Class GeneSet

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<GeneSet>, java.lang.Iterable<java.lang.String>

    public class GeneSet
    extends java.lang.Object
    implements java.lang.Comparable<GeneSet>, java.lang.Iterable<java.lang.String>, java.io.Serializable
    An set of genes (that belongs to a collection of gene-sets)
    Author:
    Pablo Cingolani
    See Also:
    Serialized Form
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean debug  
    • Constructor Summary

      Constructors 
      Constructor Description
      GeneSet​(java.lang.String name, java.lang.String description, GeneSets geneSets)
      Create an empty gene set (that belongs to a collection of gene sets 'geneSets')
      GeneSet​(java.util.List<GeneSet> geneSetList, GeneSets geneSets)
      Create a new GeneSet by joining all GeneSets in the list
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addGene​(java.lang.String gene)
      Add one gene to genesSet
      int compareTo​(GeneSet geneSet)
      Comparable interface (to order terms)
      int compareToNumbers​(double n1, double n2, java.lang.String name1, java.lang.String name2, boolean descending)
      Compare 2 numbers and 2 'names' (if both numbers are equal) - NaN sorted in a way that they remain at the end of a sorted list - When two numbers are equal, the sort is done alphabetically by name
      int countOverlap​(GeneSet gs)
      COunt how many genes are in both GeneSets
      java.util.List<java.lang.String> genesSorted()
      Return a sorted list of genes
      java.lang.String getDescription()  
      int getGeneCount()
      Number of symbols in this node (total = interesting + not-interesting)
      java.util.HashSet<java.lang.String> getGenes()  
      GeneSets getGeneSets()  
      java.util.HashSet<java.lang.String> getInterestingGenes()
      Get 'interesting' genes
      int getInterestingGenesCount()
      Number of 'interesting' symbols
      int getMaxRank()  
      java.lang.String getName()  
      int getRankedGenesCount()  
      long getRankSum()  
      boolean hasGene​(java.lang.String gene)  
      void intersection​(GeneSet geneSet)
      Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').
      java.util.Iterator<java.lang.String> iterator()  
      long rankSum()
      Calculate rankSum, rankedSymbols and maxRank
      void setDescription​(java.lang.String description)  
      void setGeneSets​(GeneSets geneSets)  
      void setMaxRank​(int maxRank)  
      void setMinus​(GeneSet geneSet)
      Perform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').
      void setName​(java.lang.String geneSetName)  
      int size()  
      int sizeEffective()
      Number of genes that have a value
      java.lang.String toString()  
      java.lang.String toStringAll()  
      void union​(GeneSet geneSet)
      Union this term with 'geneSet' (union for 'geneSet' and 'interestingGeneSet').
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator
    • Field Detail

      • debug

        public static boolean debug
    • Constructor Detail

      • GeneSet

        public GeneSet​(java.util.List<GeneSet> geneSetList,
                       GeneSets geneSets)
        Create a new GeneSet by joining all GeneSets in the list
        Parameters:
        geneSetList -
      • GeneSet

        public GeneSet​(java.lang.String name,
                       java.lang.String description,
                       GeneSets geneSets)
        Create an empty gene set (that belongs to a collection of gene sets 'geneSets')
        Parameters:
        name -
        geneSets -
    • Method Detail

      • addGene

        public void addGene​(java.lang.String gene)
        Add one gene to genesSet
        Parameters:
        gene -
      • compareTo

        public int compareTo​(GeneSet geneSet)
        Comparable interface (to order terms)
        Specified by:
        compareTo in interface java.lang.Comparable<GeneSet>
      • compareToNumbers

        public int compareToNumbers​(double n1,
                                    double n2,
                                    java.lang.String name1,
                                    java.lang.String name2,
                                    boolean descending)
        Compare 2 numbers and 2 'names' (if both numbers are equal) - NaN sorted in a way that they remain at the end of a sorted list - When two numbers are equal, the sort is done alphabetically by name
        Parameters:
        n1 -
        n2 -
        name1 -
        name2 -
        Returns:
      • countOverlap

        public int countOverlap​(GeneSet gs)
        COunt how many genes are in both GeneSets
        Parameters:
        gs -
        Returns:
      • genesSorted

        public java.util.List<java.lang.String> genesSorted()
        Return a sorted list of genes
        Returns:
      • getDescription

        public java.lang.String getDescription()
      • getGeneCount

        public int getGeneCount()
        Number of symbols in this node (total = interesting + not-interesting)
        Returns:
      • getGenes

        public java.util.HashSet<java.lang.String> getGenes()
      • getGeneSets

        public GeneSets getGeneSets()
      • getInterestingGenes

        public java.util.HashSet<java.lang.String> getInterestingGenes()
        Get 'interesting' genes
        Returns:
      • getInterestingGenesCount

        public int getInterestingGenesCount()
        Number of 'interesting' symbols
        Returns:
      • getMaxRank

        public int getMaxRank()
      • getName

        public java.lang.String getName()
      • getRankedGenesCount

        public int getRankedGenesCount()
      • getRankSum

        public long getRankSum()
      • hasGene

        public boolean hasGene​(java.lang.String gene)
      • intersection

        public void intersection​(GeneSet geneSet)
        Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').
        Parameters:
        geneSet - : GeneSet to intercept
      • iterator

        public java.util.Iterator<java.lang.String> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<java.lang.String>
      • rankSum

        public long rankSum()
        Calculate rankSum, rankedSymbols and maxRank
        Returns:
        rankSum
      • setDescription

        public void setDescription​(java.lang.String description)
      • setGeneSets

        public void setGeneSets​(GeneSets geneSets)
      • setMaxRank

        public void setMaxRank​(int maxRank)
      • setMinus

        public void setMinus​(GeneSet geneSet)
        Perform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').
        Parameters:
        geneSet - : GeneSet to use for 'set minus' operation
      • setName

        public void setName​(java.lang.String geneSetName)
      • size

        public int size()
      • sizeEffective

        public int sizeEffective()
        Number of genes that have a value
        Returns:
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • toStringAll

        public java.lang.String toStringAll()
      • union

        public void union​(GeneSet geneSet)
        Union this term with 'geneSet' (union for 'geneSet' and 'interestingGeneSet').
        Parameters:
        geneSet - : GeneSet to use for union