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classes.org.forester.application.surfacing.class Maven / Gradle / Ivy

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InnerClasses
,MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING

I

ConstantValue?
3DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
Ljava/lang/String;
7DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS\
FPARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS]
*DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX
(PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS^
4PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS_
(PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS`
4PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONSa
/PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINSb
;PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONSc
/PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINSd
;PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONSe
PARSIMONY_OUTPUT_FITCH_GAINS_BCf
$PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BCg
 PARSIMONY_OUTPUT_FITCH_LOSSES_BCh
%PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BCi
!PARSIMONY_OUTPUT_FITCH_PRESENT_BCj
&PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BCk
PARSIMONY_OUTPUT_DOLLO_GAINS_Dl
#PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_Dm
PARSIMONY_OUTPUT_DOLLO_LOSSES_Dn
$PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_Do
 PARSIMONY_OUTPUT_DOLLO_PRESENT_Dp
%PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_Dq
DOMAINS_PRESENT_NEXUS
BDC_PRESENT_NEXUS
PRG_NAME
*DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLOr
*DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCHs
=BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLOt
=BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCHu
NEXUS_EXTERNAL_DOMAINS
"NEXUS_EXTERNAL_DOMAIN_COMBINATIONS
NEXUS_SECONDARY_FEATURESv
3PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURESw
:PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURESx
/PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURESy
0PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURESz
1PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES{
5SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO|
0PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES}
1PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES~

HELP_OPTION_1

HELP_OPTION_2
OUTPUT_DIR_OPTION
SCORING_OPTION
SCORING_DEFAULT?
DomainSimilarityScoring
ALorg/forester/surfacing/DomainSimilarity$DomainSimilarityScoring;
SCORING_DOMAIN_COUNT_BASED
SCORING_PROTEIN_COUNT_BASED
SCORING_COMBINATION_BASED
DETAILEDNESS_OPTION
DETAILEDNESS_DEFAULT?
Detailedness
@Lorg/forester/surfacing/DomainSimilarityCalculator$Detailedness;
SPECIES_MATRIX_OPTION
DETAILEDNESS_BASIC
DETAILEDNESS_LIST_IDS
DETAILEDNESS_PUNCTILIOUS
DOMAIN_SIMILARITY_SORT_OPTION
DOMAIN_SORT_FILD_DEFAULT?
DomainSimilaritySortField
CLorg/forester/surfacing/DomainSimilarity$DomainSimilaritySortField;
DOMAIN_SIMILARITY_SORT_MIN
DOMAIN_SIMILARITY_SORT_MAX
DOMAIN_SIMILARITY_SORT_SD
DOMAIN_SIMILARITY_SORT_MEAN
DOMAIN_SIMILARITY_SORT_DIFF
"DOMAIN_SIMILARITY_SORT_COUNTS_DIFF
&DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF
$DOMAIN_SIMILARITY_SORT_SPECIES_COUNT
DOMAIN_SIMILARITY_SORT_ALPHA
4DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
DOMAIN_COUNT_SORT_OPTION
DOMAINS_SORT_ORDER_DEFAULT?
$GenomeWideCombinableDomainsSortOrder
YLorg/forester/surfacing/GenomeWideCombinableDomains$GenomeWideCombinableDomainsSortOrder;
DOMAIN_COUNT_SORT_ALPHA
"DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT
+DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT
$DOMAIN_COUNT_SORT_COMBINATIONS_COUNT
CUTOFF_SCORE_FILE_OPTION
NOT_IGNORE_DUFS_OPTION
MAX_E_VALUE_OPTION
MAX_ALLOWED_OVERLAP_OPTION
NO_ENGULFING_OVERLAP_OPTION
#IGNORE_COMBINATION_WITH_SAME_OPTION
"PAIRWISE_DOMAIN_COMPARISONS_PREFIX
"PAIRWISE_DOMAIN_COMPARISONS_OPTION
OUTPUT_FILE_OPTION
PFAM_TO_GO_FILE_USE_OPTION
GO_OBO_FILE_USE_OPTION
GO_NAMESPACE_LIMIT_OPTION
,GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION
,GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS
,GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT
%SECONDARY_FEATURES_PARSIMONY_MAP_FILE
3DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED
*DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML
,DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML
DOMAIN_SIMILARITY_PRINT_OPTION
&DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT?
PRINT_OPTION
?Lorg/forester/surfacing/PrintableDomainSimilarity$PRINT_OPTION;
9IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
IGNORE_VIRAL_IDS
:IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT

Z
-IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
5IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT
.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX
2MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX
;MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX
/NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX
3NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX
OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX
DOMAIN_LENGTHS_ANALYSIS_SUFFIX
PERFORM_DOMAIN_LENGTH_ANALYSIS
ALL_PFAMS_ENCOUNTERED_SUFFIX?
/ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX?
 ENCOUNTERED_PFAMS_SUMMARY_SUFFIX?
"ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX?
 ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX?
ALL_PFAMS_GAINED_AS_DC_SUFFIX?
ALL_PFAMS_LOST_AS_DC_SUFFIX?
.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES?
1BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES?
D_PROMISCUITY_FILE_SUFFIX
LOG_FILE_SUFFIX
DATA_FILE_SUFFIX
DATA_FILE_DESC
INDIVIDUAL_SCORE_CUTOFF_DEFAULT?
INDIVIDUAL_SCORE_CUTOFF
MLorg/forester/io/parsers/HmmscanPerDomainTableParser$INDIVIDUAL_SCORE_CUTOFF;
4INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX?
0INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX?
?INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX?
FINDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX?
LIMIT_SPEC_FOR_PROT_EX
DBINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED?
;INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX?
7INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX?
FINDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX?
MINDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX?
 PERFORM_DC_REGAIN_PROTEINS_STATS

