Package org.forester.application

Class surfacing

java.lang.Object
org.forester.application.surfacing
public class surfacing extends Object

  • Field Details

    • DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS

      public static final String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
      See Also:

    • DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION

      public static final String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION
      See Also:

    • DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

      public static final String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
      See Also:

    • PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

      public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
      See Also:

    • DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX

      public static final String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
      See Also:

    • PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS

      public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
      See Also:

    • PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS

      public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
      See Also:

    • PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS

      public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
      See Also:

    • PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS

      public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
      See Also:

    • PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS

      public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
      See Also:

    • PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS

      public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
      See Also:

    • PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS

      public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
      See Also:

    • PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS

      public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
      See Also:

    • PARSIMONY_OUTPUT_FITCH_GAINS_BC

      public static final String PARSIMONY_OUTPUT_FITCH_GAINS_BC
      See Also:

    • PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC

      public static final String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
      See Also:

    • PARSIMONY_OUTPUT_FITCH_LOSSES_BC

      public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_BC
      See Also:

    • PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC

      public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
      See Also:

    • PARSIMONY_OUTPUT_FITCH_PRESENT_BC

      public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC
      See Also:

    • PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC

      public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_GAINS_D

      public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_D
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D

      public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_LOSSES_D

      public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_D
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D

      public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_PRESENT_D

      public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_D
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D

      public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
      See Also:

    • DOMAINS_PRESENT_NEXUS

      public static final String DOMAINS_PRESENT_NEXUS
      See Also:

    • BDC_PRESENT_NEXUS

      public static final String BDC_PRESENT_NEXUS
      See Also:

    • PRG_NAME

      public static final String PRG_NAME
      See Also:

    • DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

      public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
      See Also:

    • DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

      public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
      See Also:

    • BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

      public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
      See Also:

    • BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

      public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
      See Also:

    • NEXUS_EXTERNAL_DOMAINS

      public static final String NEXUS_EXTERNAL_DOMAINS
      See Also:

    • NEXUS_EXTERNAL_DOMAIN_COMBINATIONS

      public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
      See Also:

    • NEXUS_SECONDARY_FEATURES

      public static final String NEXUS_SECONDARY_FEATURES
      See Also:

    • PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES

      public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
      See Also:

    • PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES

      public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES

      public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES

      public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES

      public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
      See Also:

    • SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

      public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
      See Also:

    • PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES

      public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
      See Also:

    • PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES

      public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
      See Also:

    • PAIRWISE_DOMAIN_COMPARISONS_PREFIX

      public static final String PAIRWISE_DOMAIN_COMPARISONS_PREFIX
      See Also:

    • MAX_ALLOWED_OVERLAP_DEFAULT

      public static final int MAX_ALLOWED_OVERLAP_DEFAULT
      See Also:

    • SEQ_EXTRACT_SUFFIX

      public static final String SEQ_EXTRACT_SUFFIX
      See Also:

    • PLUS_MINUS_ANALYSIS_OPTION

      public static final String PLUS_MINUS_ANALYSIS_OPTION
      See Also:

    • PLUS_MINUS_DOM_SUFFIX

      public static final String PLUS_MINUS_DOM_SUFFIX
      See Also:

    • PLUS_MINUS_DOM_SUFFIX_HTML

      public static final String PLUS_MINUS_DOM_SUFFIX_HTML
      See Also:

    • PLUS_MINUS_DC_SUFFIX_HTML

      public static final String PLUS_MINUS_DC_SUFFIX_HTML
      See Also:

    • PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT

      public static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT
      See Also:

    • PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT

      public static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT
      See Also:

    • PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX

      public static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX
      See Also:

    • PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX

      public static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX
      See Also:

    • VERBOSE

      public static final boolean VERBOSE
      See Also:

    • ALL_PFAMS_ENCOUNTERED_SUFFIX

      public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX
      See Also:

    • ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX

      public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
      See Also:

    • ENCOUNTERED_PFAMS_SUMMARY_SUFFIX

      public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
      See Also:

    • ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX

      public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
      See Also:

    • ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX

      public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
      See Also:

    • ALL_PFAMS_GAINED_AS_DC_SUFFIX

      public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX
      See Also:

    • ALL_PFAMS_LOST_AS_DC_SUFFIX

      public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX
      See Also:

    • BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES

      public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
      See Also:

    • BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES

      public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
      See Also:

    • D_PROMISCUITY_FILE_SUFFIX

      public static final String D_PROMISCUITY_FILE_SUFFIX
      See Also:

    • INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX

      public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX
      See Also:

    • INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX

      public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX
      See Also:

    • 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
      See Also:

    • 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
      See Also:

    • 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
      See Also:

    • INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX

      public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX
      See Also:

    • INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX

      public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX
      See Also:

    • 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
      See Also:

    • 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
      See Also:

  • Constructor Details

    • surfacing

      public surfacing()

  • Method Details

    • main

      public static void main(String[] args)