Modifier and Type | Constant Field | Value |
---|---|---|
public static final char |
group1 |
49 |
public static final char |
group2 |
50 |
public static final char |
group3 |
51 |
public static final char |
unknownGroup |
48 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
INFINITY |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
PFAM |
"PFAM" |
public static final java.lang.String |
RFAM |
"RFAM" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
EXPERT |
"EXPERT" |
public static final java.lang.String |
HOMSTRAD |
"HOMSTRAD" |
public static final java.lang.String |
INTERPRO |
"INTERPRO" |
public static final java.lang.String |
LOAD |
"LOAD" |
public static final java.lang.String |
MIM |
"MIM" |
public static final java.lang.String |
PDB |
"PDB" |
public static final java.lang.String |
PFAMB |
"PFAMB" |
public static final java.lang.String |
PRINTS |
"PRINTS" |
public static final java.lang.String |
PROSITE |
"PROSITE" |
public static final java.lang.String |
PROSITE_PROFILE |
"PROSITE_PROFILE" |
public static final java.lang.String |
SCOP |
"SCOP" |
public static final java.lang.String |
SMART |
"SMART" |
public static final java.lang.String |
URL |
"URL" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ENDOFFILE |
"end of file" |
public static final java.lang.String |
SECTIONKEYNULL |
"section key is null" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final java.lang.String |
ACCESSION_TAG |
"ACCESSION" |
protected static final java.lang.String |
AUTHORS_TAG |
"AUTHORS" |
protected static final java.lang.String |
BASE_COUNT_TAG |
"BASE" |
protected static final java.lang.String |
BASE_COUNT_TAG_FULL |
"BASE COUNT" |
protected static final java.lang.String |
COMMENT_TAG |
"COMMENT" |
protected static final java.lang.String |
CONSORTIUM_TAG |
"CONSRTM" |
protected static final java.lang.String |
DEFINITION_TAG |
"DEFINITION" |
protected static final java.lang.String |
END_SEQUENCE_TAG |
"//" |
protected static final java.lang.String |
FEATURE_TAG |
"FEATURES" |
public static final java.lang.String |
GENBANK_FORMAT |
"GENBANK" |
protected static final java.lang.String |
JOURNAL_TAG |
"JOURNAL" |
protected static final java.lang.String |
KEYWORDS_TAG |
"KEYWORDS" |
protected static final java.lang.String |
LOCUS_TAG |
"LOCUS" |
protected static final java.lang.String |
MEDLINE_TAG |
"MEDLINE" |
protected static final java.lang.String |
ORGANISM_TAG |
"ORGANISM" |
protected static final java.lang.String |
PUBMED_TAG |
"PUBMED" |
protected static final java.lang.String |
REFERENCE_TAG |
"REFERENCE" |
protected static final java.lang.String |
REMARK_TAG |
"REMARK" |
protected static final java.lang.String |
SOURCE_TAG |
"SOURCE" |
protected static final java.lang.String |
START_SEQUENCE_TAG |
"ORIGIN" |
protected static final java.lang.String |
TITLE_TAG |
"TITLE" |
protected static final java.lang.String |
VERSION_TAG |
"VERSION" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CIRCULAR_DNA |
"circular" |
public static final java.lang.String |
LINEAR_DNA |
"linear" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MAX_WIDTH |
80 |
protected static final int |
QUALIFIER_INDENT |
21 |
protected static final java.lang.String |
QUALIFIER_INDENT_STR |
" " |
protected static final java.lang.String |
QUALIFIER_INDENT_TMP |
" %s " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
IUPAC_LOCATION |
"org/biojava/nbio/core/sequence/iupac.txt" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
UNKNOWN_DNA |
"UNK" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final java.lang.String |
locationSplitPattern |
",(?=([^\\(|\\)]+\\([^\\(|\\)]+\\))[^\\(|\\)]+)" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BYTES_PER_INT |
32 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
PRIME |
79 |
public static final int |
SEED |
9 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CACHE_PROPERTY |
"biojava.cache.files" |
public static final int |
GZIP_MAGIC |
8075 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final java.lang.String |
NUCLEOTIDE_LETTERS |
"GCTAUXN" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_LIMIT |
1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_LOCATION |
"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_MAPPING_URL |
"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_GENENAMES_URL |
"https://www.genenames.org/cgi-bin/download?title=HGNC+output+data&hgnc_dbtag=on&col=gd_app_sym&col=gd_app_name&col=gd_status&col=gd_prev_sym&col=gd_prev_name&col=gd_aliases&col=gd_pub_chrom_map&col=gd_pub_acc_ids&col=md_mim_id&col=gd_pub_refseq_ids&col=md_ensembl_id&col=md_prot_id&col=gd_hgnc_id&status=Approved&status_opt=2&where=((gd_pub_chrom_map%20not%20like%20%27%patch%%27%20and%20gd_pub_chrom_map%20not%20like%20%27%ALT_REF%%27)%20or%20gd_pub_chrom_map%20IS%20NULL)%20and%20gd_locus_group%20%3d%20%27protein-coding%20gene%27&order_by=gd_app_sym_sort&format=text&limit=&submit=submit&.cgifields=&.cgifields=chr&.cgifields=status&.cgifields=hgnc_dbtag" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CDS |
"CDS" |
public static final java.lang.String |
CHROMOSOME |
"CHROMOSOME" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BROAD_SYNONYM |
3 |
public static final int |
EXACT_SYNONYM |
1 |
public static final int |
NARROW_SYNONYM |
2 |
public static final int |
RELATED_SYNONYM |
0 |
public static final int |
UNKNOWN_SCOPE |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ALT_ID |
"alt_id" |
public static final java.lang.String |
BROAD_SYNONYM |
"broad_synonym" |
public static final java.lang.String |
COMMENT |
"comment" |
public static final java.lang.String |
DEF |
"def" |
public static final java.lang.String |
DISJOINT_FROM |
"disjoint_from" |
public static final java.lang.String |
EXACT_SYNONYM |
"exact_synonym" |
public static final java.lang.String |
ID_KEY |
"id" |
public static final java.lang.String |
INTERSECTION_OF |
"intersection_of" |
public static final java.lang.String |
IS_A |
"is_a" |
public static final java.lang.String |
IS_OBSOLETE |
"is_obsolete" |
public static final java.lang.String |
NAME |
"name" |
public static final java.lang.String |
NARROW_SYNONYM |
"narrow_synonym" |
public static final java.lang.String |
ONTOLOGY |
"ontologys" |
public static final java.lang.String |
REL_SYNONYM |
"related_synonym" |
public static final java.lang.String |
RELATIONSHIP |
"relationship" |
public static final java.lang.String |
SUBSET |
"subset" |
public static final java.lang.String |
SYNONYM |
"synonym" |
public static final java.lang.String |
TERM |
"Term" |
public static final java.lang.String |
TYPEDEF |
"Typedef" |
public static final java.lang.String |
XREF_ANALOG |
"xref_analog" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ACETYLATION |
"https://www.phosphosite.org/downloads/Acetylation_site_dataset.gz" |
public static final java.lang.String |
DISEASE_ASSOC |
"https://www.phosphosite.org/downloads/Disease-associated_sites.gz" |
public static final java.lang.String |
METHYLATION |
"https://www.phosphosite.org/downloads/Methylation_site_dataset.gz" |
public static final java.lang.String |
PHOSPHORYLATION |
"https://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz" |
public static final java.lang.String |
REGULATORY |
"https://www.phosphosite.org/downloads/Regulatory_sites.gz" |
public static final java.lang.String |
SUMOYLATION |
"https://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz" |
public static final java.lang.String |
UBIQUITINATION |
"https://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
DEFAULT_DISORDER |
0.5299999713897705f |
public static final float |
DEFAULT_ORDER |
0.4699999988079071f |
public static final float |
DEFAULT_RANGE_PROBABILITY_THRESHOLD |
0.5f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ATOMRECORD |
"ATOM" |
public static final java.lang.String |
SEQRESRECORD |