()V
Code
LineNumberTable
'checkWriteabilityForPairwiseComparisons
v(Lorg/forester/surfacing/PrintableDomainSimilarity$PRINT_OPTION;[[Ljava/lang/String;Ljava/lang/String;Ljava/io/File;)V

StackMapTablew?
createParametersAsString?
DomainCombinationType
q(ZDIZLjava/io/File;Lorg/forester/protein/BinaryDomainCombination$DomainCombinationType;)Ljava/lang/StringBuilder;?
executeFitchGainsAnalysis
8(Ljava/io/File;Ljava/util/List;ILjava/util/SortedSet;Z)V?????Z!

Exceptions
	Signature
?(Ljava/io/File;Ljava/util/List;ILjava/util/SortedSet;Z)V
executePlusMinusAnalysis
?(Ljava/io/File;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/SortedMap;Ljava/util/Map;Ljava/util/Map;Ljava/util/List;)V?^Q

?(Ljava/io/File;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/SortedMap;>;Ljava/util/Map;>;Ljava/util/Map;Ljava/util/List;)V

getIntrees
I([Ljava/io/File;I[[Ljava/lang/String;)[Lorg/forester/phylogeny/Phylogeny;??Vc
inferSpeciesTrees
0(Ljava/io/File;Ljava/util/List;)Ljava/util/List;?y
?(Ljava/io/File;Ljava/util/List;)Ljava/util/List;
log
%(Ljava/lang/String;Ljava/io/Writer;)V
main
([Ljava/lang/String;)V??????.???????V??NR????????
createSplitWriters
2(Ljava/io/File;Ljava/lang/String;Ljava/util/Map;)V
Y(Ljava/io/File;Ljava/lang/String;Ljava/util/Map;)V
'printOutPercentageOfMultidomainProteins
((Ljava/util/SortedMap;Ljava/io/Writer;)V
P(Ljava/util/SortedMap;Ljava/io/Writer;)V
$preparePhylogenyForParsimonyAnalyses
9(Lorg/forester/phylogeny/Phylogeny;[[Ljava/lang/String;)V??
	printHelp

processFilter
&(Ljava/io/File;Ljava/util/SortedSet;)V
G(Ljava/io/File;Ljava/util/SortedSet;)V
processInputFileNames
)([Ljava/lang/String;)[[Ljava/lang/String;
processPlusMinusAnalysisOption
k(Lorg/forester/util/CommandLineArguments;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/List;)V
?(Lorg/forester/util/CommandLineArguments;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/List;)V
processPlusMinusFile
Q(Ljava/io/File;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/List;)VE
?(Ljava/io/File;Ljava/util/List;Ljava/util/List;Ljava/util/List;Ljava/util/List;)V
writePresentToNexus
D(Ljava/io/File;Ljava/io/File;Ljava/util/SortedSet;Ljava/util/List;)V
?(Ljava/io/File;Ljava/io/File;Ljava/util/SortedSet;Ljava/util/List;)V
writeProteinListsForAllSpecies
6(Ljava/io/File;Ljava/util/SortedMap;Ljava/util/List;)V?
?(Ljava/io/File;Ljava/util/SortedMap;>;Ljava/util/List;)V


SourceFile
surfacing.java??
java/lang/StringBuilder
pwc_??

_??????
.html??
java/io/File???????????
	surfacing??
	E-value: ??
, Cutoff-scores-file: 
, Cutoff-scores-file: not-set
, Max-overlap: ??
, Max-overlap: not-set
!, Engulfing-overlaps: not-allowed
, Engulfing-overlaps: allowed
, Ignore-dufs: true
, Ignore-dufs: false
, DC type (if applicable): ???????
java/util/TreeSet???????????
,org/forester/protein/BinaryDomainCombination??
java/lang/Integer??

count < 1 ??

	????????????????

0
GSum of all distinct domain combinations appearing once               : 
GSum of all distinct domain combinations appearing more than once     : 
GSum of all distinct domains in combinations apppearing only once     : 
GSum of all distinct domains in combinations apppearing more than once: 
GSum of all distinct domain combinations never lost                   : 
GSum of all distinct domain combinations lost once                    : 
GSum of all distinct domain combinations lost more than once          : 
GSum of all distinct domains in combinations lost only once           : 
ASum of all distinct domains in combinations lost more than once: 
GAll binary combinations                                              : 
GAll domains                                                          : ??

