Package org.forester.application
Class surfacing
- java.lang.Object
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- org.forester.application.surfacing
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public class surfacing extends java.lang.Object
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Field Summary
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Constructor Summary
Constructors Constructor Description surfacing()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
main(java.lang.String[] args)
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Field Detail
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DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
public static final java.lang.String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
- See Also:
- Constant Field Values
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DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION
public static final java.lang.String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION
- See Also:
- Constant Field Values
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DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
public static final java.lang.String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
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- Constant Field Values
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DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
public static final java.lang.String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
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- Constant Field Values
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PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
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- Constant Field Values
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PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
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- Constant Field Values
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PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
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- Constant Field Values
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PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
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- Constant Field Values
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
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- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_GAINS_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_GAINS_BC
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_LOSSES_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_LOSSES_BC
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_PRESENT_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_BC
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_GAINS_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_D
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
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- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_LOSSES_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_D
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_PRESENT_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_D
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
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- Constant Field Values
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DOMAINS_PRESENT_NEXUS
public static final java.lang.String DOMAINS_PRESENT_NEXUS
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- Constant Field Values
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BDC_PRESENT_NEXUS
public static final java.lang.String BDC_PRESENT_NEXUS
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- Constant Field Values
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PRG_NAME
public static final java.lang.String PRG_NAME
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- Constant Field Values
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DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final java.lang.String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
- See Also:
- Constant Field Values
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DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
public static final java.lang.String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
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- Constant Field Values
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BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
- See Also:
- Constant Field Values
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BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
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- Constant Field Values
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NEXUS_EXTERNAL_DOMAINS
public static final java.lang.String NEXUS_EXTERNAL_DOMAINS
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- Constant Field Values
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NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
public static final java.lang.String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
- See Also:
- Constant Field Values
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NEXUS_SECONDARY_FEATURES
public static final java.lang.String NEXUS_SECONDARY_FEATURES
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
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- Constant Field Values
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SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final java.lang.String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
- See Also:
- Constant Field Values
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PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
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- Constant Field Values
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PAIRWISE_DOMAIN_COMPARISONS_PREFIX
public static final java.lang.String PAIRWISE_DOMAIN_COMPARISONS_PREFIX
- See Also:
- Constant Field Values
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MAX_ALLOWED_OVERLAP_DEFAULT
public static final int MAX_ALLOWED_OVERLAP_DEFAULT
- See Also:
- Constant Field Values
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SEQ_EXTRACT_SUFFIX
public static final java.lang.String SEQ_EXTRACT_SUFFIX
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- Constant Field Values
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PLUS_MINUS_ANALYSIS_OPTION
public static final java.lang.String PLUS_MINUS_ANALYSIS_OPTION
- See Also:
- Constant Field Values
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PLUS_MINUS_DOM_SUFFIX
public static final java.lang.String PLUS_MINUS_DOM_SUFFIX
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- Constant Field Values
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PLUS_MINUS_DOM_SUFFIX_HTML
public static final java.lang.String PLUS_MINUS_DOM_SUFFIX_HTML
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- Constant Field Values
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PLUS_MINUS_DC_SUFFIX_HTML
public static final java.lang.String PLUS_MINUS_DC_SUFFIX_HTML
- See Also:
- Constant Field Values
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PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT
public static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT
- See Also:
- Constant Field Values
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PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT
public static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT
- See Also:
- Constant Field Values
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PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX
public static final java.lang.String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX
- See Also:
- Constant Field Values
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PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX
public static final java.lang.String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX
- See Also:
- Constant Field Values
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VERBOSE
public static final boolean VERBOSE
- See Also:
- Constant Field Values
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ALL_PFAMS_ENCOUNTERED_SUFFIX
public static final java.lang.String ALL_PFAMS_ENCOUNTERED_SUFFIX
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- Constant Field Values
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ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
public static final java.lang.String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
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- Constant Field Values
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ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
public static final java.lang.String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
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- Constant Field Values
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ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
public static final java.lang.String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
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- Constant Field Values
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ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
public static final java.lang.String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
- See Also:
- Constant Field Values
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ALL_PFAMS_GAINED_AS_DC_SUFFIX
public static final java.lang.String ALL_PFAMS_GAINED_AS_DC_SUFFIX
- See Also:
- Constant Field Values
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ALL_PFAMS_LOST_AS_DC_SUFFIX
public static final java.lang.String ALL_PFAMS_LOST_AS_DC_SUFFIX
- See Also:
- Constant Field Values
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BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
public static final java.lang.String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
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- Constant Field Values
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BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
public static final java.lang.String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
- See Also:
- Constant Field Values
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D_PROMISCUITY_FILE_SUFFIX
public static final java.lang.String D_PROMISCUITY_FILE_SUFFIX
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- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX
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- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX
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- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX
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- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX
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- Constant Field Values
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LIMIT_SPEC_FOR_PROT_EX
public static final java.lang.String LIMIT_SPEC_FOR_PROT_EX
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BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED
public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED
- See Also:
- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX
- See Also:
- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX
- See Also:
- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX
- See Also:
- Constant Field Values
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INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX
- See Also:
- Constant Field Values
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