Package bacnet.datamodel.expdesign

Class BioCondition

java.lang.Object
bacnet.datamodel.expdesign.BioCondition
All Implemented Interfaces:
Serializable
public class BioCondition extends Object implements Serializable
This class is used for the different bioconds declared in the experiment It contains the biocond name, and all the related data. IMPORTANT, MAJ 04102011 : WT data are only used as indication on experimental design, in all analysis if we want WT we need to add it in the Experiment
See Also:

  • Field Details

    • SEPARATOR

      public static String SEPARATOR
      BioConditoon separator for comparisons
      equal to " vs "

  • Constructor Details

    • BioCondition

      public BioCondition()

    • BioCondition

      public BioCondition(String bioCondName)

  • Method Details

    • containTranscriptomes

      public boolean containTranscriptomes()

    • containRNASeq

      public boolean containRNASeq()

    • containProteomes

      public boolean containProteomes()

    • getExpressionData

      public ArrayList<ExpressionData> getExpressionData()
      Put all ExpressionData in a list
      Returns:

    • getTranscriptomesData

      public ArrayList<OmicsData> getTranscriptomesData()
      Put all TranscriptomeData in a list
      Returns:

    • getTranscriptomesGenomes

      public static ArrayList<String> getTranscriptomesGenomes()
      Get all genomes associated to a transcriptomes dataset
      Returns:

    • getRNASeqGenomes

      public static ArrayList<String> getRNASeqGenomes()
      Get all genomes associated to a transcriptomes dataset
      Returns:

    • getOmicsData

      public ArrayList<OmicsData> getOmicsData()
      Put all OmicsData in a list
      Returns:

    • getProteomicsData

      public ArrayList<OmicsData> getProteomicsData()
      Put all OmicsData in a list
      Returns:

    • getProteomeGenomes

      public static ArrayList<String> getProteomeGenomes()
      Get all genomes associated to a proteomics dataset
      Returns:

    • getComparisonDataNames

      public ArrayList<String> getComparisonDataNames()
      Get every names of the Comparison which can be found:
    • Tiling arrays
    • Gene Expression arrays
    • ExpressionMatrix
      • Returns:
      a list of all the data

    • getGenome

      public Genome getGenome()
      Return corresponding Genome given by this.genomeName
      Load it if necessary
      Returns:

    • getComparisonNames

      public ArrayList<String> getComparisonNames()
      Return a list of all Comparisons: bioCondName vs comparisons.get(i)
      Returns:

    • compare

      public BioCondition compare(BioCondition bioCond2, boolean calcData)
      Create a BioCondition containing the different data for comparing this BioCondition to bioCond2
      Parameters:
      bioCond2 -
      Returns:
      Throws:
      IOException

    • getBioCondition

      public static BioCondition getBioCondition(String bioCondName)
      From a biological condition name load the corresponding BioCondition object
      Parameters:
      bioCondName -
      Returns:

    • getBioCondition

      public static BioCondition getBioCondition(String bioCondName, boolean modelProvider)
      From a biological condition name, get from the ModelProvider the corresponding BioCondition object
      If not available it will load them for the hard drive
      Parameters:
      bioCondName -
      true - if you want to get BioCondition from pre-loaded BioCondition
      Returns:

    • parseName

      public static String[] parseName(String name)
      Parse a Comparison name, extracting leftBioCondition and rightBiocondition
      Parameters:
      name -
      Returns:
      {leftBioCond,rightBioCond}

    • getAllBioConditionNames

      public static ArrayList<String> getAllBioConditionNames()
      Get all available BioCondition names by reading the text file Experiment.INCLUDE_COND_PATH
      Returns:

    • getAllBioConditions

      public static ArrayList<BioCondition> getAllBioConditions()
      Return all BioCondition available
      Returns:

    • getAllPublishedBioConditions

      public static ArrayList<BioCondition> getAllPublishedBioConditions()
      Return all BioCondition available
      Returns:

    • getAllUnPublishedBioConditions

      public static ArrayList<BioCondition> getAllUnPublishedBioConditions()
      Return all BioCondition available
      Returns:

    • load

      public static BioCondition load(String fileName)
      Read compressed, serialized data with a FileInputStream. Uncompress that data with a GZIPInputStream. Deserialize the vector of lines with a ObjectInputStream. Replace current data with new data, and redraw everything.

