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Constant Field Values

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apollo.analysis.*

apollo.analysis.SeqAnalysisGUI
public static final int MAX_HISTORY_LENGTH 5

apollo.dataadapter.*

apollo.dataadapter.DataLoadEvent
public static final int DATA_RETRIEVE_BEGIN 0
public static final int DATA_RETRIEVE_DONE 1

apollo.dataadapter.EnsCGIAdapterGUI
public static final int MAX_HISTORY_LENGTH 5
public static final int RANGE 2
public static final int REGION 1

apollo.dataadapter.GbrowseAdapterGUI
public static final int MAX_HISTORY_LENGTH 5

apollo.dataadapter.StateInformation
public static final java.lang.String ADD_RESULT_GENES_AS_ANNOTATIONS "addResultAsAnnotation.Gene"
public static final java.lang.String ADD_TRANSCRIPT_SUPPORT "addSupport.Transcript"
public static final java.lang.String AGGRESSIVE_GENE_NAMING "aggressiveNaming.Gene"
public static final java.lang.String AUTHOR "AnnotationAuthor"
public static final java.lang.String AUTHOR_EMAIL "AnnotationAuthorEmail"
public static final java.lang.String CONNECTION_STRING "connection_string"
public static final java.lang.String DATA_ADAPTER "adapter"
public static final java.lang.String DATA_FILE_NAME "dataFileName"
public static final java.lang.String DATABASE "database"
public static final java.lang.String DSN_DESCRIPTION "DSN_description"
public static final java.lang.String DSN_MAP_MASTER "DSN_mapMaster"
public static final java.lang.String DSN_SOURCE "DSN_source"
public static final java.lang.String DSN_SOURCE_ID "DSN_sourceId"
public static final java.lang.String DSN_SOURCE_VERSION "DSN_sourceVersion"
public static final java.lang.String ENSEMBL_DRIVER "ensembl_driver"
public static final java.lang.String HOST "host"
public static final java.lang.String HTTP_PROXY_HOST "http.proxyHost"
public static final java.lang.String HTTP_PROXY_PORT "http.proxyPort"
public static final java.lang.String HTTP_PROXY_SET "http.proxySet"
public static final java.lang.String INCLUDE_CONTIG_FEATURE "include.ContigFeature"
public static final java.lang.String INCLUDE_CONTIG_FEATURE_TYPES "INCLUDE_CONTIG_FEATURE_TYPES"
public static final java.lang.String INCLUDE_DITAG_FEATURE "include.DitagFeature"
public static final java.lang.String INCLUDE_DITAG_TYPES "INCLUDE_DITAG_FEATURE_TYPES"
public static final java.lang.String INCLUDE_DNA_DNA_ALIGNMENT "include.DnaDnaAlignment"
public static final java.lang.String INCLUDE_DNA_DNA_ALIGNMENT_TYPES "INCLUDE_DNA_DNA_ALIGNMENT_TYPES"
public static final java.lang.String INCLUDE_DNA_PROTEIN_ALIGNMENT "include.DnaProteinAlignment"
public static final java.lang.String INCLUDE_DNA_PROTEIN_ALIGNMENT_TYPES "INCLUDE_DNA_PROTEIN_ALIGNMENT_TYPES"
public static final java.lang.String INCLUDE_FEATURE "include.Feature"
public static final java.lang.String INCLUDE_FEATURE_TYPES "INCLUDE_FEATURE"
public static final java.lang.String INCLUDE_GENE "include.Gene"
public static final java.lang.String INCLUDE_GENE_TYPES "INCLUDE_GENE_TYPES"
public static final java.lang.String INCLUDE_PREDICTION_TRANSCRIPT "include.PredictionTranscript"
public static final java.lang.String INCLUDE_PREDICTION_TRANSCRIPT_TYPES "INCLUDE_PREDICTION_TRANSCRIPT_TYPES"
public static final java.lang.String INCLUDE_REPEAT_FEATURE "include.RepeatFeature"
public static final java.lang.String INCLUDE_REPEAT_FEATURE_TYPES "INCLUDE_REPEAT_FEATURE_TYPES"
public static final java.lang.String INCLUDE_SIMPLE_PEPTIDE_FEATURE "include.SimplePeptideFeature"
public static final java.lang.String INCLUDE_SIMPLE_PEPTIDE_FEATURE_TYPES "INCLUDE_SIMPLE_PEPTIDE_FEATURE_TYPES"
public static final java.lang.String INCLUDE_VARIATION "include.Variation"
public static final java.lang.String INPUT_DATA_SET "AnnotationInputDataSet"
public static final java.lang.String INPUT_FILE_NAME "AnnotationInputFile"
public static final java.lang.String INPUT_ID "Input"
public static final java.lang.String INPUT_SERVER_NAME "AnnotationInputServer"
public static final java.lang.String INPUT_STRING "InputString"
public static final java.lang.String INPUT_TYPE "Input Type"
public static final java.lang.String JDBC_DRIVER "jdbc_driver"
public static final java.lang.String LOCK "AnnotationLock"
public static final java.lang.String LOGGING_FILE "loggingFile"
public static final java.lang.String NAME "name"
public static final java.lang.String OUTPUT_DATA_SET "AnnotationOutputDataSet"
public static final java.lang.String OUTPUT_FILE_NAME "AnnotationOutputFile"
public static final java.lang.String OUTPUT_SERVER_NAME "AnnotationOutputServer"
public static final java.lang.String PASSWORD "password"
public static final java.lang.String PORT "port"
public static final java.lang.String REGION "region"
public static final java.lang.String RESET_GENE_START_AND_STOP "resetStartAndStop.Gene"
public static final java.lang.String SCHEMA_VERSION "schema_version"
public static final java.lang.String SEGMENT_ID "Segment_id"
public static final java.lang.String SEGMENT_LENGTH "Segment_length"
public static final java.lang.String SEGMENT_ORIENTATION "Segment_orientation"
public static final java.lang.String SEGMENT_SEGMENT "Segment_segment"
public static final java.lang.String SEGMENT_START "Segment_start"
public static final java.lang.String SEGMENT_STOP "Segment_stop"
public static final java.lang.String SEGMENT_SUBPARTS "Segment_subparts"
public static final java.lang.String SEQUENCE_FILE_NAME "sequenceFileName"
public static final java.lang.String SERVER_PORT "AnnotationServerPort"
public static final java.lang.String SERVER_URL "DAS_server_url"
public static final java.lang.String SIGNATURE "signature"
public static final java.lang.String TYPE_PREFIX_STRING "typePrefix.Gene"
public static final java.lang.String USER "user"

