Constant Field Values


Contents
org.biojava.*

org.biojava.bio.structure.AminoAcid
public static final String ATOMRECORD "ATOM"
public static final String SEQRESRECORD "SEQRES"

org.biojava.bio.structure.AminoAcidImpl
public static final 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 String AMINOACID "amino"
public static final String HETATM "hetatm"
public static final String NUCLEOTIDE "nucleotide"

org.biojava.bio.structure.HetatomImpl
public static final String type "hetatm"

org.biojava.bio.structure.NucleotideImpl
public static final String type "nucleotide"

org.biojava.bio.structure.PDBHeader
public static final float DEFAULT_RESOLUTION 99.0f

org.biojava.bio.structure.PDBStatus
public static final String DEFAULT_PDB_SERVER "www.rcsb.org"
public static final 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 String caAtomName " CA "
public static final String cbAtomName "CB"
public static final String nAtomName "N"
public static final String oAtomName "O"

org.biojava.bio.structure.align.BioJavaStructureAlignment
public static final 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 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 String algorithmName "jCE Circular Permutation"
public static final int DEFAULT_MIN_CP_LENGTH 5
public static final String version "1.3"

org.biojava.bio.structure.align.ce.CeMain
public static final String algorithmName "jCE"
public static final 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 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 String algorithmName "jCE-sidechain"

org.biojava.bio.structure.align.ce.OptimalCECPMain
public static final String algorithmName "jCE Optimal Circular Permutation"
public static final 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 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 String PDB_DIR "PDB_DIR"

org.biojava.bio.structure.align.gui.DisplayAFP
public static final boolean debug false

org.biojava.bio.structure.align.gui.MenuCreator
public static final String ALIGNMENT_PANEL "Alignment Panel"
public static final String EQR_COLOR "Color By EQR"
public static final String FATCAT_BLOCK "Color By Alignment Block"
public static final String FATCAT_TEXT "View as FATCAT result"
public static final String LOAD_ALIGNMENT_XML "Load Alignment XML"
public static final String LOAD_DB_RESULTS "Load DB search results"
public static final String PAIRS_ONLY "View Aligned Pairs"
public static final String PRINT "Print"
public static final String SAVE_ALIGNMENT_XML "Save Alignment XML"
public static final String SELECT_EQR "Select Equivalent Positions"
public static final String SIMILARITY_COLOR "Color By Similarity"
public static final String TEXT_ONLY "View Text Only"

org.biojava.bio.structure.align.gui.SystemInfo
public static final 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 String hexPropertyNames " file.separator line.separator path.separator "
public static final 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 String COMMAND_LINE_HELP "enter Jmol scripting command..."

org.biojava.bio.structure.align.model.AFPChain
public static final String DEFAULT_ALGORITHM_NAME "jFatCat_rigid"

org.biojava.bio.structure.align.seq.SmithWaterman3Daligner
public static final String algorithmName "Smith-Waterman superposition"

org.biojava.bio.structure.align.util.AtomCache
public static final String CHAIN_NR_SYMBOL ":"
public static final String CHAIN_SPLIT_SYMBOL "."
public static final String PDP_DOMAIN_IDENTIFIER "PDP:"
public static final String UNDERSCORE "_"

org.biojava.bio.structure.align.util.HTTPConnectionTools
public static final int DEFAULT_CONNECTION_TIMEOUT 15000
public static final String USERAGENT "JFatCat Java client"

org.biojava.bio.structure.align.util.UserConfiguration
public static final String MMCIF_FORMAT "mmCif"
public static final String PDB_DIR "PDB_DIR"
public static final String PDB_FORMAT "PDB"
public static final String TMP_DIR "java.io.tmpdir"

org.biojava.bio.structure.domain.RemotePDPProvider
public static final 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 String adapter "org.jmol.api.JmolAdapter"
public static final String smartAdapter "org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final 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 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 String HELIX "HELIX"
public static final String PDB_AUTHOR_ASSIGNMENT "PDB_AUTHOR_ASSIGNMENT"
public static final String STRAND "STRAND"
public static final String TURN "TURN"

org.biojava.bio.structure.io.PDBFileReader
public static final String DEFAULT_PDB_FILE_SERVER "ftp.wwpdb.org"
public static final String LOAD_CHEM_COMP_PROPERTY "loadChemCompInfo"
public static final 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 String FIELD_LINE "_"
public static final String LOOP_END "#"
public static final String LOOP_START "loop_"
public static final String STRING_LIMIT ";"

org.biojava.bio.structure.scop.BerkeleyScopInstallation
public static final String claFileName "dir.cla.scop."
public static final String desFileName "dir.des.scop."
public static final String hieFileName "dir.hie.scop."

