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

Package org.moltools.apps.probemaker.modules

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

org.moltools.apps.probemaker.modules.TestDescriptor
A representation of a test. Each AnalysisModule defines a number of tests. The user interface allow setting which of these tests to perform. This is done by calling the setPerform method of the corresponding Test object. The Test object does not implement the test itself, but represents a test for user interface purposes. @author Johan Stenberg @version 1.0

  transient protected double magnesiumConc;
  transient protected HttpClient client = null;
  
  
  public DINAMeltSecStructModule() {
    super(new TestDescriptor[] { new TestDescriptor("Secondary structure")}, //$NON-NLS-1$
        new DataDescriptor[] {
        new DoubleDescriptor("dG limit","Maximum dG allowed for highest quality (usually a negative number)",KEY_DG_LIMIT,-100.0,100.0), //$NON-NLS-1$ //$NON-NLS-2$ 
        new DoubleDescriptor("dG span","Maximum dG above limit allowed for intermediate quality",KEY_DG_SPAN,0,100), //$NON-NLS-1$ //$NON-NLS-2$ 
        new DoubleDescriptor("Folding temperature (�C)","The temperature in degrees celsius to use for the folding calculations",KEY_FOLD_TEMP,0,100), //$NON-NLS-1$ //$NON-NLS-2$ 
        new DoubleDescriptor("Na+ conc. (M)","The sodium ion concentration (molar) to use for the folding calculations",KEY_NA_CONC,0.01,1), //$NON-NLS-1$ //$NON-NLS-2$

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    "An error message is given if a matching sequence is found.</html>"; //$NON-NLS-1$
  }


  public GapFillPadlockTSSLigationModule() {
    super(new TestDescriptor[] {
        new TestDescriptor("Templating by own target"), //$NON-NLS-1$
        new TestDescriptor("Templating by other targets"), //$NON-NLS-1$
        new TestDescriptor("Templating by other probes") //$NON-NLS-1$
    },new DataDescriptor[] {
        new IntegerDescriptor("Min. target 5' match length", //$NON-NLS-1$
            "Minimum number of matching bases on 5' end for targets", //$NON-NLS-1$
            PadlockLigationCalculator.
            PROPERTY_TARGET_5_MATCH_LENGTH, 1, 100),

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  }


  public SelectorLigationModule() {
    super(
        new TestDescriptor[] {
            new TestDescriptor("Ligation to self on 5' end"), //$NON-NLS-1$
            new TestDescriptor("Ligation to self on 3' end"), //$NON-NLS-1$
            new TestDescriptor("Ligation to target's 5' end"), //$NON-NLS-1$
            new TestDescriptor("Ligation to other selector on 5' end"), //$NON-NLS-1$
            new TestDescriptor("Ligation to other selector on 3' end"), //$NON-NLS-1$
            new TestDescriptor("Other selector ligates on 5' end"), //$NON-NLS-1$
            new TestDescriptor("Other selector ligates on 3' end"), //$NON-NLS-1$
            new TestDescriptor("Ligation to other target's 5' end"), //$NON-NLS-1$
            new TestDescriptor("Ligation to other target's 3' end"), //$NON-NLS-1$
        },
        new DataDescriptor[] {
            new IntegerDescriptor("Min. target 5' match length", //$NON-NLS-1$
                "Minimum number of matching bases on 5' end for targets", //$NON-NLS-1$
                KEY_TARGET_5_MATCH_LENGTH, 1, 100),

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    "<i>Nucleic Acids Res.</i>, <b>31</b>, 1796-1802.</html>";  //$NON-NLS-1$
  }


  public PadlockTSSLigationModule() {
    super(new TestDescriptor[] {
        new TestDescriptor("Templating by own target"),  //$NON-NLS-1$
        new TestDescriptor("Templating by self"),  //$NON-NLS-1$
        new TestDescriptor("Templating by other targets"),  //$NON-NLS-1$
        new TestDescriptor("Templating by other probes"),  //$NON-NLS-1$
        new TestDescriptor("Template of other probes"),  //$NON-NLS-1$
    },new DataDescriptor[] {
        new IntegerDescriptor("Min. target 5' match length",  //$NON-NLS-1$
            "Minimum number of matching bases on 5' end for targets",  //$NON-NLS-1$
            PadlockLigationCalculator.PROPERTY_TARGET_5_MATCH_LENGTH, 1, 100),
            new IntegerDescriptor("Min. target 3' match length",  //$NON-NLS-1$

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    "If the cutoff mode is used, only the lower temperature limit is considered.</html>"; //$NON-NLS-1$
  }


  public TSSLengthAndTmModule() {
    super(new TestDescriptor[] {
          new TestDescriptor("5' hybridization temparature"), //$NON-NLS-1$
          new TestDescriptor("3' hybridization temperature"), //$NON-NLS-1$
          new TestDescriptor("5' TSS length"), //$NON-NLS-1$
          new TestDescriptor("3' TSS length")},  //$NON-NLS-1$
          new DataDescriptor[] {
        new BooleanDescriptor("Use cutoff mode", //$NON-NLS-1$
                           "Give warning and error messages only for values below the preferred Tm. Allow all values above the limit.", //$NON-NLS-1$
                           PROP_USE_CUTOFF_MODE)});
    setData(PROP_USE_CUTOFF_MODE,new Boolean(false));

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  public GCContentModule() {
    
    //Set values in super class.
    super(
            new TestDescriptor[] { new TestDescriptor("%GC Content") }, //$NON-NLS-1$
            new DataDescriptor[] {
                new IntegerDescriptor("Max %GC", "Max allowed GC content in per cent.", //$NON-NLS-1$ //$NON-NLS-2$
                    "MAX_GC", 0, 100), //$NON-NLS-1$
            new IntegerDescriptor("Min %GC", "Min allowed GC content in per cent.", //$NON-NLS-1$ //$NON-NLS-2$
                "MIN_GC", 0, 100)                   //$NON-NLS-1$

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    "If all tags have not been allocated, a fatal message is given.</html>"; //$NON-NLS-1$
  }


  public TagAllocationModule() {
    super(new TestDescriptor[] {
            new TestDescriptor("Tag allocation")}, //$NON-NLS-1$
            new DataDescriptor[0]
          );
  }

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  }; 
  
  
  public StringHeteroDimerModule() {
    super(new TestDescriptor[] {
           new TestDescriptor("Probe-probe heterodimer formation") //$NON-NLS-1$
          },descriptors);
    
    setData(KEY_WINDOW,new Integer(10));
    setData(KEY_STRINGENCY,new Integer(6));
  }

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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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  static final String KEY_ALLOWED_COMPLEMENTARITY_SCORE = "ALLOWED_COMPLEMENTARITY_SCORE"; //$NON-NLS-1$
  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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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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