test/jalview/ws/jabaws/RNAStructExportImport.java

   1 package jalview.ws.jabaws;
   2
   3 import static org.junit.Assert.*;
   4
   5 import java.util.ArrayList;
   6 import java.util.Arrays;
   7 import java.util.List;
   8 import java.util.Vector;
   9
  10 import jalview.api.AlignCalcManagerI;
  11 import jalview.datamodel.AlignmentAnnotation;
  12 import jalview.datamodel.AlignmentI;
  13 import jalview.datamodel.Annotation;
  14 import jalview.io.AnnotationFile;
  15 import jalview.io.FormatAdapter;
  16 import jalview.io.StockholmFileTest;
  17 import jalview.ws.jws2.AADisorderClient;
  18 import jalview.ws.jws2.Jws2Discoverer;
  19 import jalview.ws.jws2.RNAalifoldClient;
  20 import jalview.ws.jws2.jabaws2.Jws2Instance;
  21
  22 import org.junit.AfterClass;
  23 import org.junit.BeforeClass;
  24 import org.junit.Test;
  25
  26 public class RNAStructExportImport
  27 {
  28   public static String testseqs = "examples/unfolded_RF00031.aln";
  29
  30   public static Jws2Discoverer disc;
  31
  32   public static Jws2Instance rnaalifoldws;
  33
  34   jalview.ws.jws2.RNAalifoldClient alifoldClient;
  35
  36   public static jalview.gui.AlignFrame af = null;
  37
  38   @BeforeClass
  39   public static void setUpBeforeClass() throws Exception
  40   {
  41
  42
  43     jalview.bin.Cache.initLogger();
  44     disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
  45
  46     for (Jws2Instance svc : disc.getServices())
  47     {
  48
  49       if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
  50       {
  51         rnaalifoldws = svc;
  52       }
  53     }
  54
  55     System.out.println("State of rnaalifoldws: " + rnaalifoldws);
  56
  57     if (rnaalifoldws == null) System.exit(0);
  58
  59     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
  60
  61     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
  62
  63     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
  64
  65   }
  66
  67   @AfterClass
  68   public static void tearDownAfterClass() throws Exception
  69   {
  70     if (af != null)
  71     {
  72       af.setVisible(false);
  73       af.dispose();
  74     }
  75   }
  76
  77   @Test
  78   public void testRNAStructExport()
  79   {
  80
  81
  82     alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
  83
  84     af.getViewport().getCalcManager().startWorker(alifoldClient);
  85
  86
  87     do
  88     {
  89       try
  90       {
  91         Thread.sleep(50);
  92       } catch (InterruptedException x)
  93       {
  94       }
  95       ;
  96     } while (af.getViewport().getCalcManager().isWorking());
  97
  98
  99     AlignmentI orig_alig = af.getViewport().getAlignment();
 100
 101     testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 102
 103   }
 104
 105   public static void testAnnotationFileIO(String testname, AlignmentI al)
 106   {
 107     try
 108     {
 109         // what format would be appropriate for RNAalifold annotations?
 110       String aligfileout = new FormatAdapter().formatSequences("PFAM",
 111               al.getSequencesArray());
 112
 113
 114       String anfileout = new AnnotationFile().printAnnotations(
 115               al.getAlignmentAnnotation(), al.getGroups(),
 116               al.getProperties());
 117       assertTrue(
 118               "Test "
 119                       + testname
 120                       + "\nAlignment annotation file was not regenerated. Null string",
 121               anfileout != null);
 122       assertTrue(
 123               "Test "
 124                       + testname
 125                       + "\nAlignment annotation file was not regenerated. Empty string",
 126               anfileout.length() > "JALVIEW_ANNOTATION".length());
 127
 128       System.out.println("Output annotation file:\n" + anfileout
 129               + "\n<<EOF\n");
 130
 131       // again what format would be appropriate?
 132       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
 133               FormatAdapter.PASTE, "PFAM");
 134       assertTrue(
 135               "Test "
 136                       + testname
 137                       + "\nregenerated annotation file did not annotate alignment.",
 138               new AnnotationFile().readAnnotationFile(al_new, anfileout,
 139                       FormatAdapter.PASTE));
 140
 141       // test for consistency in io
 142       StockholmFileTest.testAlignmentEquivalence(al, al_new);
 143       return;
 144     } catch (Exception e)
 145     {
 146       e.printStackTrace();
 147     }
 148     fail("Test "
 149             + testname
 150             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
 151   }
 152
 153 }