org.biojava.bio.structure.scop.RemoteScopInstallation
public static final String DEFAULT_SERVER "http://source.rcsb.org/jfatcatserver/domains/"

org.biojava.bio.structure.scop.ScopInstallation
public static final String claFileName "dir.cla.scop.txt_"
public static final String DEFAULT_VERSION "1.75"
public static final String desFileName "dir.des.scop.txt_"
public static final String hieFileName "dir.hie.scop.txt_"
public static final 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 String DEFAUL_CHAIN_FILE "chaininfo.txt"
public static final 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.core.sequence.io.IUPACParser
public static final 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 String CACHE_PROPERTY "biojava.cache.files"
public static final int GZIP_MAGIC 8075

org.biojava3.core.util.SequenceTools
protected static final 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 String adapter "org.jmol.api.JmolAdapter"
public static final String smartAdapter "org.jmol.adapter.smarter.SmarterJmolAdapter"
public static final 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.surfacing
public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX "_all_encountered_pfams"
public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX "_all_encountered_pfams_with_go_annotation"
public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX "_all_pfams_gained_as_dc"
public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX "_all_pfams_gained_as_domains"
public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX "_all_pfams_lost_as_dc"
public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX "_all_pfams_lost_as_domains"
public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES "PER_NODE_EVENTS"
public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES "PER_SUBTREE_EVENTS"
public static final String BDC_PRESENT_NEXUS "_dc.nex"
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO "_dc_dollo.xml"
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH "_dc_fitch.xml"
public static final String D_PROMISCUITY_FILE_SUFFIX "_domain_promiscuities"
public static final String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX ".dcc"
public static final String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS "graph_analysis_out"
public static final String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS "_dc.dot"
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO "_d_dollo.xml"
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH "_d_fitch.xml"
public static final String DOMAINS_PRESENT_NEXUS "_dom.nex"
public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX "_encountered_pfams_summary"
public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS "_dc.nex"
public static final String NEXUS_EXTERNAL_DOMAINS "_dom.nex"
public static final String NEXUS_SECONDARY_FEATURES "_secondary_features.nex"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES "_dollo_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS "_dollo_biol_proc_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT "_dollo_cell_comp_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION "_dollo_mol_funct_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_D "_dollo_gains_d"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D "_dollo_gains_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D "_dollo_gains_d.html"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES "_dollo_gains_secondary_features"
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_D "_dollo_losses_d"
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D "_dollo_losses_d.html"
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES "_dollo_losses_secondary_features"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_D "_dollo_present_d"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D "_dollo_present_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D "_dollo_present_d.html"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES "_dollo_present_secondary_features"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES "_fitch_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS "_fitch_biol_proc_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT "_fitch_cell_comp_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION "_fitch_mol_funct_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_GAINS_BC "_fitch_gains_dc"
public static final String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC "_fitch_gains_dc.html"
public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_BC "_fitch_losses_dc"
public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC "_fitch_losses_dc.html"
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC "_fitch_present_dc"
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS "_fitch_present_dc.dot"
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC "_fitch_present_dc.html"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS "_dollo_glc_dc"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS "_dollo_glc_d"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES "_dollo_glc_secondary_features"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS "_fitch_glc_dc"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS "_fitch_glc_d"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS "_dollo_gl_dc"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS "_dollo_gl_d"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES "_dollo_gl_secondary_features"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS "_fitch_gl_dc"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS "_fitch_gl_d"
public static final String PRG_NAME "surfacing"
public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO "_secondary_features_dollo.xml"