apollo.dataadapter.chado.ChadoTransaction
public static final java.lang.String MAP_POSITION_ID "genomicSequence"

apollo.dataadapter.das.simple.SimpleDASAdapterGUI
public static final int MAX_HISTORY_LENGTH 5

apollo.dataadapter.das2.DAS2AdapterGUI
public static final int MAX_HISTORY_LENGTH 5

apollo.dataadapter.ensj.EnsJAdapter
public static final java.lang.String COORD_SYSTEM "COORD_SYSTEM"
public static final java.lang.String END "END"
public static final java.lang.String ID "ID"
public static final java.lang.String ID_PATTERN "ID: (\\S*)"
public static final java.lang.String NUMBER_OF_FEATURES "NUMBER_OF_FEATURES"
public static final java.lang.String REGION_PATTERN "REGION: ([^--]*)--(.*):(\\S*):(\\S*)-(\\S*)"
public static final java.lang.String REGION_PATTERN_2 "Chr ([^--]*)--(.*):(\\S*) (\\S*) (\\S*)"
public static final java.lang.String REGION_PATTERN_3 "Chr (\\S*) (\\S*) (\\S*)"
public static final java.lang.String SEQ_REGION "SEQ_REGION"
public static final java.lang.String STABLE_ID_PREFIX "ID: "
public static final java.lang.String START "START"
public static final java.lang.String VERSION "VERSION"

apollo.dataadapter.ensj.EnsJConnectionUtil
public static final java.lang.String DRIVER "org.gjt.mm.mysql.Driver"

