Constant Field Values

Contents

• com.biomatters.*

com.biomatters.*

com.biomatters.geneious.publicapi.components.Dialogs

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_FOCUSED_TEXT_COMPONENT_KEY	"Dialogs.defaultFocusedComponent"
public static final String	DONT_INITIALLY_FOCUS_KEY	"Dialogs.dontInitiallyFocus"
public static final String	DONT_SHOW_AGAIN	"Don\'t show this again"

com.biomatters.geneious.publicapi.components.OptionsPanel.RoundedLineBorder

Modifier and Type	Constant Field	Value
public static final int	CORNER_WIDTH	5

com.biomatters.geneious.publicapi.databaseservice.TextOrSimilaritySearchOption

Modifier and Type	Constant Field	Value
public static final String	NUCLEOTIDE_SIMILARITY_SEARCH_TYPE	"Nucleotide Similarity"
public static final String	PROTEIN_SIMILARITY_SEARCH_TYPE	"Protein Similarity"
public static final String	TEXT_NAME_SEARCH_TYPE	"Name"
public static final String	TEXT_SEARCH_TYPE	"Any"

com.biomatters.geneious.publicapi.databaseservice.WritableDatabaseService

Modifier and Type	Constant Field	Value
public static final String	KEY_PROCESS_SPECIAL_QUERY_SYMBOLS	"processSpecialQuerySymbols"
public static final String	KEY_SEARCH_INDEX_CORRUPT_OR_MISSING_FAIL_WITH_EXCEPTION	"searchIndexCorruptOrMissingFailWithException"
public static final String	KEY_SEARCH_SUBFOLDERS	"includeSubfolders"
public static final String	KEY_SEARCH_TYPE	"searchType"
public static final String	KEY_WHOLE_WORDS_ONLY	"wholeWordsOnly"

com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument

Modifier and Type	Constant Field	Value
public static final String	TEMPORARY_FIELD_KEY_ANNOTATED_DOCUMENT_LOCATION	"annotatedDocumentLocation"
public static final String	TEMPORARY_FIELD_KEY_PLUGIN_DOCUMENT_LOCATION	"pluginDocumentLocation"

com.biomatters.geneious.publicapi.documents.DocumentHistory

Modifier and Type	Constant Field	Value
public static final String	DOCUMENT_HISTORY_ADDITIONAL_XML_ELEMENT_NAME	"DocumentHistory"

com.biomatters.geneious.publicapi.documents.DocumentHistoryEntryField

Modifier and Type	Constant Field	Value
public static final String	DESCRIPTION_CODE	"description"

com.biomatters.geneious.publicapi.documents.OperationRecordDocument

Modifier and Type	Constant Field	Value
public static final String	FAKE_OPERATION_ID_PREFIX	"FAKE_OPERATION_ID:"

com.biomatters.geneious.publicapi.documents.PluginDocument

Modifier and Type	Constant Field	Value
public static final String	FILE_DATA_ATTRIBUTE_NAME	"xmlFileData"
public static final int	MAXIMUM_HTML_LENGTH	70000

com.biomatters.geneious.publicapi.documents.XMLSerializable

Modifier and Type	Constant Field	Value
public static final String	ROOT_ELEMENT_NAME	"XMLSerialisableRootElement"

com.biomatters.geneious.publicapi.documents.sequence.AminoAcidSequenceDocument

Modifier and Type	Constant Field	Value
public static final String	NICE_NAME	"Amino Acid Sequence"

com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph

Modifier and Type	Constant Field	Value
public static final int	EDITED_NUCLEOTIDE_QUALITY	63

com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument

Modifier and Type	Constant Field	Value
public static final String	NICE_NAME	"Nucleotide Sequence"