0Produced by:surfacing
(Version:2.250
2Release Date:2012.05.07
6Contact:[email protected]
PWWW:www.phylosoft.org/forester/applications/surfacing
&org/forester/util/CommandLineArguments??
help	?

h??			
java/util/ArrayList
dufs

e
detail

o
sort
smatrix
scoring
mo
no_eo
dc_sort
cos

species_first
out_dir
ignore_self_comb
p2g
obo
	ds_output
go_namespace
pwc
ignore_singlet_domains
consider_bdc_direction
jack
seed

jack_ratio
species_tree

pos_filter

neg_filter
input
random_seed
neg_dom_filter
ignore_viral_ids
prot_extract
	secondary

plus_minus
graph_analysis_out
all_prot
consider_bdc_adj			?
unknown option(s): 		
'no acceptable value for E-value maximum		
6no acceptable value for maximal allowed domain overlap
ignore_species_specific_domains	?
Dno value for domain combinations similarities output file: -o=		
>no value for individual domain score cutoffs file: -cos=
2cannot read individual domain score cutoffs file: 

 				 	!	"
0cannot read from individual score cutoffs file: 	#	$	%	$	&	$
-no value for output directory: -out_dir=	'?	(	)
 " aready exists and is not empty	*?
failed to create "	+?
cannot write to "
8attempt to use both negative and positive protein filter
_attempt to use both negative or positive protein filter together wirh a negative domains filter
0no value for negative filter: -neg_filter=
can not read from "
": 
0no value for positive filter: -pos_filter=
??
,no value for input files file: -input=	,	-
failed to read from "	.?
SNo hmmpfam output file indicated is input: use comand line directly or input=??
uno value for scoring method for domain combinations similarity calculation: -scoring="
domains	/?	0?
combinations	1?
proteins	2?
unknown value "
G" for scoring method for domain combinations similarity calculation: "-
=<

|
>"??
2no value for -detail="	3?
basic	#?
list_ids	4?
punctilious	5?
" for detailedness: "-
?no domain ids given for sequences with given domains to be extracted : -prot_extract=??
|no value for domain combinations similarities sorting: -sort="
alpha	6?
max	7?
min	8?
mean	9?
species	:?
sd?
diff	;?
abs_count_diff	<?

count_diff	=?
2" for domain combinations similarities sorting: "-
Bno value for print option: -detailed_html|simple_html|simple_tab>"

detailed_html?
simple_html
)simple HTML output not implemented yet :(

simple_tab	>
" for print option: -??
Fno value for sorting of domain counts: -dc_sort="	??
dom	@?
prot	A?
comb	B?
"" for sorting of domain counts: "-
[[Ljava/lang/String;??	C	D
"cannot analyze less than two files
Xcannot use : -pwc= to turn on pairwise analyses with less than three input files??
.dcc
1no value for Pfam to GO mapping file: -p2g=
%cannot read Pfam to GO mapping file: 
org/forester/go/PfamToGoParser??		E	F	G	H?
9parser.getMappingCount() < domain_id_to_go_ids_map.size()
*cannot read from Pfam to GO mapping file: 
%no value for GO OBO file: -obo=
Qcannot use GO OBO file (-obo=) without Pfam to GO mapping file (p2g=)
cannot read GO OBO file: 
org/forester/go/OBOparser	I	K	L?	M	N?
*parser.getGoTermCount() != go_terms.size()
cannot read from GO OBO file: 	O	P	G
?cannot use GO namespace limit (-go_namespace=) without Pfam to GO mapping file (p2g=) and GO OBO file (-obo=)
kno value for GO namespace limit: "-go_namespace="
molecular_function?	Q	R
biological_process	S	R
cellular_component	T	R
" for GO namespace limit: "-
?cannot use jacknife resampling analysis (-jack[=]) without pairwise analyses (pwc=)	U?
(illegal format for number of resamplings
&attempt to use less than 2 resamplings
!illegal format for jacknife ratio
1attempt to use illegal value for jacknife ratio: 	V	W
(illegal format for random generator seed
?cannot infer gains and losses on input species trees (-species_tree without pairwise analyses (pwc=)
Eno value for input tree: -species_tree=

#	X		Y	Z	[???
4no value for random number seed: -random_seed=??
_domain_lengths_analysis
;no value for secondary features map file: -secondary=

java/util/Map
)cannot read secondary features map file: 	\	]
,problem with contents of features map file [
.no output directory indicated (-out_dir=)
4no name for (main) output file indicated (-o=)
Rno (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-p2g=)
Qno (acceptable) go id to term mapping file provided ('GO OBO file') (-obo=)	^	_
Output directory            : ?	`?
Input files names from      : 
 [

 input files]
(Input files names from:
 input files]
Positive protein filter     : 
 domain ids]
)Positive protein filter:
 domain ids]
Negative protein filter     : 
)Negative protein filter:
Negative domain filter      : 
(Negative domain filter:
java/lang/String

+

*

-
Plus-minus analysis         : 
&& 
%Plus-minus analysis:


Cutoff scores file          : 
$Cutoff scores file:
E-value maximum (inclusive) : 
-E-value maximum (inclusive):
Ignore DUFs                 : ?	a
Ignore virus like ids       : 
@Ignore virus, phage, transposition related ids:
Ignore DUFs:
Max allowed domain overlap  : 
,Max allowed domain overlap:
Ignore engulfed domains     : 
<Ignore (lower confidence) engulfed domains:
Ignore singlet domains      : 
pIgnore singlet domains for domain combination similarity analyses (not for parsimony analyses):
Ignore species specific doms: 
yIgnore species specific domains for domain combination similarity analyses (not for parsimony analyses):
Ignore combination with self: 
YIgnore combination with self for domain combination similarity analyses:
Consider directedness       : 
EConsider directedness of binary domain combinations:
Consider adjacency          : 
AConsider djacency of binary domain combinations:
Domain counts sort order    : 	b?	c?
alphabetical
domain count
domain proteins count
domain combinations count
unknown value for dc sort order
Pfam to GO mappings from    : 

 mappings]
*Pfam to GO mappings from:
GO terms from               : 
 terms]
GO terms from:
Limit GO terms to           : 
"Limit GO terms to
Suffix for PWC files        : 
%Suffix for PWC files
Query domains (ordered)     : 

