msaservice = (MsaWS) Jws2Client.connect(url, service);
-					if (msaservice != null) {
-						break;
-					}
-				}
-			}
-			if (msaservice == null) {
-				fail("couldn't find a clustalO service on the public registry");
-			}
-			FastaSequence fsq = new FastaSequence("seqA",
-					"SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
-			List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
-			for (int i = 0; i < 9; i++) {
-				iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
-						+ fsq.getSequence().substring(i + 3, i + 3 + i)));
-			}
+      String jobid = msaservice.align(iseqs);
+      if (jobid != null)
+      {
+        JobStatus js = null;
+        do
+        {
+          try
+          {
+            Thread.sleep(500);
+          } catch (InterruptedException q)
+          {
+          }
+          ;
+          js = msaservice.getJobStatus(jobid);
+        } while (!js.equals(JobStatus.FAILED)
+                && !js.equals(JobStatus.CANCELLED)
+                && !js.equals(JobStatus.FINISHED));
+        assertEquals("Trial alignment failed. State was " + js.name(), js,
+                JobStatus.FINISHED);
+        assertEquals(
+                "Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
+                msaservice.getResult(jobid).getSequences().size(),
+                iseqs.size());
 
-			String jobid = msaservice.align(iseqs);
-			if (jobid != null) {
-				JobStatus js = null;
-				do {
-					try {
-						Thread.sleep(500);
-					} catch (InterruptedException q) {
-					}
-					;
-					js = msaservice.getJobStatus(jobid);
-				} while (!js.equals(JobStatus.FAILED)
-						&& !js.equals(JobStatus.CANCELLED)
-						&& !js.equals(JobStatus.FINISHED));
-				assertEquals("Trial alignment failed. State was " + js.name(),
-						js, JobStatus.FINISHED);
-				assertEquals(
-						"Mismatch in number of input and result sequences - assume alignment service wasn't interacted with correctly",
-						msaservice.getResult(jobid).getSequences().size(),
-						iseqs.size());
-				msaservice.getResult(jobid).getSequences()
-						.forEach(new Consumer<FastaSequence>() {
-							@Override
-							public void accept(FastaSequence t) {
-								System.out.println(">"+t.getId());
-								System.out.println(t.getFormattedFasta());
-							}
-						});
-			}
+        List<FastaSequence> fastaSequences = msaservice.getResult(jobid).getSequences();
+        for(FastaSequence fastaSequence : fastaSequences){
+          System.out.println(">" + fastaSequence.getId());
+          System.out.println(fastaSequence.getFormattedFasta());
+        }
+      }
 
-		}
-	}
+      //        msaservice.getResult(jobid).getSequences()
+      //        .forEach(new Consumer<FastaSequence>()
+      //                {
+      //                  @Override
+      //                  public void accept(FastaSequence t)
+      //                  {
+      //                    System.out.println(">" + t.getId());
+      //                    System.out.println(t.getFormattedFasta());
+      //                  }
+      //                });
+    }
+
+  }
 }
+