"SEQRES" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BONDS_INITIAL_CAPACITY |
3 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SEC_STRUC |
"secstruc" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
DEFAULT_RESOLUTION |
99.0f |
public static final float |
DEFAULT_RFREE |
1.0f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_PDB_SERVER |
"www.rcsb.org" |
public static final java.lang.String |
PDB_SERVER_PROPERTY |
"PDB.SERVER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
62946250941673093L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
C_ATOM_NAME |
"C" |
public static final java.lang.String |
C1_ATOM_NAME |
"C1\'" |
public static final java.lang.String |
C2_ATOM_NAME |
"C2\'" |
public static final java.lang.String |
C3_ATOM_NAME |
"C3\'" |
public static final java.lang.String |
C4_ATOM_NAME |
"C4\'" |
public static final java.lang.String |
CA_ATOM_NAME |
"CA" |
public static final java.lang.String |
CB_ATOM_NAME |
"CB" |
public static final java.lang.String |
N_ATOM_NAME |
"N" |
public static final java.lang.String |
NUCLEOTIDE_REPRESENTATIVE |
"P" |
public static final java.lang.String |
O_ATOM_NAME |
"O" |
public static final java.lang.String |
O2_ATOM_NAME |
"O2\'" |
public static final java.lang.String |
O3_ATOM_NAME |
"O3\'" |
public static final java.lang.String |
O4_ATOM_NAME |
"O4\'" |
public static final java.lang.String |
O5_ATOM_NAME |
"O5\'" |
public static final java.lang.String |
OP1_ATOM_NAME |
"OP1" |
public static final java.lang.String |
OP2_ATOM_NAME |
"OP2" |
public static final java.lang.String |
P_ATOM_NAME |
"P" |
public static final double |
RATIO_RESIDUES_TO_TOTAL |
0.95 |
public static final char |
UNKNOWN_GROUP_LABEL |
88 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CHAINID_PARAM |
"chainid" |
public static final java.lang.String |
FORMAT_PARAM |
"format" |
public static final java.lang.String |
PDBID_PARAM |
"pdbid" |
public static final java.lang.String |
RESIDUES_PARAM |
"residues" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"BioJava_structure" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_CLUSTER_CUTOFF |
95 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final boolean |
isPrint |
false |
protected static final int |
nIter |
1 |
protected static final double |
zThr |
-0.1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
GLOBAL_ALIGN1 |
false |
public static final boolean |
GLOBAL_ALIGN2 |
false |
protected static final boolean |
isPrint |
true |
protected static final int |
nIter |
1 |
protected static final double |
zThr |
-0.1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jCE Circular Permutation" |
public static final java.lang.String |
version |
"1.5" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_MIN_CP_LENGTH |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jCE" |
public static final java.lang.String |
version |
"1.2" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final double |
DEFAULT_GAP_EXTENSION |
0.5 |
protected static final double |
DEFAULT_GAP_OPEN |
5.0 |
protected static final double |
DEFAULT_oRmsdThr |
2.0 |
protected static final java.lang.String |
DEFAULT_SUBSTITUTION_MATRIX |
"PRLA000101" |
protected static final double |
DISTANCE_INCREMENT |
0.5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jCE-sidechain" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jCE Optimal Circular Permutation" |
public static final java.lang.String |
version |
"1.0" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_BATCH_SIZE |
100 |
public static final int |
DEFAULT_JOB_TIME |
-1 |
public static final int |
DEFAULT_NR_ALIGNMENTS |
-1 |
public static final int |
DEFAULT_NR_THREADS |
1 |
public static final java.lang.String |
DEFAULT_PDB_PATH |
"/tmp/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jFatCat" |
public static final java.lang.String |
VERSION |
"1.1" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jFatCat_flexible" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jFatCat_rigid" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
debug |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
debug |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
debug |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
debug |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
debug |
false |
public static final boolean |
printTimeStamps |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_FRAGLEN |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
0L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
56289234782130L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
2387409854370432908L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ALIGNMENT_PANEL |
"Alignment Panel" |
public static final java.lang.String |
DIST_MATRICES |
"Show Distance Matrices" |
public static final java.lang.String |
DOT_PLOT |
"Show Dot Plot" |
public static final java.lang.String |
EQR_COLOR |
"Color By EQR" |
public static final java.lang.String |
FASTA_FORMAT |
"View FASTA Alignment" |
public static final java.lang.String |
FATCAT_BLOCK |
"Color By Alignment Block" |
public static final java.lang.String |
FATCAT_TEXT |
"View as FATCAT result" |
public static final java.lang.String |
LOAD_ALIGNMENT_XML |
"Load Alignment XML" |
public static final java.lang.String |
LOAD_DB_RESULTS |
"Load DB search results" |
public static final java.lang.String |
MULTIPLE_ALIGN |
"New Multiple Alignment" |
public static final java.lang.String |
PAIRS_ONLY |
"View Aligned Pairs" |
public static final java.lang.String |
PAIRWISE_ALIGN |
"New Pairwise Alignment" |
public static final java.lang.String |
PHYLOGENETIC_TREE |
"Phylogenetic Tree" |
public static final java.lang.String |
PRINT |
"Print" |
public static final java.lang.String |
SAVE_ALIGNMENT_XML |
"Save Alignment XML" |
public static final java.lang.String |
SELECT_EQR |
"Select Equivalent Positions" |
public static final java.lang.String |
SIMILARITY_COLOR |
"Color By Similarity" |
public static final java.lang.String |
TEXT_ONLY |
"View Text Only" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
defaultProperties |
"browser file.separator java.class.version java.vendor java.vendor.url java.version line.separator os.arch os.name os.version path.separator " |
public static final java.lang.String |
hexPropertyNames |
" file.separator line.separator path.separator " |
public static final java.lang.String |
urlPropertyNames |
" browser.vendor.url java.class.path java.home user.dir user.home user.name " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_CHAR_SIZE |
12 |
public static final int |
DEFAULT_LINE_LENGTH |
70 |
public static final int |
DEFAULT_LINE_SEPARATION |
20 |
public static final int |
DEFAULT_RIGHT_SPACER |
10 |
public static final int |
DEFAULT_X_SPACE |
20 |
public static final int |
DEFAULT_Y_SPACE |
40 |
public static final int |
DEFAULT_Y_STEP |
60 |
public static final int |
SUMMARY_POS |
20 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_CHAR_SIZE |
12 |
public static final int |
DEFAULT_LINE_LENGTH |
70 |
public static final int |
DEFAULT_LINE_SEPARATION |
20 |
public static final int |
DEFAULT_RIGHT_SPACER |
10 |
public static final int |
DEFAULT_X_SPACE |
20 |
public static final int |
DEFAULT_Y_SPACE |
40 |
public static final int |
SUMMARY_POS |
20 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final java.lang.String |
COMMAND_LINE_HELP |
"enter Jmol scripting command..." |
protected static final int |
DEFAULT_HEIGHT |
500 |
protected static final int |
DEFAULT_WIDTH |
500 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
UNKNOWN_ALGORITHM |
"unknown" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jMultipleMC" |
public static final java.lang.String |
version |
"1.1" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
AVGTM_SCORE |
"AvgTM-score" |
public static final java.lang.String |
