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org.biojava.* |
org.biojava.bibliography.BiblioCriterion | ||
public static final int |
QUERY_CRITERION |
0 |
public static final int |
SORT_CRITERION |
1 |
org.biojava.bibliography.BibRefQuery | ||
public static final java.lang.String |
PROP_CRITERIONS |
"criterions" |
public static final java.lang.String |
PROP_EXCLUDED_ATTRS |
"excluded" |
org.biojava.bibliography.BibRefSupport | ||
public static final java.lang.String |
ATTR_FORMAT |
"format" |
public static final java.lang.String |
ATTR_PROPERTIES |
"properties" |
public static final java.lang.String |
ATTR_SCOPE |
"scope" |
public static final java.lang.String |
ENTRY_PROPERTIES |
"entry_properties" |
public static final java.lang.String |
GENERIC_PROVIDER |
"Provider" |
public static final java.lang.String |
INIT_PROP_LOG |
"log" |
public static final java.lang.String |
INIT_PROP_SUPPORT |
"bibrefsupport" |
public static final java.lang.String |
JOURNAL_ABBREV |
"journal_abbreviations" |
public static final java.lang.String |
JOURNAL_TITLES |
"journal_titles" |
public static final java.lang.String |
LANGUAGES |
"languages" |
public static final java.lang.String |
PROVIDER_ORGANISATION |
"Organisation" |
public static final java.lang.String |
PROVIDER_PERSON |
"Person" |
public static final java.lang.String |
PROVIDER_SERVICE |
"Service" |
public static final java.lang.String |
REPOSITORY_SUBSETS |
"repository_subsets" |
public static final java.lang.String |
RESOURCE_TYPES |
"resource_types" |
public static final java.lang.String |
ROLE_ATTR_QUERYABLE |
"queryable" |
public static final java.lang.String |
ROLE_ATTR_RETRIEVABLE |
"retrievable" |
public static final java.lang.String |
SUBJECT_HEADINGS |
"subject_headings" |
public static final java.lang.String |
TYPE_ARTICLE |
"Article" |
public static final java.lang.String |
TYPE_BOOK |
"Book" |
public static final java.lang.String |
TYPE_BOOK_ARTICLE |
"BookArticle" |
public static final java.lang.String |
TYPE_JOURNAL_ARTICLE |
"JournalArticle" |
public static final java.lang.String |
TYPE_PATENT |
"Patent" |
public static final java.lang.String |
TYPE_PROCEEDING |
"Proceeding" |
public static final java.lang.String |
TYPE_TECH_REPORT |
"TechReport" |
public static final java.lang.String |
TYPE_THESIS |
"Thesis" |
public static final java.lang.String |
TYPE_WEB_RESOURCE |
"WebResource" |
org.biojava.bio.chromatogram.ChromatogramFactory | ||
public static final int |
ABI_MAGIC |
1094863174 |
public static final int |
SCF_MAGIC |
779314022 |
org.biojava.bio.dp.SimpleMarkovModel | ||
public static final long |
serialVersionUID |
-3043028839927615753l |
org.biojava.bio.gui.sequence.ImageMap | ||
public static final java.lang.String |
CIRCLE |
"circle" |
public static final java.lang.String |
POLY |
"poly" |
public static final java.lang.String |
RECT |
"rect" |
org.biojava.bio.gui.sequence.RulerRenderer | ||
public static final int |
TICKS_DOWN |
1 |
public static final int |
TICKS_UP |
0 |
org.biojava.bio.molbio.RestrictionEnzyme | ||
public static final int |
BLUNT |
2 |
public static final int |
CUT_COMPOUND |
1 |
public static final int |
CUT_SIMPLE |
0 |
public static final int |
OVERHANG_3PRIME |
1 |
public static final int |
OVERHANG_5PRIME |
0 |