Write similarities to       : 
  Scoring method            : 
 Scoring method:	d?
domain combinations based
#domain combinations based
domain counts based
domain counts based
domain proteins counts based
&domain proteins counts based
%unknown value for sorting for scoring
  Sort by                   : 
Sort by:	e?

score minimum

score maximum

score mean
score standard deviation
species number
alphabetical domain identifier
(maximal) difference
$absolute (maximal) counts difference
(maximal) counts difference
(maximal) counts  difference
*unknown value for sorting for similarities
 (sort by species count first)	`?
  Detailedness              : 	f?
'list combining domains for each species
*unknown value for sorting for detailedness
  Print option              : 
HTML
simple tab delimited
unknown value for print option
  Species matrix            : 
_domain_combination_data.txt
Domain comb data output     : 
1Domain combination data output: 
 
Pairwise comparisons: 
0Pairwise comparisons:

difference
absolute counts difference
counts difference
Jacknife:
 resamplings
 Jacknife ratio:	g	h
-Jacknife random number seed:?	i
  Jacknife                  : 
 resamplings
    Ratio                   : 
    Random number seed      : 
9Intree for gain/loss parsimony analysis:
  Intree for gain/loss pars.: 
E    Random number seed for Fitch parsimony analysis:
-Secondary features map file:
Secondary features map file : 
 [mappings for 
Command line:
	j?


Command line                : 
java/io/BufferedWriter

~
org/forester/protein/DomainId	k	l
.prot
java/io/FileWriter?	m
Could not open [
java/util/TreeMap?	
)org/forester/surfacing/DomainLengthsTable
_domain_promiscuities
	Species:	
Mean:	
SD:	
Median:	
Min:	
Max:	
N:	
Max Promiscuous Domains:
_log.txt
?#SPECIES	PRTEIN_ID	N_TERM_DOMAIN	C_TERM_DOMAIN	N_TERM_DOMAIN_PER_DOMAIN_E_VALUE	C_TERM_DOMAIN_PER_DOMAIN_E_VALUE	N_TERM_DOMAIN_COUNTS_PER_PROTEIN	C_TERM_DOMAIN_COUNTS_PER_PROTEIN
,org/forester/util/BasicDescriptiveStatistics
__domains_per_potein_stats.txt
Genome
Mean
SD
Median

N
Min
Max


	n?
java/util/HashMap

/??
1Processing                                     : 
1Genome                                         : 	osps?	o	p	q	p	r	p	s	p
3org/forester/io/parsers/HmmscanPerDomainTableParser?	t?	u	v	w	x	y	z	y	{	y	|		}	~		?	?	?	??	?	??	?	w
1Number of proteins encountered                 : 
1Number of proteins stored                      : 
1Coverage                                       : 	?	?

%
1Domains encountered                            : 	??
1Domains stored                                 : 	??
1Distinct domains stored                        : 	?	?
1Domains ignored due to individual score cutoffs: 	??
1Domains ignored due to E-value                 : 	??
1Domains ignored due to DUF designation         : 	??
1Domains ignored due virus like ids             : 	??
1Domains ignored due negative domain filter     : 	??
1Domains ignored due to overlap                 : 	??
1Proteins ignored due to negative filter        : 	??
1Proteins ignored due to positive filter        : 
1Time for processing                            : 
ms

 [species: 
:domains analyzed: 
'; domains ignored: [ind score cutoffs: 
] [E-value cutoff: 
] [DUF: 
] [virus like ids: 
] [negative domain filter: 
] [overlap: 
+; proteins ignored due to negative filter: 
+; proteins ignored due to positive filter: 
org/forester/protein/Protein	?	?	?	?	E
org/forester/protein/Domain	??	??	?	?
'org/forester/util/DescriptiveStatistics	??	?	?
!org/forester/species/BasicSpecies	?		?	?	?	??	?	?	?	?	?	?	?	?|?	?	?	??	??
Wrote domain promiscuities to: 
ALL	??	??	??	??	??	????
*__all_genomes_domains_per_potein_histo.txt	?	?
__domains_always_single_.txt	?	?
 __domains_single_or_combined.txt
__domains_always_combined.txt
6Average of proteins with a least one domain assigned: 
% (+/-
%)
4Range of proteins with a least one domain assigned: 
%-
1Average of prot with a least one dom assigned  : 
1Range of prot with a least one dom assigned    : 	?	?
Wrote domain length data to: 
6org/forester/surfacing/BasicDomainSimilarityCalculator?	?
Jorg/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator
Dorg/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator
Korg/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator?	o	?g	??	?	?	?	?	?	???
9Sum of all distinct binary combinations:
-Sum of all distinct domains:
$Analysis date/time:
java/text/SimpleDateFormat
yyyy.MM.dd HH:mm:ss	?	?

 genomes	?	?
6Wrote main output (includes domain similarities) to: "
!Failed to write similarites to: "
" [
org/forester/species/Species
/org/forester/surfacing/PairwiseGenomeComparator	?	?	X	?
_mean_score.pwd	?	E	?	?
_bin_combinations.pwd	?	E
_domains.pwd	?	E
_mean_score_NJ.xml
8org/forester/evoinference/matrix/distance/DistanceMatrix	?	?
_bin_combinations_NJ.xml
_domains_NJ.xml	?	?????	?	?		?	?	?		?	?	?
Mapping to secondary features:
%org/forester/surfacing/MappingResults	??	??

