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| PREV NEXT | FRAMES NO FRAMES | ||||||||
| org.biojava.* |
|---|
| org.biojava.bio.structure.AminoAcid | ||
|---|---|---|
public static final java.lang.String |
ATOMRECORD |
"ATOM" |
public static final java.lang.String |
SEQRESRECORD |
"SEQRES" |
| org.biojava.bio.structure.AminoAcidImpl | ||
|---|---|---|
public static final java.lang.String |
type |
"amino" |
| org.biojava.bio.structure.Calc | ||
|---|---|---|
public static final float |
degreesPerRadian |
57.295780181884766f |
public static final float |
radiansPerDegree |
0.01745329238474369f |
| org.biojava.bio.structure.GroupType | ||
|---|---|---|
public static final java.lang.String |
AMINOACID |
"amino" |
public static final java.lang.String |
HETATM |
"hetatm" |
public static final java.lang.String |
NUCLEOTIDE |
"nucleotide" |
| org.biojava.bio.structure.HetatomImpl | ||
|---|---|---|
public static final java.lang.String |
type |
"hetatm" |
| org.biojava.bio.structure.NucleotideImpl | ||
|---|---|---|
public static final java.lang.String |
type |
"nucleotide" |
| org.biojava.bio.structure.PDBHeader | ||
|---|---|---|
public static final float |
DEFAULT_RESOLUTION |
99.0f |
| org.biojava.bio.structure.PDBStatus | ||
|---|---|---|
public static final java.lang.String |
DEFAULT_PDB_SERVER |
"www.rcsb.org" |
public static final java.lang.String |
PDB_SERVER_PROPERTY |
"PDB.SERVER" |
| org.biojava.bio.structure.StructureException | ||
|---|---|---|
public static final long |
serialVersionUID |
62946250941673093L |
| org.biojava.bio.structure.StructureTools | ||
|---|---|---|
public static final java.lang.String |
caAtomName |
" CA " |
public static final java.lang.String |
cbAtomName |
"CB" |
public static final java.lang.String |
nAtomName |
"N" |
public static final java.lang.String |
oAtomName |
"O" |
| org.biojava.bio.structure.align.BioJavaStructureAlignment | ||
|---|---|---|
public static final java.lang.String |
algorithmName |
"BioJava_structure" |
| org.biojava.bio.structure.align.ClusterAltAligs | ||
|---|---|---|
public static final int |
DEFAULT_CLUSTER_CUTOFF |
95 |
| org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor | ||
|---|---|---|
public static final java.lang.String |
PDB_DIR |
"PDB_DIR" |
| org.biojava.bio.structure.align.ce.CECalculator | ||
|---|---|---|
protected static final boolean |
isPrint |
false |
protected static final int |
nIter |
1 |
protected static final double |
zThr |
-0.1 |
| org.biojava.bio.structure.align.ce.CeCalculatorEnhanced | ||
|---|---|---|
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 |
| org.biojava.bio.structure.align.ce.CeCPMain | ||
|---|---|---|
public static final java.lang.String |
algorithmName |
"jCE Circular Permutation" |
public static final int |
DEFAULT_MIN_CP_LENGTH |
5 |
public static final java.lang.String |
version |
"1.3" |
| org.biojava.bio.structure.align.ce.CeMain | ||
|---|---|---|
public static final java.lang.String |
algorithmName |
"jCE" |
public static final java.lang.String |
version |
"1.1" |
| org.biojava.bio.structure.align.ce.CeParameters | ||
|---|---|---|
public static final int |
CA_AND_SIDE_CHAIN_ANGLE_SCORING |
3 |
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 |
public static final int |
DEFAULT_SCORING_STRATEGY |
0 |
protected static final double |
DISTANCE_INCREMENT |
0.5 |
public static final java.lang.String |
SCORING_STRATEGY |
"ScoringStrategy" |
public static final int |
SEQUENCE_CONSERVATION |
4 |
public static final int |
SIDE_CHAIN_ANGLE_SCORING |
2 |
public static final int |
SIDE_CHAIN_SCORING |
1 |
| org.biojava.bio.structure.align.ce.CeSideChainMain | ||
|---|---|---|
public static final java.lang.String |
algorithmName |
"jCE-sidechain" |
| org.biojava.bio.structure.align.ce.OptimalCECPMain | ||
|---|---|---|
public static final java.lang.String |
algorithmName |
