Package org.moltools.apps.probemaker.project

Examples of org.moltools.apps.probemaker.project.Project

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    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    pm.setProject(proj);
  }
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  }
 
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultProbeDesigner.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultTSSConstructor.defaultParameters);
   
    ProbeMakerTarget pt1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
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    pm = new ProbeMakerPlugIn();
    ProbeMakerTarget t1 = new AlleleSpecificPadlockTarget("T1","ACTACGAGCGACGAGC|ACACGCTACATCGAGC","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    VariantTarget t2 = new MinisequencingTarget("T2","ACTACGAGCGACGAGCSACACGCTACATCGAGC","Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    t2.setVariant(t2.getVariants()[0]);
    ProbeMakerTarget t3 = new UnchangedTarget("T3","ACGTCAGCGAGCGACGACTACTACGAC","Target 3"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    project = new Project("IOTest"); //$NON-NLS-1$
    pm.setProject(project);
    project.getTargets().addSequence(t1);
    project.getTargets().addSequence(t2);
    project.getTargets().addSequence(t3);
    ListSequenceDB<NucleotideSequence> tags1 = new ListSequenceDB<NucleotideSequence>();
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  }
 
  public void testOne() throws Exception {
   
    pm = new ProbeMakerPlugIn();
    Project proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
       
    pm.setProject(proj);
   
    AlleleSpecificPadlockTarget t1 = new AlleleSpecificPadlockTarget("T1", "GGGGGGGGGGGGGGGGGGGGGG|GGGGGGGGGGGGGGGGGGGGGGGG", "Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    AlleleSpecificPadlockTarget t2 = new AlleleSpecificPadlockTarget("T2", "GGGGGGGGGGGGGGGGGGGGGG|GGGGGGGGGGGGGGGGGGGGGGGG", "Target 2"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
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  }
 
  @Override
  protected void setUp() throws DuplicateIDException, FileNotFoundException, IOException, SequenceFormatException {
    pm = new ProbeMakerPlugIn();
    project = new Project("Mfold_test"); //$NON-NLS-1$
    pm.setProject(project);
    m = new DINAMeltSecStructModule();   
    project.getSettings().addCandidateModuleStage1(m);   
    Collection<Probe> seqs = SequenceIO.readSequences(new InputStreamReader(getClass().getResourceAsStream("mfold_test.lib")),new IDAndNameFastaFormatter<Probe>(),DefaultProbe.getSequenceBuilder()); //$NON-NLS-1$
    project.getProbes().addSequences(seqs);
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    tags = new DefaultTagLibrary(new ListSequenceDB<NucleotideSequence>(),"Tag library 10"); //$NON-NLS-1$
    tags.setMode(TagLibrary.USE_UNIQUE_TAG);
    tags.addSequence(new SimpleNucleotideSequence("Tag1","GAAAAAAAAAAAAAAAAAAT", NucleotideSequence.DNA)); //$NON-NLS-1$ //$NON-NLS-2$
   
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    pm.setProject(proj);
  }
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  }
 
  @Override
  protected void setUp() throws DuplicateIDException {
    pm = new ProbeMakerPlugIn();
    proj = new Project("Test project"); //$NON-NLS-1$
    proj.getSettings().addDesignerProperties(GreedyTagAllocator.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultProbeDesigner.defaultParameters);
    proj.getSettings().addDesignerProperties(DefaultTSSConstructor.defaultParameters);
   
    ProbeMakerTarget pt1 = new AlleleSpecificPadlockTarget("T1","CCCCCCCCCCCCCCCCCCCC|AAAAAAAAAAAAAAAAAAAAAAAAA","Target 1"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
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  public void testTagOccurrenceModule() throws Exception {
    tom.setData(DefaultTagOccurrenceModule.KEY_PERCENT_SIMILARITY,new Integer(100));
    tom.getAllTests()[2].setPerform(false);
    tom.getAllTests()[3].setPerform(false);
    pm.setProject(new Project("test project")); //$NON-NLS-1$
    pm.getProject().getSettings().addCandidateModuleStage1(tom);
    pm.getProject().getTargets().addSequence(t1);
    pm.getProject().getTargets().addSequence(t2);
    pm.getProject().getTagAllocationTable().clearUsed();
    lib1.addSequence(new SimpleNucleotideSequence("TAG_A","AAAAAAAAAAAAA")); //$NON-NLS-1$ //$NON-NLS-2$
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            CoreMessages.getString("ProbeMakerPlugIn.MESSAGE_DEFAULT_SETTINGS_NOT_READ"),                                       //$NON-NLS-1$
            iox);
      }
    }

    final Project newp = new Project(name);
    newp.setSettings(s);

    //If template was selected, get template properties
    if (template != null) {
      final String fileName = template.getSettingsFileName();
      if (fileName == null || fileName.length() == 0) {
        platform.getUI().sendMessage("No settings file set for this template. Using default settings.", "No settings file", PlatformUI.NO_QUERY);
      }
      else {
        final File f = new File(fileName);
        try {
          final Reader in = new FileReader(f);
          newp.setSettings(SettingsIO.inputSettings(in));
        }
        catch (final FileNotFoundException e) {
          platform.handleError("Template settings file not found: " + f.getAbsolutePath(),e); //$NON-NLS-1$
        }
        catch (final Exception e) {
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            CoreMessages.getString("ProbeMakerPlugIn.MESSAGE_DEFAULT_SETTINGS_NOT_READ"),                                       //$NON-NLS-1$
            iox);
      }
    }

    final Project newp = new Project(name);
    newp.setSettings(s);

    //If template was selected, get template properties
    if (template != null) {
      final String fileName = template.getSettingsFileName();
      if (fileName == null || fileName.length() == 0) {
        platform.getUI().sendMessage("No settings file set for this template. Using default settings.", "No settings file", PlatformUI.NO_QUERY);
      }
      else {
        final File f = new File(fileName);
        try {
          final Reader in = new FileReader(f);
          newp.setSettings(SettingsIO.inputSettings(in));
        }
        catch (final FileNotFoundException e) {
          platform.handleError("Template settings file not found: " + f.getAbsolutePath(),e); //$NON-NLS-1$
        }
        catch (final Exception e) {
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Related Classes of org.moltools.apps.probemaker.project.Project

  • org.moltools.apps.probemaker.design.TagAllocationTable
  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.ProbeMakerPlugIn
  • org.moltools.apps.probemaker.test.DINAMeltModuleTest
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
  • org.moltools.apps.probemaker.test.TagOccurrenceModuleTest
  • org.moltools.apps.probemaker.test.TSSConstructionTest
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