com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation

Modifier and Type	Constant Field	Value
public static final String	HIDDEN_TYPE_FOR_ACTIVELY_LINKED_PARENTS	"invisible_Parent"
public static final String	INVISIBLE_ANNOTATION_TYPE_PREFIX	"invisible_"
public static final String	KEY_ANNOTATION_GROUP	"annotation group"
public static final String	KEY_CREATED_BY	"created by"
public static final String	KEY_MODIFIED_BY	"modified by"
public static final String	TYPE_CDS	"CDS"
public static final String	TYPE_CHAIN	"chain"
public static final String	TYPE_CLONING_FRAGMENT	"Fragment"
public static final String	TYPE_COIL	"coil"
public static final String	TYPE_COILED_COIL	"coiled-coil region"
public static final String	TYPE_CONCATENATED_SEQUENCE	"Concatenated sequence"
public static final String	TYPE_CONFLICT	"conflict"
public static final String	TYPE_CRISPR	"CRISPR"
public static final String	TYPE_DISULFIDE_BOND	"disulfide bond"
public static final String	TYPE_DNA_PROBE	"DNA probe bind"
public static final String	TYPE_DOMAIN	"domain"
public static final String	TYPE_EDITING_HISTORY_DELETION	"Editing History Deletion"
public static final String	TYPE_EDITING_HISTORY_INSERTION	"Editing History Insertion"
public static final String	TYPE_EDITING_HISTORY_REPLACEMENT	"Editing History Replacement"
public static final String	TYPE_EXCLUDED_REGION	"Excluded Region"
public static final String	TYPE_EXON	"exon"
public static final String	TYPE_EXPRESSION_DIFFERENCE	"Expression Difference"
public static final String	TYPE_EXPRESSION_LEVEL	"Expression Level"
public static final String	TYPE_EXTRACTED_REGION	"extracted region"
public static final String	TYPE_GENE	"gene"
public static final String	TYPE_GIBSON_PRIMER_EXTENSION	"Gibson Primer Extension"
public static final String	TYPE_HELIX	"helix"
public static final String	TYPE_HIGH_COVERAGE	"Coverage - High"
public static final String	TYPE_INSERTED_SEQUENCE	"Inserted sequence"
public static final String	TYPE_INTRON	"intron"
public static final String	TYPE_JUNCTION	"Junction"
public static final String	TYPE_LIGATION	"ligation"
public static final String	TYPE_LONG_TERMINAL_REPEAT	"LTR"
public static final String	TYPE_LOW_COVERAGE	"Coverage - Low"
public static final String	TYPE_LOW_QUALITY	"low quality"
public static final String	TYPE_MASKED	"Masked"
public static final String	TYPE_MATURE_PEPTIDE	"mat_peptide"
public static final String	TYPE_MISC_DIFFERENCE	"misc_difference"
public static final String	TYPE_MISC_FEATURE	"misc_feature"
public static final String	TYPE_MISC_RNA	"misc_RNA"
public static final String	TYPE_MOTIF	"motif"
public static final String	TYPE_MRNA	"mRNA"
public static final String	TYPE_NCRNA	"ncRNA"
public static final String	TYPE_OPTIMIZED_CODON	"Optimized Codon"
public static final String	TYPE_ORF	"ORF"
public static final String	TYPE_ORIGIN	"origin"
public static final String	TYPE_ORIGIN_OF_REPLICATION	"rep_origin"
public static final String	TYPE_OVERHANG	"overhang"
public static final String	TYPE_PEPTIDE	"peptide"
public static final String	TYPE_POLYA_SIGNAL	"polyA_signal"
public static final String	TYPE_POLYA_SITE	"polyA_site"
public static final String	TYPE_POLYLINKER	"polylinker"
public static final String	TYPE_POLYMORPHISM	"Polymorphism"
public static final String	TYPE_POTENTIAL_RESTRICTION_SITE	"potential restriction site"
public static final String	TYPE_PRECURSOR_RNA	"precursor_RNA"
public static final String	TYPE_PRIMER_BIND	"primer_bind"
public static final String	TYPE_PRIMER_BIND_REVERSE	"primer_bind_reverse"
public static final String	TYPE_PROMOTER	"promoter"
public static final String	TYPE_PROTEIN_BIND	"protein_bind"
public static final String	TYPE_REGULATORY	"regulatory"
public static final String	TYPE_REPEAT_REGION	"repeat_region"
public static final String	TYPE_REPEAT_UNIT	"repeat_unit"
public static final String	TYPE_RESTRICTION_SITE	"restriction site"
public static final String	TYPE_RRNA	"rRNA"
public static final String	TYPE_SEARCH_HIT	"Search Hit"
public static final String	TYPE_SIGNAL_PEPTIDE	"sig_peptide"
public static final String	TYPE_SITE	"site"
public static final String	TYPE_SOURCE	"source"
public static final String	TYPE_SPACER	"Att Site Spacer"
public static final String	TYPE_STATISTICS	"Statistics"
public static final String	TYPE_STRAND	"strand"
public static final String	TYPE_TERMINATOR	"terminator"
public static final String	TYPE_TMRNA	"tmRNA"
public static final String	TYPE_TRANSLATED_REGION	"translated region"
public static final String	TYPE_TRANSMEMBRANE	"transmembrane region"
public static final String	TYPE_TRIMMED	"trimmed"
public static final String	TYPE_TRNA	"tRNA"
public static final String	TYPE_TURN	"turn"
public static final String	TYPE_UTR_3	"3\'UTR"
public static final String	TYPE_UTR_5	"5\'UTR"
public static final String	TYPE_VECTOR_MODERATE	"vector_moderate"
public static final String	TYPE_VECTOR_SEGMENT_OF_SUSPECT_ORIGIN	"vector_suspect"
public static final String	TYPE_VECTOR_STRONG	"vector_strong"
public static final String	TYPE_VECTOR_WEAK	"vector_weak"
public static final String	TYPE_WIG	"wiggle"