CE_SCORE |
"CE-score" |
public static final java.lang.String |
MC_SCORE |
"MC-score" |
public static final java.lang.String |
PROBABILITY |
"Probability" |
public static final java.lang.String |
REF_RMSD |
"Ref-RMSD" |
public static final java.lang.String |
REFTM_SCORE |
"RefTM-score" |
public static final java.lang.String |
RMSD |
"RMSD" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"Smith-Waterman superposition" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
BIOL_ASSEMBLY_IDENTIFIER |
"BIO:" |
public static final java.lang.String |
CHAIN_NR_SYMBOL |
":" |
public static final java.lang.String |
CHAIN_SPLIT_SYMBOL |
"." |
public static final java.lang.String |
PDP_DOMAIN_IDENTIFIER |
"PDP:" |
public static final java.lang.String |
UNDERSCORE |
"_" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_CONNECTION_TIMEOUT |
15000 |
public static final java.lang.String |
USERAGENT |
"JFatCat Java client" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
MMCIF_FORMAT |
"mmCif" |
public static final java.lang.String |
PDB_CACHE_DIR |
"PDB_CACHE_DIR" |
public static final java.lang.String |
PDB_DIR |
"PDB_DIR" |
public static final java.lang.String |
PDB_FORMAT |
"PDB" |
public static final java.lang.String |
TMP_DIR |
"java.io.tmpdir" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_ALGORITHM_NAME |
"jFatCat_rigid" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_METHOD_NAME |
"jFatCat_rigid" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_N_SPHERE_POINTS |
960 |
public static final int |
DEFAULT_NTHREADS |
1 |
public static final double |
DEFAULT_PROBE_SIZE |
1.4 |
public static final double |
NUC_CARBON_VDW |
1.8 |
public static final double |
NUC_NITROGEN_VDW |
1.6 |
public static final double |
OXIGEN_VDW |
1.4 |
public static final double |
PHOSPHOROUS_VDW |
1.9 |
public static final double |
SULFUR_VDW |
1.85 |
public static final double |
TETRAHEDRAL_CARBON_VDW |
1.87 |
public static final double |
TETRAHEDRAL_NITROGEN_VDW |
1.5 |
public static final double |
TRIGONAL_CARBON_VDW |
1.76 |
public static final double |
TRIGONAL_NITROGEN_VDW |
1.65 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_VERSION |
"4_1_0" |
public static final java.lang.String |
LATEST_VERSION |
"4_1_0" |
public static final java.lang.String |
VERSION_3_5_0 |
"3_5_0" |
public static final java.lang.String |
VERSION_4_0_0 |
"4_0_0" |
public static final java.lang.String |
VERSION_4_1_0 |
"4_1_0" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CATH_DOWNLOAD_ALL_RELEASES_DIR |
"all-releases" |
public static final java.lang.String |
CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR |
"cath-classification-data" |
public static final java.lang.String |
CATH_DOWNLOAD_URL |
"http://download.cathdb.info/cath/releases/" |
public static final java.lang.String |
DEFAULT_VERSION |
"4_1_0" |
public static final java.lang.String |
domainDescriptionFileName |
"cath-domain-description-file-v%s.txt" |
public static final java.lang.String |
domainListFileName |
"cath-domain-list-v%s.txt" |
public static final java.lang.String |
domallFileName |
"cath-domain-boundaries-v%s.txt" |
public static final java.lang.String |
nodeListFileName |
"cath-names-v%s.txt" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_ASA_SPHERE_POINTS |
3000 |
public static final double |
DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF |
0.2 |
public static final int |
DEFAULT_MIN_COFACTOR_SIZE |
40 |
public static final double |
DEFAULT_MINIMUM_INTERFACE_AREA |
35.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_PDB_API_URL |
"http://www.rcsb.org/pdb/rest/" |
public static final java.lang.String |
DEFAULT_PDB_HOST |
"http://www.rcsb.org" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_SERVER |
"http://source.rcsb.org/jfatcatserver/domains/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final float |
CUT_OFF_VALUE |
0.5f |
public static final float |
CUT_OFF_VALUE1 |
0.28999999165534973f |
public static final float |
CUT_OFF_VALUE1M |
0.20999999344348907f |
public static final float |
CUT_OFF_VALUE1S |
0.1899999976158142f |
public static final float |
CUT_OFF_VALUE2 |
0.4399999976158142f |
public static final float |
DBL |
0.05000000074505806f |
public static final int |
ENDS |
12 |
public static final int |
ENDSEND |
9 |
public static final int |
MAX_CUTS |
80 |
public static final int |
MAXCONT |
900 |
public static final int |
MAXDOM |
30 |
public static final int |
MAXLEN |
3200 |
public static final int |
MAXSIZE |
350 |
public static final int |
MIN_DOMAIN_LENGTH |
35 |
public static final float |
RG |
0.0f |
public static final float |
RG1 |
1.0f |
public static final float |
TD |
25.0f |
public static final float |
TD1 |
40.0f |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_VERSION |
"latest" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_VERSION |
"latest" |
public static final java.lang.String |
DOMAINS_PATH |
"/ecod/distributions/" |
public static final java.lang.String |
ECOD_URL |
"http://prodata.swmed.edu" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
F_UNCLASSIFIED |
"F_UNCLASSIFIED" |
public static final java.lang.String |
IS_DOMAIN_ASSEMBLY |
"IS_DOMAIN_ASSEMBLY" |
public static final java.lang.String |
IS_REPRESENTATIVE |
"MANUAL_REP" |
public static final java.lang.String |
NOT_DOMAIN_ASSEMBLY |
"NOT_DOMAIN_ASSEMBLY" |
public static final java.lang.String |
NOT_REPRESENTATIVE |
"AUTO_NONREP" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
adapter |
"org.jmol.api.JmolAdapter" |
public static final java.lang.String |
smartAdapter |
"org.jmol.adapter.smarter.SmarterJmolAdapter" |
public static final java.lang.String |
viewer |
"org.jmol.api.JmolSimpleViewer" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
adapter |
"org.jmol.api.JmolAdapter" |
public static final java.lang.String |
smartAdapter |
"org.jmol.adapter.smarter.SmarterJmolAdapter" |
public static final java.lang.String |
viewer |
"org.jmol.api.JmolSimpleViewer" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
SLIDER_STEPS |
8 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MAX_SCALE |
10 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
EQUIVALENT |
1 |
public static final int |
NOT_ALIGNED |
0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_X_RIGHT_BORDER |
40 |
public static final int |
DEFAULT_X_START |
10 |
public static final int |
DEFAULT_Y_BOTTOM |
16 |
public static final int |
DEFAULT_Y_HEIGHT |
8 |
public static final int |
DEFAULT_Y_START |
0 |
public static final int |
DEFAULT_Y_STEP |
10 |
public static final int |
LINE_HEIGHT |
10 |
public static final int |
MINIMUM_HEIGHT |
20 |
public static final int |
SIZE |
20 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
BLACK_WHITE_GRADIENT |
1 |
public static final int |
RAINBOW_GRADIENT |
4 |
public static final int |
RAINBOW_INTENSITY_GRADIENT |
5 |
public static final int |
RED_BLUE_GRADIENT |
3 |
public static final int |
WHITE_BLACK_GRADIENT |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CS_HSV |
1007 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
GAP_COVERAGE_THRESHOLD |
0.3 |
public static final double |
IDENTITY_THRESHOLD |
0.99999 |
public static final double |
RATIO_GAPS_FOR_MISMATCH |
0.5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
ATOM_CA_THRESHOLD |
500000 |
public static final int |
MAX_ATOMS |
2147483647 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_PDB_FILE_SERVER |
"http://ftp.wwpdb.org" |
public static final java.lang.String |
PDB_FILE_SERVER_PROPERTY |
"PDB.FILE.SERVER" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
219047230178423923L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
COMPONENTS_FILE_LOCATION |
"pub/pdb/data/monomers/components.cif.gz" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
CHEM_COMP_CACHE_DIRECTORY |
"chemcomp" |