org.forester.application.surfacing_old
public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX "_all_encountered_pfams"
public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX "_all_encountered_pfams_with_go_annotation"
public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX "_all_pfams_gained_as_dc"
public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX "_all_pfams_gained_as_domains"
public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX "_all_pfams_lost_as_dc"
public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX "_all_pfams_lost_as_domains"
public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES "PER_NODE_EVENTS"
public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES "PER_SUBTREE_EVENTS"
public static final String BDC_PRESENT_NEXUS "_dc.nex"
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO "_dc_dollo.xml"
public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH "_dc_fitch.xml"
public static final String D_PROMISCUITY_FILE_SUFFIX "_domain_promiscuities"
public static final String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX ".dcc"
public static final String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS "graph_analysis_out"
public static final String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS "_dc.dot"
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO "_d_dollo.xml"
public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH "_d_fitch.xml"
public static final String DOMAINS_PRESENT_NEXUS "_dom.nex"
public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX "_encountered_pfams_summary"
public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS "_dc.nex"
public static final String NEXUS_EXTERNAL_DOMAINS "_dom.nex"
public static final String NEXUS_SECONDARY_FEATURES "_secondary_features.nex"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES "_dollo_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS "_dollo_biol_proc_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT "_dollo_cell_comp_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION "_dollo_mol_funct_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_D "_dollo_gains_d"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D "_dollo_gains_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D "_dollo_gains_d.html"
public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES "_dollo_gains_secondary_features"
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_D "_dollo_losses_d"
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D "_dollo_losses_d.html"
public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES "_dollo_losses_secondary_features"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_D "_dollo_present_d"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D "_dollo_present_goid_d"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D "_dollo_present_d.html"
public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES "_dollo_present_secondary_features"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES "_fitch_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS "_fitch_biol_proc_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT "_fitch_cell_comp_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION "_fitch_mol_funct_goid_dc"
public static final String PARSIMONY_OUTPUT_FITCH_GAINS_BC "_fitch_gains_dc"
public static final String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC "_fitch_gains_dc.html"
public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_BC "_fitch_losses_dc"
public static final String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC "_fitch_losses_dc.html"
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC "_fitch_present_dc"
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS "_fitch_present_dc.dot"
public static final String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC "_fitch_present_dc.html"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS "_dollo_glc_dc"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS "_dollo_glc_d"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES "_dollo_glc_secondary_features"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS "_fitch_glc_dc"
public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS "_fitch_glc_d"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS "_dollo_gl_dc"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS "_dollo_gl_d"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES "_dollo_gl_secondary_features"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS "_fitch_gl_dc"
public static final String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS "_fitch_gl_d"
public static final String PRG_NAME "surfacing"
public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO "_secondary_features_dollo.xml"

org.forester.archaeopteryx.ArchaeopteryxA
public static final String NAME "ArchaeopteryxA"

org.forester.archaeopteryx.Constants
public static final boolean NH_PARSING_IGNORE_QUOTES_DEFAULT true

org.forester.archaeopteryx.FontChooser
public static final long serialVersionUID 62256323L

org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient
public static final String QUERY_PLACEHOLDER "__query__"

org.forester.archaeopteryx.webservices.WebserviceUtil
public static final String PFAM_INST "pfam"
public static final String PFAM_NAME "Pfam"
public static final String PFAM_SERVER "http://pfam.janelia.org"
public static final String TAX_CODE_TO_SCI_NAME "tax_code_to_sci_name"
public static final String TOL_NAME "Tree of Life"
public static final String TOL_WEBSERVER "http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=__query__"
public static final String TREE_BASE_NAME "TreeBase"
public static final String TREE_FAM_INST "tree_fam"
public static final String TREE_FAM_NAME "TreeFam"

org.forester.development.AminoAcid
public static final char GAP 45
public static final byte GAP_CODE 21
public static final char TERMINATE 42
public static final byte TERMINATE_CODE 22
public static final char UNKNOWN 63
public static final byte UNKNOWN_CODE 20

org.forester.go.GoNameSpace
public final String BIOLOGICAL_PROCESS_STR "biological_process"
public final String CELLULAR_COMPONENT_STR "cellular_component"
public final String MOLECULAR_FUNCTION_STR "molecular_function"
public final String UNASSIGNED_STR "unassigned"

org.forester.go.GoRelationship
public static final String NEGATIVELY_REGULATES_STR "negatively_regulates"
public static final String PART_OF_STR "part_of"
public static final String POSITIVELY_REGULATES_STR "positively_regulates"
public static final String REGULATES_STR "regulates"

org.forester.go.GoSubset
public static final String GOSLIM_CANDIDA_STR "goslim_candida"
public static final String GOSLIM_GENERIC_STR "goslim_generic"
public static final String GOSLIM_GOA_STR "goslim_goa"
public static final String GOSLIM_PIR_STR "goslim_pir"
public static final String GOSLIM_PLANT_STR "goslim_plant"
public static final String GOSLIM_POMBE_STR "goslim_pombe"
public static final String GOSLIM_YEAST_STR "goslim_yeast"
public static final String GOSUBSET_PROK_STR "gosubset_prok"

