Constant Field Values


Contents
org.geworkbench.*

org.geworkbench.analysis.AbstractAnalysis
public static final int AFFY_DETECTION_CALL_FILTER 0
public static final int ALLELIC_FREQUENCY_TYPE 24
public static final int BLAST_TYPE 33
public static final int DEVIATION_BASED_FILTER_TYPE 2
public static final int EXPRESSION_THRESHOLD_FILTER_TYPE 3
public static final int FOLD_CHANGE_TYPE 32
public static final int GENEPIX_FlAGS_FILTER_TYPE 22
public static final int HIERARCHICAL_CLUSTERING_TYPE 11
public static final int HOUSEKEEPINGGENES_VALUE_NORMALIZER_TYPE 21
public static final int IGNORE_TYPE 12
public static final int LOG_TRANSFORMATION_NORMALIZER_TYPE 4
public static final int MARKER_MEAN_MEDIAN_CENTERING_NORMALIZER_TYPE 6
public static final int MARKER_MEAN_VARIANCE_NORMALIZER_TYPE 8
public static final int MARKUS_TYPE 27
public static final int MAX_TYPE 15
public static final int MEAN_TYPE 17
public static final int MEDIAN_TYPE 18
public static final int MEDUSA_TYPE 31
public static final int MICROARRAY_MEAN_MEDIAN_CENTERING_NORMALIZER_TYPE 7
public static final int MIN_TYPE 14
public static final int MISSING_VALUE_NORMALIZER_TYPE 9
public static final int MISSING_VALUES_FILTER_TYPE 1
public static final int MRA_TYPE 28
public static final int NETBOOST_TYPE 25
public static final int PUDGE_TYPE 30
public static final int QUANTILE_NORMALIZER_TYPE 23
public static final int REPLACE_TYPE 13
public static final int SKYBASE_TYPE 29
public static final int SKYLINE_TYPE 26
public static final int SOM_CLUSTERING_TYPE 10
public static final int THRESHOLD_NORMALIZER_TYPE 5
public static final int TTEST_TYPE 20
public static final int TWO_CHANNEL_THRESHOLD_FILTER_TYPE 19
public static final int ZERO_TYPE 16

org.geworkbench.bison.annotation.CSAnnotationContext<T extends DSNamed>
public static final java.lang.String CLASS_CASE "Case"
public static final java.lang.String CLASS_CONTROL "Control"
public static final java.lang.String CLASS_IGNORE "Ignore"
public static final java.lang.String CLASS_TEST "Test"
public static final java.lang.String SELECTION "Selection"

org.geworkbench.bison.annotation.CSAnnotationContextManager
public static final java.lang.String DEFAULT_CONTEXT_NAME "Default"

org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrixDataSet
public static final java.lang.String ADJ_FORMART "adj format"
public static final java.lang.String ENTREZ_ID "entrez id"
public static final java.lang.String GENE_NAME "gene name"
public static final java.lang.String OTHER "other"
public static final java.lang.String PROBESET_ID "probeset id"
public static final java.lang.String SIF_FORMART "sif format"

org.geworkbench.bison.datastructure.biocollections.microarrays.DSMicroarraySet
public static final int affyTxtType 6
public static final int DO_NOT_CREATE_VALUE_OBJECT 0
public static final int expPvalueType 3
public static final int genepixGPRType 5

org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser
public static final java.lang.String ABREV "Gene Symbol"
public static final java.lang.String DESCRIPTION "Gene Title"
public static final java.lang.String GENE_ONTOLOGY_BIOLOGICAL_PROCESS "Gene Ontology Biological Process"
public static final java.lang.String GENE_ONTOLOGY_CELLULAR_COMPONENT "Gene Ontology Cellular Component"
public static final java.lang.String GENE_ONTOLOGY_MOLECULAR_FUNCTION "Gene Ontology Molecular Function"
public static final java.lang.String GENE_SYMBOL "Gene Symbol"
public static final java.lang.String GOTERM "Gene Ontology Biological Process"
public static final java.lang.String LOCUSLINK "Entrez Gene"
public static final java.lang.String MAIN_DELIMITER "\\s*///\\s*"
public static final java.lang.String REFSEQ "RefSeq Transcript ID"
public static final java.lang.String SWISSPROT "SwissProt"
public static final java.lang.String UNIGENE "UniGene ID"