org.biojava.bio.molbio.RestrictionEnzymeManager | ||
public static final java.lang.String |
REBASE_DATA_KEY |
"rebase.data.file" |
public static final java.lang.String |
REBASE_TAG_COMM |
"<7>" |
public static final java.lang.String |
REBASE_TAG_ISZR |
"<2>" |
public static final java.lang.String |
REBASE_TAG_METH |
"<4>" |
public static final java.lang.String |
REBASE_TAG_NAME |
"<1>" |
public static final java.lang.String |
REBASE_TAG_ORGN |
"<5>" |
public static final java.lang.String |
REBASE_TAG_REFS |
"<8>" |
public static final java.lang.String |
REBASE_TAG_SITE |
"<3>" |
public static final java.lang.String |
REBASE_TAG_SRCE |
"<6>" |
org.biojava.bio.molbio.RestrictionMapper | ||
public static final java.lang.String |
SITE_FEATURE_SOURCE |
"regex" |
public static final java.lang.String |
SITE_FEATURE_TYPE |
"misc_binding" |
org.biojava.bio.program.abi.ABIFParser.TaggedDataRecord | ||
public static final int |
DATA_TYPE_ASCII_ARRAY |
2 |
public static final int |
DATA_TYPE_DATE |
10 |
public static final int |
DATA_TYPE_FLOAT |
7 |
public static final int |
DATA_TYPE_INTEGER |
4 |
public static final int |
DATA_TYPE_PSTRING |
18 |
public static final int |
DATA_TYPE_TIME |
11 |
org.biojava.bio.program.das.DASSequence | ||
public static final java.lang.String |
PROPERTY_ANNOTATIONSERVER |
"org.biojava.bio.program.das.annotation_server" |
public static final java.lang.String |
PROPERTY_FEATUREID |
"org.biojava.bio.program.das.feature_id" |
public static final java.lang.String |
PROPERTY_FEATURELABEL |
"org.biojava.bio.program.das.feature_label" |
public static final java.lang.String |
PROPERTY_LINKS |
"org.biojava.bio.program.das.links" |
public static final java.lang.String |
PROPERTY_SEQUENCEVERSION |
"org.biojava.bio.program.das.sequence_version" |
public static final int |
SIZE_THRESHOLD |
500000 |
org.biojava.bio.program.gff.GFFEntrySet | ||
public static final java.lang.String |
PROPERTY_GFF_SCORE |
"org.biojava.bio.program.gff.gff_feature_score" |
org.biojava.bio.program.indexdb.BioStoreFactory | ||
public static final java.lang.String |
KEYS |
"secondary_namespaces" |
public static final java.lang.String |
PRIMARY_KEY_NAME |
"primary_namespace" |
public static final java.lang.String |
SEQUENCE_FORMAT |
"format" |
public static final java.lang.String |
STORE_NAME |
"name" |
org.biojava.bio.program.phred.PhredFormat | ||
public static final java.lang.String |
DEFAULT |
"PHRED" |
public static final java.lang.String |
PROPERTY_DESCRIPTIONLINE |
"description_line" |
org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder | ||
public static final java.lang.String |
HOMOLOGY_FEATURE_TYPE |
"homology" |
org.biojava.bio.program.ssbind.SeqSimilarityStAXAdapter | ||
public static final java.lang.String |
NAMESPACE |
"http://www.biojava.org" |
org.biojava.bio.program.ssbind.SimilarityPairBuilder | ||
public static final java.lang.String |
SIMILARITY_PAIR_FEATURE_TYPE |
"similarity" |
org.biojava.bio.program.tagvalue.TagValueParser | ||
public static final java.lang.String |
EMPTY_LINE_EOR |
"" |
org.biojava.bio.program.xff.XFFFeatureSetHandler | ||
public static final java.lang.String |
PROPERTY_XFF_ID |
"org.biojava.bio.program.xff.id" |
org.biojava.bio.proteomics.MassCalc | ||
public static final double |
Cavg |
12.011d |
public static final double |