apollo.dataadapter.ensj.controller.Controller
public static final java.lang.String CHANGE_DATABASE "CHANGE_DATABASE"
public static final java.lang.String CLEAR_SEQ_REGIONS "CLEAR_SEQ_REGIONS"
public static final java.lang.String FIND_COORD_SYSTEMS "FIND_COORD_SYSTEMS"
public static final java.lang.String FIND_ENSEMBL_DATABASE_NAMES "FIND_ENSEMBL_DATABASE_NAMES"
public static final java.lang.String FIND_SEQ_REGIONS "FIND_SEQ_REGIONS"
public static final java.lang.String FIND_START_ENDS "FIND_START_ENDS"
public static final java.lang.String HIDE_OR_SHOW_ANNOTATIONS "HIDE_OR_SHOW_ANNOTATIONS"
public static final java.lang.String HIDE_OR_SHOW_DATABASE "HIDE_OR_SHOW_DATABASE"
public static final java.lang.String HIDE_OR_SHOW_LOCATION "HIDE_OR_SHOW_LOCATION"
public static final java.lang.String HIDE_OR_SHOW_OPTIONS "HIDE_OR_SHOW_OPTIONS"
public static final java.lang.String HIDE_OR_SHOW_TYPES "HIDE_OR_SHOW_TYPES"
public static final java.lang.String LOAD_SEQ_REGION_BY_HISTORY "LOAD_SEQ_REGION_BY_HISTORY"
public static final java.lang.String OPEN_FILE_CHOOSER "OPEN_FILE_CHOOSER"
public static final java.lang.String READ "READ"
public static final java.lang.String SELECT_NEW_ENSEMBL_DATABASE "SELECT_NEW_ENSEMBL_DATABASE"
public static final java.lang.String SELECT_SEQ_REGION "SELECT_SEQ_REGION"
public static final java.lang.String SHOW_AB_INITIO_COUNTS_BY_TYPE "SHOW_AB_INITIO_COUNTS_BY_TYPE"
public static final java.lang.String SHOW_DITAG_FEATURE_COUNTS_BY_TYPE "SHOW_DITAG_FEATURE_COUNTS_BY_TYPE"
public static final java.lang.String SHOW_DNA_DNA_COUNTS_BY_TYPE "SHOW_DNA_DNA_COUNTS_BY_TYPE"
public static final java.lang.String SHOW_DNA_PROTEIN_COUNTS_BY_TYPE "SHOW_DNA_PROTEIN_COUNTS_BY_TYPE"
public static final java.lang.String SHOW_GENE_COUNTS_BY_TYPE "SHOW_GENE_COUNTS_BY_TYPE"
public static final java.lang.String SHOW_SIMPLE_FEATURE_COUNTS_BY_TYPE "SHOW_SIMPLE_FEATURE_COUNTS_BY_TYPE"
public static final java.lang.String UPDATE "UPDATE"
public static final java.lang.String USE_SEQ_REGION_LOCATION "USE_SEQ_REGION_LOCATION"
public static final java.lang.String USE_STABLE_ID_LOCATION "USE_STABLE_ID_LOCATION"

apollo.dataadapter.ensj.controller.EventHandler
public static final java.lang.String NULL_VERSION "(No Version)"

apollo.dataadapter.ensj.controller.FindSeqRegionsHandler
public static final java.lang.String PATTERN "([^--]*)--(.*)"

apollo.dataadapter.ensj.controller.LoadSeqRegionByHistoryHandler
public static final java.lang.String PATTERN "([^--]*)--(.*):(.*):(.*)-(.*)"

apollo.dataadapter.ensj.model.OptionsModel
public static final java.lang.String NONE "NONE"

apollo.dataadapter.ensj.model.TypesModel
public static final java.lang.String ABINITIO "ABINITIO"
public static final java.lang.String DITAGFEATURE "DITAGFEATURE"
public static final java.lang.String DNADNA "DNADNA"
public static final java.lang.String DNAPROTEIN "DNAPROTEIN"
public static final java.lang.String GENE "GENE"
public static final java.lang.String NONE "NONE"
public static final java.lang.String SIMPLEFEATURE "SIMPLEFEATURE"
public static final java.lang.String SIMPLEPEPTIDE "SIMPLEPEPTIDE"

apollo.dataadapter.ensj.view.OptionsPanel
public static final java.lang.String ADD_RESULT_GENES_LABEL "Add result genes as annotations"
public static final java.lang.String ADD_TRANSCRIPT_SUPPORT_LABEL "Add support to transcripts"
public static final java.lang.String AGGRESSIVE_NAMING_LABEL "Aggressive naming"
public static final java.lang.String S_AND_S_RESET_LABEL "Start+Stop reset"
public static final java.lang.String TYPE_PREFIX_LABEL "Prefix to add to types"