:
 mapped domains = 
, not mapped domains = 
, mapped ratio = 
), mapped ratio = n/a (total domains = 0 )????
_fitch_dc_gains_counts??
_fitch_dc_losses_counts	?	?	?	?		?	
Time for analysis : 
Total running time: 
ms 
Free memory       : 
MB, total memory: 
MB
2If this application is useful to you, please cite:
OK	??	?
_domains_A.html
_domains_B.html
_domains_C.html
_domains_D.html
_domains_E.html
_domains_F.html
_domains_G.html
_domains_H.html
_domains_I.html
_domains_J.html
_domains_K.html
_domains_L.html
_domains_M.html
_domains_N.html
_domains_O.html
_domains_P.html
_domains_Q.html
_domains_R.html
_domains_S.html
_domains_T.html
_domains_U.html
_domains_V.html
_domains_W.html
_domains_X.html
_domains_Y.html
_domains_Z.html
_domains_0.html	??
java/util/Map$Entry
Entry	???	?
$Percentage of multidomain proteins: 
1Percentage of multidomain proteins:            : 	?	?
node named [
] is not unique in input tree 	??	?	???	??	?	?	?	??	?	?	?	??	??	??	??
Inode with no name, scientific name, common name, or taxonomy code present	?	?	?
Not using the following 
 nodes:
: 
--	?	?
"java/lang/IllegalArgumentException
&] not present/not unique in input tree
Usage:
?% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications.surfacing [options]  [external node name 1] [name 2] ... [name n]
L Note: This software might need a significant amount of memory (heap space);
Y       hence use "-Xms128m -Xmx512m" (or more) to prevent a "java.lang.OutOfMemoryError".

 Options: 
>detail: level of detail for similarities output file (default:

)
Kignore_self_comb: to ignore combinations with self (default: not to ignore)
?ignore_singlet_domains: to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)
?ignore_species_specific_domains: to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)
Qdufs: to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)
|ignore_viral_ids: to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'
)sort: sorting for similarities (default: 
*o: name for (main) output file (mandatory)
e: max (inclusive) E-value
"mo: maximal allowed domain overlap
2no_eo: to ignore engulfed lower confidence domains
smatrix: species matrix
scoring: scoring (default:
,dc_sort: sorting for domain counts (default:
3ds_output: domain similarity print option (default:
cos: cutoff score file
*species_first: sort by species count first
out_dir: output directory
p2g: Pfam to GO mapping file
obo: GO terms file (OBO format)
/go_namespace: limit GO term to one GO namespace
bpwc[=]: to perform pairwise comparison based analyses
Hspecies_tree: species tree, to perform (Dollo, Fitch) parismony analyses
}jack: perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: 100]
8jack_ratio: ratio for jacknife resampling [default: 0.5]
Lseed: seed for random number generator for jacknife resampling [default: 19]
?species_tree=: to infer domain/binary domain combination gains/losses on given species trees
]pos_filter=: to filter out proteins not containing at least one domain listed in 
Yneg_filter=: to filter out proteins containing at least one domain listed in 
Fneg_dom_filter=: to filter out (ignore) domains listed in 
-input=: to read input files from 
?random_seed=: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence
Xconsider_bdc_direction: to consider directedness in binary combinations: e.g. A-B != B-A
Oconsider_bdc_adj: to consider directedness and adjacency in binary combinations
?prot_extract=: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')
Dsecondary=: to perfom parsimony analysis on secondary features
6plus_minus=: to presence/absence genome analysis
Xgraph_analysis_out: to output binary domain combinations for (downstream) graph analysis
+all_prot: to output all proteins per domain

Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1 -no_eo -mo=0 -input=genomes_limited.txt -out_dir=out -o=o  -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot

TExample 2: java -Xms128m -Xmx512m -cp path/to/forester.jar org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo -dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo -ds_output=detailed_html -scoring=domains -sort=alpha human mouse brafl strpu	?	?
[Ljava/lang/String;
?properties for the input files (hmmpfam output) are expected to be in the following format "#" (or just one word, which is both the filename and the species id), instead received "
2no value for 'plus-minus' file: -plus_minus=??	?	?	??
?
\species/genome names can not appear with both '+' and '-' suffix, as appears the case for: "
\species/genome names can not appear with both '*' and '-' suffix, as appears the case for: "
cspecies/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: "
$D

	
java/lang/NumberFormatException
' minimal Difference (default is 1), '$F=' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: "
'plus minus' file [
] appears empty


_dom.nex


		?




_dc.nex

	?
?	?