org.forester.go.GoXRef
public static final String ARACYC_STR "AraCyc"
public static final String EC_STR "EC"
public static final String GOC_STR "GOC"
public static final String IMG_STR "IMG"
public static final String KEGG_STR "KEGG"
public static final String META_CYC_STR "MetaCyc"
public static final String PMID_STR "PMID"
public static final String REACTOME_STR "Reactome"
public static final String RESID_STR "RESID"
public static final String TC_STR "TC"
public static final String UM_BBD_ENZYME_ID_STR "UM-BBD_enzymeID"
public static final String UM_BBD_PATHWAY_ID_STR "UM-BBD_pathwayID"
public static final String UM_BBD_REACTIONID_STR "UM-BBD_reactionID"
public static final String WIKIPEDIA_STR "Wikipedia"
public static final String XX_STR "XX"

org.forester.io.parsers.nexus.NexusConstants
public static final String BEGIN_CHARACTERS "Begin Characters;"
public static final String BEGIN_TAXA "Begin Taxa;"
public static final String BEGIN_TREES "Begin Trees;"
public static final String CHARSTATELABELS "CharStateLabels"
public static final String DATATYPE "DataType"
public static final String DIMENSIONS "Dimensions"
public static final String END "End;"
public static final String FORMAT "Format"
public static final String MATRIX "Matrix"
public static final String NCHAR "NChar"
public static final String NEXUS "#NEXUS"
public static final String NTAX "NTax"
public static final String STANDARD "Standard"
public static final String SYMBOLS "Symbols"
public static final String TAXLABELS "TaxLabels"
public static final String TRANSLATE "Translate"
public static final String TREE "Tree"
public static final String UTREE "UTREE"

org.forester.io.parsers.nhx.NHXParser
public static final boolean LIMIT_SPECIES_NAMES_TO_FIVE_CHARS true
public static final boolean REPLACE_UNDERSCORES_DEFAULT false

org.forester.io.parsers.nhx.NHXtags
public static final String ANNOTATION "AN="
public static final String BINARY_DOMAIN_COMBINATIONS "GDC="
public static final String COLOR "C="
public static final String CUSTOM_DATA_ON_NODE "XN="
public static final String DOMAIN_STRUCTURE "DS="
public static final String DOMAINS "GD="
public static final String DOMAINS_SEPARATOR "\\|"
public static final String EC_NUMBER "E="
public static final String GENE_NAME "GN="
public static final String GENE_NAME_SYNONYM "G="
public static final String IS_DUPLICATION "D="
public static final String NODE_IDENTIFIER "ID="
public static final String ORTHOLOGOUS "On="
public static final String PARENT_BRANCH_WIDTH "W="
public static final String SEQUENCE_ACCESSION "AC="
public static final String SPECIES_NAME "S="
public static final String SUBTREE_NEIGHBORS "SNn="
public static final String SUPER_ORTHOLOGOUS "SOn="
public static final String SUPPORT "B="
public static final String TAXONOMY_ID "T="

