Class GoTerms

Method Details

• add

  public GoTerm add(GoTerm goTerm)

  Add a GOTerm (if not already in this GOTerms) WARNING: Creates 'fake' symbolNames based on symbolIds. This method is used mostly for testing / debugging

• addInterestingSymbol

  public void addInterestingSymbol(String symbolId, int rank, HashSet<String> noGoTermFound)

  Add a symbol as 'interesting' symbol (to every corresponding GOTerm in this set)

  Parameters:

  symbolName - : Symbol's name

  rank - : symbol's rank

  noGoTermFound - : Add symbol here if there are no GOTerms associated with this symbol

• addSymbolId

  public boolean addSymbolId(GoTerm goTerm, String symbolId)

  Add a symbolId (as well as all needed mappings)

  Parameters:

  goTermAcc -

  symbolId -

  symbolName -

  goTermType -

  description -

  Returns:

  true if OK, false on error (GOTerm 'goTermAcc' not found)

• addSymbolsFromChilds

  public void addSymbolsFromChilds()

  Use symbols for chids in DAG For every GOTerm, each child's symbols are added to the term so that root term contains every symbol and every interestingSymbol

• allSymbols

  public Set<String> allSymbols()

  Create a set with all the symbols

• checkInterestingSymbolIds

  public void checkInterestingSymbolIds(Set<String> interestingSymbolIds)

  Checks that every symboolID is in the set (as 'interesting' symbols)

  Parameters:

  interestingSymbolIds - : A set of interesting symbols Throws an exception on error

• disjointSet

  public GoTerm disjointSet(List<GoTerm> goTermList, int activeSets)

  Produce a GOTerm based on a list of GOTerms and a 'mask'

  Parameters:

  goTermList - : A list of GOTerms

  activeSets - : An integer (binary mask) that specifies weather a set in the list should be taken into account or not. The operation performed is: Intersection{ GOTerms where mask_bit == 1 } - Union{ GOTerms where mask_bit == 0 } ) where the minus sign '-' is actually a 'set minus' operation. This operation is done for both sets in GOTerm (i.e. symbolIds and interestingSymbolIds)

  Returns:

  A GOTerm

• getGoTerm

  public GoTerm getGoTerm(String goTermAcc)

• getGoTermsByGoTermAcc

  public HashMap<String,GoTerm> getGoTermsByGoTermAcc()

• getGoTermsBySymbolId

  public HashMap<String,Set<GoTerm>> getGoTermsBySymbolId()

• getGoTermsBySymbolId

  public Set<GoTerm> getGoTermsBySymbolId(String symbolId)

• getInterestingSymbolIdsSet

  public HashSet<String> getInterestingSymbolIdsSet()

• getInterestingSymbolIdsSize

  public int getInterestingSymbolIdsSize()

• getLabel

  public String getLabel()

• getMaxRank

  public int getMaxRank()

• getNameSpace

  public String getNameSpace()

• getRank

  public int getRank(String symbolId)

  Get symbol's rank

  Parameters:

  symbolId -

  Returns:

• getRankSymbolId

  public HashMap<String,Integer> getRankSymbolId()

• iterator

  public Iterator<GoTerm> iterator()

  Iterate through each GOterm in this GOTerms

  Specified by:

  iterator in interface Iterable<GoTerm>

• keySet

  public Set<String> keySet()

• levels

  public int levels()

  Calculate each node's level (in DAG)

  Returns:

  maximum level

• listTopTerms

  public List<GoTerm> listTopTerms(int numberToSelect)

  Select a number of GOTerms

  Parameters:

  numberToSelect -

  Returns:

• numberOfInterestingSymbols

  public int numberOfInterestingSymbols()

  Calculate how many interesting symbol-IDs in are there in all these GOTerms

  Returns:

  Number of interesting symbols

• numberOfNodes

  public int numberOfNodes()

  Number of nodes in this DAG

  Returns:

• numberOfNodesWithOneInterestingSymbol

  public int numberOfNodesWithOneInterestingSymbol()

  Calculate the number of nodes in that have at least one interesting symbol

  Returns:

• numberOfNodesWithOneSymbol

  public int numberOfNodesWithOneSymbol()

  Calculate the number of nodes in that have at least one annotated symbol

  Returns:

• numberOfSymbols

  public int numberOfSymbols()

  Calculate how many symbol-IDs in are there in all these GOTerms

  Returns:

  Number of interesting symbols

• readGeneAssocFile

  public void readGeneAssocFile(String goGenesFile, boolean useGeneId)

  Reads a file containing every gene (names and ids) associated GO terms

  Parameters:

  goGenesFile - : A file containing gene associations to GO terms

• readInterestingSymbolIdsFile

  public void readInterestingSymbolIdsFile(String fileName)

  Reads a file with a list of 'interesting' genes (one per line)

  Parameters:

  fileName - : Can be "-" for no-file

• readOboFile

  public void readOboFile(String oboFile, boolean removeObsolete)

  Read an OBO file

  Parameters:

  oboFile -

  nameSpace -

• removeGOTerm

  public void removeGOTerm(String goTermAcc)

  Remove a GOTerm

• resetInterestingSymbolIds

  public void resetInterestingSymbolIds()

  Reset every 'interesting' symbolId (on every single GOTerm in this GOTerms)

• rootNodes

  public Set<GoTerm> rootNodes()

• saveGseaGeneSets

  public void saveGseaGeneSets(String fileName)

  Save gene sets file for GSEA analysis Format specification: http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29

  Parameters:

  fileName -

• setLabel

  public void setLabel(String label)

• toString

  public String toString()

  Overrides:

  toString in class Object

• values

  public Collection<GoTerm> values()