Package org.moltools.apps.probemaker.ext.mod

Examples of org.moltools.apps.probemaker.ext.mod.DefaultHybInterferenceModule

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    Probe p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 0 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 0); //$NON-NLS-1$ //$NON-NLS-2$
   
   
//  Design again with test
    proj.getSettings().addCandidateModuleStage1(new DefaultHybInterferenceModule());   
   
    pm.getProbeDesignTask(false, true, true, new AllAcceptor(),new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();   
    p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 2 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 2);     //$NON-NLS-1$ //$NON-NLS-2$
   
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    Probe p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 0 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 0); //$NON-NLS-1$ //$NON-NLS-2$
   
   
//  Design again with test
    proj.getSettings().addCandidateModuleStage1(new DefaultHybInterferenceModule());   
   
    pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new AllAcceptor(),new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();   
    p = proj.getProbes().getSequenceAt(0);   
    assertTrue("Hyb. interference, 2 messages expected, " + ProbeMakerPropertyUtils.getAllMessages(p).size() + " generated.",ProbeMakerPropertyUtils.getAllMessages(p).size() == 2);     //$NON-NLS-1$ //$NON-NLS-2$
   
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Related Classes of org.moltools.apps.probemaker.ext.mod.DefaultHybInterferenceModule

  • org.moltools.apps.probemaker.calculators.SWStructureCalculator
  • org.moltools.apps.probemaker.messages.Message
  • org.moltools.apps.probemaker.modules.TestDescriptor
  • org.moltools.apps.probemaker.seq.ProbeMakerTarget
  • org.moltools.apps.probemaker.test.HybInterferenceModuleTest
  • org.moltools.design.calc.ComplementCalculator
  • org.moltools.design.data.impl.SimpleSubSequenceTemplate
  • org.moltools.design.data.PropertyAcceptorNucleotideSequence
  • org.moltools.design.data.TargettedSubSequence
  • org.moltools.lib.struct.NAHybridStructure
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