apollo.dataadapter.ensj.view.TypesPanel
public static final java.lang.String AB_INITIO_LABEL "Ab Initio Predictions"
public static final java.lang.String CONTIG_LABEL "Contigs"
public static final java.lang.String DITAG_FEATURE_LABEL "Ditag Features"
public static final java.lang.String DNA_DNA_ALIGN_LABEL "Dna Dna Alignments"
public static final java.lang.String DNA_PROTEIN_ALIGN_LABEL "Dna Protein Alignments"
public static final java.lang.String GENE_LABEL "Genes"
public static final java.lang.String PROTEIN_ANNOTATIONS_LABEL "Protein Annotations"
public static final java.lang.String REPEAT_LABEL "Repeats"
public static final java.lang.String SIMPLE_FEATURE_LABEL "Simple Features"

apollo.dataadapter.ensj.view.View
public static final java.lang.String SHOW_ANNOTATIONS_LABEL "Show / Hide Annotations..."
public static final java.lang.String SHOW_DATABASES_LABEL "Show / Hide Databases..."
public static final java.lang.String SHOW_OPTIONS_LABEL "Show / Hide Options..."
public static final java.lang.String SHOW_TYPES_LABEL "Show / Hide Types..."

apollo.dataadapter.ensj19.EnsJAdapter
public static final java.lang.String STABLE_ID_PREFIX "STABLE_ID "

apollo.dataadapter.ensj19.EnsJAdapterGUI
protected static final java.lang.String DEFAULT_CONFIG_FILE "conf/ensj_defaults.conf"

apollo.dataadapter.gamexml.TransactionXMLAdapter
public static final java.lang.String EXT_NAME ".tnxml"

apollo.dataadapter.gff3.GFF3Entry
public static final int NUM_FIELDS 9

apollo.dataadapter.sample.SampleAdapter
public static final java.lang.String NUMBER_OF_FEATURES "NUMBER_OF_FEATURES"

apollo.dataadapter.synteny.SyntenyComparaAdapterGUI
public static final java.lang.String PATTERN "([^,]*),$"

apollo.datamodel.*

apollo.datamodel.CodingPropertiesI
public static final int CODING 4
public static final int MIXED_3PRIME 2
public static final int MIXED_5PRIME 1
public static final int MIXED_BOTH 3
public static final int UNKNOWN 7
public static final int UTR_3PRIME 5
public static final int UTR_5PRIME 6

apollo.datamodel.EvidenceConstants
public static final int FIVE_AND_THREE_PRIME 4
public static final int FIVE_PRIME 2
public static final int SIMILARITY 1
public static final int THREE_PRIME 3

apollo.datamodel.RangeI
public static final java.lang.String NO_NAME "no_name"
public static final java.lang.String NO_TYPE "no_type"

apollo.datamodel.SequenceI
public static final java.lang.String AA "AA"
public static final java.lang.String CLEAR_EDIT "NOP"
public static final java.lang.String DELETION "nucleotide_deletion"
public static final java.lang.String DNA "DNA"
public static final java.lang.String INSERTION "nucleotide_insertion"
public static final java.lang.String RNA "RNA"
public static final java.lang.String SUBSTITUTION "substitution"

apollo.datamodel.Transcript
public static final java.lang.String TRANSCRIPT_TYPE "transcript"

apollo.editor.*

apollo.editor.FeatureChangeEvent
public static final int ADD 1
public static final int DELETE 2
public static final int MERGE 21
public static final int REDRAW 5
public static final int REPLACE 22
public static final int SPLIT 20
public static final int SYNC 6

apollo.editor.ResultChangeEvent
public static final int ANALYSIS 18
public static final int RESULTSET 17
public static final int RESULTSPAN 16

apollo.gui.*

apollo.gui.DetailInfo
public static final int BIOTYPE 20
public static final int CODING_PROPERTIES 22
public static final int END 13
public static final int END_PHASE 21
public static final int EVIDENCE 9
public static final int GENOMIC_LENGTH 0
public static final int GENOMIC_RANGE 2
public static final int GENOMIC_SEQUENCE 10
public static final int HIGH 15
public static final int ID 5
public static final int LOW 14
public static final int MATCH_LENGTH 1
public static final int MATCH_RANGE 3
public static final int MATCH_SEQUENCE 11
public static final int NAME 8
public static final int PHASE 19
public static final int Range 18
public static final int SCORE 4
public static final int START 12
public static final int STRAND 16
public static final int TIER 7
public static final int Type 17
public static final int TYPE 6

apollo.gui.GenericFileAdapterGUI
public static final int MAX_HISTORY_LENGTH 5

apollo.gui.Orientations
public static final int HORIZONTAL 2
public static final int VERTICAL 1