Wrote proteins list to "
s
"org/forester/application/surfacing
java/lang/Object
$org/forester/application/surfacing$1
_dc.dot
_fitch_present_dc.dot
_dollo_gl_d
_dollo_gl_dc
_fitch_gl_d
_fitch_gl_dc
_dollo_glc_d

_dollo_glc_dc
_fitch_glc_d

_fitch_glc_dc
_fitch_gains_dc
_fitch_gains_dc.html
_fitch_losses_dc
_fitch_losses_dc.html
_fitch_present_dc
_fitch_present_dc.html
_dollo_gains_d
_dollo_gains_d.html
_dollo_losses_d
_dollo_losses_d.html
_dollo_present_d
_dollo_present_d.html
_d_dollo.xml
_d_fitch.xml

_dc_dollo.xml

_dc_fitch.xml
_secondary_features.nex
_dollo_gl_secondary_features
_dollo_glc_secondary_features
_dollo_gains_secondary_features
 _dollo_losses_secondary_features
!_dollo_present_secondary_features
_secondary_features_dollo.xml

_dollo_goid_d
_fitch_goid_dc

?org/forester/surfacing/DomainSimilarity$DomainSimilarityScoring
>org/forester/surfacing/DomainSimilarityCalculator$Detailedness
Aorg/forester/surfacing/DomainSimilarity$DomainSimilaritySortField
Worg/forester/surfacing/GenomeWideCombinableDomains$GenomeWideCombinableDomainsSortOrder

=org/forester/surfacing/PrintableDomainSimilarity$PRINT_OPTION
	_sd_nj.nh

_sbc_nj.nh
_all_encountered_pfams
)_all_encountered_pfams_with_go_annotation
_encountered_pfams_summary
_all_pfams_gained_as_domains
_all_pfams_lost_as_domains
_all_pfams_gained_as_dc
_all_pfams_lost_as_dc
PER_NODE_EVENTS
PER_SUBTREE_EVENTS
Korg/forester/io/parsers/HmmscanPerDomainTableParser$INDIVIDUAL_SCORE_CUTOFF
 _indep_dc_gains_fitch_counts.txt
_indep_dc_gains_fitch_lists.txt
._indep_dc_gains_fitch_lists_for_go_mapping.txt
5_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt
'_dc_MAPPED_secondary_features_fitch.xml
'_indep_dc_gains_fitch_counts_MAPPED.txt
&_indep_dc_gains_fitch_lists_MAPPED.txt
5_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt
<_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt
Borg/forester/protein/BinaryDomainCombination$DomainCombinationType
java/util/List
java/util/SortedSet
java/io/Writer
java/util/SortedMap
java/util/Iterator

java/util/Set
[Ljava/io/File;
#[Lorg/forester/phylogeny/Phylogeny;
2org/forester/evoinference/distance/NeighborJoining
org/forester/go/GoNameSpace
[Ljava/util/Map;
java/io/PrintStream
[Ljava/io/BufferedWriter;
[Ljava/util/List;

FilterType
>org/forester/io/parsers/HmmscanPerDomainTableParser$FilterType
9org/forester/surfacing/PairwiseDomainSimilarityCalculator
1org/forester/surfacing/DomainSimilarityCalculator
GoAnnotationOutput
Dorg/forester/surfacing/DomainSimilarityCalculator$GoAnnotationOutput
[Lorg/forester/species/Species;
0org/forester/surfacing/DomainParsimonyCalculator
6org/forester/phylogeny/iterators/PhylogenyNodeIterator
$org/forester/phylogeny/PhylogenyNode
append
-(Ljava/lang/String;)Ljava/lang/StringBuilder;
toString
()Ljava/lang/String;
H$SwitchMap$org$forester$surfacing$PrintableDomainSimilarity$PRINT_OPTION
[I
ordinal
()I
endsWith
(Ljava/lang/String;)Z
-(Ljava/lang/Object;)Ljava/lang/StringBuilder;
org/forester/util/ForesterUtil
FILE_SEPARATOR
(Ljava/lang/String;)V
isWritableFile
"(Ljava/io/File;)Ljava/lang/String;
isEmpty

fatalError
'(Ljava/lang/String;Ljava/lang/String;)V
(D)Ljava/lang/StringBuilder;
(I)Ljava/lang/StringBuilder;
$org/forester/surfacing/SurfacingUtil
checkForOutputFileWriteability
(Ljava/io/File;)V
createBufferedWriter
((Ljava/io/File;)Ljava/io/BufferedWriter;
listToSortedCountsMap
'(Ljava/util/List;)Ljava/util/SortedMap;
keySet
()Ljava/util/Set;
iterator
()Ljava/util/Iterator;
hasNext
()Z
next
()Ljava/lang/Object;
get
&(Ljava/lang/Object;)Ljava/lang/Object;
intValue
unexpectedFatalError
LINE_SEPARATOR
write
getId0
!()Lorg/forester/protein/DomainId;
add
(Ljava/lang/Object;)Z
getId1
size
	removeAll
(Ljava/util/Collection;)Z
close
programMessage

getSpecies
 ()Lorg/forester/species/Species;
getSpeciesId
(I)Ljava/lang/Object;
doubleValue
()D
valueOf
(D)Ljava/lang/Double;
1org/forester/surfacing/DomainCountsDifferenceUtil
calculateCopyNumberDifferences
?(Ljava/util/List;Ljava/util/SortedMap;Ljava/util/List;Ljava/util/List;Ljava/util/List;ILjava/lang/Double;Ljava/io/File;Ljava/io/File;Ljava/io/File;Ljava/util/Map;Ljava/util/Map;Ljava/io/File;Ljava/io/File;Ljava/io/File;)V
getLocalizedMessage
isReadableFile
(Lorg/forester/phylogeny/Phylogeny;Ljava/lang/StringBuilder;)I
isCompletelyBinary
printWarningMessage
createInstance
6()Lorg/forester/evoinference/distance/NeighborJoining;
execute
"(Ljava/util/List;)Ljava/util/List;
toNewHampshire
5(Ljava/util/List;ZZLjava/io/File;Ljava/lang/String;)V

