Package org.moltools.apps.probemaker.design

Examples of org.moltools.apps.probemaker.design.TagLibrary

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        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;

      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);

      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.
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   * messages added until thisProbe is confirmed.*/
  protected byte compareTag(Probe thisProbe, Probe otherProbe, int tagpos, boolean allowsSequence, boolean allowsComplement,
      TagLibrary[] taglibraries,
      TagSimilarityCalculator tsc1) {
   
    TagLibrary tl = taglibraries[tagpos];
    byte mode = tl.getMode();
    Group<?> thisGroup = DesignUtils.getGroupWithType(thisProbe, ProbeGroup.GROUP_TYPE);
    Group<?> otherGroup = DesignUtils.getGroupWithType(otherProbe, ProbeGroup.GROUP_TYPE);
    boolean sameGroup = thisGroup == otherGroup;
   
    boolean checkSequence = !allowsSequence && tests[2].perform();
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        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;

      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);

      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.
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        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;

      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);

      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.
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Related Classes of org.moltools.apps.probemaker.design.TagLibrary

  • org.moltools.apps.probemaker.ext.mod.DefaultTagOccurrenceModule
  • org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator
  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.swingui.TagLibraryViewFactory
  • org.moltools.apps.probemaker.swingui.TagSetupPanel
  • org.moltools.apps.probemaker.swingui.TagSetupPanel$LibraryLabel
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
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