test/jalview/ws/jabaws/DisorderAnnotExportImport.java

   1 package jalview.ws.jabaws;
   2
   3 import static org.junit.Assert.*;
   4
   5 import java.util.ArrayList;
   6 import java.util.List;
   7
   8 import jalview.datamodel.AlignmentAnnotation;
   9 import jalview.datamodel.AlignmentI;
  10 import jalview.io.AnnotationFile;
  11 import jalview.io.FormatAdapter;
  12 import jalview.io.StockholmFileTest;
  13 import jalview.ws.jws2.AADisorderClient;
  14 import jalview.ws.jws2.Jws2Discoverer;
  15 import jalview.ws.jws2.jabaws2.Jws2Instance;
  16
  17 import org.junit.AfterClass;
  18 import org.junit.BeforeClass;
  19 import org.junit.Test;
  20
  21 public class DisorderAnnotExportImport
  22 {
  23   public static String testseqs = "examples/uniref50.fa";
  24
  25   public static Jws2Discoverer disc;
  26
  27   public static List<Jws2Instance> iupreds;
  28
  29   jalview.ws.jws2.AADisorderClient disorderClient;
  30
  31   public static jalview.gui.AlignFrame af = null;
  32
  33   @BeforeClass
  34   public static void setUpBeforeClass() throws Exception
  35   {
  36
  37     jalview.bin.Cache.initLogger();
  38     disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
  39     iupreds = new ArrayList<Jws2Instance>();
  40     for (Jws2Instance svc : disc.getServices())
  41     {
  42       if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
  43       {
  44         iupreds.add(svc);
  45       }
  46     }
  47     assertTrue("Couldn't discover any IUPred services to use to test.",
  48             iupreds.size() > 0);
  49     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
  50     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
  51     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
  52   }
  53
  54   @AfterClass
  55   public static void tearDownAfterClass() throws Exception
  56   {
  57     if (af != null)
  58     {
  59       af.setVisible(false);
  60       af.dispose();
  61     }
  62   }
  63
  64   /**
  65    * test for patches to JAL-1294
  66    */
  67   @Test
  68   public void testDisorderAnnotExport()
  69   {
  70     disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
  71     af.getViewport().getCalcManager().startWorker(disorderClient);
  72     do
  73     {
  74       try
  75       {
  76         Thread.sleep(50);
  77       } catch (InterruptedException x)
  78       {
  79       }
  80       ;
  81     } while (af.getViewport().getCalcManager().isWorking());
  82     AlignmentI orig_alig = af.getViewport().getAlignment();
  83     // NOTE: Consensus annotation row cannot be exported and reimported faithfully - so we remove them
  84     List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
  85     for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
  86     {
  87       if (aa.autoCalculated)
  88       {
  89         toremove.add(aa);
  90       }
  91     }
  92     for (AlignmentAnnotation aa:toremove)
  93     {
  94       orig_alig.deleteAnnotation(aa);
  95     }
  96     testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
  97
  98   }
  99
 100   public static void testAnnotationFileIO(String testname, AlignmentI al)
 101   {
 102     try
 103     {
 104       String aligfileout = new FormatAdapter().formatSequences("PFAM",
 105               al.getSequencesArray());
 106       String anfileout = new AnnotationFile().printAnnotations(
 107               al.getAlignmentAnnotation(), al.getGroups(),
 108               al.getProperties());
 109       assertTrue(
 110               "Test "
 111                       + testname
 112                       + "\nAlignment annotation file was not regenerated. Null string",
 113               anfileout != null);
 114       assertTrue(
 115               "Test "
 116                       + testname
 117                       + "\nAlignment annotation file was not regenerated. Empty string",
 118               anfileout.length() > "JALVIEW_ANNOTATION".length());
 119
 120       System.out.println("Output annotation file:\n" + anfileout
 121               + "\n<<EOF\n");
 122
 123       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
 124               FormatAdapter.PASTE, "PFAM");
 125       assertTrue(
 126               "Test "
 127                       + testname
 128                       + "\nregenerated annotation file did not annotate alignment.",
 129               new AnnotationFile().readAnnotationFile(al_new, anfileout,
 130                       FormatAdapter.PASTE));
 131
 132       // test for consistency in io
 133       StockholmFileTest.testAlignmentEquivalence(al, al_new);
 134       return;
 135     } catch (Exception e)
 136     {
 137       e.printStackTrace();
 138     }
 139     fail("Test "
 140             + testname
 141             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
 142   }
 143
 144 }