    • save

      public void save(String fileName)
      Prompt the user for a filename, and save the scribble in that file. Serialize the vector of lines with an ObjectOutputStream. Compress the serialized objects with a GZIPOutputStream. Write the compressed, serialized data to a file with a FileOutputStream. Don't forget to flush and close the stream.

    • getName

      public String getName()

    • setName

      public void setName(String name)

    • getGenomeName

      public String getGenomeName()

    • setGenomeName

      public void setGenomeName(String genomeName)

    • getDate

      public String getDate()

    • setDate

      public void setDate(String date)

    • getExperienceNb

      public int getExperienceNb()

    • setExperienceNb

      public void setExperienceNb(int experienceNb)

    • isWildType

      public boolean isWildType()

    • setWildType

      public void setWildType(boolean wildType)

    • getComment

      public String getComment()

    • setComment

      public void setComment(String comment)

    • getGeneExprs

      public ArrayList<GeneExpression> getGeneExprs()

    • setGeneExprs

      public void setGeneExprs(ArrayList<GeneExpression> geneExprs)

    • getTilings

      public ArrayList<Tiling> getTilings()

    • setTilings

      public void setTilings(ArrayList<Tiling> tilings)

    • getMatrices

      public ArrayList<ExpressionMatrix> getMatrices()

    • setMatrices

      public void setMatrices(ArrayList<ExpressionMatrix> matrices)

    • getArrayExpressId

      public String getArrayExpressId()

    • setArrayExpressId

      public void setArrayExpressId(String arrayExpressId)

    • getArrayExpressTechnoId

      public String getArrayExpressTechnoId()

    • isNoData

      public boolean isNoData()

    • setNoData

      public void setNoData(boolean noData)

    • setArrayExpressTechnoId

      public void setArrayExpressTechnoId(String arrayExpressTechnoId)

    • getGenomeUsed

      public String getGenomeUsed()

    • setGenomeUsed

      public void setGenomeUsed(String genomeUsed)

    • getMutant

      public ArrayList<String> getMutant()

    • setMutant

      public void setMutant(ArrayList<String> mutant)

    • getMediaGrowthProperties

      public ArrayList<String> getMediaGrowthProperties()

    • setMediaGrowthProperties

      public void setMediaGrowthProperties(ArrayList<String> mediaGrowthProperties)

    • getGrowth

      public ArrayList<String> getGrowth()

    • setGrowth

      public void setGrowth(ArrayList<String> growth)

    • getTemperature

      public String getTemperature()

    • setTemperature

      public void setTemperature(String temperature)

    • getTime

      public String getTime()

    • setTime

      public void setTime(String time)

    • getMedia

      public ArrayList<String> getMedia()

    • setMedia

      public void setMedia(ArrayList<String> media)

    • getLinkedBioCondition

      public ArrayList<String> getLinkedBioCondition()

    • setLinkedBioCondition

      public void setLinkedBioCondition(ArrayList<String> linkedBioCondition)

    • getComparisons

      public ArrayList<String> getComparisons()

    • setComparisons

      public void setComparisons(ArrayList<String> comparisons)

    • getTypeDataContained

      public TreeSet<OmicsData.TypeData> getTypeDataContained()

    • getnTerms

      public ArrayList<NTermData> getnTerms()

    • getNGSSeqs

      public ArrayList<NGS> getNGSSeqs()

    • setNGSSeqs

      public void setNGSSeqs(ArrayList<NGS> rnaSeqs)

    • setnTerms

      public void setnTerms(ArrayList<NTermData> nTerms)

    • getProteomes

      public ArrayList<ProteomicsData> getProteomes()

    • setProteomes

      public void setProteomes(ArrayList<ProteomicsData> proteomes)

    • setTypeDataContained

      public void setTypeDataContained(TreeSet<OmicsData.TypeData> typeDataContained)

    • getReference

      public String getReference()

    • setReference

      public void setReference(String reference)

    • getStudyName

      public String getStudyName()

    • setStudyName

      public void setStudyName(String studyName)

    • getAntiComparisons

      public ArrayList<String> getAntiComparisons()

    • setAntiComparisons

      public void setAntiComparisons(ArrayList<String> antiComparisons)

    • getLocalization

      public ArrayList<String> getLocalization()

    • setLocalization

      public void setLocalization(ArrayList<String> localization)