"jCE Optimal Circular Permutation" |
public static final java.lang.String |
version |
"1.0" |
| org.biojava.bio.structure.align.client.FarmJobParameters | ||
|---|---|---|
public static final int |
DEFAULT_BATCH_SIZE |
100 |
public static final boolean |
DEFAULT_DIR_SPLIT |
true |
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/" |
| org.biojava.bio.structure.align.fatcat.FatCat | ||
|---|---|---|
public static final float |
VERSION |
1.0f |
| org.biojava.bio.structure.align.fatcat.calc.AFPCalculator | ||
|---|---|---|
public static final boolean |
debug |
false |
| org.biojava.bio.structure.align.fatcat.calc.AFPChainer | ||
|---|---|---|
public static final boolean |
debug |
false |
| org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer | ||
|---|---|---|
public static final boolean |
debug |
false |
| org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor | ||
|---|---|---|
public static final boolean |
debug |
false |
| org.biojava.bio.structure.align.fatcat.calc.FatCatAligner | ||
|---|---|---|
public static final boolean |
debug |
false |
public static final boolean |
printTimeStamps |
false |
| org.biojava.bio.structure.align.fatcat.calc.FatCatParameters | ||
|---|---|---|
public static final int |
DEFAULT_FRAGLEN |
8 |
| org.biojava.bio.structure.align.gui.ChooseDirAction | ||
|---|---|---|
public static final long |
serialVersionUID |
0L |
| org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel | ||
|---|---|---|
public static final java.lang.String |
PDB_DIR |
"PDB_DIR" |
| org.biojava.bio.structure.align.gui.DisplayAFP | ||
|---|---|---|
public static final boolean |
debug |
false |
| org.biojava.bio.structure.align.gui.MemoryMonitor | ||
|---|---|---|
public static final long |
serialVersionUID |
56289234782130L |
| org.biojava.bio.structure.align.gui.MemoryMonitor.Surface | ||
|---|---|---|
public static final long |
serialVersionUID |
2387409854370432908L |
| org.biojava.bio.structure.align.gui.MenuCreator | ||
|---|---|---|
public static final java.lang.String |
ALIGNMENT_PANEL |
"Alignment Panel" |
public static final java.lang.String |
EQR_COLOR |
"Color By EQR" |
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 |
PAIRS_ONLY |
"View Aligned Pairs" |
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" |
| org.biojava.bio.structure.align.gui.SystemInfo | ||
|---|---|---|
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 " |
| org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager | ||
|---|---|---|
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 |
| org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol | ||
|---|---|---|
protected static final java.lang.String |
COMMAND_LINE_HELP |
"enter Jmol scripting command..." |
| org.biojava.bio.structure.align.model.AFPChain | ||
|---|---|---|
public static final java.lang.String |
DEFAULT_ALGORITHM_NAME |
"jFatCat_rigid" |
| org.biojava.bio.structure.align.seq.SmithWaterman3Daligner | ||
|---|---|---|
public static final java.lang.String |
algorithmName |
"Smith-Waterman superposition" |
| org.biojava.bio.structure.align.util.AtomCache | ||
|---|---|---|
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 |
"_" |
| org.biojava.bio.structure.align.util.HTTPConnectionTools | ||
|---|---|---|
public static final int |
DEFAULT_CONNECTION_TIMEOUT |
15000 |
public static final java.lang.String |
USERAGENT |
"JFatCat Java client" |
| org.biojava.bio.structure.align.util.UserConfiguration | ||
|---|---|---|
public static final java.lang.String |
MMCIF_FORMAT |
"mmCif" |
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" |
| org.biojava.bio.structure.cath.CathDomain | ||
|---|---|---|
public static final long |
serialVersionUID |
1L |
| org.biojava.bio.structure.cath.CathFragment | ||
|---|---|---|
public static final long |
serialVersionUID |
1L |
| org.biojava.bio.structure.cath.CathInstallation | ||
|---|---|---|
