Constant Field Values

org.biojava.*

org.biojava.bio.structure.AminoAcid
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`ATOMRECORD`	`"ATOM"`
`public static final java.lang.String`	`SEQRESRECORD`	`"SEQRES"`

org.biojava.bio.structure.AminoAcidImpl
Modifier and Type Constant Field Value

public static final java.lang.String type "amino"

org.biojava.bio.structure.AminoAcidImpl
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`type`	`"amino"`

org.biojava.bio.structure.Calc
Modifier and Type	Constant Field	Value
`public static final float`	`degreesPerRadian`	`57.295780181884766f`
`public static final float`	`radiansPerDegree`	`0.01745329238474369f`

org.biojava.bio.structure.GroupType
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final java.lang.String type "hetatm"
org.biojava.bio.structure.NucleotideImpl
Modifier and Type Constant Field Value

public static final java.lang.String type "nucleotide"
org.biojava.bio.structure.PDBHeader
Modifier and Type Constant Field Value

public static final float DEFAULT_RESOLUTION 99.0f

org.biojava.bio.structure.HetatomImpl
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`type`	`"hetatm"`

org.biojava.bio.structure.NucleotideImpl
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`type`	`"nucleotide"`

org.biojava.bio.structure.PDBHeader
Modifier and Type	Constant Field	Value
`public static final float`	`DEFAULT_RESOLUTION`	`99.0f`

org.biojava.bio.structure.PDBStatus
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"`

org.biojava.bio.structure.ResidueRange
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`RANGE_REGEX`	`"^([a-zA-Z])+[_:](?:(-?\\d+[a-zA-Z]?)-(-?\\d+[a-zA-Z]?))?$"`

org.biojava.bio.structure.StructureException
Modifier and Type Constant Field Value

public static final long serialVersionUID 62946250941673093L

org.biojava.bio.structure.StructureException
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`62946250941673093L`

org.biojava.bio.structure.StructureTools
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final java.lang.String algorithmName "BioJava_structure"
org.biojava.bio.structure.align.ClusterAltAligs
Modifier and Type Constant Field Value

public static final int DEFAULT_CLUSTER_CUTOFF 95

org.biojava.bio.structure.align.BioJavaStructureAlignment
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`algorithmName`	`"BioJava_structure"`

org.biojava.bio.structure.align.ClusterAltAligs
Modifier and Type	Constant Field	Value
`public static final int`	`DEFAULT_CLUSTER_CUTOFF`	`95`

org.biojava.bio.structure.align.ce.AbstractUserArgumentProcessor
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`CACHE_DIR`	`"PDB_CACHE_DIR"`
`public static final java.lang.String`	`PDB_DIR`	`"PDB_DIR"`

org.biojava.bio.structure.align.ce.CECalculator
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`

org.biojava.bio.structure.align.ce.CeCalculatorEnhanced
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`

org.biojava.bio.structure.align.ce.CeCPMain
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`algorithmName`	`"jCE Circular Permutation"`
`public static final java.lang.String`	`version`	`"1.4"`

org.biojava.bio.structure.align.ce.CECPParameters
Modifier and Type Constant Field Value

public static final int DEFAULT_MIN_CP_LENGTH 5

org.biojava.bio.structure.align.ce.CECPParameters
Modifier and Type	Constant Field	Value
`public static final int`	`DEFAULT_MIN_CP_LENGTH`	`5`

org.biojava.bio.structure.align.ce.CeMain
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`algorithmName`	`"jCE"`
`public static final java.lang.String`	`version`	`"1.1"`

org.biojava.bio.structure.align.ce.CeParameters
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final java.lang.String algorithmName "jCE-sidechain"

org.biojava.bio.structure.align.ce.CeSideChainMain
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`algorithmName`	`"jCE-sidechain"`

org.biojava.bio.structure.align.ce.OptimalCECPMain
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"`

org.biojava.bio.structure.align.client.FarmJobParameters
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final float VERSION 1.0f