public static final java.lang.String |
SERVER_LOCATION |
"http://files.rcsb.org/ligands/download/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
MMCIF_DEFAULT_VALUE |
"." |
public static final java.lang.String |
MMCIF_MISSING_VALUE |
"?" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
COMMENT_CHAR |
"#" |
public static final java.lang.String |
FIELD_LINE |
"_" |
public static final java.lang.String |
LOOP_START |
"loop_" |
public static final java.lang.String |
MMCIF_TOP_HEADER |
"data_" |
public static final java.lang.String |
STRING_LIMIT |
";" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
BIO_ASSEMBLY |
"bioAssembly?structureId=%s&nr=%s" |
public static final java.lang.String |
DEFAULT_SERVERNAME |
"http://pepper.rcsb.org:8080/pdb/rest/biolassembly/" |
public static final java.lang.String |
NR_BIOL_APPEND |
"nrBiolAssemblies?structureId=%s" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SERVICELOCATION |
"http://www.rcsb.org/pdb/rest/search" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
baseURL |
"ftp://ftp.rcsb.org/pub/pdb/data/status/latest/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DEFAULT_SERVER |
"http://source.rcsb.org/jfatcatserver/domains/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
LATEST_VERSION |
"2.05" |
public static final java.lang.String |
VERSION_1_55 |
"1.55" |
public static final java.lang.String |
VERSION_1_57 |
"1.57" |
public static final java.lang.String |
VERSION_1_59 |
"1.59" |
public static final java.lang.String |
VERSION_1_61 |
"1.61" |
public static final java.lang.String |
VERSION_1_63 |
"1.63" |
public static final java.lang.String |
VERSION_1_65 |
"1.65" |
public static final java.lang.String |
VERSION_1_67 |
"1.67" |
public static final java.lang.String |
VERSION_1_69 |
"1.69" |
public static final java.lang.String |
VERSION_1_71 |
"1.71" |
public static final java.lang.String |
VERSION_1_73 |
"1.73" |
public static final java.lang.String |
VERSION_1_75 |
"1.75" |
public static final java.lang.String |
VERSION_1_75A |
"2.01" |
public static final java.lang.String |
VERSION_1_75B |
"2.02" |
public static final java.lang.String |
VERSION_1_75C |
"2.03" |
public static final java.lang.String |
VERSION_2_0_1 |
"2.01" |
public static final java.lang.String |
VERSION_2_0_2 |
"2.02" |
public static final java.lang.String |
VERSION_2_0_3 |
"2.03" |
public static final java.lang.String |
VERSION_2_0_4 |
"2.04" |
public static final java.lang.String |
VERSION_2_0_5 |
"2.05" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
claFileName |
"dir.cla.scop.txt_" |
public static final java.lang.String |
comFileName |
"dir.com.scop.txt_" |
public static final java.lang.String |
DEFAULT_VERSION |
"1.75" |
public static final java.lang.String |
desFileName |
"dir.des.scop.txt_" |
public static final java.lang.String |
hieFileName |
"dir.hie.scop.txt_" |
public static final java.lang.String |
SCOP_DOWNLOAD |
"http://scop.berkeley.edu/downloads/parse/" |
public static final java.lang.String |
SCOP_DOWNLOAD_ALTERNATE |
"http://scop.berkeley.edu/downloads/parse/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
CA_MIN_DIST |
9.0 |
public static final double |
HBONDHIGHENERGY |
-500.0 |
public static final int |
HBONDLOWENERGY |
-9900 |
public static final double |
MAX_PEPTIDE_BOND_LENGTH |
2.5 |
public static final double |
MINDIST |
0.5 |
public static final double |
Q |
-27888.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
BIOJAVA_ASSIGNMENT |
"BIOJAVA_ASSIGNMENT" |
public static final java.lang.String |
DSSP_ASSIGNMENT |
"DSSP_ASSIGNMENT" |
public static final java.lang.String |
PDB_AUTHOR_ASSIGNMENT |
"PDB_AUTHOR_ASSIGNMENT" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
algorithmName |
"jCE-symm" |
public static final java.lang.String |
version |
"2.2" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_SYMMETRY_THRESHOLD |
0.4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEF_NUM_CELLS |
12 |
public static final double |
DEFAULT_INTERFACE_DISTANCE_CUTOFF |
5.5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MIN_VALID_CELL_SIZE |
10.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final double |
DELTA |
1.0E-7 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
WAIT_INCREMENT |
3000L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
HMMER_SERVICE |
"https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ALL_PFAMS_ENCOUNTERED_SUFFIX |
"_all_encountered_pfams" |
public static final java.lang.String |
ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX |
"_all_encountered_pfams_with_go_annotation" |
public static final java.lang.String |
ALL_PFAMS_GAINED_AS_DC_SUFFIX |
"_all_pfams_gained_as_dc" |
public static final java.lang.String |
ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX |
"_all_pfams_gained_as_domains" |
public static final java.lang.String |
ALL_PFAMS_LOST_AS_DC_SUFFIX |
"_all_pfams_lost_as_dc" |
public static final java.lang.String |
ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX |
"_all_pfams_lost_as_domains" |
public static final java.lang.String |
BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES |
"PER_NODE_EVENTS" |
public static final java.lang.String |
BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES |
"PER_SUBTREE_EVENTS" |
public static final java.lang.String |
BDC_PRESENT_NEXUS |
"_dc.nex" |
public static final java.lang.String |
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO |
"_dc_dollo.xml" |
public static final java.lang.String |
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH |
"_dc_fitch.xml" |
public static final java.lang.String |
BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED |
"_dc_MAPPED_secondary_features_fitch.xml" |
public static final java.lang.String |
D_PROMISCUITY_FILE_SUFFIX |
"_domain_promiscuities" |
public static final java.lang.String |
DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX |
".dcc" |
public static final java.lang.String |
DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION |
"dcc" |
public static final java.lang.String |
DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS |
"graph_analysis_out" |
public static final java.lang.String |
DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS |
"_dc.dot" |
public static final java.lang.String |
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO |
"_d_dollo.xml" |
public static final java.lang.String |
DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH |
"_d_fitch.xml" |
public static final java.lang.String |
DOMAINS_PRESENT_NEXUS |
"_dom.nex" |
public static final java.lang.String |
ENCOUNTERED_PFAMS_SUMMARY_SUFFIX |
"_encountered_pfams_summary" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX |
"_indep_dc_gains_fitch_counts_MAPPED.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX |
"_indep_dc_gains_fitch_counts.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX |
"_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX |
"_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX |
"_indep_dc_gains_fitch_lists_for_go_mapping.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX |
"_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX |
"_indep_dc_gains_fitch_lists_MAPPED.txt" |
public static final java.lang.String |
INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX |
"_indep_dc_gains_fitch_lists.txt" |
public static final int |
MAX_ALLOWED_OVERLAP_DEFAULT |
-1 |
public static final java.lang.String |
NEXUS_EXTERNAL_DOMAIN_COMBINATIONS |
"_dc.nex" |
public static final java.lang.String |
NEXUS_EXTERNAL_DOMAINS |
"_dom.nex" |
public static final java.lang.String |
NEXUS_SECONDARY_FEATURES |
"_secondary_features.nex" |
public static final java.lang.String |
PAIRWISE_DOMAIN_COMPARISONS_PREFIX |
"pwc_" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES |
