softparsmap
Class DataSourceIndexXmlNcbiTaxonomy

java.lang.Object
  extended bysoftparsmap.DataSourceIndexXmlNcbiTaxonomy
All Implemented Interfaces:
java.io.Serializable

public class DataSourceIndexXmlNcbiTaxonomy
extends java.lang.Object
implements java.io.Serializable

Index for data source DataSourceXmlNcbiTaxonomy.

See Also:
Serialized Form

Field Summary
 java.util.Map childToParent
          This map contain the tree and is created from the file nodes.dmp.
 java.util.Map databaseIdToFilePointerPart
          A map from the database id numbers (Integer) to a position (FilePointerPart) in the database that holds the sequence part.
 java.util.Map databaseIdToNodesId
          A map from the database id number (Integer) to the tax id number in NCBI (Integer).
 java.util.Map nodesIdToNamesFilePointer
          A map from NCBI's tax id's (Integer) to file pointer into the file names.dmp such that when reading one line from that position will get the name row for that species.
 
Constructor Summary
DataSourceIndexXmlNcbiTaxonomy()
          Constructor creates empty maps.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

childToParent

public java.util.Map childToParent
This map contain the tree and is created from the file nodes.dmp. The key and value is tax id's in Integer class. The key is the tax id of the child and the value is the tax value of the parent.


nodesIdToNamesFilePointer

public java.util.Map nodesIdToNamesFilePointer
A map from NCBI's tax id's (Integer) to file pointer into the file names.dmp such that when reading one line from that position will get the name row for that species.


databaseIdToNodesId

public java.util.Map databaseIdToNodesId
A map from the database id number (Integer) to the tax id number in NCBI (Integer).


databaseIdToFilePointerPart

public java.util.Map databaseIdToFilePointerPart
A map from the database id numbers (Integer) to a position (FilePointerPart) in the database that holds the sequence part.

Constructor Detail

DataSourceIndexXmlNcbiTaxonomy

public DataSourceIndexXmlNcbiTaxonomy()
Constructor creates empty maps.