public class surfacing
extends java.lang.Object
Constructor and Description |
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surfacing() |
Modifier and Type | Method and Description |
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static void |
main(java.lang.String[] args) |
public static final java.lang.String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
public static final java.lang.String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
public static final java.lang.String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_GAINS_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_LOSSES_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_BC
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_D
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
public static final java.lang.String DOMAINS_PRESENT_NEXUS
public static final java.lang.String BDC_PRESENT_NEXUS
public static final java.lang.String PRG_NAME
public static final java.lang.String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final java.lang.String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
public static final java.lang.String NEXUS_EXTERNAL_DOMAINS
public static final java.lang.String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
public static final java.lang.String NEXUS_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
public static final java.lang.String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final java.lang.String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
public static final java.lang.String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
public static final java.lang.String ALL_PFAMS_ENCOUNTERED_SUFFIX
public static final java.lang.String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
public static final java.lang.String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
public static final java.lang.String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
public static final java.lang.String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
public static final java.lang.String ALL_PFAMS_GAINED_AS_DC_SUFFIX
public static final java.lang.String ALL_PFAMS_LOST_AS_DC_SUFFIX
public static final java.lang.String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
public static final java.lang.String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
public static final java.lang.String D_PROMISCUITY_FILE_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX
public static final java.lang.String 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_UNIQUE_SUFFIX
public static final java.lang.String LIMIT_SPEC_FOR_PROT_EX
public static final java.lang.String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX
public static final java.lang.String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX
public static final java.lang.String 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_UNIQUE_SUFFIX