org.biojava.bio.structure.align.fatcat.FatCat
Modifier and Type	Constant Field	Value
`public static final float`	`VERSION`	`1.0f`

org.biojava.bio.structure.align.fatcat.calc.AFPCalculator
Modifier and Type Constant Field Value

public static final boolean debug false
org.biojava.bio.structure.align.fatcat.calc.AFPChainer
Modifier and Type Constant Field Value

public static final boolean debug false
org.biojava.bio.structure.align.fatcat.calc.AFPOptimizer
Modifier and Type Constant Field Value

public static final boolean debug false
org.biojava.bio.structure.align.fatcat.calc.AFPPostProcessor
Modifier and Type Constant Field Value

public static final boolean debug false

org.biojava.bio.structure.align.fatcat.calc.FatCatAligner
Modifier and Type	Constant Field	Value
`public static final boolean`	`debug`	`false`
`public static final boolean`	`printTimeStamps`	`false`

org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
Modifier and Type Constant Field Value

public static final int DEFAULT_FRAGLEN 8

org.biojava.bio.structure.align.fatcat.calc.FatCatParameters
Modifier and Type	Constant Field	Value
`public static final int`	`DEFAULT_FRAGLEN`	`8`

org.biojava.bio.structure.align.gui.ChooseDirAction
Modifier and Type Constant Field Value

public static final long serialVersionUID 0L
org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
Modifier and Type Constant Field Value

public static final java.lang.String PDB_DIR "PDB_DIR"
org.biojava.bio.structure.align.gui.DisplayAFP
Modifier and Type Constant Field Value

public static final boolean debug false
org.biojava.bio.structure.align.gui.MemoryMonitor
Modifier and Type Constant Field Value

public static final long serialVersionUID 56289234782130L
org.biojava.bio.structure.align.gui.MemoryMonitor.Surface
Modifier and Type Constant Field Value

public static final long serialVersionUID 2387409854370432908L

org.biojava.bio.structure.align.gui.ChooseDirAction
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`0L`

org.biojava.bio.structure.align.gui.ConfigPDBInstallPanel
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`PDB_DIR`	`"PDB_DIR"`

org.biojava.bio.structure.align.gui.MemoryMonitor
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`56289234782130L`

org.biojava.bio.structure.align.gui.MemoryMonitor.Surface
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`2387409854370432908L`

org.biojava.bio.structure.align.gui.MenuCreator
Modifier and Type	Constant Field	Value
`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
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 "`

org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager
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`

org.biojava.bio.structure.align.gui.jmol.StructureAlignmentJmol
Modifier and Type	Constant Field	Value
`protected static final java.lang.String`	`COMMAND_LINE_HELP`	`"enter Jmol scripting command..."`

org.biojava.bio.structure.align.model.AFPChain
Modifier and Type Constant Field Value

public static final java.lang.String DEFAULT_ALGORITHM_NAME "jFatCat_rigid"

org.biojava.bio.structure.align.model.AFPChain
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`DEFAULT_ALGORITHM_NAME`	`"jFatCat_rigid"`

org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
Modifier and Type Constant Field Value

public static final java.lang.String algorithmName "Smith-Waterman superposition"

org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`algorithmName`	`"Smith-Waterman superposition"`

org.biojava.bio.structure.align.util.AtomCache
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`	`"_"`

org.biojava.bio.structure.align.util.HTTPConnectionTools
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`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.asa.AsaCalculator
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`

org.biojava.bio.structure.cath.CathDomain
Modifier and Type Constant Field Value

public static final long serialVersionUID 1L

org.biojava.bio.structure.cath.CathDomain
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`1L`

org.biojava.bio.structure.cath.CathFactory
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`LATEST_VERSION`	`"3.5.0"`
`public static final java.lang.String`	`VERSION_3_5_0`	`"3.5.0"`

org.biojava.bio.structure.cath.CathFragment
Modifier and Type Constant Field Value

public static final long serialVersionUID 1L

org.biojava.bio.structure.cath.CathFragment
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`1L`