"_dollo_goid_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_GAINS_D |
"_dollo_gains_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D |
"_dollo_gains_d.html" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES |
"_dollo_gains_secondary_features" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_LOSSES_D |
"_dollo_losses_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D |
"_dollo_losses_d.html" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES |
"_dollo_losses_secondary_features" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_PRESENT_D |
"_dollo_present_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D |
"_dollo_present_d.html" |
public static final java.lang.String |
PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES |
"_dollo_present_secondary_features" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES |
"_fitch_goid_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_GAINS_BC |
"_fitch_gains_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC |
"_fitch_gains_dc.html" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_LOSSES_BC |
"_fitch_losses_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC |
"_fitch_losses_dc.html" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_PRESENT_BC |
"_fitch_present_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS |
"_fitch_present_dc.dot" |
public static final java.lang.String |
PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC |
"_fitch_present_dc.html" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS |
"_dollo_glc_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS |
"_dollo_glc_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES |
"_dollo_glc_secondary_features" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS |
"_fitch_glc_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS |
"_fitch_glc_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS |
"_dollo_gl_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS |
"_dollo_gl_d" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES |
"_dollo_gl_secondary_features" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS |
"_fitch_gl_dc" |
public static final java.lang.String |
PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS |
"_fitch_gl_d" |
public static final java.lang.String |
PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX |
"_plus_minus_go_ids_all.txt" |
public static final double |
PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT |
1.0 |
public static final int |
PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT |
0 |
public static final java.lang.String |
PLUS_MINUS_ANALYSIS_OPTION |
"plus_minus" |
public static final java.lang.String |
PLUS_MINUS_DC_SUFFIX_HTML |
"_plus_minus_dc.html" |
public static final java.lang.String |
PLUS_MINUS_DOM_SUFFIX |
"_plus_minus_dom.txt" |
public static final java.lang.String |
PLUS_MINUS_DOM_SUFFIX_HTML |
"_plus_minus_dom.html" |
public static final java.lang.String |
PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX |
"_plus_minus_go_ids_passing.txt" |
public static final java.lang.String |
PRG_NAME |
"surfacing" |
public static final java.lang.String |
SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO |
"_secondary_features_dollo.xml" |
public static final java.lang.String |
SEQ_EXTRACT_SUFFIX |
".prot" |
public static final boolean |
VERBOSE |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MIN_LENGTH |
85 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEBUG |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
NAME |
"ArchaeopteryxA" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
__RELEASE |
false |
public static final boolean |
__SNAPSHOT_RELEASE |
false |
public static final boolean |
__SYNTH_LF |
false |
public static final boolean |
ALLOW_DDBJ_BLAST |
false |
public static final boolean |
NH_PARSING_IGNORE_QUOTES_DEFAULT |
false |
public static final java.lang.String |
PRG_NAME |
"Archaeopteryx" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
serialVersionUID |
62256323L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ANNOTATION |
"Annotation" |
public static final java.lang.String |
BACKGROUND |
"Background" |
public static final java.lang.String |
BACKGROUND_GRADIENT_BOTTOM |
"Background Gradient Bottom" |
public static final java.lang.String |
BINARY_DOMAIN_COMBINATIONS |
"Binary Domain Combinations" |
public static final java.lang.String |
BRANCH |
"Branch" |
public static final java.lang.String |
BRANCH_LENGTH |
"Branch Length" |
public static final java.lang.String |
COLLAPSED |
"Collapsed" |
public static final java.lang.String |
CONFIDENCE |
"Confidence" |
public static final java.lang.String |
DOMAIN_BASE |
"Domain Base" |
public static final java.lang.String |
DOMAIN_LABEL |
"Domain Label" |
public static final java.lang.String |
DUPLICATION |
"Duplication" |
public static final java.lang.String |
DUPLICATION_OR_SPECATION |
"Duplication or Specation" |
public static final java.lang.String |
MATCHING_NODES_A |
"Matching A" |
public static final java.lang.String |
MATCHING_NODES_A_AND_B |
"Matching A and B" |
public static final java.lang.String |
MATCHING_NODES_B |
"Matching B" |
public static final java.lang.String |
NODE_BOX |
"Node Box" |
public static final java.lang.String |
OVERVIEW |
"Overview" |
public static final java.lang.String |
SEQUENCE |
"Sequence" |
public static final java.lang.String |
SPECIATION |
"Speciation" |
public static final java.lang.String |
TAXONOMY |
"Taxonomy" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
SPECIAL_DOMAIN_COLORING |
true |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_WIDTH |
400 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
VECTOR_DEFAULT_WIDTH |
120 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final long |
RANDOM_NUMBER_SEED_DEFAULT |
42L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
MSA_FILE_SUFFIX |
".aln" |
public static final java.lang.String |
PWD_FILE_SUFFIX |
".pwd" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEBUG |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
QUERY_PLACEHOLDER |
"__query__" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
PFAM_INST |
"pfam" |
public static final java.lang.String |
PFAM_NAME |
"Pfam" |
public static final java.lang.String |
PFAM_SERVER |
"http://pfam.xfam.org" |
public static final java.lang.String |
TOL_NAME |
"Tree of Life (ToL)" |
public static final java.lang.String |
TOL_URL_BASE |
"http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=" |
public static final java.lang.String |
TOL_WEBSERVER |
"http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=__query__" |
public static final java.lang.String |
TREE_BASE_DESC |
"This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment." |
public static final java.lang.String |
TREE_BASE_INST |
"treebase" |
public static final java.lang.String |
TREE_BASE_NAME |
"TreeBASE" |
public static final java.lang.String |
TREE_FAM_INST |
"tree_fam" |
public static final java.lang.String |
TREE_FAM_NAME |
"TreeFam" |
public static final java.lang.String |
TREE_FAM_URL_BASE |
"http://www.treefam.org/family/TF" |
public static final java.lang.String |
TREEBASE_PHYLOWS_STUDY_URL_BASE |
"http://purl.org/phylo/treebase/phylows/study/TB2:S" |
public static final java.lang.String |
TREEBASE_PHYLOWS_TREE_URL_BASE |
"http://purl.org/phylo/treebase/phylows/tree/TB2:Tr" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA |
10.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
FACTOR |
1000000 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
FACTOR |
1000000 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
BIOLOGICAL_PROCESS_STR |
"biological_process" |
public static final java.lang.String |
CELLULAR_COMPONENT_STR |
"cellular_component" |
public static final java.lang.String |
MOLECULAR_FUNCTION_STR |
"molecular_function" |