org.geworkbench.bison.datastructure.bioobjects.markers.goterms.GeneOntologyTree
public static final java.lang.String OBO_FILENAME "gene_ontology.1_2.obo"

org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue
protected static final float MISSING 1000.0f

org.geworkbench.bison.datastructure.bioobjects.microarray.DSMasterRagulatorResultSet<T extends DSGeneMarker>
public static final char ACTIVATOR 43
public static final char REPRESSOR 45

org.geworkbench.bison.datastructure.bioobjects.microarray.DSSignificanceResultSet<T extends DSGeneMarker>
public static final int CASE 0
public static final int CONTROL 1

org.geworkbench.bison.datastructure.complex.pattern.PatternResult
public static final java.lang.String DISCOVER "discovery"
public static final java.lang.String EXHAUSTIVE "exhaustive"

org.geworkbench.bison.parsers.AffymetrixParser
public static final char DETECTION_ABSENT 65
public static final char DETECTION_MARGINAL 77
public static final char DETECTION_PRESENT 80

org.geworkbench.bison.parsers.GenepixParseContext
public static final java.lang.String TYPE_DOUBLE "Double"
public static final java.lang.String TYPE_INTEGER "Integer"
public static final java.lang.String TYPE_STRING "String"

org.geworkbench.builtin.projects.OboSourcePreference
public static final java.lang.String DEFAULT_OBO_FILE "data/gene_ontology.1_2.obo"
public static final java.lang.String DEFAULT_REMOTE_LOCATION "http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo"

org.geworkbench.builtin.projects.RWspHandler
protected static final int AccessID 4
protected static final int DirtyID 6
protected static final int IdID 1
protected static final int LastChangeID 9
protected static final int LastSyncID 8
protected static final int LDHeight 330
protected static final int LDWidth 790
protected static final int LkUsrID 5
protected static final int LocalID 0
protected static final int SLDHeight 300
protected static final int SyncID 7
protected static final java.lang.String USER_INFO "userinfo"
protected static final java.lang.String USER_INFO_DELIMIETER "=="

org.geworkbench.builtin.projects.history.HistoryPanel
public static final java.lang.String HISTORY "History"
public static final java.lang.String HISTORYDETAIL "HistoryDetail"

org.geworkbench.builtin.projects.remoteresources.CaArrayFilteringDialog
public static final java.lang.String CHIPPROVIDER "Array Provider"
public static final java.lang.String ORGANISM "Organism"
public static final java.lang.String PINAME "Principal Investigator"

org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog
public static final int ADD 0
public static final int DELETE 1
public static final int EDIT 2

org.geworkbench.engine.config.GUIFramework
public static final java.lang.String COMMAND_AREA "CommandArea"
public static final java.lang.String PROJECT_AREA "ProjectArea"
public static final java.lang.String SELECTION_AREA "SelectionArea"
public static final java.lang.String TOOL_AREA "Toolbar"
public static final java.lang.String VISUAL_AREA "VisualArea"

org.geworkbench.engine.config.rules.PluginObject
public static final java.lang.String COMPONENT_DESCRIPTOR_EXTENSION ".cwb.xml"
public static final java.lang.String escapedMenuItemDelimiter "\\dot"

org.geworkbench.engine.management.ComponentResource
public static final java.lang.String CLASSES_DIR "classes"
public static final java.lang.String CONF_DIR "conf"
public static final java.lang.String LIB_DIR "lib"

org.geworkbench.engine.preferences.GlobalPreferences
public static final java.lang.String DEFAULT_R_LIBPATH ""
public static final java.lang.String DEFAULT_R_LOCATION ""
public static final java.lang.String DEFAULT_RWSP_URL "http://genspace.cs.columbia.edu:8080/axis2/services"
public static final java.lang.String DEFAULT_TEXT_EDITOR "c:/windows/system32/notepad.exe"
public static final java.lang.String DEFAULT_TEXT_EDITOR_MAC ""
public static final int MAX_INTERACTION_NUM 5000
public static final java.lang.String MAX_NETWORK_OBJECT_NUMBER "Soft Limit on Cytoscape Network Objects (nodes+edges)"
public static final int ORIGINAL 0
public static final java.lang.String PREF_GENEPIX_COMPUTATION "Genepix Value Computation"
public static final java.lang.String PREF_MARKER_LOAD "Marker Load Options"
public static final java.lang.String PREF_TEXT_EDITOR "Text Editor"
public static final java.lang.String PREF_VISUALIZATION "Visualization"
public static final java.lang.String R_LIBPATH "R package directory (leave it blank for default path)"
public static final java.lang.String R_LOCATION "R Location (Rscript.exe and it\'s folder)"
public static final java.lang.String RCM_URL "Remote Components URL"
public static final java.lang.String RWSP_URL "Remote Workspaces URL"
public static final int SORTED_GENE 1
public static final int SORTED_PROBE 2

