Package net.sf.apptools.data

Examples of net.sf.apptools.data.IntegerDescriptor

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    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.
                             PROPERTY_PROBE_5_MATCH_LENGTH, 1, 100),
        new IntegerDescriptor("Min. 3' match length", //$NON-NLS-1$
                             "Minimum number of matching bases on 3' end", //$NON-NLS-1$
                             PadlockLigationCalculator.
                             PROPERTY_PROBE_3_MATCH_LENGTH, 1, 100)
    });
    setData(PadlockLigationCalculator.PROPERTY_PROBE_5_MATCH_LENGTH,new Integer(ltc.getParameters().get(PadlockLigationCalculator.PROPERTY_PROBE_5_MATCH_LENGTH).toString()));
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        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", //$NON-NLS-1$
            "The value in percent of the maximum alignment score required to yield a match. If 100 % regular string search used.", //$NON-NLS-1$
            KEY_PERCENT_SIMILARITY, 1, 100),
        new StringDataDescriptor("Positions to check sequence", //$NON-NLS-1$
            "A comma-separated list of tag positions for which to check if the sequence occurs elsewhere", //$NON-NLS-1$
            KEY_SEQUENCE_POSITIONS,false),
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  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),
            new IntegerDescriptor("Min. 3' match length", //$NON-NLS-1$
                "Minimum number of matching bases on 3' end", //$NON-NLS-1$
                PadlockLigationCalculator.
                PROPERTY_PROBE_3_MATCH_LENGTH, 1, 100),
                new BooleanDescriptor("Use Tm limit", //$NON-NLS-1$
                    "Use a limit for Tm of probe-target hybrid", //$NON-NLS-1$
                    PadlockLigationCalculator.PROPERTY_USE_TM),           
                    new IntegerDescriptor("Max. Tm", //$NON-NLS-1$
                        "Maximum Tm of probe-target hybrid at site of match.", //$NON-NLS-1$
                        PadlockLigationCalculator.PROPERTY_TM_LIMIT, 0, 100)                   
    });
    setMin5MatchLength(Integer.parseInt(ltc.getParameters().get(PadlockLigationCalculator.PROPERTY_PROBE_5_MATCH_LENGTH)));
    setMin3MatchLength(Integer.parseInt(ltc.getParameters().get(PadlockLigationCalculator.PROPERTY_PROBE_3_MATCH_LENGTH)));
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  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)
    });
    setData(KEY_WARNING_CHANCE,new Integer(90));
  }
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  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 {
      fmpc = new FractionalMeltingPointCalculator(new FractionalNNParameters());
    }
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            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),
                new IntegerDescriptor("Min. target 3' match length", //$NON-NLS-1$
                    "Minimum number of matching bases on 3' end for targets", //$NON-NLS-1$
                    KEY_TARGET_3_MATCH_LENGTH, 1, 100),
                    new IntegerDescriptor("Min. selectors 5' match length", //$NON-NLS-1$
                        "Minimum number of matching bases on 5' end for selectors", //$NON-NLS-1$
                        KEY_SELECTOR_5_MATCH_LENGTH, 1, 100),
                        new IntegerDescriptor("Min. selectors 3' match length", //$NON-NLS-1$
                            "Minimum number of matching bases on 3' end for selectors", //$NON-NLS-1$
                            KEY_SELECTOR_3_MATCH_LENGTH, 1, 100)
        });

    setData(KEY_TARGET_5_MATCH_LENGTH,new Integer(PROPERTY_TARGET_5_MATCH_LENGTH));
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    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),
            new IntegerDescriptor("Min. target 3' match length", //$NON-NLS-1$
                "Minimum number of matching bases on 3' end for targets", //$NON-NLS-1$
                PadlockLigationCalculator.
                PROPERTY_TARGET_3_MATCH_LENGTH, 1, 100),
                new IntegerDescriptor("Min. probe 5' match length", //$NON-NLS-1$
                    "Minimum number of matching bases on 5' end for probes", //$NON-NLS-1$
                    PadlockLigationCalculator.
                    PROPERTY_PROBE_5_MATCH_LENGTH, 1, 100),
                    new IntegerDescriptor("Min. probe 3' match length", //$NON-NLS-1$
                        "Minimum number of matching bases on 3' end for probes", //$NON-NLS-1$
                        PadlockLigationCalculator.
                        PROPERTY_PROBE_3_MATCH_LENGTH, 1, 100)
    });
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        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",  //$NON-NLS-1$
                "Minimum number of matching bases on 3' end for targets",  //$NON-NLS-1$
                PadlockLigationCalculator.PROPERTY_TARGET_3_MATCH_LENGTH, 1, 100),
                new IntegerDescriptor("Min. probe 5' match length",  //$NON-NLS-1$
                    "Minimum number of matching bases on 5' end for probes",  //$NON-NLS-1$
                    PadlockLigationCalculator.PROPERTY_PROBE_5_MATCH_LENGTH, 1, 100),
                    new IntegerDescriptor("Min. probe 3' match length",  //$NON-NLS-1$
                        "Minimum number of matching bases on 3' end for probes",  //$NON-NLS-1$
                        PadlockLigationCalculator.PROPERTY_PROBE_3_MATCH_LENGTH, 1, 100),
                        new BooleanDescriptor("Use Tm limit",  //$NON-NLS-1$
                            "Use a limit for Tm of probe-target hybrid",  //$NON-NLS-1$
                            PadlockLigationCalculator.PROPERTY_USE_TM),
                            new IntegerDescriptor("Max. Tm",  //$NON-NLS-1$
                                "Maximum Tm of probe-target hybrid at site of match.",  //$NON-NLS-1$
                                PadlockLigationCalculator.PROPERTY_TM_LIMIT, 0, 100)
    });
    setData(PadlockLigationCalculator.PROPERTY_TARGET_5_MATCH_LENGTH,new Integer(ltc.getParameters().get(
        PadlockLigationCalculator.PROPERTY_TARGET_5_MATCH_LENGTH).toString()));
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    //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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  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),
            new IntegerDescriptor("Min. 3' match length", //$NON-NLS-1$
                "Minimum number of matching bases on 3' end", //$NON-NLS-1$
                PadlockLigationCalculator.
                PROPERTY_PROBE_3_MATCH_LENGTH, 1, 100),
                new BooleanDescriptor("Use Tm limit", //$NON-NLS-1$
                    "Use a limit for Tm of probe-target hybrid", //$NON-NLS-1$
                    PadlockLigationCalculator.PROPERTY_USE_TM),           
                    new IntegerDescriptor("Max. Tm", //$NON-NLS-1$
                        "Maximum Tm of probe-target hybrid at site of match.", //$NON-NLS-1$
                        PadlockLigationCalculator.PROPERTY_TM_LIMIT, 0, 100)                   
    });
    setData(PadlockLigationCalculator.PROPERTY_PROBE_5_MATCH_LENGTH,new Integer(ltc.getParameters().get(
        PadlockLigationCalculator.PROPERTY_PROBE_5_MATCH_LENGTH).toString()));
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Related Classes of net.sf.apptools.data.IntegerDescriptor

  • org.moltools.apps.probemaker.ext.mod.DefaultTagOccurrenceModule
  • 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
  • org.moltools.apps.probemaker.ext.mod.SelectorLigationModule
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