softparsmap
Class FamilyGroupTreesInFiles

java.lang.Object
  ooc.LinkedTagInstance
      softparsmap.AbstractFamilyGroup
          softparsmap.FamilyGroupTreesInFiles

All Implemented Interfaces:

Dependencies, FamilyGroup

Direct Known Subclasses:

FamilyGroupTreesInFilesInfoPerRow

public class FamilyGroupTreesInFiles

extends AbstractFamilyGroup

This family group assume that there is one file per family and that the family number can be found in the file name. Further the parser is used to parse in the gene tree found in the file. See the def.xml file for more information.

Constructor Summary

FamilyGroupTreesInFiles()

Method Summary

java.util.Set	getFamilies() Returns the set of Family instances that this this family group is responsible for.
GeneNode	getGeneTree(java.lang.Integer familyNumber) Returns the gene tree given a family number.
TreeParser	getTreeParserIn()

Methods inherited from class softparsmap.AbstractFamilyGroup

getDataSource, getGroupName, getPropertyFile

Methods inherited from class ooc.LinkedTagInstance

containsKey, get, getAttribute, getAttributeBoolean, getAttributeDouble, getAttributeFloat, getAttributeInteger, getAttributeList, getAttributeRef, getAttributeShort, getAttributeString, getAttributeTag, getChildIterator, getChildIteratorByName, getContainer, getContainerTag, getFirstChildTagByName, getTag, getTagId, getTagInstance, getTagInstance, getTagRef, hasAttributeValue, hasChildTagByName, hasChildTags, hasTag, isMutable, keySet, put, remove, setTag, setupInstance

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FamilyGroupTreesInFiles

public FamilyGroupTreesInFiles()

Method Detail

getTreeParserIn

public TreeParser getTreeParserIn()

getGeneTree

public GeneNode getGeneTree(java.lang.Integer familyNumber)

Description copied from interface: FamilyGroup

Returns the gene tree given a family number.

Returns:

the gene node which is the root of the gene tree

See Also:

GeneNode

getFamilies

public java.util.Set getFamilies()

Description copied from interface: FamilyGroup

Returns the set of Family instances that this this family group is responsible for.

Returns:

a set of Family instances

See Also:

Family