org.biojava.bio.structure.cath.CathInstallation
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final long serialVersionUID 1L
org.biojava.bio.structure.cath.CathSegment
Modifier and Type Constant Field Value

public static final long serialVersionUID 1L

org.biojava.bio.structure.cath.CathNode
Modifier and Type	Constant Field	Value
`public static final long`	`serialVersionUID`	`1L`

org.biojava.bio.structure.domain.PDBDomainProvider
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"`

org.biojava.bio.structure.domain.RemotePDPProvider
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`DEFAULT_SERVER`	`"http://source.rcsb.org/jfatcatserver/domains/"`

org.biojava.bio.structure.domain.pdp.PDPParameters
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`

org.biojava.bio.structure.gui.BiojavaJmol
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"`

org.biojava.bio.structure.gui.ScaleableMatrixPanel
Modifier and Type Constant Field Value

protected static final int SLIDER_STEPS 8
org.biojava.bio.structure.gui.SequenceDisplay
Modifier and Type Constant Field Value

public static final int MAX_SCALE 10

org.biojava.bio.structure.gui.util.AlignedPosition
Modifier and Type Constant Field Value

public static final int EQUIVALENT 1

public static final int NOT_ALIGNED 0
org.biojava.bio.structure.gui.util.PDBDirPanel
Modifier and Type Constant Field Value

public static final java.lang.String PDB_DIR "PDB_DIR"

org.biojava.bio.structure.gui.util.SequenceScalePanel
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`

org.biojava.bio.structure.gui.util.color.GradientMapper
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`

org.biojava.bio.structure.gui.util.color.HSVColorSpace
Modifier and Type Constant Field Value

public static final int CS_HSV 1007

org.biojava.bio.structure.io.FileParsingParameters
Modifier and Type	Constant Field	Value
`public static final int`	`ATOM_CA_THRESHOLD`	`500000`
`public static final int`	`MAX_ATOMS`	`2147483647`

org.biojava.bio.structure.io.PDBFileParser
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final long serialVersionUID 219047230178423923L

org.biojava.bio.structure.io.mmcif.SimpleMMcifParser
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`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.RemoteScopInstallation
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`DEFAULT_SERVER`	`"http://source.rcsb.org/jfatcatserver/domains/"`

org.biojava.bio.structure.scop.ScopFactory
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`LATEST_VERSION`	`"2.04"`
`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"`

org.biojava.bio.structure.scop.ScopInstallation
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.mrc-lmb.cam.ac.uk/scop/parse/"`
`public static final java.lang.String`	`SCOP_DOWNLOAD_ALTERNATE`	`"http://scop.berkeley.edu/downloads/parse/"`

org.biojava.bio.structure.secstruc.BigSqrt
Modifier and Type Constant Field Value

public static final int DEFAULT_MAX_ITERATIONS 50

public static final int DEFAULT_SCALE 3

org.biojava.bio.structure.server.FlatFileInstallation
Modifier and Type	Constant Field	Value
`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
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`

org.biojava3.alignment.io.StockholmFileParser
Modifier and Type Constant Field Value

public static final int INFINITY -1

org.biojava3.alignment.io.StockholmStructure
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`PFAM`	`"PFAM"`
`public static final java.lang.String`	`RFAM`	`"RFAM"`

org.biojava3.alignment.io.StockholmStructure.DatabaseReference
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"`

org.biojava3.core.sequence.io.GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>
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"`

org.biojava3.core.sequence.io.GenbankWriterHelper
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`CIRCULAR_DNA`	`"circular"`
`public static final java.lang.String`	`LINEAR_DNA`	`"linear"`

org.biojava3.core.sequence.io.GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
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 "`

org.biojava3.core.sequence.io.IUPACParser
Modifier and Type Constant Field Value

public static final java.lang.String IUPAC_LOCATION "org/biojava3/core/sequence/iupac.txt"

org.biojava3.core.sequence.io.template.GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound>
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`UNKNOWN_DNA`	`"UNK"`