org.forester.io.parsers.phyloxml.PhyloXmlMapping
public static final String ACCESSION "accession"
public static final String ACCESSION_SOURCE_ATTR "source"
public static final String ANNOTATION "annotation"
public static final String ANNOTATION_DESC "desc"
public static final String ANNOTATION_EVIDENCE_ATTR "evidence"
public static final String ANNOTATION_REF_ATTR "ref"
public static final String ANNOTATION_SOURCE_ATTR "source"
public static final String ANNOTATION_TYPE_ATTR "type"
public static final String BINARY_CHARACTER "bc"
public static final String BINARY_CHARACTERS "binary_characters"
public static final String BINARY_CHARACTERS_GAINED "gained"
public static final String BINARY_CHARACTERS_GAINED_COUNT_ATTR "gained_count"
public static final String BINARY_CHARACTERS_LOST "lost"
public static final String BINARY_CHARACTERS_LOST_COUNT_ATTR "lost_count"
public static final String BINARY_CHARACTERS_PRESENT "present"
public static final String BINARY_CHARACTERS_PRESENT_COUNT_ATTR "present_count"
public static final String BINARY_CHARACTERS_TYPE_ATTR "type"
public static final String BRANCH_LENGTH "branch_length"
public static final String CLADE "clade"
public static final String CLADE_DATE "date"
public static final String CLADE_DATE_DESC "desc"
public static final String CLADE_DATE_MAX "maximum"
public static final String CLADE_DATE_MIN "minimum"
public static final String CLADE_DATE_UNIT "unit"
public static final String CLADE_DATE_VALUE "value"
public static final String COLOR "color"
public static final String COLOR_BLUE "blue"
public static final String COLOR_GREEN "green"
public static final String COLOR_RED "red"
public static final String CONFIDENCE "confidence"
public static final String CONFIDENCE_TYPE_ATTR "type"
public static final String DISTRIBUTION "distribution"
public static final String DISTRIBUTION_DESC "desc"
public static final String EVENT_DUPLICATIONS "duplications"
public static final String EVENT_LOSSES "losses"
public static final String EVENT_SPECIATIONS "speciations"
public static final String EVENT_TYPE "type"
public static final String EVENTS "events"
public static final String ID_REF "id_ref"
public static final String IDENTIFIER "id"
public static final String IDENTIFIER_PROVIDER_ATTR "provider"
public static final String NODE_NAME "name"
public static final String PHYLOGENY "phylogeny"
public static final String PHYLOGENY_BRANCHLENGTH_UNIT_ATTR "branch_length_unit"
public static final String PHYLOGENY_DESCRIPTION "description"
public static final String PHYLOGENY_IS_REROOTABLE_ATTR "rerootable"
public static final String PHYLOGENY_IS_ROOTED_ATTR "rooted"
public static final String PHYLOGENY_NAME "name"
public static final String PHYLOGENY_TYPE_ATTR "type"
public static final String POINT "point"
public static final String POINT_ALTITUDE "alt"
public static final String POINT_ALTITUDE_UNIT_ATTR "alt_unit"
public static final String POINT_GEODETIC_DATUM "geodetic_datum"
public static final String POINT_LATITUDE "latitude"
public static final String POINT_LONGITUDE "longitude"
public static final String PROPERTY "property"
public static final String PROPERTY_APPLIES_TO "applies_to"
public static final String PROPERTY_DATATYPE "datatype"
public static final String PROPERTY_REF "ref"
public static final String PROPERTY_UNIT "unit"
public static final String REFERENCE "reference"
public static final String REFERENCE_DESC "desc"
public static final String REFERENCE_DOI_ATTR "doi"
public static final String SEQUENCE "sequence"
public static final String SEQUENCE_DOMAIN_ARCHITECTURE_DOMAIN "domain"
public static final String SEQUENCE_DOMAIN_ARCHITECTURE_LENGTH "length"
public static final String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_CONFIDENCE "confidence"
public static final String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_FROM "from"
public static final String SEQUENCE_DOMAIN_ARCHITECTURE_PROT_DOMAIN_TO "to"
public static final String SEQUENCE_DOMAIN_ARCHITECURE "domain_architecture"
public static final String SEQUENCE_LOCATION "location"
public static final String SEQUENCE_MOL_SEQ "mol_seq"
public static final String SEQUENCE_NAME "name"
public static final String SEQUENCE_SYMBOL "symbol"
public static final String SEQUENCE_TYPE "type"
public static final String TAXONOMY "taxonomy"
public static final String TAXONOMY_AUTHORITY "authority"
public static final String TAXONOMY_CODE "code"
public static final String TAXONOMY_COMMON_NAME "common_name"
public static final String TAXONOMY_RANK "rank"
public static final String TAXONOMY_SCIENTIFIC_NAME "scientific_name"
public static final String TAXONOMY_SYNONYM "synonym"
public static final String TYPE_ATTR "type"
public static final String URI "uri"
public static final String URI_DESC_ATTR "desc"
public static final String WIDTH "width"

org.forester.io.parsers.phyloxml.PhyloXmlParser
public static final String APACHE_FEATURES_VALIDATION_SCHEMA "http://apache.org/xml/features/validation/schema"
public static final String APACHE_FEATURES_VALIDATION_SCHEMA_FULL "http://apache.org/xml/features/validation/schema-full-checking"
public static final String APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION "http://apache.org/xml/properties/schema/external-schemaLocation"
public static final String JAXP_SCHEMA_LANGUAGE "http://java.sun.com/xml/jaxp/properties/schemaLanguage"
public static final String JAXP_SCHEMA_SOURCE "http://java.sun.com/xml/jaxp/properties/schemaSource"
public static final String SAX_FEATURES_VALIDATION "http://xml.org/sax/features/validation"
public static final String W3C_XML_SCHEMA "http://www.w3.org/2001/XMLSchema"

org.forester.io.parsers.phyloxml.PhyloXmlUtil
public static final int ROUNDING_DIGITS_FOR_PHYLOXML_DOUBLE_OUTPUT 9

