org.forester.application
Class surfacing

java.lang.Object
  extended by org.forester.application.surfacing

public class surfacing
extends Object


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

Field Detail

DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS

public static final String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
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Constant Field Values

DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS

public static final String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS
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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
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Constant Field Values

DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX

public static final String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS
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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS
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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS
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PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS
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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS
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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS
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PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS
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Constant Field Values

PARSIMONY_OUTPUT_FITCH_GAINS_BC

public static final String PARSIMONY_OUTPUT_FITCH_GAINS_BC
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Constant Field Values

PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC

public static final String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC
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PARSIMONY_OUTPUT_FITCH_LOSSES_BC

public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_BC
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PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC

public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC
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PARSIMONY_OUTPUT_FITCH_PRESENT_BC

public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC
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PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC

public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC
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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_GAINS_D

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_D
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PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D
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PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D
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PARSIMONY_OUTPUT_DOLLO_LOSSES_D

public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_D
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PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D

public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D
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PARSIMONY_OUTPUT_DOLLO_PRESENT_D

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_D
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PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D
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PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D
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DOMAINS_PRESENT_NEXUS

public static final String DOMAINS_PRESENT_NEXUS
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Constant Field Values

BDC_PRESENT_NEXUS

public static final String BDC_PRESENT_NEXUS
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Constant Field Values

PRG_NAME

public static final String PRG_NAME
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Constant Field Values

DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
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Constant Field Values

DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
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BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
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Constant Field Values

BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH

public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH
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Constant Field Values

NEXUS_EXTERNAL_DOMAINS

public static final String NEXUS_EXTERNAL_DOMAINS
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Constant Field Values

NEXUS_EXTERNAL_DOMAIN_COMBINATIONS

public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
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Constant Field Values

NEXUS_SECONDARY_FEATURES

public static final String NEXUS_SECONDARY_FEATURES
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Constant Field Values

PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES
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Constant Field Values

PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES
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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES
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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES
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PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES

public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES
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Constant Field Values

SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO

public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO
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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS

public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS
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PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT

public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT
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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION

public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION
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Constant Field Values

PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES

public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES
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Constant Field Values

PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS

public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS
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Constant Field Values

PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT

public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT
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PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION

public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION
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Constant Field Values

PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES

public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES
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Constant Field Values

ALL_PFAMS_ENCOUNTERED_SUFFIX

public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX
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Constant Field Values

ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX

public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX
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Constant Field Values

ENCOUNTERED_PFAMS_SUMMARY_SUFFIX

public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX
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ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX

public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX
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ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX

public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX
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ALL_PFAMS_GAINED_AS_DC_SUFFIX

public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX
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ALL_PFAMS_LOST_AS_DC_SUFFIX

public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX
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Constant Field Values

BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES

public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES
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BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES

public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES
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Constant Field Values

D_PROMISCUITY_FILE_SUFFIX

public static final String D_PROMISCUITY_FILE_SUFFIX
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Constant Field Values
Constructor Detail

surfacing

public surfacing()
Method Detail

main

public static void main(String[] args)