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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CORNER_WIDTH |
5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
NUCLEOTIDE_SIMILARITY_SEARCH_TYPE |
"Nucleotide Similarity Search" |
public static final String |
PROTEIN_SIMILARITY_SEARCH_TYPE |
"Protein Similarity Search" |
public static final String |
TEXT_SEARCH_TYPE |
"Text Search" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
KEY_SEARCH_SUBFOLDERS |
"includeSubfolders" |
public static final String |
KEY_SEARCH_TYPE |
"searchType" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DESCRIPTION_CODE |
"description" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
FILE_DATA_ATTRIBUTE_NAME |
"xmlFileData" |
public static final int |
MAXIMUM_HTML_LENGTH |
70000 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ROOT_ELEMENT_NAME |
"XMLSerialisableRootElement" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
NICE_NAME |
"Amino Acid Sequence" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
NICE_NAME |
"Nucleotide Sequence" |
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_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_LEVEL |
"Expression Level" |
public static final String |
TYPE_EXTRACTED_REGION |
"extracted region" |
public static final String |
TYPE_GENE |
"gene" |
public static final String |
TYPE_HELIX |
"helix" |
public static final String |
TYPE_INSERTED_SEQUENCE |
"Inserted sequence" |
public static final String |
TYPE_INTRON |
"intron" |
public static final String |
TYPE_LIGATION |
"ligation" |
public static final String |
TYPE_LONG_TERMINAL_REPEAT |
"LTR" |
public static final String |
TYPE_LOW_QUALITY |
"low quality" |
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_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_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_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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
COLOR |
"Color" |
public static final String |
EDITING_HISTORY_ORIGINAL_BASES |
"Original Bases" |
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_FOR_ACTIVELY_LINKED_PARENTS |
".hidden_Parent" |
public static final String |
NCBI_CODON_START |
"codon_start" |
public static final String |
NCBI_TRANSL_TABLE |
"transl_table" |
public static final String |
RECOGNITION_PATTERN |
"Recognition pattern" |
public static final String |
REFERENCED_DOCUMENT_LABEL_PREFIX |
" label: " |
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_NUCLEOTIDES |
"Variant Nucleotide(s)" |
public static final String |
VARIANT_REFERENCE_NUCLEOTIDES |
"Reference Nucleotide(s)" |
public static final String |
WEAK_REFERENCED_DOCUMENT_PREFIX |
"referenceToDocument: " |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
GENOME_SEQUENCE_THRESHOLD |
100000 |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
REVERSED_NAME_SUFFIX |
" (reversed)" |
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 |
SOURCE_QUALIFIER_NAME |
".hidden_source_urn" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DESCRIPTION_QUALIFIER |
"Description" |
Modifier and Type | Constant Field | Value |
---|---|---|
protected static final int |
MAXIMUM_HTML_TEXT_LENGTH |
30000 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
OVERRIDE_DOCUMENT_TYPE_KEY |
"overrideDocumentType" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
DESC |
"GeneiousActionDescription" |
public static final String |
ICON |
"GeneiousActionIcon" |
public static final String |
NAME |
"GeneiousActionName" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
TOGGLED_PROPERTY_NAME |
"GeneiousActionToggled" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final double |
DEFAULT_POSITION |
0.5 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
ASSOCIATED_OPTION_PROPERTY |
"AssociatedOption" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
CENTER |
1 |
public static final int |
LEFT |
0 |
public static final int |
RIGHT |
2 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final String |
LOCAL_DATABASE_SERVICE_UNIQUE_ID |
"LocalDocuments" |
public static final String |
SEARCH_RESULTS_SERVICE_UNIQUE_ID |
"SearchResults" |
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 |
RELATIVE_POSITION_BELOW |
0.01 |
public static final double |
RELATIVE_POSITION_DIRECTLY_BELOW |
0.005 |
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 |
8984 |