com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier

Modifier and Type	Constant Field	Value
public static final String	ALL_LOCATIONS	"All Locations"
public static final String	COLOR	"Color"
public static final String	DIFFERENTIAL_EXPRESSION_ABSOLUTE_CONFIDENCE_QUALIFIER	"Differential Expression Absolute Confidence"
public static final String	DIFFERENTIAL_EXPRESSION_ADJUSTED_P_VALUE	"Differential Expression Adjusted p-value"
public static final String	DIFFERENTIAL_EXPRESSION_BASE_MEAN	"Differential Expression Base Mean"
public static final String	DIFFERENTIAL_EXPRESSION_CONFIDENCE_QUALIFIER	"Differential Expression Confidence"
public static final String	DIFFERENTIAL_EXPRESSION_LOG_FOLD_STANDARD_ERROR_QUALIFIER	"Differential Expression Log2 Standard Error"
public static final String	DIFFERENTIAL_EXPRESSION_LOG2_RATIO_QUALIFIER	"Differential Expression Log2 Ratio"
public static final String	DIFFERENTIAL_EXPRESSION_METHOD	"Differential Expression Method Used"
public static final String	DIFFERENTIAL_EXPRESSION_P_VALUE	"Differential Expression p-value"
public static final String	DIFFERENTIAL_EXPRESSION_RATIO_QUALIFIER	"Differential Expression Ratio"
public static final String	DIFFERENTIAL_EXPRESSION_WALD_STAT	"Differential Expression Wald Statistic"
public static final String	EDITING_HISTORY_ORIGINAL_BASES	"Original Bases"
public static final String	EXPRESSION_FPKM	"FPKM"
public static final String	EXPRESSION_RAW_FRAGMENT_COUNT	"Raw Fragment Count"
public static final String	EXPRESSION_RAW_READ_COUNT	"Raw Read Count"
public static final String	EXPRESSION_RAW_TRANSCRIPT_COUNT	"Raw Transcript Count"
public static final String	EXPRESSION_RPKM	"RPKM"
public static final String	EXPRESSION_TPM	"TPM"
public static final String	EXTRACTED_REGION_INTERVALS_NAME	"Extracted interval"
public static final String	EXTRACTED_REGION_ORIGINAL_CIRCULAR_SEQUENCE_LENGTH	"Original Circular Sequence Length"
public static final String	GENETIC_CODE_NAME	"Genetic code"
public static final String	HIDDEN_PREFIX	".hidden_"
public static final String	HIDDEN_QUALIFIER_BACKGROUND_COLOR	".hidden_Background Color"
public static final String	HIDDEN_QUALIFIER_EXCLUDE_FROM_ANNOTATION_RESULT_COUNTER	".hidden_Do Not Count As Generated Result"
public static final String	HIDDEN_QUALIFIER_FOR_ACTIVELY_LINKED_PARENTS	".hidden_Parent"
public static final String	HIDDEN_QUALIFIER_FORCE_BOLD	".hidden_Force Bold"
public static final String	HIDDEN_QUALIFIER_FORCE_FADED	".hidden_Force Faded"
public static final String	HIDDEN_QUALIFIER_HIGH_VIEW_PRIORITY	".hidden_High View Priority"
public static final String	HIDE_QUALIFIER_IN_SEQUENCE_VIEWER_TOOLTIP	".hidden_SequenceViewerToolTip"