public static final java.lang.String |
CATH_DOWNLOAD |
"http://release.cathdb.info/" |
public static final java.lang.String |
DEFAULT_VERSION |
"3.5.0" |
public static final java.lang.String |
domainDescriptionFileName |
"CathDomainDescriptionFile" |
public static final java.lang.String |
domainListFileName |
"CathDomainList" |
public static final java.lang.String |
domallFileName |
"CathDomall" |
public static final java.lang.String |
nodeListFileName |
"CathNames" |
| org.biojava.bio.structure.cath.CathNode | ||
|---|---|---|
public static final long |
serialVersionUID |
1L |
| org.biojava.bio.structure.cath.CathSegment | ||
|---|---|---|
public static final long |
serialVersionUID |
1L |
| org.biojava.bio.structure.domain.PDBDomainProvider | ||
|---|---|---|
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" |
| org.biojava.bio.structure.domain.RemotePDPProvider | ||
|---|---|---|
public static final java.lang.String |
DEFAULT_SERVER |
"http://source.rcsb.org/jfatcatserver/domains/" |
| org.biojava.bio.structure.domain.pdp.PDPParameters | ||
|---|---|---|
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 |
| org.biojava.bio.structure.gui.BiojavaJmol | ||
|---|---|---|
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" |
| org.biojava.bio.structure.gui.ScaleableMatrixPanel | ||
|---|---|---|
protected static final int |
SLIDER_STEPS |
8 |
| org.biojava.bio.structure.gui.SequenceDisplay | ||
|---|---|---|
public static final int |
MAX_SCALE |
10 |
| org.biojava.bio.structure.gui.util.AlignedPosition | ||
|---|---|---|
public static final int |
EQUIVALENT |
1 |
public static final int |
NOT_ALIGNED |
0 |
| org.biojava.bio.structure.gui.util.PDBDirPanel | ||
|---|---|---|
public static final java.lang.String |
PDB_DIR |
"PDB_DIR" |
| org.biojava.bio.structure.gui.util.SequenceScalePanel | ||
|---|---|---|
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 |
| org.biojava.bio.structure.gui.util.color.GradientMapper | ||
|---|---|---|
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 |
| org.biojava.bio.structure.gui.util.color.HSVColorSpace | ||
|---|---|---|
public static final int |
CS_HSV |
1007 |
| org.biojava.bio.structure.io.FileParsingParameters | ||
|---|---|---|
public static final int |
ATOM_CA_THRESHOLD |
500000 |
public static final int |
MAX_ATOMS |
2147483647 |
| org.biojava.bio.structure.io.PDBFileParser | ||
|---|---|---|
public static final java.lang.String |
HELIX |
"HELIX" |
public static final java.lang.String |
PDB_AUTHOR_ASSIGNMENT |
"PDB_AUTHOR_ASSIGNMENT" |
public static final java.lang.String |
STRAND |
"STRAND" |
public static final java.lang.String |
TURN |
"TURN" |
| org.biojava.bio.structure.io.PDBFileReader | ||
|---|---|---|
public static final java.lang.String |
DEFAULT_PDB_FILE_SERVER |
"ftp.wwpdb.org" |
public static final java.lang.String |
LOAD_CHEM_COMP_PROPERTY |
"loadChemCompInfo" |
public static final java.lang.String |
PDB_FILE_SERVER_PROPERTY |
"PDB.FILE.SERVER" |
| org.biojava.bio.structure.io.PDBParseException | ||
|---|---|---|
public static final long |
serialVersionUID |
219047230178423923L |
| org.biojava.bio.structure.io.mmcif.SimpleMMcifParser | ||
|---|---|---|
public static final java.lang.String |
FIELD_LINE |
"_" |
public static final java.lang.String |
LOOP_END |
"#" |
public static final java.lang.String |
LOOP_START |
"loop_" |
public static final java.lang.String |
STRING_LIMIT |
";" |
| org.biojava.bio.structure.quaternary.io.BioUnitDataProviderFactory | ||
|---|---|---|
public static final java.lang.String |
fileBasedProviderClassName |
"org.biojava.bio.structure.quaternary.io.FileBasedPDBBioUnitDataProvider" |
public static final java.lang.String |
mmcifProviderClassName |
"org.biojava.bio.structure.quaternary.io.MmCifBiolAssemblyProvider" |
public static final java.lang.String |
pdbProviderClassName |