Cmono |
12.0d |
public static final double |
Havg |
1.00794d |
public static final double |
Hmono |
1.007825d |
public static final double |
Navg |
14.00674d |
public static final double |
Nmono |
14.003074d |
public static final double |
Oavg |
15.9994d |
public static final double |
Omono |
15.9949146d |
org.biojava.bio.proteomics.Protease | ||
public static final java.lang.String |
ARG_C |
"Arg-C" |
public static final java.lang.String |
ASP_N |
"Asp-N" |
public static final java.lang.String |
CHYMOTRYP |
"Chymotrypsin" |
public static final java.lang.String |
CNBr |
"CNBr" |
public static final java.lang.String |
GLU_C_BICARB |
"Glu-C-bicarbonate" |
public static final java.lang.String |
GLU_C_PHOS |
"Glu-C-phosphate" |
public static final java.lang.String |
LYS_C |
"Lys-C" |
public static final java.lang.String |
TRYPSIN |
"Trypsin" |
org.biojava.bio.proteomics.ProteaseManager | ||
public static final java.lang.String |
ARG_C |
"Arg-C" |
public static final java.lang.String |
ASP_N |
"Asp-N" |
public static final java.lang.String |
CHYMOTRYP |
"Chymotrypsin" |
public static final java.lang.String |
CNBr |
"CNBr" |
public static final java.lang.String |
GLU_C_BICARB |
"Glu-C-bicarbonate" |
public static final java.lang.String |
GLU_C_PHOS |
"Glu-C-phosphate" |
public static final java.lang.String |
LYS_C |
"Lys-C" |
public static final java.lang.String |
TRYPSIN |
"Trypsin" |
org.biojava.bio.search.SeqSimilaritySearchSubHit | ||
public static final java.lang.String |
QUERY_LABEL |
"Query" |
org.biojava.bio.seq.Feature | ||
public static final java.lang.String |
PROPERTY_DATA_KEY |
"internal_data" |
org.biojava.bio.seq.FeatureTypes | ||
public static final java.lang.String |
URI_PREFIX |
"uri:biojava.org:types" |
org.biojava.bio.seq.Frame | ||
public static final int |
FRAME_0 |
0 |
public static final int |
FRAME_1 |
1 |
public static final int |
FRAME_2 |
2 |
org.biojava.bio.seq.db.NCBISequenceDB | ||
public static final java.lang.String |
DB_NUCLEOTIDE |
"nucleotide" |
public static final java.lang.String |
DB_PROTEIN |
"protein" |
org.biojava.bio.seq.homol.SimilarityPairFeature | ||
public static final java.lang.String |
QUERY_LABEL |
"query" |
public static final java.lang.String |
SUBJECT_LABEL |
"subject" |
org.biojava.bio.seq.io.AlignIOConstants | ||
public static final int |
CLUSTAL |
103 |
public static final int |
CLUSTAL_AA |
524391 |
public static final int |
CLUSTAL_DNA |
131175 |
public static final int |
CLUSTAL_RNA |
262247 |
public static final int |
FASTA |
102 |
public static final int |
FASTA_AA |
524390 |
public static final int |
FASTA_DNA |
131174 |
public static final int |
FASTA_RNA |
262246 |
public static final int |
MSF |
104 |
public static final int |
MSF_AA |
524392 |
public static final int |
MSF_DNA |
131176 |
public static final int |
MSF_RNA |
262248 |
public static final int |
RAW |
101 |
public static final int |
RAW_AA |
524389 |
public static final int |
RAW_DNA |
131173 |
public static final int |
RAW_RNA |
262245 |
public static final int |
UNKNOWN |
100 |
org.biojava.bio.seq.io.EmblLikeFormat | ||
protected static final java.lang.String |
ACCESSION_TAG |
"AC" |
protected static final java.lang.String |
AUTHORS_TAG |
"RA" |
protected static final java.lang.String |
CIRCULAR_TAG |
"CIRCULAR" |
