test/jalview/io/Jalview2xmlTests.java

   1 package jalview.io;
   2
   3 import static org.junit.Assert.*;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.gui.AlignFrame;
   7
   8 import java.io.File;
   9
  10 import org.junit.AfterClass;
  11 import org.junit.BeforeClass;
  12 import org.junit.Test;
  13
  14 public class Jalview2xmlTests
  15 {
  16
  17   /**
  18    * @throws java.lang.Exception
  19    */
  20   @BeforeClass
  21   public static void setUpBeforeClass() throws Exception
  22   {
  23     jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
  24   }
  25
  26   /**
  27    * @throws java.lang.Exception
  28    */
  29   @AfterClass
  30   public static void tearDownAfterClass() throws Exception
  31   {
  32     jalview.gui.Desktop.instance.quit();
  33   }
  34   public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
  35   {
  36     int numdsann=0;
  37     for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
  38       if (sq.getAnnotation() != null)
  39       {
  40         for (AlignmentAnnotation dssa : sq.getAnnotation())
  41         {
  42           if (dssa.isValidStruc())
  43           {
  44             numdsann++;
  45           }
  46         }
  47       }
  48     }
  49     return numdsann;
  50   }
  51   @Test
  52   public void testRNAStructureRecovery() throws Exception
  53   {
  54     String inFile = "examples/RF00031_folded.stk";
  55     String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
  56     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
  57     assertTrue("Didn't read input file "+inFile, af!=null);
  58     int olddsann=countDsAnn(af.getViewport());
  59     assertTrue("Didn't find any dataset annotations",olddsann>0);
  60     assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
  61     af.closeMenuItem_actionPerformed(true);
  62     af=null;
  63     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
  64     assertTrue("Failed to import new project", af!=null);
  65     int newdsann=countDsAnn(af.getViewport());
  66     assertTrue("Differing numbers of dataset sequence annotation\nOriginally "+olddsann+" and now "+newdsann,olddsann==newdsann);
  67     System.out.println("Read in same number of annotations as originally present ("+olddsann+")");
  68   }
  69   @Test
  70   public void testTCoffeeScores() throws Exception
  71   {
  72     String inFile = "examples/uniref50.fa",inAnnot="examples/uniref50.score_ascii";
  73     String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
  74     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
  75     assertTrue("Didn't read input file "+inFile, af!=null);
  76     af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null,null);
  77     assertTrue(
  78             "Didn't set T-coffee colourscheme",
  79             af.getViewport().getGlobalColourScheme().getClass()
  80                     .equals(jalview.schemes.TCoffeeColourScheme.class));
  81     assertTrue(
  82             "Recognise T-Coffee score from string",
  83             jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
  84                     .getAlignment(),
  85                     jalview.schemes.ColourSchemeProperty.getColourName(af
  86                             .getViewport().getGlobalColourScheme())) != null);
  87
  88     assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
  89     af.closeMenuItem_actionPerformed(true);
  90     af=null;
  91     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
  92     assertTrue("Failed to import new project", af!=null);
  93     assertTrue("Didn't set T-coffee colourscheme for imported project.",af.getViewport().getGlobalColourScheme().getClass().equals(jalview.schemes.TCoffeeColourScheme.class));
  94     System.out.println("T-Coffee score shading successfully recovered from project.");
  95   }
  96
  97 }