getMessage
getTime
()J
printProgramInformation
](Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;Ljava/lang/String;)V
isOptionSet
java/lang/System
exit
(I)V
validateAllowedOptionsAsString
$(Ljava/util/List;)Ljava/lang/String;
length
getOptionValueAsDouble
(Ljava/lang/String;)D
getOptionValueAsInt
(Ljava/lang/String;)I
isOptionValueSet
getOptionValue
&(Ljava/lang/String;)Ljava/lang/String;
"org/forester/util/BasicTableParser
parse
D(Ljava/lang/Object;Ljava/lang/String;)Lorg/forester/util/BasicTable;
org/forester/util/BasicTable
getColumnsAsMapDouble
(II)Ljava/util/Map;
BASIC
DLorg/forester/protein/BinaryDomainCombination$DomainCombinationType;
DIRECTED
DIRECTED_ADJACTANT
exists
	listFiles
()[Ljava/io/File;
mkdir
canWrite

file2array
#(Ljava/io/File;)[Ljava/lang/String;
getNumberOfNames
equals
DOMAINS
COMBINATIONS
PROTEINS
toLowerCase
&LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES
PUNCTILIOUS
	DOMAIN_ID
MAX
MIN
MEAN

SPECIES_COUNT
MAX_DIFFERENCE
ABS_MAX_COUNTS_DIFFERENCE
MAX_COUNTS_DIFFERENCE
SIMPLE_TAB_DELIMITED
ALPHABETICAL_KEY_ID
KEY_DOMAIN_COUNT
KEY_DOMAIN_PROTEINS_COUNT
COMBINATIONS_COUNT
getNames
()[Ljava/lang/String;
()Ljava/util/List;
createDomainIdToGoIdMap
!(Ljava/util/List;)Ljava/util/Map;
getMappingCount
$org/forester/go/OBOparser$ReturnType

ReturnType

BASIC_GO_TERM
&Lorg/forester/go/OBOparser$ReturnType;
7(Ljava/io/File;Lorg/forester/go/OBOparser$ReturnType;)V
getGoTermCount
org/forester/go/GoUtils
createGoIdToGoTermMap
createMolecularFunction
()Lorg/forester/go/GoNameSpace;
createBiologicalProcess
createCellularComponent
isOptionHasAValue
getOptionValueAsLong
(Ljava/lang/String;)J
indexOf
split
'(Ljava/lang/String;)[Ljava/lang/String;
trim
$createDomainIdToSecondaryFeaturesMap
(Ljava/io/File;)Ljava/util/Map;
out
Ljava/io/PrintStream;
println
(Z)Ljava/lang/StringBuilder;
print
b$SwitchMap$org$forester$surfacing$GenomeWideCombinableDomains$GenomeWideCombinableDomainsSortOrder
J$SwitchMap$org$forester$surfacing$DomainSimilarity$DomainSimilarityScoring
L$SwitchMap$org$forester$surfacing$DomainSimilarity$DomainSimilaritySortField
I$SwitchMap$org$forester$surfacing$DomainSimilarityCalculator$Detailedness
round
(DI)D
(J)Ljava/lang/StringBuilder;
getCommandLineArgsAsString
replace
(CC)Ljava/lang/String;
(Ljava/io/Writer;)V
printStackTrace
NONE
@Lorg/forester/io/parsers/HmmscanPerDomainTableParser$FilterType;
POSITIVE_PROTEIN
NEGATIVE_PROTEIN
NEGATIVE_DOMAIN
?(Ljava/io/File;Ljava/lang/String;Ljava/util/Set;Lorg/forester/io/parsers/HmmscanPerDomainTableParser$FilterType;Lorg/forester/io/parsers/HmmscanPerDomainTableParser$INDIVIDUAL_SCORE_CUTOFF;Z)V
q(Ljava/io/File;Ljava/lang/String;Lorg/forester/io/parsers/HmmscanPerDomainTableParser$INDIVIDUAL_SCORE_CUTOFF;Z)V
setEValueMaximum
(D)V

setIgnoreDufs
(Z)V
setIgnoreVirusLikeIds
setIgnoreEngulfedDomains
setMaxAllowedOverlap
>org/forester/io/parsers/HmmscanPerDomainTableParser$ReturnType
/UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN
@Lorg/forester/io/parsers/HmmscanPerDomainTableParser$ReturnType;

setReturnType
C(Lorg/forester/io/parsers/HmmscanPerDomainTableParser$ReturnType;)V
setIndividualScoreCutoffs
(Ljava/util/Map;)V
<(Ljava/lang/String;Ljava/lang/String;Ljava/lang/Exception;)V
getProteinsEncountered
addValue