public static final java.lang.String |
UNASSIGNED_STR |
"unassigned" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
HAS_PART_STR |
"has_part" |
public static final java.lang.String |
NEGATIVELY_REGULATES_STR |
"negatively_regulates" |
public static final java.lang.String |
OCCURS_IN_STR |
"occurs_in" |
public static final java.lang.String |
PART_OF_STR |
"part_of" |
public static final java.lang.String |
POSITIVELY_REGULATES_STR |
"positively_regulates" |
public static final java.lang.String |
REGULATES_STR |
"regulates" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
GOSLIM_ASPERGILLUS_STR |
"goslim_aspergillus" |
public static final java.lang.String |
GOSLIM_CANDIDA_STR |
"goslim_candida" |
public static final java.lang.String |
GOSLIM_GENERIC_STR |
"goslim_generic" |
public static final java.lang.String |
GOSLIM_GOA_STR |
"goslim_goa" |
public static final java.lang.String |
GOSLIM_PIR_STR |
"goslim_pir" |
public static final java.lang.String |
GOSLIM_PLANT_STR |
"goslim_plant" |
public static final java.lang.String |
GOSLIM_POMBE_STR |
"goslim_pombe" |
public static final java.lang.String |
GOSLIM_YEAST_STR |
"goslim_yeast" |
public static final java.lang.String |
GOSUBSET_PROK_STR |
"gosubset_prok" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ARACYC_STR |
"AraCyc" |
public static final java.lang.String |
CORUM_STR |
"CORUM" |
public static final java.lang.String |
EC_STR |
"EC" |
public static final java.lang.String |
GOC_STR |
"GOC" |
public static final java.lang.String |
IMG_STR |
"IMG" |
public static final java.lang.String |
KEGG_STR |
"KEGG" |
public static final java.lang.String |
META_CYC_STR |
"MetaCyc" |
public static final java.lang.String |
NIF_SUBCELLULAR_STR |
"NIF_Subcellular" |
public static final java.lang.String |
PMID_STR |
"PMID" |
public static final java.lang.String |
PO_STR |
"PO" |
public static final java.lang.String |
REACTOME_STR |
"Reactome" |
public static final java.lang.String |
RESID_STR |
"RESID" |
public static final java.lang.String |
RHEA_STR |
"RHEA" |
public static final java.lang.String |
SABIO_RK_STR |
"SABIO-RK" |
public static final java.lang.String |
TC_STR |
"TC" |
public static final java.lang.String |
UM_BBD_ENZYME_ID_STR |
"UM-BBD_enzymeID" |
public static final java.lang.String |
UM_BBD_PATHWAY_ID_STR |
"UM-BBD_pathwayID" |
public static final java.lang.String |
UM_BBD_REACTIONID_STR |
"UM-BBD_reactionID" |
public static final java.lang.String |
UNIPATHWAY_STR |
"UniPathway" |
public static final java.lang.String |
WIKIPEDIA_STR |
"Wikipedia" |
public static final java.lang.String |
XX_STR |
"XX" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
BEGIN_CHARACTERS |
"Begin Characters;" |
public static final java.lang.String |
BEGIN_DATA |
"Begin Data;" |
public static final java.lang.String |
BEGIN_TAXA |
"Begin Taxa;" |
public static final java.lang.String |
BEGIN_TREES |
"Begin Trees;" |
public static final java.lang.String |
CHARSTATELABELS |
"CharStateLabels" |
public static final java.lang.String |
DATATYPE |
"DataType" |
public static final java.lang.String |
DIMENSIONS |
"Dimensions" |
public static final java.lang.String |
END |
"End;" |
public static final java.lang.String |
FORMAT |
"Format" |
public static final java.lang.String |
MATRIX |
"Matrix" |
public static final java.lang.String |
NCHAR |
"NChar" |
public static final java.lang.String |
NEXUS |
"#NEXUS" |
public static final java.lang.String |
NTAX |
"NTax" |
public static final java.lang.String |
STANDARD |
"Standard" |
public static final java.lang.String |
SYMBOLS |
"Symbols" |
public static final java.lang.String |
TAXLABELS |
"TaxLabels" |
public static final java.lang.String |
TRANSLATE |
"Translate" |
public static final java.lang.String |
TREE |
"Tree" |
public static final java.lang.String |
UTREE |
"UTREE" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
REPLACE_UNDERSCORES_DEFAULT |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
DOMAIN_STRUCTURE |
"DS=" |
public static final java.lang.String |
GENE_NAME |
"GN=" |
public static final java.lang.String |
IS_DUPLICATION |
"D=" |
public static final java.lang.String |
SEQUENCE_ACCESSION |
"AC=" |
public static final java.lang.String |
SPECIES_NAME |
"S=" |
public static final java.lang.String |
SUPPORT |
"B=" |
public static final java.lang.String |
TAXONOMY_ID |
"T=" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ACCESSION |
"accession" |
public static final java.lang.String |
ACCESSION_COMMENT_ATTR |
"comment" |
public static final java.lang.String |
ACCESSION_SOURCE_ATTR |
"source" |
public static final java.lang.String |
ANNOTATION |
"annotation" |
public static final java.lang.String |
ANNOTATION_DESC |
"desc" |
public static final java.lang.String |
ANNOTATION_EVIDENCE_ATTR |
"evidence" |
public static final java.lang.String |
ANNOTATION_REF_ATTR |
"ref" |
public static final java.lang.String |
ANNOTATION_SOURCE_ATTR |
"source" |
public static final java.lang.String |
ANNOTATION_TYPE_ATTR |
"type" |
public static final java.lang.String |
BINARY_CHARACTER |
"bc" |
public static final java.lang.String |
BINARY_CHARACTERS |
"binary_characters" |
public static final java.lang.String |
BINARY_CHARACTERS_GAINED |
"gained" |
public static final java.lang.String |
BINARY_CHARACTERS_GAINED_COUNT_ATTR |
"gained_count" |
public static final java.lang.String |
BINARY_CHARACTERS_LOST |
"lost" |
public static final java.lang.String |
BINARY_CHARACTERS_LOST_COUNT_ATTR |
"lost_count" |
public static final java.lang.String |
BINARY_CHARACTERS_PRESENT |
"present" |
public static final java.lang.String |
BINARY_CHARACTERS_PRESENT_COUNT_ATTR |
"present_count" |
public static final java.lang.String |
BINARY_CHARACTERS_TYPE_ATTR |
"type" |
public static final java.lang.String |
BRANCH_LENGTH |
"branch_length" |
public static final java.lang.String |
CLADE |
"clade" |
public static final java.lang.String |
CLADE_DATE |
"date" |
public static final java.lang.String |
CLADE_DATE_DESC |
"desc" |
public static final java.lang.String |
CLADE_DATE_MAX |
"maximum" |
public static final java.lang.String |
CLADE_DATE_MIN |
"minimum" |
public static final java.lang.String |
CLADE_DATE_UNIT |
"unit" |
public static final java.lang.String |
CLADE_DATE_VALUE |
"value" |
public static final java.lang.String |
COLOR |
"color" |
public static final java.lang.String |
COLOR_BLUE |
"blue" |
public static final java.lang.String |
COLOR_GREEN |
"green" |
public static final java.lang.String |
COLOR_RED |
"red" |
public static final java.lang.String |
CONFIDENCE |
"confidence" |
public static final java.lang.String |
CONFIDENCE_SD_ATTR |
"stddev" |
public static final java.lang.String |
CONFIDENCE_TYPE_ATTR |
"type" |
public static final java.lang.String |
DISTRIBUTION |
"distribution" |
public static final java.lang.String |
DISTRIBUTION_DESC |
"desc" |
public static final java.lang.String |
EVENT_DUPLICATIONS |
"duplications" |
public static final java.lang.String |
EVENT_LOSSES |
"losses" |
public static final java.lang.String |
EVENT_SPECIATIONS |
"speciations" |
public static final java.lang.String |
EVENT_TYPE |
"type" |
public static final java.lang.String |
EVENTS |
"events" |
public static final java.lang.String |
ID_REF |
"id_ref" |
public static final java.lang.String |
IDENTIFIER |
"id" |
public static final java.lang.String |
IDENTIFIER_PROVIDER_ATTR |
"provider" |
public static final java.lang.String |
NODE_COLLAPSE |
"collapse" |
public static final java.lang.String |
NODE_NAME |
"name" |
public static final java.lang.String |
PHYLOGENY |
"phylogeny" |
public static final java.lang.String |
PHYLOGENY_BRANCHLENGTH_UNIT_ATTR |
"branch_length_unit" |
public static final java.lang.String |
PHYLOGENY_DESCRIPTION |
"description" |
public static final java.lang.String |
PHYLOGENY_IS_REROOTABLE_ATTR |
"rerootable" |