protected static final java.lang.String |
COMMENT_TAG |
"CC" |
protected static final java.lang.String |
COORDINATE_TAG |
"RP" |
protected static final java.lang.String |
DATE_TAG |
"DT" |
public static final java.lang.String |
DEFAULT |
"EMBL" |
protected static final java.lang.String |
DEFINITION_TAG |
"DE" |
protected static final java.lang.String |
DIVISION_TAG |
"DIVISION" |
protected static final java.lang.String |
END_SEQUENCE_TAG |
"//" |
protected static final java.lang.String |
FEATURE_TABLE_TAG |
"FT" |
protected static final java.lang.String |
FEATURE_TAG |
"FH" |
protected static final java.lang.String |
ID_TAG |
"ID" |
protected static final java.lang.String |
JOURNAL_TAG |
"RL" |
protected static final java.lang.String |
KEYWORDS_TAG |
"KW" |
protected static final java.lang.String |
ORGANISM_TAG |
"OC" |
protected static final java.lang.String |
REF_ACCESSION_TAG |
"RX" |
protected static final java.lang.String |
REFERENCE_TAG |
"RN" |
protected static final java.lang.String |
SEPARATOR_TAG |
"XX" |
protected static final java.lang.String |
SIZE_TAG |
"SIZE" |
protected static final java.lang.String |
SOURCE_TAG |
"OS" |
protected static final java.lang.String |
START_SEQUENCE_TAG |
"SQ" |
protected static final java.lang.String |
STRAND_NUMBER_TAG |
"STRANDS" |
protected static final java.lang.String |
TITLE_TAG |
"RT" |
protected static final java.lang.String |
TYPE_TAG |
"TYPE" |
protected static final java.lang.String |
VERSION_TAG |
"SV" |
org.biojava.bio.seq.io.EmblProcessor | ||
public static final java.lang.String |
PROPERTY_EMBL_ACCESSIONS |
"embl_accessions" |
org.biojava.bio.seq.io.FastaAlignmentFormat | ||
public static final int |
DNA |
1 |
public static final int |
PROTEIN |
2 |
org.biojava.bio.seq.io.FastaFormat | ||
public static final java.lang.String |
DEFAULT |
"FASTA" |
public static final java.lang.String |
PROPERTY_DESCRIPTIONLINE |
"description_line" |
org.biojava.bio.seq.io.GAMEFormat | ||
public static final java.lang.String |
DEFAULT |
"GAME1.2" |
org.biojava.bio.seq.io.GenbankFormat | ||
protected static final java.lang.String |
ACCESSION_TAG |
"ACCESSION" |
protected static final java.lang.String |
AUTHORS_TAG |
"AUTHORS" |
protected static final java.lang.String |
CIRCULAR_TAG |
"CIRCULAR" |
protected static final java.lang.String |
COMMENT_TAG |
"COMMENT" |
protected static final java.lang.String |
COORDINATE_TAG |
"COORDINATE" |
protected static final java.lang.String |
DATE_TAG |
"MDAT" |
public static final java.lang.String |
DEFAULT |
"GENBANK" |
protected static final java.lang.String |
DEFINITION_TAG |
"DEFINITION" |
protected static final java.lang.String |
DIVISION_TAG |
"DIVISION" |
protected static final java.lang.String |
END_SEQUENCE_TAG |
"//" |
protected static final java.lang.String |
FEATURE_FLAG |
"FT" |
protected static final java.lang.String |
FEATURE_LINE_PREFIX |
" " |
protected static final java.lang.String |
FEATURE_TAG |
"FEATURES" |
protected static final java.lang.String |
GI_TAG |
"GI" |
protected static final java.lang.String |
JOURNAL_TAG |
"JOURNAL" |
protected static final java.lang.String |
KEYWORDS_TAG |
"KW" |
protected static final java.lang.String |
LOCUS_TAG |
"LOCUS" |
protected static final java.lang.String |
ORGANISM_TAG |
"ORGANISM" |