"org.biojava.bio.structure.quaternary.io.PDBBioUnitDataProvider" |
public static final java.lang.String |
remoteProviderClassName |
"org.biojava.bio.structure.quaternary.io.RemoteBioUnitDataProvider" |
| org.biojava.bio.structure.scop.BerkeleyScopInstallation | ||
|---|---|---|
public static final java.lang.String |
claFileName |
"dir.cla.scop." |
public static final java.lang.String |
desFileName |
"dir.des.scop." |
public static final java.lang.String |
hieFileName |
"dir.hie.scop." |
| org.biojava.bio.structure.scop.RemoteScopInstallation | ||
|---|---|---|
public static final java.lang.String |
DEFAULT_SERVER |
"http://source.rcsb.org/jfatcatserver/domains/" |
| org.biojava.bio.structure.scop.ScopInstallation | ||
|---|---|---|
public static final java.lang.String |
claFileName |
"dir.cla.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.mrc-lmb.cam.ac.uk/scop/parse/" |
| org.biojava.bio.structure.secstruc.BigSqrt | ||
|---|---|---|
public static final int |
DEFAULT_MAX_ITERATIONS |
50 |
public static final int |
DEFAULT_SCALE |
3 |
| org.biojava.bio.structure.server.FlatFileInstallation | ||
|---|---|---|
public static final java.lang.String |
DEFAUL_CHAIN_FILE |
"chaininfo.txt" |
public static final java.lang.String |
DEFAULT_INDEX_FILE |
"pdbinfo.txt" |
| org.biojava3.* |
|---|
| org.biojava3.aaproperties.profeat.convertor.Convertor | ||
|---|---|---|
public static final char |
group1 |
49 |
public static final char |
group2 |
50 |
public static final char |
group3 |
51 |
public static final char |
unknownGroup |
48 |
| org.biojava3.alignment.io.StockholmFileParser | ||
|---|---|---|
public static final int |
INFINITY |
-1 |
| org.biojava3.alignment.io.StockholmStructure.DatabaseReference | ||
|---|---|---|
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" |
| org.biojava3.core.sequence.io.IUPACParser | ||
|---|---|---|
public static final java.lang.String |
IUPAC_LOCATION |
"org/biojava3/core/sequence/iupac.txt" |
| org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C extends Compound> | ||
|---|---|---|
public static final int |
BYTES_PER_INT |
32 |
| org.biojava3.core.util.Hashcoder | ||
|---|---|---|
public static final int |
PRIME |
79 |
public static final int |
SEED |
9 |
| org.biojava3.core.util.InputStreamProvider | ||
|---|---|---|
public static final java.lang.String |
CACHE_PROPERTY |
"biojava.cache.files" |
public static final int |
GZIP_MAGIC |
8075 |
| org.biojava3.core.util.SequenceTools | ||
|---|---|---|
protected static final java.lang.String |
NUCLEOTIDE_LETTERS |
"GCTAUXN" |
| org.biojava3.core.util.SoftHashMap<K,V> | ||
|---|---|---|
public static final boolean |
DEBUG |
false |
public static final int |
DEFAULT_LIMIT |
1 |
| org.biojava3.phylo.ResidueProperties | ||
|---|---|---|
public static final double |
buriedmax |
4.6 |
public static final double |
buriedmin |
0.05 |
public static final double |
helixmax |
1.51 |
public static final double |
helixmin |
0.57 |
public static final double |
hydmax |
4.5 |
public static final double |
hydmin |
-3.9 |
public static final double |
strandmax |
1.7 |
public static final double |
strandmin |
0.37 |
public static final double |
turnmax |
1.56 |
public static final double |
turnmin |
0.47 |
| org.biojava3.ronn.RonnConstraint | ||
|---|---|---|
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 |
| org.biojava3.structure.gui.JmolViewerImpl | ||
|---|---|---|
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" |
| org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties | ||
|---|---|---|
public static final long |
serialVersionUID |
1L |
| org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties | ||
|---|---|---|
public static final long |
serialVersionUID |
1L |
| org.biojava3.ws.alignment.qblast.NCBIQBlastService | ||
|---|---|---|
public static final long |
WAIT_INCREMENT |
3000L |
| org.forester.* |
|---|
| org.forester.application.gsdi | ||
