Package GNormPluslib

Class GNormPlus

java.lang.Object

GNormPluslib.GNormPlus

public class GNormPlus
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static HashMap<String,String>	Abb2Longformtok_hash
static HashMap<String,String>	ent_hash
static HashMap<String,String>	Filtering_WithLongForm_hash
static HashMap<String,String>	GeneIDs_hash
static HashMap<String,String>	GeneScoring_hash
static HashMap<String,Double>	GeneScoringDF_hash
static HashMap<String,String>	GeneWithoutSPPrefix_hash
static HashMap<String,String>	GenusID_hash
static HashMap<String,String>	HomologeneID_hash
static boolean	initialized
static HashMap<String,String>	Normalization2Protein_hash
static HashMap<String,String>	PrefixID_hash
static PrefixTree	PT_Cell
static PrefixTree	PT_CTDGene
static PrefixTree	PT_FamilyName
static PrefixTree	PT_Gene
static PrefixTree	PT_GeneChromosome
static PrefixTree	PT_Species
static HashMap<String,String>	setup_hash
static String	SetupFile
static HashMap<String,String>	SimConceptMention2Type_hash
static HashMap<String,String>	SP_Virus2Human_hash
static HashMap<String,String>	StrainID_ancestor2tax_hash
static HashMap<String,String>	StrainID_taxid2names_hash
static HashMap<String,String>	suffixprefix_orig2modified
static HashMap<String,String>	SuffixTranslationMap_hash
static HashMap<String,String>	SuffixTranslationMap2_hash
static HashMap<String,Double>	TaxFreq_hash
static ArrayList<String>	taxid4gene

Constructor Summary

Constructors

Constructor	Description
GNormPlus()

Method Summary

Modifier and Type	Method	Description
static void	loadConfiguration(InputStream setupFileStream, String FocusSpecies)
static String	loadResources(String FocusSpecies, double startTime)
static void	main(String[] args)
static void	processFile(String inputFilePath, String InputFile, String outputFilePath, double startTime, String TrainTest)

Methods inherited from class java.lang.Object

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

Field Detail

initialized

public static boolean initialized

PT_Species

public static PrefixTree PT_Species

PT_Cell

public static PrefixTree PT_Cell

PT_CTDGene

public static PrefixTree PT_CTDGene

PT_Gene

public static PrefixTree PT_Gene

PT_GeneChromosome

public static PrefixTree PT_GeneChromosome

PT_FamilyName

public static PrefixTree PT_FamilyName

ent_hash

public static HashMap<String,String> ent_hash

GenusID_hash

public static HashMap<String,String> GenusID_hash

PrefixID_hash

public static HashMap<String,String> PrefixID_hash

TaxFreq_hash

public static HashMap<String,Double> TaxFreq_hash

GeneScoring_hash

public static HashMap<String,String> GeneScoring_hash

GeneScoringDF_hash

public static HashMap<String,Double> GeneScoringDF_hash

GeneIDs_hash

public static HashMap<String,String> GeneIDs_hash

Normalization2Protein_hash

public static HashMap<String,String> Normalization2Protein_hash

HomologeneID_hash

public static HashMap<String,String> HomologeneID_hash

SuffixTranslationMap_hash

public static HashMap<String,String> SuffixTranslationMap_hash

SuffixTranslationMap2_hash

public static HashMap<String,String> SuffixTranslationMap2_hash

SimConceptMention2Type_hash

public static HashMap<String,String> SimConceptMention2Type_hash

Filtering_WithLongForm_hash

public static HashMap<String,String> Filtering_WithLongForm_hash

SP_Virus2Human_hash

public static HashMap<String,String> SP_Virus2Human_hash

GeneWithoutSPPrefix_hash

public static HashMap<String,String> GeneWithoutSPPrefix_hash

taxid4gene

public static ArrayList<String> taxid4gene

setup_hash

public static HashMap<String,String> setup_hash

suffixprefix_orig2modified

public static HashMap<String,String> suffixprefix_orig2modified

Abb2Longformtok_hash

public static HashMap<String,String> Abb2Longformtok_hash

StrainID_ancestor2tax_hash

public static HashMap<String,String> StrainID_ancestor2tax_hash

StrainID_taxid2names_hash

public static HashMap<String,String> StrainID_taxid2names_hash

SetupFile

public static String SetupFile

Constructor Detail

GNormPlus

public GNormPlus()

Method Detail

main

public static void main(String[] args)
                 throws IOException,
                        InterruptedException,
                        XMLStreamException,
                        SQLException

Throws:

IOException

InterruptedException

XMLStreamException

SQLException

processFile

public static void processFile(String inputFilePath,
                               String InputFile,
                               String outputFilePath,
                               double startTime,
                               String TrainTest)
                        throws IOException,
                               XMLStreamException

Throws:

IOException

XMLStreamException

loadResources

public static String loadResources(String FocusSpecies,
                                   double startTime)
                            throws IOException

Throws:

IOException

loadConfiguration

public static void loadConfiguration(InputStream setupFileStream,
                                     String FocusSpecies)
                              throws IOException

Throws:

IOException