protected static final java.lang.String |
REF_ACCESSION_TAG |
"" |
protected static final java.lang.String |
REFERENCE_TAG |
"REFERENCE" |
protected static final java.lang.String |
SIZE_TAG |
"SIZE" |
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 |
STRAND_NUMBER_TAG |
"STRANDS" |
protected static final java.lang.String |
TITLE_TAG |
"TITLE" |
protected static final java.lang.String |
TYPE_TAG |
"TYPE" |
protected static final java.lang.String |
VERSION_TAG |
"VERSION" |
org.biojava.bio.seq.io.GenbankProcessor | ||
public static final java.lang.String |
PROPERTY_GENBANK_ACCESSIONS |
"genbank_accessions" |
org.biojava.bio.seq.io.SeqAlignReadWrite | ||
public static final int |
EMBL |
3 |
public static final int |
FASTA |
8 |
public static final int |
FASTAALIGN |
9 |
public static final int |
FASTADNA |
1 |
public static final int |
FASTAPROTEIN |
2 |
public static final int |
GENBANK |
4 |
public static final int |
GENPEPT |
6 |
public static final int |
MSFDNA |
7 |
public static final int |
MSFPROTEIN |
10 |
public static final int |
SWISSPROT |
5 |
org.biojava.bio.seq.io.SeqIOConstants | ||
public static final int |
AA |
524288 |
public static final int |
AMBIGUOUS |
65536 |
public static final int |
DNA |
131072 |
public static final int |
EMBL |
10 |
public static final int |
EMBL_AA |
524298 |
public static final int |
EMBL_DNA |
131082 |
public static final int |
EMBL_RNA |
262154 |
public static final int |
FASTA |
2 |
public static final int |
FASTA_AA |
524290 |
public static final int |
FASTA_DNA |
131074 |
public static final int |
FASTA_RNA |
262146 |
public static final int |
GCG |
15 |
public static final int |
GENBANK |
12 |
public static final int |
GENBANK_AA |
524300 |
public static final int |
GENBANK_DNA |
131084 |
public static final int |
GENBANK_RNA |
262156 |
public static final int |
GENPEPT |
524301 |
public static final int |
GFF |
20 |
public static final int |
IG |
4 |
public static final int |
INTEGER |
1048576 |
public static final int |
NBRF |
3 |
public static final int |
PDB |
524309 |
public static final int |
PHRED |
1179678 |
public static final int |
RAW |
1 |
public static final int |
REFSEQ |
14 |
public static final int |
REFSEQ_AA |
524302 |
public static final int |
REFSEQ_DNA |
131086 |
public static final int |
REFSEQ_RNA |
262158 |
public static final int |
RNA |
262144 |
public static final int |
SWISSPROT |
524299 |
public static final int |
UNKNOWN |
0 |
org.biojava.bio.seq.io.SequenceDBSequenceBuilder | ||
public static final int |
ANNOTATE_EXISTING |
1 |
public static final int |
CREATE_DUMMYSEQ |
2 |
public static final int |
CREATE_REALSEQ |
3 |
org.biojava.bio.seq.io.SwissprotProcessor | ||
public static final java.lang.String |
PROPERTY_SWISSPROT_ACCESSIONS |
"swissprot.accessions" |
public static final java.lang.String |
PROPERTY_SWISSPROT_COMMENT |
"swissprot.comment" |
public static final java.lang.String |
PROPERTY_SWISSPROT_FEATUREATTRIBUTE |
"swissprot.featureattribute" |
org.biojava.bio.seq.io.agave.AGAVEAnnotFilter | ||
public static final int |
BOTH_FORWARD_COMPLEMENT |
0 |
public static final int |
COMPLEMENT |
-1 |
public static final int |
FORWARD |
1 |
org.biojava.bio.seq.io.agave.AGAVEProperty | ||
public static final java.lang.String |
QUALIFIER |
"qualifier" |