roundToInt
(D)I
getDomainsEncountered
getDomainsStored
getDomainsStoredSet
()Ljava/util/SortedSet;
+getDomainsIgnoredDueToIndividualScoreCutoff
getDomainsIgnoredDueToEval
getDomainsIgnoredDueToDuf
"getDomainsIgnoredDueToVirusLikeIds
*getDomainsIgnoredDueToNegativeDomainFilter
getDomainsIgnoredDueToOverlap
getProteinsIgnoredDueToFilter
proteinToDomainCombinations
\(Lorg/forester/protein/Protein;Ljava/lang/String;Ljava/lang/String;)Ljava/lang/StringBuffer;
java/lang/StringBuffer
getProteinDomains
getDomainId
containsKey
put
8(Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/Object;
	getLength
domainsPerProteinsStatistics
?(Ljava/lang/String;Ljava/util/List;Lorg/forester/util/DescriptiveStatistics;Ljava/util/SortedMap;Ljava/util/SortedSet;Ljava/util/SortedSet;Ljava/util/SortedSet;Ljava/io/Writer;)V
7org/forester/surfacing/BasicGenomeWideCombinableDomains
?(Ljava/util/List;ZLorg/forester/species/Species;Ljava/util/Map;Lorg/forester/protein/BinaryDomainCombination$DomainCombinationType;Ljava/util/Map;Ljava/util/Map;)Lorg/forester/surfacing/BasicGenomeWideCombinableDomains;

addLengths
(Ljava/util/List;)V
getSize
!writeDomainCombinationsCountsFile
?([[Ljava/lang/String;Ljava/io/File;Ljava/io/Writer;Lorg/forester/surfacing/GenomeWideCombinableDomains;ILorg/forester/surfacing/GenomeWideCombinableDomains$GenomeWideCombinableDomainsSortOrder;)V
1writeBinaryDomainCombinationsFileForGraphAnalysis
?([[Ljava/lang/String;Ljava/io/File;Lorg/forester/surfacing/GenomeWideCombinableDomains;ILorg/forester/surfacing/GenomeWideCombinableDomains$GenomeWideCombinableDomainsSortOrder;)V
addAllDomainIdsToSet
L(Lorg/forester/surfacing/GenomeWideCombinableDomains;Ljava/util/SortedSet;)V
"addAllBinaryDomainCombinationToSet
extractProteinNames
W(Ljava/util/List;Ljava/util/List;Ljava/io/Writer;Ljava/lang/String;Ljava/lang/String;)V
flush
gc
arithmeticMean
sampleStandardDeviation
median
getN
getMin
getMax
map2file
D(Ljava/io/File;Ljava/util/Map;Ljava/lang/String;Ljava/lang/String;)V
collection2file
9(Ljava/io/File;Ljava/util/Collection;Ljava/lang/String;)V
executeDomainLengthAnalysis
Q([[Ljava/lang/String;ILorg/forester/surfacing/DomainLengthsTable;Ljava/io/File;)V
H(Lorg/forester/surfacing/DomainSimilarity$DomainSimilaritySortField;ZZ)V
FLorg/forester/surfacing/DomainSimilarityCalculator$GoAnnotationOutput;
calculateSimilarities
d(Lorg/forester/surfacing/PairwiseDomainSimilarityCalculator;Ljava/util/List;ZZ)Ljava/util/SortedSet;
#decoratePrintableDomainSimilarities
?(Ljava/util/SortedSet;Lorg/forester/surfacing/DomainSimilarityCalculator$Detailedness;Lorg/forester/surfacing/DomainSimilarityCalculator$GoAnnotationOutput;Ljava/util/Map;Lorg/forester/go/GoNameSpace;)V
	substring
(II)Ljava/lang/String;
format
$(Ljava/util/Date;)Ljava/lang/String;
writeDomainSimilaritiesToFile

f(Ljava/lang/StringBuilder;Ljava/lang/StringBuilder;Ljava/io/Writer;Ljava/util/Map;Ljava/util/SortedSet;ZLjava/util/List;Lorg/forester/surfacing/PrintableDomainSimilarity$PRINT_OPTION;Lorg/forester/surfacing/DomainSimilarity$DomainSimilaritySortField;Lorg/forester/surfacing/DomainSimilarity$DomainSimilarityScoring;Z)Lorg/forester/util/DescriptiveStatistics;
performPairwiseComparisons
(Ljava/lang/StringBuilder;ZLorg/forester/surfacing/DomainSimilarityCalculator$Detailedness;ZZLorg/forester/surfacing/DomainSimilarity$DomainSimilaritySortField;Lorg/forester/surfacing/PrintableDomainSimilarity$PRINT_OPTION;Lorg/forester/surfacing/DomainSimilarity$DomainSimilarityScoring;Ljava/util/Map;Ljava/util/Map;Lorg/forester/go/GoNameSpace;[Lorg/forester/species/Species;ILjava/util/List;Lorg/forester/surfacing/PairwiseDomainSimilarityCalculator;Ljava/lang/String;ZLjava/lang/String;Ljava/lang/String;Ljava/io/File;Z)V
(I)I
getDomainDistanceScoresMeans
writeMatrixToFile
!(Ljava/io/File;Ljava/util/List;)V
)getSharedBinaryCombinationsBasedDistances
getSharedDomainsBasedDistances
createNjTreeBasedOnMatrixToFile
l(Ljava/io/File;Lorg/forester/evoinference/matrix/distance/DistanceMatrix;)Lorg/forester/phylogeny/Phylogeny;
#performPairwiseComparisonsJacknifed
7([Lorg/forester/species/Species;ILjava/util/List;ZIDJ)V
removeSuffix
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FULL_SEQUENCE
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