public static final java.lang.String |
PHYLOGENY_IS_ROOTED_ATTR |
"rooted" |
public static final java.lang.String |
PHYLOGENY_NAME |
"name" |
public static final java.lang.String |
PHYLOGENY_TYPE_ATTR |
"type" |
public static final java.lang.String |
POINT |
"point" |
public static final java.lang.String |
POINT_ALTITUDE |
"alt" |
public static final java.lang.String |
POINT_ALTITUDE_UNIT_ATTR |
"alt_unit" |
public static final java.lang.String |
POINT_GEODETIC_DATUM |
"geodetic_datum" |
public static final java.lang.String |
POINT_LATITUDE |
"lat" |
public static final java.lang.String |
POINT_LONGITUDE |
"long" |
public static final java.lang.String |
POLYGON |
"polygon" |
public static final java.lang.String |
PROPERTY |
"property" |
public static final java.lang.String |
PROPERTY_APPLIES_TO |
"applies_to" |
public static final java.lang.String |
PROPERTY_DATATYPE |
"datatype" |
public static final java.lang.String |
PROPERTY_REF |
"ref" |
public static final java.lang.String |
PROPERTY_UNIT |
"unit" |
public static final java.lang.String |
REFERENCE |
"reference" |
public static final java.lang.String |
REFERENCE_DESC |
"desc" |
public static final java.lang.String |
REFERENCE_DOI_ATTR |
"doi" |
public static final java.lang.String |
SEQUENCE |
"sequence" |
public static final java.lang.String |
SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN |
"domain" |
public static final java.lang.String |
SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH |
"length" |
public static final java.lang.String |
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE |
"confidence" |
public static final java.lang.String |
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM |
"from" |
public static final java.lang.String |
SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO |
"to" |
public static final java.lang.String |
SEQUENCE_DOMAIN_ARCHITECURE |
"domain_architecture" |
public static final java.lang.String |
SEQUENCE_GENE_NAME |
"gene_name" |
public static final java.lang.String |
SEQUENCE_LOCATION |
"location" |
public static final java.lang.String |
SEQUENCE_MOL_SEQ |
"mol_seq" |
public static final java.lang.String |
SEQUENCE_MOL_SEQ_ALIGNED_ATTR |
"is_aligned" |
public static final java.lang.String |
SEQUENCE_NAME |
"name" |
public static final java.lang.String |
SEQUENCE_RELATION |
"sequence_relation" |
public static final java.lang.String |
SEQUENCE_RELATION_DISTANCE |
"distance" |
public static final java.lang.String |
SEQUENCE_RELATION_ID_REF0 |
"id_ref_0" |
public static final java.lang.String |
SEQUENCE_RELATION_ID_REF1 |
"id_ref_1" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE |
"type" |
public static final java.lang.String |
SEQUENCE_SOURCE_ID |
"id_source" |
public static final java.lang.String |
SEQUENCE_SYMBOL |
"symbol" |
public static final java.lang.String |
SEQUENCE_TYPE |
"type" |
public static final java.lang.String |
SEQUENCE_X_REFS |
"cross_references" |
public static final java.lang.String |
TAXONOMY |
"taxonomy" |
public static final java.lang.String |
TAXONOMY_AUTHORITY |
"authority" |
public static final java.lang.String |
TAXONOMY_CODE |
"code" |
public static final java.lang.String |
TAXONOMY_COMMON_NAME |
"common_name" |
public static final java.lang.String |
TAXONOMY_RANK |
"rank" |
public static final java.lang.String |
TAXONOMY_SCIENTIFIC_NAME |
"scientific_name" |
public static final java.lang.String |
TAXONOMY_SYNONYM |
"synonym" |
public static final java.lang.String |
TYPE_ATTR |
"type" |
public static final java.lang.String |
URI |
"uri" |
public static final java.lang.String |
URI_DESC_ATTR |
"desc" |
public static final java.lang.String |
WIDTH |
"width" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
APACHE_FEATURES_VALIDATION_SCHEMA |
"http://apache.org/xml/features/validation/schema" |
public static final java.lang.String |
APACHE_FEATURES_VALIDATION_SCHEMA_FULL |
"http://apache.org/xml/features/validation/schema-full-checking" |
public static final java.lang.String |
APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION |
"http://apache.org/xml/properties/schema/external-schemaLocation" |
public static final java.lang.String |
JAXP_SCHEMA_LANGUAGE |
"http://java.sun.com/xml/jaxp/properties/schemaLanguage" |
public static final java.lang.String |
JAXP_SCHEMA_SOURCE |
"http://java.sun.com/xml/jaxp/properties/schemaSource" |
public static final java.lang.String |
SAX_FEATURES_VALIDATION |
"http://xml.org/sax/features/validation" |
public static final java.lang.String |
W3C_XML_SCHEMA |
"http://www.w3.org/2001/XMLSchema" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
OTHER |
"other" |
public static final int |
ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT |
9 |
public static final java.lang.String |
SEQ_TYPE_DNA |
"dna" |
public static final java.lang.String |
SEQ_TYPE_PROTEIN |
"protein" |
public static final java.lang.String |
SEQ_TYPE_RNA |
"rna" |
public static final java.lang.String |
UNIPROT_TAX_PROVIDER |
"uniprot" |
public static final java.lang.String |
UNKNOWN |
"unknown" |
public static final java.lang.String |
VECTOR_PROPERTY_REF |
"vector:index=" |
public static final java.lang.String |
VECTOR_PROPERTY_TYPE |
"xsd:decimal" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
DEBUG |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
APACHE_FEATURES_VALIDATION_SCHEMA |
"http://apache.org/xml/features/validation/schema" |
public static final java.lang.String |
APACHE_FEATURES_VALIDATION_SCHEMA_FULL |
"http://apache.org/xml/features/validation/schema-full-checking" |
public static final java.lang.String |
APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION |
"http://apache.org/xml/properties/schema/external-schemaLocation" |
public static final java.lang.String |
JAXP_SCHEMA_LANGUAGE |
"http://java.sun.com/xml/jaxp/properties/schemaLanguage" |
public static final java.lang.String |
JAXP_SCHEMA_SOURCE |
"http://java.sun.com/xml/jaxp/properties/schemaSource" |
public static final java.lang.String |
SAX_FEATURES_VALIDATION |
"http://xml.org/sax/features/validation" |
public static final java.lang.String |
W3C_XML_SCHEMA |
"http://www.w3.org/2001/XMLSchema" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
AUTHDATE |
"AUTHDATE" |
public static final java.lang.String |
AUTHORITY |
"AUTHORITY" |
public static final java.lang.String |
CLADE |
"NODE" |
public static final java.lang.String |
NODE_ID_ATTR |
"ID" |
public static final java.lang.String |
NODE_ITALICIZENAME_ATTR |
"ITALICIZENAME" |
public static final java.lang.String |
OTHERNAME |
"OTHERNAME" |
public static final java.lang.String |
OTHERNAME_NAME |
"NAME" |
public static final java.lang.String |
OTHERNAMES |
"OTHERNAMES" |
public static final java.lang.String |
PHYLOGENY |
"TREE" |
public static final java.lang.String |
TAXONOMY_NAME |
"NAME" |
public static final java.lang.String |
TOL_TAXONOMY_ID_TYPE |
"tol" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
TAX_CODE |
"(?:[A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA" |
public static final java.lang.String |
TAX_CODE_LO |
"(?:[A-Z]{5})|RAT|PIG|PEA" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
INDENT_PHYLOXML_DEAFULT |
true |
public static final java.lang.String |
PHYLO_XML_END |
"</phyloxml>" |
public static final java.lang.String |
PHYLO_XML_INTENDATION_BASE |
" " |
public static final java.lang.String |
PHYLO_XML_NAMESPACE_LINE |
"<phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd\" xmlns=\"http://www.phyloxml.org\">" |
public static final java.lang.String |
PHYLO_XML_VERSION_ENCODING_LINE |
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MIN_ALLOWED_BL_VALUE |
0.001 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MAX_ALLOWED_BL_VALUE |
1.0 |
public static final double |
MIN_ALLOWED_BL_VALUE |
1.0E-4 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final boolean |
