Class surfacing


  • public class surfacing
    extends java.lang.Object
    • Field Detail

      • DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS

        public static final java.lang.String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
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      • DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION

        public static final java.lang.String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION
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      • DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

        public static final java.lang.String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
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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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      • DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX

        public static final java.lang.String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
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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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      • PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS

        public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
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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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      • PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS

        public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
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      • PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS

        public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
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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
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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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      • 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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      • PARSIMONY_OUTPUT_FITCH_GAINS_BC

        public static final java.lang.String PARSIMONY_OUTPUT_FITCH_GAINS_BC
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      • PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC

        public static final java.lang.String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
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      • PARSIMONY_OUTPUT_FITCH_LOSSES_BC

        public static final java.lang.String PARSIMONY_OUTPUT_FITCH_LOSSES_BC
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      • PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC

        public static final java.lang.String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
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      • PARSIMONY_OUTPUT_FITCH_PRESENT_BC

        public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_BC
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      • PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC

        public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
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      • PARSIMONY_OUTPUT_DOLLO_GAINS_D

        public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_D
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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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      • PARSIMONY_OUTPUT_DOLLO_LOSSES_D

        public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_D
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      • PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D

        public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
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      • PARSIMONY_OUTPUT_DOLLO_PRESENT_D

        public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_D
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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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      • DOMAINS_PRESENT_NEXUS

        public static final java.lang.String DOMAINS_PRESENT_NEXUS
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      • BDC_PRESENT_NEXUS

        public static final java.lang.String BDC_PRESENT_NEXUS
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      • DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

        public static final java.lang.String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
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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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      • BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

        public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
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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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      • NEXUS_EXTERNAL_DOMAINS

        public static final java.lang.String NEXUS_EXTERNAL_DOMAINS
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      • NEXUS_EXTERNAL_DOMAIN_COMBINATIONS

        public static final java.lang.String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
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      • NEXUS_SECONDARY_FEATURES

        public static final java.lang.String NEXUS_SECONDARY_FEATURES
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      • PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES

        public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
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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
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      • PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES

        public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
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      • PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES

        public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
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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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      • SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

        public static final java.lang.String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
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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
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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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      • PAIRWISE_DOMAIN_COMPARISONS_PREFIX

        public static final java.lang.String PAIRWISE_DOMAIN_COMPARISONS_PREFIX
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      • MAX_ALLOWED_OVERLAP_DEFAULT

        public static final int MAX_ALLOWED_OVERLAP_DEFAULT
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      • SEQ_EXTRACT_SUFFIX

        public static final java.lang.String SEQ_EXTRACT_SUFFIX
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      • PLUS_MINUS_ANALYSIS_OPTION

        public static final java.lang.String PLUS_MINUS_ANALYSIS_OPTION
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      • PLUS_MINUS_DOM_SUFFIX

        public static final java.lang.String PLUS_MINUS_DOM_SUFFIX
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      • PLUS_MINUS_DOM_SUFFIX_HTML

        public static final java.lang.String PLUS_MINUS_DOM_SUFFIX_HTML
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      • PLUS_MINUS_DC_SUFFIX_HTML

        public static final java.lang.String PLUS_MINUS_DC_SUFFIX_HTML
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      • PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT

        public static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT
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      • PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT

        public static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT
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      • PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX

        public static final java.lang.String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX
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      • PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX

        public static final java.lang.String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX
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      • ALL_PFAMS_ENCOUNTERED_SUFFIX

        public static final java.lang.String ALL_PFAMS_ENCOUNTERED_SUFFIX
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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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      • ENCOUNTERED_PFAMS_SUMMARY_SUFFIX

        public static final java.lang.String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
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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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      • ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX

        public static final java.lang.String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
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      • ALL_PFAMS_GAINED_AS_DC_SUFFIX

        public static final java.lang.String ALL_PFAMS_GAINED_AS_DC_SUFFIX
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      • ALL_PFAMS_LOST_AS_DC_SUFFIX

        public static final java.lang.String ALL_PFAMS_LOST_AS_DC_SUFFIX
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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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      • BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES

        public static final java.lang.String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
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      • D_PROMISCUITY_FILE_SUFFIX

        public static final java.lang.String D_PROMISCUITY_FILE_SUFFIX
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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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      • 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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      • 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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      • 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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      • LIMIT_SPEC_FOR_PROT_EX

        public static final java.lang.String LIMIT_SPEC_FOR_PROT_EX
      • BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED

        public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED
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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
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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
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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
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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
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    • Constructor Detail

      • surfacing

        public surfacing()
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)