X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=0a9cb19472d648b19ef1a742e47f2bd85305190c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=7fe645c2cf4583033a6dcf98e80ca01e28a165d4;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 7fe645c..0a9cb19 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertTrue; import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.gui.JvOptionPane; @@ -89,7 +90,7 @@ public class RNAStructExportImport public static void setUpBeforeClass() throws Exception { Cache.loadProperties("test/jalview/io/testProps.jvprops"); - Cache.initLogger(); + Console.initLogger(); disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false); while (disc.isRunning()) @@ -101,7 +102,8 @@ public class RNAStructExportImport for (ServiceWithParameters svc : disc.getServices()) { - if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("rnaalifoldws")) + if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT) + .contains("rnaalifoldws")) { rnaalifoldws = (Jws2Instance) svc; } @@ -116,7 +118,8 @@ public class RNAStructExportImport jalview.io.FileLoader fl = new jalview.io.FileLoader(false); - af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE); + af = fl.LoadFileWaitTillLoaded(testseqs, + jalview.io.DataSourceType.FILE); assertNotNull("Couldn't load test data ('" + testseqs + "')", af); @@ -219,32 +222,26 @@ public class RNAStructExportImport try { // what format would be appropriate for RNAalifold annotations? - String aligfileout = FileFormat.Pfam.getWriter(null).print( - al.getSequencesArray(), true); + String aligfileout = FileFormat.Pfam.getWriter(null) + .print(al.getSequencesArray(), true); String anfileout = new AnnotationFile() .printAnnotationsForAlignment(al); - assertNotNull( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Null string", + assertNotNull("Test " + testname + + "\nAlignment annotation file was not regenerated. Null string", anfileout); - assertTrue( - "Test " - + testname - + "\nAlignment annotation file was not regenerated. Empty string", + assertTrue("Test " + testname + + "\nAlignment annotation file was not regenerated. Empty string", anfileout.length() > "JALVIEW_ANNOTATION".length()); - System.out.println("Output annotation file:\n" + anfileout - + "\n<