owltools.panther
Class PANTHERForest

java.lang.Object
  extended by owltools.panther.PANTHERForest

public class PANTHERForest
extends Object

Methods to simplify the work with sets of PANTHER trees. See: PANTHERTree.


Field Summary
 int fileCount
           
 
Constructor Summary
PANTHERForest(File pantherDir)
          Create an instance for the given privitve array of files.
 
Method Summary
 Set<PANTHERTree> getAssociatedTrees(String identifier)
          Return the number of unique bioentity identifiers found in the set.
 int getNumberOfFilesInSet()
          Return the number of files read into the set.
 int getNumberOfIdentifiersInSet()
          Return the number of unique identifiers found in the set.
 PANTHERTree getTreeByID(String tree_id)
          Return the tree for the tree unique identifier, If nothing was found, return null.
 Set<String> getTreeIDSet()
          Return the unique tree identifiers found in the forest.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

fileCount

public int fileCount
Constructor Detail

PANTHERForest

public PANTHERForest(File pantherDir)
              throws IOException
Create an instance for the given privitve array of files.

Parameters:
pantherDir -
Throws:
IOException
Method Detail

getNumberOfFilesInSet

public int getNumberOfFilesInSet()
Return the number of files read into the set.

Returns:
count

getNumberOfIdentifiersInSet

public int getNumberOfIdentifiersInSet()
Return the number of unique identifiers found in the set.

Returns:
count

getAssociatedTrees

public Set<PANTHERTree> getAssociatedTrees(String identifier)
Return the number of unique bioentity identifiers found in the set. If nothing was found, return null.

Parameters:
identifier -
Returns:
set of trees

getTreeIDSet

public Set<String> getTreeIDSet()
Return the unique tree identifiers found in the forest. If nothing was found, return null.

Returns:
set

getTreeByID

public PANTHERTree getTreeByID(String tree_id)
Return the tree for the tree unique identifier, If nothing was found, return null.

Parameters:
tree_id - the id of the tree we want
Returns:
tree


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