org.geworkbench.engine.preferences.PreferencesDialog
public static final int MARGIN 20
public static final int SPACING 8

org.geworkbench.engine.properties.PropertiesManager
public static final java.lang.String GLOBAL_PROPERTIES "configuration.xml"

org.geworkbench.engine.skin.Skin
public static final java.lang.String APP_SIZE_FILE "appCoords.txt"

org.geworkbench.events.CaArrayEvent
public static final java.lang.String BIOASSAY "BIOASSAY"
public static final java.lang.String EXPERIMENT "EXP"

org.geworkbench.events.CaArrayQueryEvent
public static final java.lang.String GOTEXPERIMENTS "getexperiments"
public static final java.lang.String GOTVALIDVALUES "getvalidvalues"

org.geworkbench.events.CaArrayRequestEvent
public static final java.lang.String BIOASSAY "BIOASSAY"
public static final java.lang.String CANCEL "CANCEL"
public static final java.lang.String EXPERIMENT "EXP"

org.geworkbench.events.GeneSelectorEvent
public static final int MARKER_SELECTION 1
public static final int PANEL_SELECTION 2

org.geworkbench.events.GeneTaggedEvent
public static final int HIGHLIGHT 1
public static final int USE_VISUAL_PROPERTY 2

org.geworkbench.events.ProgressBarEvent
public static final int INITIALIZE 0
public static final int UPDATE 1

org.geworkbench.events.SubpanelChangedEvent<T extends DSNamed>
public static final int DELETE 4
public static final int NEW 2
public static final int SET_CONTENTS 1

org.geworkbench.parsers.AdjacencyMatrixFileFormat
public static final java.lang.String INTERACTIONS_SERVLET_CONNECTION_TIMEOUT "interactions_servlet_connection_timeout"
public static final java.lang.String INTERACTIONS_SERVLET_URL "interactions_servlet_url"
public static final java.lang.String PROPERTIES_FILE "conf/application.properties"

org.geworkbench.util.BinaryEncodeDecode
public static final int MASK 255
public static final int SIZE_OF_INT 4

org.geworkbench.util.JAutoList
public static final java.lang.String NEXT_BUTTON_TEXT "Find Next"
public static final java.lang.String SEARCH_LABEL_TEXT "Search:"

org.geworkbench.util.ProgressBar
public static final int BOUNDED_TYPE 0
public static final int INDETERMINATE_TYPE 1

org.geworkbench.util.ProgressBarT
public static final int BOUNDED_TYPE 0
public static final int INDETERMINATE_TYPE 1

org.geworkbench.util.ProgressDialog
public static final int MODAL_TYPE 0
public static final int NONMODAL_TYPE 1

org.geworkbench.util.ProgressItem
public static final int BOUNDED_TYPE 0
public static final int INDETERMINATE_TYPE 1

org.geworkbench.util.PropertiesMonitor
public static final java.lang.String SOAP_CONFIG_FILE "soap.ini"

org.geworkbench.util.QSort
public static final int ASCENDING 1
public static final int DESCENDING 2

org.geworkbench.util.ResultSetlUtil
public static final java.lang.String DEL "|"
public static final java.lang.String NULL_STR "null"
public static final java.lang.String REGEX_DEL "\\|"
public static final int SPLIT_ALL -2

org.geworkbench.util.network.InteractionDetail
public static final java.lang.String ENTREZ_GENE "Entrez Gene"

org.geworkbench.util.patterns.PatternLocations
public static final java.lang.String DEFAULTTYPE "splash"
public static final java.lang.String TFTYPE "TFBS"

org.geworkbench.util.sequences.PatternTableModel
public static final int PTMPattern 4
public static final int PTMSeqNo 1
public static final int PTMSupport 0
public static final int PTMTokNo 2
public static final int PTMZScore 3

org.geworkbench.util.sequences.PatternTableView
public static final java.lang.String ROWSELECTION "rowselection"

org.geworkbench.util.sequences.SequenceViewWidget
protected static final java.lang.String LINEVIEW "Line"