org.biojava3.core.sequence.storage.BitSequenceReader.BitArrayWorker<C extends Compound>
Modifier and Type Constant Field Value

public static final int BYTES_PER_INT 32

org.biojava3.core.util.Hashcoder
Modifier and Type Constant Field Value

public static final int PRIME 79

public static final int SEED 9

org.biojava3.core.util.InputStreamProvider
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`CACHE_PROPERTY`	`"biojava.cache.files"`
`public static final int`	`GZIP_MAGIC`	`8075`

org.biojava3.core.util.SequenceTools
Modifier and Type Constant Field Value

protected static final java.lang.String NUCLEOTIDE_LETTERS "GCTAUXN"
org.biojava3.core.util.SoftHashMap<K,V>
Modifier and Type Constant Field Value

public static final boolean DEBUG false

public static final int DEFAULT_LIMIT 1

org.biojava3.genome.parsers.cytoband.CytobandParser
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"`

org.biojava3.genome.parsers.genename.GeneChromosomePositionParser
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"`

org.biojava3.genome.parsers.genename.GeneNamesParser
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`DEFAULT_GENENAMES_URL`	"http://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"

org.biojava3.ontology.Synonym
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`

org.biojava3.ontology.obo.OboFileHandler
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"`

org.biojava3.phylo.ResidueProperties
Modifier and Type	Constant Field	Value
`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
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`

org.biojava3.structure.gui.JmolViewerImpl
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"`

org.biojava3.ws.alignment.RemotePairwiseAlignmentOutputProperties
Modifier and Type Constant Field Value

public static final long serialVersionUID 1L
org.biojava3.ws.alignment.RemotePairwiseAlignmentProperties
Modifier and Type Constant Field Value

public static final long serialVersionUID 1L

org.biojava3.ws.alignment.qblast.NCBIQBlastService
Modifier and Type Constant Field Value

public static final long WAIT_INCREMENT 3000L

org.forester.*

org.forester.application.gsdi
Modifier and Type Constant Field Value

public static final boolean REPLACE_UNDERSCORES_IN_NH_SPECIES_TREE true

org.forester.application.surfacing
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_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
Modifier and Type Constant Field Value

public static final java.lang.String NAME "ArchaeopteryxA"

org.forester.archaeopteryx.Constants
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final long serialVersionUID 62256323L

org.forester.archaeopteryx.TreeColorSet
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`	`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
Modifier and Type	Constant Field	Value
`public static final int`	`DEFAULT_HEIGHT`	`12`
`public static final int`	`DEFAULT_WIDTH`	`120`

org.forester.archaeopteryx.tools.PhylogeneticInferenceOptions
Modifier and Type Constant Field Value

public static final long RANDOM_NUMBER_SEED_DEFAULT 42L

org.forester.archaeopteryx.tools.PhylogeneticInferrer
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"`

org.forester.archaeopteryx.tools.SequenceDataRetriver
Modifier and Type Constant Field Value

public static final int DEFAULT_LINES_TO_RETURN 50

org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
Modifier and Type Constant Field Value

public static final java.lang.String QUERY_PLACEHOLDER "__query__"

org.forester.archaeopteryx.webservices.WebserviceUtil
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.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
Modifier and Type	Constant Field	Value
`public static final double`	`DEFAULT_VALUE_FOR_TOO_LARGE_DISTANCE_FOR_KIMURA_FORMULA`	`10.0`

org.forester.go.GoNameSpace
Modifier and Type	Constant Field	Value
`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
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`	`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
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"`
`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
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"`

org.forester.io.parsers.nexus.NexusConstants
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final boolean REPLACE_UNDERSCORES_DEFAULT false

org.forester.io.parsers.nhx.NHXtags
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`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
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"`

org.forester.io.parsers.phyloxml.PhyloXmlUtil
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"`

org.forester.io.parsers.phyloxml.XmlElement
Modifier and Type Constant Field Value

public static final boolean DEBUG false

org.forester.io.parsers.tol.TolParser
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"`

