Package net.sf.basedb.core.data

Class FormulaData

java.lang.Object
net.sf.basedb.core.data.BasicData
net.sf.basedb.core.data.OwnedData
net.sf.basedb.core.data.SharedData
net.sf.basedb.core.data.CommonData
net.sf.basedb.core.data.FormulaData
All Implemented Interfaces:
IdentifiableData, LoggableData, NameableData, OwnableData, RegisteredData, RemovableData, ShareableData
public class FormulaData
extends CommonData
implements RegisteredData, LoggableData
This class holds information about a formula used in the analysis of raw data and bioassay sets.
Version:
2.0
Author:
Nicklas
See Also:
Formula, Developer documentation: Other classes
Hibernate: class
table="`Formulas`" lazy="false"

  • Field Details

    • entryDate

      private Date entryDate

    • averageMethod

      private int averageMethod

    • type

      private int type

    • valueType

      private Integer valueType

    • sourceIntensityTransform

      private Integer sourceIntensityTransform

    • resultIntensityTransform

      private Integer resultIntensityTransform

    • parser

      private int parser

    • MAX_RAWDATATYPE_LENGTH

      public static final int MAX_RAWDATATYPE_LENGTH
      The maximum allowed length of the raw data type name.
      See Also:
      Constant Field Values

    • rawDataType

      private String rawDataType

    • channels

      private int channels

    • MAX_FORMULA_LENGTH

      public static final int MAX_FORMULA_LENGTH
      The maximum allowed length of a formula.
      See Also:
      Constant Field Values

    • formulas

      private List<String> formulas

    • coloring

      private ColoringData coloring

  • Constructor Details

    • FormulaData

      public FormulaData()

  • Method Details

    • getEntryDate

      public Date getEntryDate()
      Description copied from interface: RegisteredData
      Get the date this item was added to the database. The value is generated at creation time and can't be modified later.
      Specified by:
      getEntryDate in interface RegisteredData

    • setEntryDate

      public void setEntryDate​(Date entryDate)

    • getAverageMethod

      public int getAverageMethod()
      The average method for thid formula:
      Since:
      2.4
      Hibernate: property
      column="`average_method`" type="int" not-null="true"

    • setAverageMethod

      public void setAverageMethod​(int averageMethod)

    • getType

      public int getType()
      The type of formula:
      • 1 = intensity expression; raw data type required, 1 formula for each channel
      • 2 = intensity transformation; raw data type or channels required, 1 formula for each channel
      • 3 = column expression; raw data type or channels required, 1 formula only
      • 4 = column restriction; raw data type or channels required, 1 formula only
      Hibernate: property
      column="`type`" type="int" not-null="true"

    • setType

      public void setType​(int type)

    • getValueType

      public Integer getValueType()
      The code for the value type. null = not known or doesn't care.
      Since:
      2.15
      Hibernate: property
      column="`value_type`" type="int" not-null="false"

    • setValueType

      public void setValueType​(Integer valueType)
      Since:
      2.15

    • getSourceIntensityTransform

      public Integer getSourceIntensityTransform()
      A flag indicating what kind of spot source data that the formula can be used with, or null if the formula can be used with any kind of source data. 0 = no transformation; 1 = 2-log; 2 = 10-log
      Since:
      2.12
      Hibernate: property
      column="`source_transform`" type="int" not-null="false"

    • setSourceIntensityTransform

      public void setSourceIntensityTransform​(Integer sourceIntensityTransform)
      Since:
      2.12

    • getResultIntensityTransform

      public Integer getResultIntensityTransform()
      A flag indicating what kind of result spot data this formula generates, or null if it generates the same kind of data that is used as source. 0 = no transformation; 1 = 2-log; 2 = 10-log
      Since:
      2.12
      Hibernate: property
      column="`result_transform`" type="int" not-null="false"

    • setResultIntensityTransform

      public void setResultIntensityTransform​(Integer resultIntensityTransform)
      Since:
      2.12

    • getParser

      public int getParser()
      Which parser to use to convert the formula to an expression or restriction. 1 = JEP
      Hibernate: property
      column="`parser`" type="int" not-null="true"

    • setParser

      public void setParser​(int parser)

    • getRawDataType

      public String getRawDataType()
      The name of raw data type this formula can be used on, or null if it can be used on any raw data type.
      Hibernate: property
      column="`rawdatatype`" type="string" length="255" not-null="false"

    • setRawDataType

      public void setRawDataType​(String rawDataType)

    • getChannels

      public int getChannels()
      The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.
      Hibernate: property
      column="`channels`" type="int" not-null="true"

    • setChannels

      public void setChannels​(int channels)

    • getFormulas

      public List<String> getFormulas()
      Get the list of formulas.
      Hibernate: list
      table="`FormulaExpressions`" lazy="true"
      Hibernate: collection-key
      column="`formula_id`"
      Hibernate: collection-index
      column="`index`" type="int"
      Hibernate: collection-element
      column="`formula`" type="string" length="255" not-null="true"

    • setFormulas

      void setFormulas​(List<String> formulas)

    • getColoring

      public ColoringData getColoring()
      Get the coloring information for this formula.
      Hibernate: component

    • setColoring

      public void setColoring​(ColoringData coloring)