ALLOW_MULTIPLE_PARENTS_DEFAULT |
false |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
COUNT_DEFAULT |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
BRANCH_WIDTH_DEFAULT_VALUE |
1.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CONFIDENCE_DEFAULT_VALUE |
-9999 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
NHX_SEPARATOR |
">" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_VALUE |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
APTX_VISUALIZATION_REF |
"style:" |
public static final int |
DEFAULT_SIZE |
-1 |
public static final java.lang.String |
FONT_COLOR_REF |
"style:font_color" |
public static final java.lang.String |
FONT_COLOR_TYPE |
"xsd:token" |
public static final java.lang.String |
FONT_REF |
"style:font" |
public static final java.lang.String |
FONT_SIZE_REF |
"style:font_size" |
public static final java.lang.String |
FONT_SIZE_TYPE |
"xsd:unsignedByte" |
public static final java.lang.String |
FONT_STYLE_BOLD |
"bold" |
public static final java.lang.String |
FONT_STYLE_BOLD_ITALIC |
"bold_italic" |
public static final java.lang.String |
FONT_STYLE_ITALIC |
"italic" |
public static final java.lang.String |
FONT_STYLE_PLAIN |
"plain" |
public static final java.lang.String |
FONT_STYLE_REF |
"style:font_style" |
public static final java.lang.String |
FONT_STYLE_TYPE |
"xsd:token" |
public static final java.lang.String |
FONT_TYPE |
"xsd:token" |
public static final java.lang.String |
NODE_COLOR_REF |
"style:node_color" |
public static final java.lang.String |
NODE_COLOR_TYPE |
"xsd:token" |
public static final java.lang.String |
NODE_FILL_GRADIENT |
"gradient" |
public static final java.lang.String |
NODE_FILL_NONE |
"none" |
public static final java.lang.String |
NODE_FILL_SOLID |
"solid" |
public static final java.lang.String |
NODE_FILL_TYPE_REF |
"style:node_fill_type" |
public static final java.lang.String |
NODE_FILL_TYPE_TYPE |
"xsd:token" |
public static final java.lang.String |
NODE_SHAPE_CIRCLE |
"circle" |
public static final java.lang.String |
NODE_SHAPE_RECTANGLE |
"rectangle" |
public static final java.lang.String |
NODE_SHAPE_REF |
"style:node_shape" |
public static final java.lang.String |
NODE_SHAPE_TYPE |
"xsd:token" |
public static final java.lang.String |
NODE_SIZE_REF |
"style:node_size" |
public static final java.lang.String |
NODE_SIZE_TYPE |
"xsd:float" |
public static final java.lang.String |
NODE_TRANSPARENCY_REF |
"style:node_transparency" |
public static final java.lang.String |
NODE_TRANSPARENCY_TYPE |
"xsd:float" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
BRANCH_LENGTH_DEFAULT |
-1024.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
UNKNOWN_GEODETIC_DATUM |
"?" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
CONFIDENCE_DEFAULT |
-1.0 |
public static final java.lang.String |
IDENTIFIER_DEFAULT |
"" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY |
"one_to_one_orthology" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_ORTHOLOGY |
"orthology" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_OTHER |
"other" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_PARALOGY |
"paralogy" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY |
"super_orthology" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY |
"ultra_paralogy" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_UNKNOWN |
"unknown" |
public static final java.lang.String |
SEQUENCE_RELATION_TYPE_XENOLOGY |
"xenology" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SEPARATOR |
"=" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
DEFAULT_RANGE |
-1 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
AA_REGEXP |
"[^ARNDBCQEZGHILKMFPSTWYVXUO\\-\\*]" |
public static final java.lang.String |
DNA_REGEXP |
"[^ACGTRYMKWSN\\-\\*]" |
public static final char |
GAP |
45 |
public static final java.lang.String |
RNA_REGEXP |
"[^ACGURYMKWSN\\-\\*]" |
public static final char |
TERMINATE |
42 |
public static final char |
UNSPECIFIED_AA |
88 |
public static final char |
UNSPECIFIED_NUC |
78 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
MAX_SIMILARITY_SCORE |
1.0 |
public static final double |
MIN_SIMILARITY_SCORE |
0.0 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
SPECIES_SEPARATOR |
" " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
AMIGO_LINK |
"http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query=" |
public static final java.lang.String |
EOL_LINK |
"http://www.eol.org/search?q=" |
public static final java.lang.String |
GO_LINK |
"http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query=" |
public static final java.lang.String |
GOOGLE_SCHOLAR_SEARCH |
"http://scholar.google.com/scholar?q=" |
public static final java.lang.String |
GOOGLE_WEB_SEARCH_LINK |
"http://www.google.com/search?q=" |
public static final java.lang.String |
NONE |
"[none]" |
public static final java.lang.String |
PFAM_FAMILY_ID_LINK |
"http://pfam.xfam.org/family/" |
public static final java.lang.String |
UNIPROT_TAXONOMY_ID_LINK |
"http://www.uniprot.org/taxonomy/" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
PLUS_MINUS |
"\u00b1" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
FORESTER_DATE |
"150513" |
public static final java.lang.String |
FORESTER_VERSION |
"1.039" |
public static final java.lang.String |
LOCAL_PHYLOXML_XSD_RESOURCE |
"resources/phyloxml.xsd" |
public static final java.lang.String |
PHYLO_XML_LOCATION |
"http://www.phyloxml.org" |
public static final java.lang.String |
PHYLO_XML_REFERENCE |
"Han MV and Zmasek CM (2009): \"phyloXML: XML for evolutionary biology and comparative genomics\", BMC Bioinformatics 10:356" |
public static final java.lang.String |
PHYLO_XML_SUFFIX |
".xml" |
public static final java.lang.String |
PHYLO_XML_VERSION |
"1.10" |
public static final java.lang.String |
PHYLO_XML_XSD |
"phyloxml.xsd" |
public static final boolean |
RELEASE |
false |
public static final java.lang.String |
UTF8 |
"UTF-8" |
public static final java.lang.String |
XML_SCHEMA_INSTANCE |
"http://www.w3.org/2001/XMLSchema-instance" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
NCBI_GI |
"http://www.ncbi.nlm.nih.gov/protein/gi:" |
public static final java.lang.String |
NCBI_NUCCORE |
"http://www.ncbi.nlm.nih.gov/nuccore/" |
public static final java.lang.String |
NCBI_PROTEIN |
"http://www.ncbi.nlm.nih.gov/protein/" |
public static final java.lang.String |
PDB |
"http://www.pdb.org/pdb/explore/explore.do?pdbId=" |
public static final java.lang.String |
UNIPROT_KB |
"http://www.uniprot.org/uniprot/" |
public static final double |
ZERO_DIFF |
1.0E-9 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
UNIPROT_KB_BASE_PATTERN_STR |
"((?:[OPQ][0-9][A-Z0-9]{3}[0-9])|(?:[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}))" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
BASE_UNIPROT_URL |
"http://www.uniprot.org/" |
public static final int |
DEFAULT_LINES_TO_RETURN |
4000 |
public static final java.lang.String |
EMBL_DBS_REFSEQ_N |
"refseqn" |
public static final java.lang.String |
EMBL_DBS_REFSEQ_P |
"refseqp" |
public static final java.lang.String |
EMBL_EMBL |
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=EMBL&style=raw&id=" |
public static final java.lang.String |
EMBL_GENBANK |
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=GENBANK&style=raw&id=" |
public static final java.lang.String |
EMBL_REFSEQ |
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=REFSEQ&style=raw&id=" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
ARCHAEA |
"Archaea" |
public static final java.lang.String |
BACTERIA |
"Bacteria" |
public static final java.lang.String |
CELLULAR_ORGANISMS |
"cellular organisms" |
public static final java.lang.String |
EUKARYOTA |
"Eukaryota" |
public static final java.lang.String |
VIRUSES |
"Viruses" |
public static final java.lang.String |
X |
"x" |