org.forester.io.parsers.tol.TolXmlMapping
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"`

org.forester.io.writers.PhylogenyWriter
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\"?>"`

org.forester.pccx.BranchLengthBasedScoringMethod
Modifier and Type Constant Field Value

public static final double MIN_ALLOWED_BL_VALUE 0.001

org.forester.pccx.LogBranchLengthBasedScoringMethod
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`

org.forester.phylogeny.Phylogeny
Modifier and Type Constant Field Value

public static final boolean ALLOW_MULTIPLE_PARENTS_DEFAULT false

org.forester.phylogeny.data.BinaryCharacters
Modifier and Type Constant Field Value

public static final int COUNT_DEFAULT -1
org.forester.phylogeny.data.BranchWidth
Modifier and Type Constant Field Value

public static final double BRANCH_WIDTH_DEFAULT_VALUE 1.0
org.forester.phylogeny.data.Confidence
Modifier and Type Constant Field Value

public static final int CONFIDENCE_DEFAULT_VALUE -9999
org.forester.phylogeny.data.DomainArchitecture
Modifier and Type Constant Field Value

public static final java.lang.String NHX_SEPARATOR ">"
org.forester.phylogeny.data.Event
Modifier and Type Constant Field Value

public static final int DEFAULT_VALUE -1

org.forester.phylogeny.data.Identifier
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`NCBI`	`"ncbi"`
`public static final java.lang.String`	`REFSEQ`	`"refseq"`

org.forester.phylogeny.data.NodeVisualization
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final double BRANCH_LENGTH_DEFAULT -1024.0
org.forester.phylogeny.data.Point
Modifier and Type Constant Field Value

public static final java.lang.String UNKNOWN_GEODETIC_DATUM "?"

org.forester.phylogeny.data.ProteinDomain
Modifier and Type	Constant Field	Value
`public static final double`	`CONFIDENCE_DEFAULT`	`0.0`
`public static final java.lang.String`	`IDENTIFIER_DEFAULT`	`""`

org.forester.phylogeny.data.SequenceRelation
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"`

org.forester.protein.BinaryDomainCombination
Modifier and Type Constant Field Value

public static final java.lang.String SEPARATOR "="

org.forester.sdi.DistanceCalculator
Modifier and Type Constant Field Value

public static final double DEFAULT -1.0

org.forester.sequence.Sequence
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`public static final double`	`MAX_SIMILARITY_SCORE`	`1.0`
`public static final double`	`MIN_SIMILARITY_SCORE`	`0.0`

org.forester.surfacing.PrintableDomainSimilarity
Modifier and Type Constant Field Value

public static final java.lang.String SPECIES_SEPARATOR " "

org.forester.surfacing.SurfacingConstants
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_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
Modifier and Type Constant Field Value

public static final boolean SANITIZE false

public static final boolean VERBOSE true

org.forester.util.DescriptiveStatistics
Modifier and Type Constant Field Value

public static final java.lang.String PLUS_MINUS "\u00b1"

org.forester.util.ForesterConstants
Modifier and Type	Constant Field	Value
`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
Modifier and Type Constant Field Value

public static final double ZERO_DIFF 1.0E-9

org.forester.ws.seqdb.SequenceDbWsTools
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`CELLULAR_ORGANISMS`	`"cellular organisms"`
`public static final java.lang.String`	`VIRUSES`	`"Viruses"`

org.forester.ws.uniprot.SequenceDbWsTools
Modifier and Type	Constant Field	Value
`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
Modifier and Type	Constant Field	Value
`public static final java.lang.String`	`CELLULAR_ORGANISMS`	`"cellular organisms"`
`public static final java.lang.String`	`VIRUSES`	`"Viruses"`

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_MAX_ITERATIONS`	`50`
`public static final int`	`DEFAULT_SCALE`	`3`

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 boolean`	`SANITIZE`	`false`
`public static final boolean`	`VERBOSE`	`true`

Constant Field Values

Contents

org.biojava.*

org.biojava3.*

org.forester.*