public static final String	JUNCTION_DESTINATION	"Junction Destination"
public static final String	JUNCTION_SOURCE	"Junction Source"
public static final String	METHYLATION_QUALIFIER	"Methylation"
public static final String	NCBI_AUTOMATIC_TRANSLATION	"translation"
public static final String	NCBI_CODON_START	"codon_start"
public static final String	NCBI_TRANSL_EXCEPT	"transl_except"
public static final String	NCBI_TRANSL_TABLE	"transl_table"
public static final String	ORIGINAL_NCBI_AUTOMATIC_TRANSLATION	"Original Translation"
public static final String	POTENTIAL_RESTRICTION_SITE_MODIFIED	"Modified"
public static final String	POTENTIAL_RESTRICTION_SITE_OFFSET	".hidden_Offset"
public static final String	POTENTIAL_RESTRICTION_SITE_ORIGINAL	"Original"
public static final String	RECOGNITION_PATTERN	"Recognition pattern"
public static final String	REFERENCED_DOCUMENT_LABEL_PREFIX	" label: "
public static final String	SOURCE_SEQUENCE_QUALIFIER	"Source Sequence"
public static final String	STRONG_REFERENCED_DOCUMENT_PREFIX	"strongReferenceToDocument: "
public static final String	TRANSLATED_REGION_INTERVALS_NAME	"Translated interval"
public static final String	VARIANT_AMINO_ACIDS	"Variant Amino Acids(s)"
public static final String	VARIANT_CHANGE	"Change"
public static final String	VARIANT_CHANGE_ARROW	" -> "
public static final String	VARIANT_ID	"Variant ID"
public static final String	VARIANT_NO_CHANGE	"No change"
public static final String	VARIANT_NUCLEOTIDES	"Variant Nucleotide(s)"
public static final String	VARIANT_REFERENCE_AMINO_ACIDS	"Reference Amino Acids(s)"
public static final String	VARIANT_REFERENCE_NUCLEOTIDES	"Reference Nucleotide(s)"
public static final String	WEAK_REFERENCED_DOCUMENT_PREFIX	"referenceToDocument: "

com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

Modifier and Type	Constant Field	Value
public static final int	GENOME_SEQUENCE_THRESHOLD	100000

com.biomatters.geneious.publicapi.implementations.DefaultAlignmentDocument

Modifier and Type	Constant Field	Value
public static final String	KEY_ALIGNMENT_OPTIONS	"alignment_options"
public static final String	KEY_ALIGNMENT_SCORE	"alignment_score"
public static final String	KEY_MATCH_REGIONS	"match_regions"

com.biomatters.geneious.publicapi.implementations.DefaultPhylogenyDocument

Modifier and Type	Constant Field	Value
public static final String	KEY_DOCUMENT_SIZE	"document_size"
public static final String	KEY_NEXUS_TREE_DISTANCE_MATRIX	"&DistanceMatrix"
public static final String	KEY_SEQUENCE_RESIDUES	"sequence_residues"

com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities

Modifier and Type	Constant Field	Value
public static final String	REVERSED_NAME_SUFFIX	" (reversed)"