|---|---|---|
public static final boolean |
REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE |
true |
| org.forester.application.surfacing | ||
|---|---|---|
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_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 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 |
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 |
PRG_NAME |
"surfacing" |
public static final java.lang.String |
SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO |
"_secondary_features_dollo.xml" |
| org.forester.archaeopteryx.ArchaeopteryxA | ||
|---|---|---|
public static final java.lang.String |
NAME |
"ArchaeopteryxA" |
| org.forester.archaeopteryx.Constants | ||
|---|---|---|
public static final boolean |
__RELEASE |
true |
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" |
| org.forester.archaeopteryx.FontChooser | ||
|---|---|---|
public static final long |
serialVersionUID |
62256323L |
| org.forester.archaeopteryx.TreeColorSet | ||
|---|---|---|
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 |
DOMAINS |
"Domains" |
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 |
"Matching Nodes" |
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" |
| org.forester.archaeopteryx.phylogeny.data.RenderableVector | ||
|---|---|---|
public static final int |
DEFAULT_HEIGHT |
12 |
public static final int |
DEFAULT_WIDTH |
120 |
| org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions | ||
|---|---|---|
public static final long |
RANDOM_NUMBER_SEED_DEFAULT |
42L |
| org.forester.archaeopteryx.tools.PhylogeneticInferrer | ||
|---|---|---|
public static final java.lang.String |
MSA_FILE_SUFFIX |
".aln" |
public static final java.lang.String |
PWD_FILE_SUFFIX |
".pwd" |
| org.forester.archaeopteryx.tools.SequenceDataRetriver | ||
|---|---|---|
public static final int |
DEFAULT_LINES_TO_RETURN |
50 |
| org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient | ||
|---|---|---|
public static final java.lang.String |
QUERY_PLACEHOLDER |
"__query__" |
| org.forester.archaeopteryx.webservices.WebserviceUtil | ||
|---|---|---|
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.janelia.org" |
public static final java.lang.String |
TAX_CODE_TO_SCI_NAME |
"tax_code_to_sci_name" |
public static final java.lang.String |
TOL_NAME |
"Tree of Life" |
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_NAME |
"TreeBASE" |
public static final java.lang.String |
TREE_FAM_INST |
"tree_fam" |
public static final java.lang.String |
TREE_FAM_NAME |
"TreeFam" |
| org.forester.evoinference.distance.PairwiseDistanceCalculator | ||
|---|---|---|
public static final double |
DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA |
10.0 |
| org.forester.go.GoNameSpace | ||
|---|---|---|
public final java.lang.String |
BIOLOGICAL_PROCESS_STR |
"biological_process" |
public final java.lang.String |
CELLULAR_COMPONENT_STR |
"cellular_component" |
public final java.lang.String |
MOLECULAR_FUNCTION_STR |
"molecular_function" |
public final java.lang.String |
UNASSIGNED_STR |
"unassigned" |
| org.forester.go.GoRelationship | ||
|---|---|---|
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 |
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" |
| org.forester.go.GoSubset | ||
|---|---|---|
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" |
public static final java.lang.String |
HIGH_LEVEL_ANNOTATION_QC_STR |
"high_level_annotation_qc" |
public static final java.lang.String |
MF_NEEDS_REVIEW_STR |
"mf_needs_review" |
public static final java.lang.String |
UNVETTED_STR |
"unvetted" |
| org.forester.go.GoXRef | ||
|---|---|---|
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" |
| org.forester.io.parsers.nexus.NexusConstants | ||
|---|---|---|
public static final java.lang.String |
BEGIN_CHARACTERS |
"Begin Characters;" |