org.forester.io.parsers.phyloxml.XmlElement
public static final boolean DEBUG false

org.forester.io.parsers.tol.TolParser
public static final String APACHE_FEATURES_VALIDATION_SCHEMA "http://apache.org/xml/features/validation/schema"
public static final String APACHE_FEATURES_VALIDATION_SCHEMA_FULL "http://apache.org/xml/features/validation/schema-full-checking"
public static final String APACHE_PROPERTIES_SCHEMA_EXTERNAL_LOCATION "http://apache.org/xml/properties/schema/external-schemaLocation"
public static final String JAXP_SCHEMA_LANGUAGE "http://java.sun.com/xml/jaxp/properties/schemaLanguage"
public static final String JAXP_SCHEMA_SOURCE "http://java.sun.com/xml/jaxp/properties/schemaSource"
public static final String SAX_FEATURES_VALIDATION "http://xml.org/sax/features/validation"
public static final String W3C_XML_SCHEMA "http://www.w3.org/2001/XMLSchema"

org.forester.io.parsers.tol.TolXmlMapping
public static final String AUTHDATE "AUTHDATE"
public static final String AUTHORITY "AUTHORITY"
public static final String CLADE "NODE"
public static final String NODE_ID_ATTR "ID"
public static final String NODE_ITALICIZENAME_ATTR "ITALICIZENAME"
public static final String OTHERNAME "OTHERNAME"
public static final String OTHERNAME_NAME "NAME"
public static final String OTHERNAMES "OTHERNAMES"
public static final String PHYLOGENY "TREE"
public static final String TAXONOMY_NAME "NAME"
public static final String TOL_TAXONOMY_ID_TYPE "tol"

org.forester.io.writers.PhylogenyWriter
public static final boolean INDENT_PHYLOXML_DEAFULT true
public static final String PHYLO_XML_END "</phyloxml>"
public static final String PHYLO_XML_INTENDATION_BASE " "
public static final 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 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.PhylogenyNode
public static final double DISTANCE_DEFAULT -1024.0

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 double CONFIDENCE_DEFAULT_VALUE -9999.0

org.forester.phylogeny.data.DomainArchitecture
public static final String NHX_SEPARATOR ">"

org.forester.phylogeny.data.Event
public static final int DEFAULT_VALUE -1

org.forester.phylogeny.data.ProteinDomain
public static final double CONFIDENCE_DEFAULT 0.0
public static final String IDENTIFIER_DEFAULT ""

org.forester.sdi.DistanceCalculator
public static final double DEFAULT -1.0

org.forester.surfacing.BinaryDomainCombination
public static final String SEPARATOR "="

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 String SPECIES_SEPARATOR " "

org.forester.surfacing.SurfacingConstants
public static final String AMIGO_LINK "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query="
public static final String EOL_LINK "http://www.eol.org/search?q="
public static final String GO_LINK "http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&query="
public static final String GOOGLE_SCHOLAR_LIMITS "&as_subj=bio&as_subj=med&as_subj=chm&num=100"
public static final String GOOGLE_SCHOLAR_LINK "http://scholar.google.com/scholar?q="
public static final String GOOGLE_WEB_SEARCH_LINK "http://www.google.com/search?q="
public static final String NONE "[none]"
public static final String PFAM_FAMILY_ID_LINK "http://pfam.sanger.ac.uk/family?id="
public static final String TAXONOMY_LINK "http://beta.uniprot.org/taxonomy/?query="
public static final String TOL_LINK "http://www.googlesyndicatedsearch.com/u/TreeofLife?q="
public static final String UNIPROT_LINK "http://beta.uniprot.org/taxonomy/?query="
public static final 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 String PLUS_MINUS "\u00b1"

org.forester.util.ForesterConstants
public static final String LOCAL_PHYLOXML_XSD_RESOURCE "resources/phyloxml.xsd"
public static final String PHYLO_XML_LOCATION "http://www.phyloxml.org"
public static final 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 String PHYLO_XML_SUFFIX ".xml"
public static final String PHYLO_XML_VERSION "1.10"
public static final String PHYLO_XML_XSD "phyloxml.xsd"
public static final boolean RELEASE false
public static final String UTF8 "UTF-8"
public static final String XML_SCHEMA_INSTANCE "http://www.w3.org/2001/XMLSchema-instance"

org.forester.util.ForesterUtil
public static final double ZERO_DIFF 1.0E-9