com.biomatters.geneious.publicapi.implementations.sequence.OligoSequenceDocument

Modifier and Type	Constant Field	Value
public static final String	BINDING_REGION_ANNOTATION_NAME	"Binding Region"
public static final String	EXTENSION_QUALIFIER_NAME	"Extension"
public static final String	PRIMER_INFO_NOTE_CODE	"primerInfo"
public static final String	PRIMER_PERCENT_GC_ANNOTATION_QUALIFIER_NAME	"%GC"
public static final String	SOURCE_QUALIFIER_NAME	".hidden_source_urn"

com.biomatters.geneious.publicapi.implementations.sequence.SequenceTrack

Modifier and Type	Constant Field	Value
public static final String	DESCRIPTION_QUALIFIER	"Description"
public static final String	NO_TRACK	"No Track"

com.biomatters.geneious.publicapi.implementations.structure.DefaultMolecularStructureDocument

Modifier and Type	Constant Field	Value
protected static final int	MAXIMUM_HTML_TEXT_LENGTH	30000

com.biomatters.geneious.publicapi.laf.UI.ClientProperties

Modifier and Type	Constant Field	Value
public static final String	BUTTON_DRAW_CHEVRON	"JButton.geneiousJButtonDrawChevron"
public static final String	COMBO_BOX_FILTER_MODE	"FilterableComboBox.FilterMode"
public static final String	COMBO_BOX_FILTER_MODE_AUTO_ENABLE_THRESHOLD	"FilterableComboBox.FilterModeAutoEnableThreshold"
public static final String	COMBO_BOX_FILTER_MODE_VALUE_ALWAYS_OFF	"AlwaysOff"
public static final String	COMBO_BOX_FILTER_MODE_VALUE_ALWAYS_ON	"AlwaysOn"
public static final String	COMBO_BOX_FILTER_MODE_VALUE_AUTO	"Auto"
public static final String	COMBO_BOX_TEXT_FIELD_WATERMARK	"ComboBox.TextFieldWatermark"
public static final String	TAB_BACKGROUND_ARC	"JTabbedPane.geneiousTabbedPaneBackgroundArc"

com.biomatters.geneious.publicapi.plugin.Assembler

Modifier and Type	Constant Field	Value
public static final String	DE_NOVO_UNIQUE_ID_SUFFIX	".deNovo"
public static final String	REFERENCE_UNIQUE_ID_SUFFIX	".reference"

com.biomatters.geneious.publicapi.plugin.DocumentFileExporter

Modifier and Type	Constant Field	Value
public static final String	REPLACE_SPACES_IN_SEQUENCE_NAMES_OPTION_NAME	"replaceSpacesInNameWithUnderscore"

com.biomatters.geneious.publicapi.plugin.DocumentType<T>

Modifier and Type	Constant Field	Value
public static final String	OVERRIDE_DOCUMENT_TYPE_KEY	"overrideDocumentType"

com.biomatters.geneious.publicapi.plugin.ExtendedPrintable

Modifier and Type	Constant Field	Value
public static final String	IS_HIGH_RESOLUTION_GRAPHICS_OPTION_NAME	"isHighResolutionGraphics"
public static final String	IS_PREVIEW_OPTION_NAME	"isPreview"
public static final String	SUPPORTS_GRADIENT_PAINTING_OPTION_NAME	"isGradientPaintingSupported"

com.biomatters.geneious.publicapi.plugin.GeneiousAction

Modifier and Type	Constant Field	Value
public static final String	DESC	"GeneiousActionDescription"
public static final String	ICON	"GeneiousActionIcon"
public static final String	NAME	"GeneiousActionName"

com.biomatters.geneious.publicapi.plugin.GeneiousAction.ToggleAction

Modifier and Type	Constant Field	Value
public static final String	TOGGLED_PROPERTY_NAME	"GeneiousActionToggled"

com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions

Modifier and Type	Constant Field	Value
public static final double	DEFAULT_POSITION	0.5

com.biomatters.geneious.publicapi.plugin.GeneiousPlugin

Modifier and Type	Constant Field	Value
public static final String	PLUGIN_NAME_LOCAL_DOCUMENTS	"Local Documents"