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" |
| org.forester.io.parsers.nhx.NHXParser | ||
|---|---|---|
public static final boolean |
REPLACE_UNDERSCORES_DEFAULT |
false |
| org.forester.io.parsers.nhx.NHXtags | ||
|---|---|---|
public static final java.lang.String |
ANNOTATION |
"AN=" |
public static final java.lang.String |
COLOR |
"C=" |
public static final java.lang.String |
CUSTOM_DATA_ON_NODE |
"XN=" |
public static final java.lang.String |
DOMAIN_STRUCTURE |
"DS=" |
public static final java.lang.String |
GENE_NAME |
"GN=" |
public static final java.lang.String |
GENE_NAME_SYNONYM |
"G=" |
public static final java.lang.String |
IS_DUPLICATION |
"D=" |
public static final java.lang.String |
NODE_IDENTIFIER |
"ID=" |
public static final java.lang.String |
ORTHOLOGOUS |
"On=" |
public static final java.lang.String |
PARENT_BRANCH_WIDTH |
"W=" |
public static final java.lang.String |
SEQUENCE_ACCESSION |
"AC=" |
public static final java.lang.String |
SPECIES_NAME |
"S=" |
public static final java.lang.String |
SUBTREE_NEIGHBORS |
"SNn=" |
public static final java.lang.String |
SUPER_ORTHOLOGOUS |
"SOn=" |
public static final java.lang.String |
SUPPORT |
"B=" |
public static final java.lang.String |
TAXONOMY_ID |
"T=" |
| org.forester.io.parsers.phyloxml.PhyloXmlMapping | ||
|---|---|---|
public static final java.lang.String |
ACCESSION |
"accession" |
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_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 |
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" |
| org.forester.io.parsers.phyloxml.PhyloXmlParser | ||
|---|---|---|
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" |
| org.forester.io.parsers.phyloxml.PhyloXmlUtil | ||
|---|---|---|
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" |
| org.forester.io.parsers.phyloxml.XmlElement | ||
|---|---|---|
public static final boolean |
DEBUG |
false |
| org.forester.io.parsers.tol.TolParser | ||
|---|---|---|
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" |
| org.forester.io.parsers.tol.TolXmlMapping | ||
|---|---|---|
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" |
| org.forester.io.writers.PhylogenyWriter | ||
|---|---|---|
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\"?>" |
| org.forester.pccx.BranchLengthBasedScoringMethod | ||
|---|---|---|
public static final double |
MIN_ALLOWED_BL_VALUE |
0.001 |
| org.forester.pccx.LogBranchLengthBasedScoringMethod | ||
|---|---|---|
public static final double |
MAX_ALLOWED_BL_VALUE |
1.0 |
public static final double |
MIN_ALLOWED_BL_VALUE |
1.0E-4 |
| org.forester.phylogeny.Phylogeny | ||
|---|---|---|
public static final boolean |
ALLOW_MULTIPLE_PARENTS_DEFAULT |
false |
| org.forester.phylogeny.data.BinaryCharacters | ||
|---|---|---|
public static final int |
COUNT_DEFAULT |
-1 |
| org.forester.phylogeny.data.BranchWidth | ||
|---|---|---|
public static final double |
BRANCH_WIDTH_DEFAULT_VALUE |
1.0 |
| org.forester.phylogeny.data.Confidence | ||
|---|---|---|
public static final int |
CONFIDENCE_DEFAULT_VALUE |
-9999 |
| org.forester.phylogeny.data.DomainArchitecture | ||
|---|---|---|
public static final java.lang.String |
NHX_SEPARATOR |
">" |
| org.forester.phylogeny.data.Event | ||
|---|---|---|
public static final int |
DEFAULT_VALUE |
-1 |
| org.forester.phylogeny.data.Identifier | ||
|---|---|---|
public static final java.lang.String |
NCBI |
"ncbi" |
public static final java.lang.String |
REFSEQ |
"refseq" |
| org.forester.phylogeny.data.NodeVisualization | ||
|---|---|---|
public static final java.lang.String |
SIZE_REF |
"aptx_visualiation:node_sise" |
public static final java.lang.String |
SIZE_TYPE |
"xsd:decimal" |
| org.forester.phylogeny.data.PhylogenyDataUtil | ||
|---|---|---|
public static final double |
BRANCH_LENGTH_DEFAULT |
-1024.0 |
| org.forester.phylogeny.data.Point | ||
|---|---|---|
