Package org.moltools.apps.probemaker.modules

Examples of org.moltools.apps.probemaker.modules.TestDescriptor

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    tssTestModel = new TestListModel(new ArrayList<CandidateAnalysisModule>());
    stage1TestModel = new TestListModel(new ArrayList<CandidateAnalysisModule>());
    stage2TestModel = new TestListModel(new ArrayList<CandidateAnalysisModule>());

    try {
      TestBox protoTestBox = new TestBox(new TestDescriptor(
          "Prototype test Prototype test Prototype test ")); //$NON-NLS-1$
     
      String ttAvail = "<html>" + SwingUIMessages.getString("ModuleSelectionPanel.TOOL_TIP_VIEW_MODULE_DESCRIPTION_HTML") + "</html>"; //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
      String ttStage = "<html>" + SwingUIMessages.getString("ModuleSelectionPanel.TOOL_TIP_SET_MODULE_PARAMETERS_HTML") + "</html>";  //$NON-NLS-1$//$NON-NLS-2$ //$NON-NLS-3$
      Object protoLabel = new AbstractProbeModule(null,null) {
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    public Component getListCellRendererComponent(JList list, Object value,
                                                  int index, boolean isSelected,
                                                  boolean cellHasFocus) {
      TestBox tb = (TestBox) value;
      TestDescriptor test1 = tb.getTest();
      if (test1 != null) {
        setText(test1.getBrief());
        setSelected(tb.isSelected());
      }
      setBackground(isSelected ? SystemColor.textHighlight : SystemColor.text);
      setForeground(isSelected ? SystemColor.textHighlightText :
                    SystemColor.textText);
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    "An error message is given if a matching sequence is found. A gap of one base is allowed between the two 5' and 3' sequences.</html>"; //$NON-NLS-1$
  }

  public GapFillPadlockLigationModule() {
    super(new TestDescriptor[] {
            new TestDescriptor("Gap-fill padlock probe self-ligation"), //$NON-NLS-1$
            new TestDescriptor("Template for other probe") //$NON-NLS-1$
          },
          new DataDescriptor[] {
        new IntegerDescriptor("Min. 5' match length", //$NON-NLS-1$
                             "Minimum number of matching bases on 5' end", //$NON-NLS-1$
                             PadlockLigationCalculator.
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    "a hybridization interference message is given.</html>"; //$NON-NLS-1$
  }

  public DefaultHybInterferenceModule() {
    super(new TestDescriptor[] {
        new TestDescriptor("5' hybridization interference"), //$NON-NLS-1$
        new TestDescriptor("3' hybridization interference") //$NON-NLS-1$
    },
    new DataDescriptor[0]);

    complementStructCalc = new SWStructureCalculator();
    ( (SWStructureCalculator) complementStructCalc).setLAC(new
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  protected int[] seqPositions;
  protected int[] compPositions;
 
  public DefaultTagOccurrenceModule() {
    super(new TestDescriptor[] {
        new TestDescriptor("Tag sequence within probe"), //$NON-NLS-1$
        new TestDescriptor("Tag complement within probe"), //$NON-NLS-1$
        new TestDescriptor("Tag sequence in other probe"), //$NON-NLS-1$
        new TestDescriptor("Tag complement in other probe") //$NON-NLS-1$
    },new DataDescriptor[1]);
    tsc = new SWTagSimilarityCalculator();
    dataDescriptors =
      new DataDescriptor[] {
        new IntegerDescriptor("Per cent of max score required for match", //$NON-NLS-1$
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    "<i>Nucleic Acids Res.</i>, <b>31</b>, 1796-1802.</html>"; //$NON-NLS-1$
  }

  public PadlockLigationModule() {
    super(new TestDescriptor[] {
        new TestDescriptor("Padlock probe self-ligation"), //$NON-NLS-1$
        new TestDescriptor("Template for other probe") //$NON-NLS-1$
    },new DataDescriptor[] {
        new IntegerDescriptor("Min. 5' match length", //$NON-NLS-1$
            "Minimum number of matching bases on 5' end", //$NON-NLS-1$
            PadlockLigationCalculator.
            PROPERTY_PROBE_5_MATCH_LENGTH, 1, 100),
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  public static final String KEY_ALLOWED_COMPLEMENTARITY_SCORE = "ALLOWED_COMPLEMENTARITY_SCORE"; //$NON-NLS-1$
  public static final String KEY_COMPLEMENTARITY_SCORE_LIMIT = "COMPLEMENTARITY_SCORE_LIMIT"; //$NON-NLS-1$
 
  public TmProbeDimerModule() {
    super(new TestDescriptor[] {
            new TestDescriptor("Probe-probe hetero-dimer formation"), //$NON-NLS-1$
            new TestDescriptor("Probe homo-dimer formation") //$NON-NLS-1$
           
          },
          new DataDescriptor[] {
              new DoubleDescriptor("Max Tm", //$NON-NLS-1$
                                  "Maximum Tm for " + //$NON-NLS-1$
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    return "<html>Dummy module that adds warning message to candidates by chance</html>"; //$NON-NLS-1$
  }

  public DummyModule() {
    super(new TestDescriptor[] {
            new TestDescriptor("Dummy test")  //$NON-NLS-1$
          },
          new DataDescriptor[] {
            new IntegerDescriptor("Chance for warning message", //$NON-NLS-1$
                     "Chance in per cent for a candidate to receive a warning message", //$NON-NLS-1$
                     KEY_WARNING_CHANCE, 0, 100)
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    "<i>Nucleic Acids Res.</i>, <b>31</b>, 1796-1802.</html>"; //$NON-NLS-1$
  }

  public FalsePrimingModule() {
    super(new TestDescriptor[] {
            new TestDescriptor("False priming on targets"),  //$NON-NLS-1$
            new TestDescriptor("False priming on primers")                   //$NON-NLS-1$
            },new DataDescriptor[] {
        new IntegerDescriptor("Max Tm for target priming","Tm limit for target priming calculations","MAX_TARGET_PRIMING_TEMP",0,100) //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    });
    setData("MAX_TARGET_PRIMING_TEMP",new Integer(40)); //$NON-NLS-1$
    try {
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    "If not, an error message is given."; //$NON-NLS-1$
  }

  public ProbeLengthModule() {
    super(new TestDescriptor[] {
            new TestDescriptor("Probe length") //$NON-NLS-1$
          },
          new DataDescriptor[0]
         );
  }
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Related Classes of org.moltools.apps.probemaker.modules.TestDescriptor

  • org.moltools.apps.probemaker.ext.mod.DefaultHybInterferenceModule
  • org.moltools.apps.probemaker.ext.mod.DefaultTagOccurrenceModule
  • org.moltools.apps.probemaker.ext.mod.DINAMeltSecStructModule
  • org.moltools.apps.probemaker.ext.mod.DummyModule
  • org.moltools.apps.probemaker.ext.mod.FalsePrimingModule
  • org.moltools.apps.probemaker.ext.mod.GapFillPadlockLigationModule
  • org.moltools.apps.probemaker.ext.mod.GapFillPadlockTSSLigationModule
  • org.moltools.apps.probemaker.ext.mod.GCContentModule
  • org.moltools.apps.probemaker.ext.mod.PadlockLigationModule
  • org.moltools.apps.probemaker.ext.mod.PadlockTSSLigationModule
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