org.forester.application
Class surfacing_old
java.lang.Object
org.forester.application.surfacing_old
public class surfacing_old
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
public static final String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
- See Also:
- Constant Field Values
DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
public static final String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
- See Also:
- 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
- See Also:
- Constant Field Values
DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
public static final String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_GAINS_BC
public static final String PARSIMONY_OUTPUT_FITCH_GAINS_BC
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
public static final String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_LOSSES_BC
public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_BC
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_PRESENT_BC
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_GAINS_D
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_LOSSES_D
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_PRESENT_D
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
- See Also:
- Constant Field Values
DOMAINS_PRESENT_NEXUS
public static final String DOMAINS_PRESENT_NEXUS
- See Also:
- Constant Field Values
BDC_PRESENT_NEXUS
public static final String BDC_PRESENT_NEXUS
- See Also:
- Constant Field Values
PRG_NAME
public static final String PRG_NAME
- See Also:
- Constant Field Values
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
- See Also:
- Constant Field Values
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
- See Also:
- Constant Field Values
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
- See Also:
- Constant Field Values
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
- See Also:
- Constant Field Values
NEXUS_EXTERNAL_DOMAINS
public static final String NEXUS_EXTERNAL_DOMAINS
- See Also:
- Constant Field Values
NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
- See Also:
- Constant Field Values
NEXUS_SECONDARY_FEATURES
public static final String NEXUS_SECONDARY_FEATURES
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
- See Also:
- Constant Field Values
SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION
- See Also:
- Constant Field Values
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
- See Also:
- Constant Field Values
ALL_PFAMS_ENCOUNTERED_SUFFIX
public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX
- See Also:
- Constant Field Values
ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
- See Also:
- Constant Field Values
ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
- See Also:
- Constant Field Values
ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
- See Also:
- Constant Field Values
ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
- See Also:
- Constant Field Values
ALL_PFAMS_GAINED_AS_DC_SUFFIX
public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX
- See Also:
- Constant Field Values
ALL_PFAMS_LOST_AS_DC_SUFFIX
public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX
- See Also:
- Constant Field Values
BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
- See Also:
- Constant Field Values
BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
- See Also:
- Constant Field Values
D_PROMISCUITY_FILE_SUFFIX
public static final String D_PROMISCUITY_FILE_SUFFIX
- See Also:
- Constant Field Values
surfacing_old
public surfacing_old()
main
public static void main(String[] args)