public static final java.lang.String |
RESULT_PROPERTY |
"result_property" |
public static final java.lang.String |
SCI_PROPERTY |
"sci_property" |
public static final java.lang.String |
XREF_PROPERTY |
"xref_property" |
org.biojava.bio.seq.io.agave.AgaveWriter | ||
public static final java.lang.String |
INDENT |
" " |
org.biojava.bio.seq.io.filterxml.XMLAnnotationTypeWriter | ||
public static final java.lang.String |
XML_ANNOTATIONTYPE_NS |
"http://www.biojava.org/AnnotationType" |
org.biojava.bio.seq.io.filterxml.XMLFilterWriter | ||
public static final java.lang.String |
XML_FILTER_NS |
"http://www.biojava.org/FeatureFilter" |
org.biojava.bio.symbol.SymbolPropertyTable | ||
public static final java.lang.String |
AVG_MASS |
"avgMass" |
public static final java.lang.String |
MONO_MASS |
"monoMass" |
public static final java.lang.String |
PK |
"pK" |
org.biojava.bio.symbol.TranslationTable | ||
public static final java.lang.String |
ALT_YEAST_NUC |
"ALTERNATIVE_YEAST_NUCLEAR" |
public static final java.lang.String |
ASCID_MITO |
"ASCIDIAN_MITOCHONDRIAL" |
public static final java.lang.String |
BLEPH_MNUC |
"BLEPHARISMA_MACRONUCLEAR" |
public static final java.lang.String |
CILIATE_NUC |
"CILIATE_NUCLEAR" |
public static final java.lang.String |
ECHIN_MITO |
"ECHINODERM_MITOCHONDRIAL" |
public static final java.lang.String |
EUPL_NUC |
"EUPLOTID_NUCLEAR" |
public static final java.lang.String |
FWORM_MITO |
"FLATWORM_MITOCHONDRIAL" |
public static final java.lang.String |
INVERT_MITO |
"INVERTEBRATE_MITOCHONDRIAL" |
public static final java.lang.String |
MOLD_MITO |
"MOLD_MITOCHONDRIAL" |
public static final java.lang.String |
UNIVERSAL |
"UNIVERSAL" |
public static final java.lang.String |
VERT_MITO |
"VERTEBRATE_MITOCHONDRIAL" |
public static final java.lang.String |
YEAST_MITO |
"YEAST_MITOCHONDRIAL" |
org.biojava.bio.symbol.UkkonenSuffixTree | ||
public static final char |
DEFAULT_TERM_CHAR |
36 |
public static final int |
TO_A_LEAF |
-1 |
org.biojava.directory.SystemRegistry | ||
public static final java.lang.String |
CONFIG_FILE |
"seqdatabase.ini" |
public static final java.lang.String |
CONFIG_LOCATOR |
"http://www.open-bio.org/registry/seqdatabase.ini" |
public static final java.lang.String |
OBDA_SEARCH_ENV |
"OBDA_SEARCH_PATH" |
org.biojava.utils.ObjectUtil | ||
public static final int |
PRIME |
1000003 |
org.biojava.utils.TypedProperties | ||
public static final java.lang.String |
DEFAULT_DELIMITERS |
",;\t" |
org.biojava.utils.candy.CandyFinder | ||
public static final java.lang.String |
DEFAULT_FINDER_NAME |
"Default vocabulary finder" |
public static final java.lang.String |
PROP_VOCABULARY |
"vocabulary" |
org.biojava.utils.candy.CandyVocabulary | ||
public static final java.lang.String |
CANDIES_NOT_SORTED |
"candies_not_sorted" |
public static final java.lang.String |
PROP_CASE_SENSITIVE |
"vocab_case_sensitive" |
public static final java.lang.String |
PROP_ENTRY_COUNT |
"entry_count" |
public static final java.lang.String |
PROP_VOCAB_DESC |
"vocab_description" |
public static final java.lang.String |
PROP_VOCAB_NAME |
"vocab_name" |
public static final java.lang.String |
PROP_VOCAB_VERSION |
"vocab_version" |
public static final java.lang.String |
PROP_VOCABULARY |
"vocabulary" |
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