org.forester.application

Class surfacing

java.lang.Object

org.forester.application.surfacing

public class surfacing
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALL_PFAMS_ENCOUNTERED_SUFFIX
static String	ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
static String	ALL_PFAMS_GAINED_AS_DC_SUFFIX
static String	ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
static String	ALL_PFAMS_LOST_AS_DC_SUFFIX
static String	ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
static String	BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
static String	BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
static String	BDC_PRESENT_NEXUS
static String	BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
static String	BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
static String	BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED
static String	D_PROMISCUITY_FILE_SUFFIX
static String	DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
static String	DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION
static String	DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
static String	DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
static String	DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
static String	DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
static String	DOMAINS_PRESENT_NEXUS
static String	ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX
static String	INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX
static String	LIMIT_SPEC_FOR_PROT_EX
static int	MAX_ALLOWED_OVERLAP_DEFAULT
static String	NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
static String	NEXUS_EXTERNAL_DOMAINS
static String	NEXUS_SECONDARY_FEATURES
static String	PAIRWISE_DOMAIN_COMPARISONS_PREFIX
static String	PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
static String	PARSIMONY_OUTPUT_DOLLO_GAINS_D
static String	PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
static String	PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
static String	PARSIMONY_OUTPUT_DOLLO_LOSSES_D
static String	PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
static String	PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
static String	PARSIMONY_OUTPUT_DOLLO_PRESENT_D
static String	PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
static String	PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
static String	PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
static String	PARSIMONY_OUTPUT_FITCH_GAINS_BC
static String	PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
static String	PARSIMONY_OUTPUT_FITCH_LOSSES_BC
static String	PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
static String	PARSIMONY_OUTPUT_FITCH_PRESENT_BC
static String	PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
static String	PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
static String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
static String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
static String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
static String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
static String	PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
static String	PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
static String	PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
static String	PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
static String	PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
static String	PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
static String	PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX
static double	PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT
static int	PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT
static String	PLUS_MINUS_ANALYSIS_OPTION
static String	PLUS_MINUS_DC_SUFFIX_HTML
static String	PLUS_MINUS_DOM_SUFFIX
static String	PLUS_MINUS_DOM_SUFFIX_HTML
static String	PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX
static String	PRG_NAME
static String	SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
static String	SEQ_EXTRACT_SUFFIX
static boolean	VERBOSE

Constructor Summary

Constructors

Constructor and Description
surfacing()

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS

public static final String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS

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Constant Field Values

DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION

public static final String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION

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Constant Field Values

DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

public static final String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

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Constant Field Values

DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX

public static final String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX

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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS

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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS

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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS

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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS

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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS

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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS

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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS

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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_GAINS_BC

public static final String PARSIMONY_OUTPUT_FITCH_GAINS_BC

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC

public static final String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_LOSSES_BC

public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_BC

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC

public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_PRESENT_BC

public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC

public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_GAINS_D

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_D

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_LOSSES_D

public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_D

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D

public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_PRESENT_D

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_D

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D

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Constant Field Values

DOMAINS_PRESENT_NEXUS

public static final String DOMAINS_PRESENT_NEXUS

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Constant Field Values

BDC_PRESENT_NEXUS

public static final String BDC_PRESENT_NEXUS

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Constant Field Values

PRG_NAME

public static final String PRG_NAME

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Constant Field Values

DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

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Constant Field Values

DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

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Constant Field Values

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

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Constant Field Values

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

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Constant Field Values

NEXUS_EXTERNAL_DOMAINS

public static final String NEXUS_EXTERNAL_DOMAINS

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Constant Field Values

NEXUS_EXTERNAL_DOMAIN_COMBINATIONS

public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS

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Constant Field Values

NEXUS_SECONDARY_FEATURES

public static final String NEXUS_SECONDARY_FEATURES

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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES

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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES

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Constant Field Values

SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES

public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES

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Constant Field Values

PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES

public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES

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Constant Field Values

PAIRWISE_DOMAIN_COMPARISONS_PREFIX

public static final String PAIRWISE_DOMAIN_COMPARISONS_PREFIX

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Constant Field Values

MAX_ALLOWED_OVERLAP_DEFAULT

public static final int MAX_ALLOWED_OVERLAP_DEFAULT

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Constant Field Values

SEQ_EXTRACT_SUFFIX

public static final String SEQ_EXTRACT_SUFFIX

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Constant Field Values

PLUS_MINUS_ANALYSIS_OPTION

public static final String PLUS_MINUS_ANALYSIS_OPTION

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Constant Field Values

PLUS_MINUS_DOM_SUFFIX

public static final String PLUS_MINUS_DOM_SUFFIX

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Constant Field Values

PLUS_MINUS_DOM_SUFFIX_HTML

public static final String PLUS_MINUS_DOM_SUFFIX_HTML

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Constant Field Values

PLUS_MINUS_DC_SUFFIX_HTML

public static final String PLUS_MINUS_DC_SUFFIX_HTML

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Constant Field Values

PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT

public static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT

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Constant Field Values

PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT

public static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT

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Constant Field Values

PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX

public static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX

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Constant Field Values

PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX

public static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX

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Constant Field Values

VERBOSE

public static final boolean VERBOSE

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Constant Field Values

ALL_PFAMS_ENCOUNTERED_SUFFIX

public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX

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Constant Field Values

ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX

public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX

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Constant Field Values

ENCOUNTERED_PFAMS_SUMMARY_SUFFIX

public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX

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Constant Field Values

ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX

public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX

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Constant Field Values

ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX

public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX

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Constant Field Values

ALL_PFAMS_GAINED_AS_DC_SUFFIX

public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX

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Constant Field Values

ALL_PFAMS_LOST_AS_DC_SUFFIX

public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX

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Constant Field Values

BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES

public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES

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Constant Field Values

BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES

public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES

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Constant Field Values

D_PROMISCUITY_FILE_SUFFIX

public static final String D_PROMISCUITY_FILE_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX

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Constant Field Values

LIMIT_SPEC_FOR_PROT_EX

public static final String LIMIT_SPEC_FOR_PROT_EX

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED

public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX

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Constant Field Values

INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX

public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX

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Constant Field Values

Constructor Detail

surfacing

public surfacing()

Method Detail

main

public static void main(String[] args)