apollo.gui.Selection
public static final int FEATURE 1
public static final int SET 2

apollo.gui.SelectionType
public static final int FEATURE 1
public static final int NONE -1
public static final int SET 2

apollo.gui.Tier
public static final int MINHEIGHT 3

apollo.gui.TierManagerI
public static final long Y_PIXELS_PER_FEATURE 10L

apollo.gui.Transformer
public static final int DOWN 1
public static final int LEFT 1
public static final int RIGHT -1
public static final int UP -1

apollo.gui.detailviewers.blixem.BlixemRunner
public static final int DNA 1
public static final int PROTEIN 2

apollo.gui.detailviewers.exonviewer.BaseEditorPanel
public static final int SEQ_SELECT_DRAG 2100

apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
public static final int CENTER_OUTLINE 2
public static final int LEFT_OUTLINE 1
public static final int NO_OUTLINE 0
public static final int RIGHT_OUTLINE 3

apollo.gui.detailviewers.exonviewer.Directions
public static final int EAST 3
public static final int NORTH 1
public static final int SOUTH 2
public static final int WEST 4

apollo.gui.detailviewers.exonviewer.SeqAlignPanel
public static final int EXON 5
public static final int INTRON 4
public static final int LEFT_BOUNDARY 1
public static final int NO_BOUNDARY 0
public static final int NO_TYPE -1
public static final int RIGHT_BOUNDARY 2
public static final int START_CODON 2
public static final int STOP_CODON 1

apollo.gui.detailviewers.sequencealigner.BaseEditorPanel
public static final int SEQ_SELECT_DRAG 2100

apollo.gui.detailviewers.sequencealigner.DefaultBaseRenderer
public static final int CENTER_OUTLINE 2
public static final int LEFT_OUTLINE 1
public static final int NO_OUTLINE 0
public static final int RIGHT_OUTLINE 3

apollo.gui.detailviewers.sequencealigner.Directions
public static final int EAST 3
public static final int NORTH 1
public static final int SOUTH 2
public static final int WEST 4

apollo.gui.detailviewers.sequencealigner.SeqAlignPanel
public static final int END_BOUNDARY 2
public static final int EXON 5
public static final int INTRON 4
public static final int NO_BOUNDARY 0
public static final int NO_TYPE -1
public static final int START_BOUNDARY 1
public static final int START_CODON 2
public static final int STOP_CODON 1

apollo.gui.detailviewers.sequencealigner.renderers.TestBaseRenderer
public static final int CENTER_OUTLINE 2
public static final int LEFT_OUTLINE 1
public static final int NO_OUTLINE 0
public static final int RIGHT_OUTLINE 3

apollo.gui.drawable.DrawableAnnotationConstants
public static final int ALLSTOPS 2
public static final int BOTHENDS 3
public static final int END 2
public static final int NOSTOPS 1
public static final int ONESTOP 3
public static final int START 1

apollo.gui.event.FeatureSelectionEvent
public static final int FEATURES 1
public static final int SEQUENCE 2
public static final int SYNLINK 3

apollo.gui.event.LazyLoadEvent
public static final int AFTER_LOAD 11
public static final int BEFORE_LOAD 10
public static final int SEQUENCE 1

apollo.gui.event.TierManagerEvent
public static final int LAYOUT_CHANGED 1

apollo.gui.event.ViewEvent
public static final int LIMITS_CHANGED 1
public static final int NEEDS_PAINT 2

apollo.gui.genomemap.ApolloLayoutManager
public static final java.lang.String BOTH "Both"
public static final java.lang.String HORIZONTAL "Horizontal"
public static final java.lang.String NONE "None"
public static final java.lang.String VERTICAL "Vertical"

apollo.gui.genomemap.ScaleView
public static final int FEATURES 2
public static final int SPLICE 1

apollo.gui.genomemap.ViewI
public static final int LEFTSIDE -1
public static final int NONE 0
public static final int RIGHTSIDE 1

apollo.gui.tweeker.Tweeker
public static final int GC 0
public static final int RESTRICTION 1

apollo.seq.*

apollo.seq.ResidueProperties
public static final int HIGH_AFFINITY 1
public static final int NO_AFFINITY -1
public static final int PERFECT_AFFINITY 2
public static final int SOME_AFFINITY 0
public static final int UNRECOGNIZED_VALUES -100

apollo.test.*

apollo.test.ApolloTest
protected final java.lang.String ROOT "/home/wgm/apolloTemp/"

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