public static final java.lang.String |
UNKNOWN_GEODETIC_DATUM |
"?" |
| org.forester.phylogeny.data.ProteinDomain | ||
|---|---|---|
public static final double |
CONFIDENCE_DEFAULT |
0.0 |
public static final java.lang.String |
IDENTIFIER_DEFAULT |
"" |
| org.forester.phylogeny.data.SequenceRelation | ||
|---|---|---|
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" |
| org.forester.protein.BinaryDomainCombination | ||
|---|---|---|
public static final java.lang.String |
SEPARATOR |
"=" |
| org.forester.sdi.DistanceCalculator | ||
|---|---|---|
public static final double |
DEFAULT |
-1.0 |
| org.forester.sequence.Sequence | ||
|---|---|---|
public static final java.lang.String |
AA_REGEXP |
"[^ARNDBCQEZGHILKMFPSTWYVXU\\-\\*]" |
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 |
| org.forester.surfacing.DomainArchitectureBasedGenomeSimilarityCalculator | ||
|---|---|---|
public static final double |
MAX_SIMILARITY_SCORE |
1.0 |
public static final double |
MIN_SIMILARITY_SCORE |
0.0 |
| org.forester.surfacing.PrintableDomainSimilarity | ||
|---|---|---|
public static final java.lang.String |
SPECIES_SEPARATOR |
" " |
| org.forester.surfacing.SurfacingConstants | ||
|---|---|---|
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_LIMITS |
"&as_subj=bio&as_subj=med&as_subj=chm&num=100" |
public static final java.lang.String |
GOOGLE_SCHOLAR_LINK |
"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.sanger.ac.uk/family?id=" |
public static final java.lang.String |
TAXONOMY_LINK |
"http://beta.uniprot.org/taxonomy/?query=" |
public static final java.lang.String |
TOL_LINK |
"http://www.googlesyndicatedsearch.com/u/TreeofLife?q=" |
public static final java.lang.String |
UNIPROT_LINK |
"http://www.uniprot.org/taxonomy/?query=" |
public static final java.lang.String |
WIKIPEDIA_LINK |
"http://wikipedia.org/wiki/" |
| org.forester.tools.PhylogenyDecorator | ||
|---|---|---|
public static final boolean |
SANITIZE |
false |
public static final boolean |
VERBOSE |
true |
| org.forester.util.DescriptiveStatistics | ||
|---|---|---|
public static final java.lang.String |
PLUS_MINUS |
"\u00b1" |
| org.forester.util.ForesterConstants | ||
|---|---|---|
public static final java.lang.String |
FORESTER_DATE |
"120629" |
public static final java.lang.String |
FORESTER_VERSION |
"1.005" |
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" |
| org.forester.util.ForesterUtil | ||
|---|---|---|
public static final double |
ZERO_DIFF |
1.0E-9 |
| org.forester.ws.seqdb.SequenceDbWsTools | ||
|---|---|---|
public static final java.lang.String |
BASE_EMBL_DB_URL |
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/" |
public static final java.lang.String |
BASE_UNIPROT_URL |
"http://www.uniprot.org/" |
public static final java.lang.String |
EMBL_DBS_EMBL |
"embl" |
public static final java.lang.String |
EMBL_DBS_REFSEQ_N |
"refseqn" |
public static final java.lang.String |
EMBL_DBS_REFSEQ_P |
"refseqp" |
| org.forester.ws.seqdb.UniProtTaxonomy | ||
|---|---|---|
public static final java.lang.String |
CELLULAR_ORGANISMS |
"cellular organisms" |
public static final java.lang.String |
VIRUSES |
"Viruses" |
| org.forester.ws.uniprot.SequenceDbWsTools | ||
|---|---|---|
public static final java.lang.String |
BASE_EMBL_DB_URL |
"http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/" |
public static final java.lang.String |
BASE_UNIPROT_URL |
"http://www.uniprot.org/" |
public static final java.lang.String |
EMBL_DBS_EMBL |
"embl" |
public static final java.lang.String |
EMBL_DBS_REFSEQ_N |
"refseqn" |
public static final java.lang.String |
EMBL_DBS_REFSEQ_P |
"refseqp" |
| org.forester.ws.uniprot.UniProtTaxonomy | ||
|---|---|---|
public static final java.lang.String |
CELLULAR_ORGANISMS |
"cellular organisms" |
public static final java.lang.String |
VIRUSES |
"Viruses" |
|
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