Serialized Form

Class softparsmap.ChildSet extends java.util.Vector implements Serializable


Class softparsmap.DataSourceIndexXmlNcbiTaxonomy extends java.lang.Object implements Serializable

Serialized Fields

childToParent

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

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

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


databaseIdToFilePointerPart

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


Class ooc.DependenciesMapped extends java.util.Hashtable implements Serializable


Class softparsmap.FatalException extends java.lang.RuntimeException implements Serializable


Class softparsmap.FilePointerPart extends java.lang.Object implements Serializable

Serialized Fields

_pointer

long _pointer

_length

int _length


Class ooc.NotValidException extends java.lang.RuntimeException implements Serializable

Serialized Fields

_tag

Tag _tag

_attribute

TagAttribute _attribute

_msg

java.lang.String _msg


Class ooc.OocException extends java.lang.RuntimeException implements Serializable

Serialized Fields

_tag

Tag _tag

_attribute

TagAttribute _attribute

_msg

java.lang.String _msg


Class ooc.SourceParseException extends java.lang.RuntimeException implements Serializable


Class ooc.TagErrorHandlerException extends java.lang.RuntimeException implements Serializable

Serialized Fields

_errorHandler

TagErrorHandler _errorHandler


Class ooc.TagIdException extends java.lang.RuntimeException implements Serializable