com.biomatters.geneious.publicapi.plugin.GeneiousService

Modifier and Type	Constant Field	Value
public static final String	SERVICE_TREE_LABEL_FAINTER_END	"</fainter>"
public static final String	SERVICE_TREE_LABEL_FAINTER_START	"<fainter>"

com.biomatters.geneious.publicapi.plugin.Options

Modifier and Type	Constant Field	Value
public static final String	ASSOCIATED_OPTION_PROPERTY	"AssociatedOption"

com.biomatters.geneious.publicapi.plugin.Options.ButtonOption

Modifier and Type	Constant Field	Value
public static final int	CENTER	1
public static final int	LEFT	0
public static final int	RIGHT	2

com.biomatters.geneious.publicapi.plugin.PluginUtilities

Modifier and Type	Constant Field	Value
public static final String	ALIAS_UNIQUE_ID_PREFIX	"Alias_"
public static final String	CLOUD_DATABASE_SERVICE_UNIQUE_ID	"CloudDocuments"
public static final String	FAVORITE_SERVICE_UNIQUE_ID	"com.biomatters.plugins.favorites.FavoritesService"
public static final String	LOCAL_DATABASE_SERVICE_UNIQUE_ID	"LocalDocuments"
public static final String	SEARCH_RESULTS_SERVICE_UNIQUE_ID	"SearchResults"

com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection

Modifier and Type	Constant Field	Value
public static final double	POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES	0.8
public static final double	POSITION_CODON_FREQUENCIES	0.9
public static final double	POSITION_COVERAGE	0.4
public static final double	POSITION_EXPECTED_ERRORS	0.62
public static final double	POSITION_FREQUENCIES	0.7
public static final double	POSITION_IDENTICAL_SITES	0.3
public static final double	POSITION_MEAN_CONFIDENCE	0.6
public static final double	POSITION_NUMBER_OF_SEQUENCES	0.25
public static final double	POSITION_PERCENTAGE_PAIRWISE_IDENTITY	0.32
public static final double	POSITION_PROTEIN_EXTINCTION_COEFFICIENT	0.54
public static final double	POSITION_PROTEIN_ISOELECTRIC_POINT	0.52
public static final double	POSITION_PROTEIN_MOLECULAR_WEIGHT	0.5
public static final double	POSITION_QUALITY_THRESHOLD_COUNTS	0.64
public static final double	POSITION_READ_LENGTHS	0.45
public static final double	POSITION_SEQUENCE_LENGTH	0.2
public static final double	POSITION_STATISTICS_HEADER	0.1
public static final double	RELATIVE_POSITION_BELOW	0.01
public static final double	RELATIVE_POSITION_DIRECTLY_BELOW	0.005

com.biomatters.geneious.publicapi.plugin.WorkflowSharingManager<O>

Modifier and Type	Constant Field	Value
public static final String	WORKFLOW_ID_PLACE_HOLDER	"newWorkflow"

com.biomatters.geneious.publicapi.utilities.FileUtilities

Modifier and Type	Constant Field	Value
public static final int	MAX_FILENAME_LENGTH	255

com.biomatters.geneious.publicapi.utilities.GuiUtilities

Modifier and Type	Constant Field	Value
public static final String	ACTION_MAP_KEY_COPY	"copy-to-clipboard"
public static final String	ACTION_MAP_KEY_CUT	"cut-to-clipboard"
public static final String	ACTION_MAP_KEY_DELETE	"delete"
public static final String	ACTION_MAP_KEY_PASTE	"paste-from-clipboard"
public static final String	ACTION_MAP_KEY_REDO	"Redo"
public static final String	ACTION_MAP_KEY_SELECT_ALL	"select-all"
public static final String	ACTION_MAP_KEY_SELECT_ALL_TABLE	"selectAll"
public static final String	ACTION_MAP_KEY_UNDO	"Undo"
public static final char	COMMAND_KEY_CHAR	'\u2318'

com.biomatters.geneious.publicapi.utilities.SystemUtilities

Modifier and Type	Constant Field	Value
public static final String	OUT_OF_MEMORY	"out of memory"