Class SequenceAnnotationQualifier
- java.lang.Object
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- com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationQualifier
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public final class SequenceAnnotationQualifier extends java.lang.Object
A named item of information (i.e. a key-value pair of Strings) on aSequenceAnnotation
. In the sequence viewer, this information is shown in the box that pops up when the mouse hovers over the annotation. Instances of this class are immutable and may therefore freely be shared without making defensive copies.
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
ALL_LOCATIONS
The name of the qualifier used to display all matching locations for repeat annotations.static java.lang.String
COLOR
Qualifier name used to override the color of an individual annotation.static java.lang.String
DIFFERENTIAL_EXPRESSION_ABSOLUTE_CONFIDENCE_QUALIFIER
Qualifier name for differential expression absolute confidencestatic java.lang.String
DIFFERENTIAL_EXPRESSION_ADJUSTED_P_VALUE
Qualifier name for differential expression adjust p-valuestatic java.lang.String
DIFFERENTIAL_EXPRESSION_BASE_MEAN
Qualifier name for differential expression base meanstatic java.lang.String
DIFFERENTIAL_EXPRESSION_CONFIDENCE_QUALIFIER
Qualifier name for differential expression confidencestatic java.lang.String
DIFFERENTIAL_EXPRESSION_LOG_FOLD_STANDARD_ERROR_QUALIFIER
Qualifier name for differential expression log fold standard errorstatic java.lang.String
DIFFERENTIAL_EXPRESSION_LOG2_RATIO_QUALIFIER
Qualifier name for differential expression log base 2 ratiostatic java.lang.String
DIFFERENTIAL_EXPRESSION_METHOD
Qualifier name for the differential expression method usedstatic java.lang.String
DIFFERENTIAL_EXPRESSION_P_VALUE
Qualifier name for differential expression p-valuestatic java.lang.String
DIFFERENTIAL_EXPRESSION_RATIO_QUALIFIER
Qualifier name for differential expression expression ratiostatic java.lang.String
DIFFERENTIAL_EXPRESSION_WALD_STAT
Qualifier name for differential expression Wald statisticstatic java.lang.String
EDITING_HISTORY_ORIGINAL_BASES
Record the bases that were originally in the location covered by an annotation of typeSequenceAnnotation.TYPE_EDITING_HISTORY_DELETION
,SequenceAnnotation.TYPE_EDITING_HISTORY_INSERTION
orSequenceAnnotation.TYPE_EDITING_HISTORY_REPLACEMENT
.static java.lang.String
EXPRESSION_FPKM
Qualifier name for expression FPKM (fragments per kilobase million)static java.lang.String
EXPRESSION_RAW_FRAGMENT_COUNT
Qualifier name for expression raw fragment countstatic java.lang.String
EXPRESSION_RAW_READ_COUNT
Qualifier name for expression raw read countstatic java.lang.String
EXPRESSION_RAW_TRANSCRIPT_COUNT
Qualifier name for expression raw transcript countstatic java.lang.String
EXPRESSION_RPKM
Qualifier name for expression RPKM (reads per kilobase million)static java.lang.String
EXPRESSION_TPM
Qualifier name for expression TPM (transcripts per million)static java.lang.String
EXTRACTED_REGION_INTERVALS_NAME
Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents an extraction (annotations of typeSequenceAnnotation.TYPE_EXTRACTED_REGION
The value of the qualifier is parsable usingSequenceAnnotationInterval(String)
.static java.lang.String
EXTRACTED_REGION_ORIGINAL_CIRCULAR_SEQUENCE_LENGTH
Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents an extraction (annotations of typeSequenceAnnotation.TYPE_EXTRACTED_REGION
from a circular sequence, in which case, this qualifier contains the length of the original circular sequence.static java.lang.String
GENETIC_CODE_NAME
Name to use for SequenceAnnotationQualifiers that specify a genetic codestatic java.lang.String
HIDDEN_PREFIX
Qualifiers that have a name that begins with this prefix will be hidden from the user interfacestatic java.lang.String
HIDDEN_QUALIFIER_BACKGROUND_COLOR
Qualifier name used to override the background color of an individual annotation.static java.lang.String
HIDDEN_QUALIFIER_EXCLUDE_FROM_ANNOTATION_RESULT_COUNTER
Qualifier name used to determine whether the annotation generator should not count this annotation as a generated result from aSequenceAnnotationGenerator
in order to report an accurate number of results that are relevant to the operation.static java.lang.String
HIDDEN_QUALIFIER_FOR_ACTIVELY_LINKED_PARENTS
The name of a qualifier that can be added to annotations on documents which are actively linked to their descendants (seeOperationRecordDocument.hasAnyActiveLinks()
).static java.lang.String
HIDDEN_QUALIFIER_FORCE_BOLD
The value of this qualifier denotes whether or not this annotation should always be shown as bold when drawn on the sequence viewer.static java.lang.String
HIDDEN_QUALIFIER_FORCE_FADED
The value of this qualifier denotes whether or not this annotation should always be shown as faded when drawn on the sequence viewer.static java.lang.String
HIDDEN_QUALIFIER_HIGH_VIEW_PRIORITY
Qualifier name used to prioritise showing an annotation even when zoomed out.static java.lang.String
HIDE_QUALIFIER_IN_SEQUENCE_VIEWER_TOOLTIP
The value of this qualifier denotes the name of another qualifier which should not appear in the tooltips displayed in the Sequence Viewer.static java.lang.String
JUNCTION_DESTINATION
The name of the qualifier used to display the destination location of a variant junction.static java.lang.String
JUNCTION_SOURCE
The name of the qualifier used to display the source location of a variant junction.static java.lang.String
METHYLATION_QUALIFIER
Qualifier name for methylation of a restriction enzymestatic java.lang.String
NCBI_AUTOMATIC_TRANSLATION
The qualifier name that NCBI uses to provide the translation of aSequenceAnnotation.TYPE_CDS
annotation, taking into account qualifiers that Geneious may not.static java.lang.String
NCBI_CODON_START
Qualifier name used by NCBI for the frame of a CDS (may be 1, 2 or 3).static java.lang.String
NCBI_TRANSL_EXCEPT
Qualifier name used by NCBI for exceptions to standard translationstatic java.lang.String
NCBI_TRANSL_TABLE
Qualifier name used by NCBI for the translation table number of a CDSstatic java.lang.String
ORIGINAL_NCBI_AUTOMATIC_TRANSLATION
When editing an annotation containing aNCBI_AUTOMATIC_TRANSLATION
property, Geneious renames this property toORIGINAL_NCBI_AUTOMATIC_TRANSLATION
static java.lang.String
POTENTIAL_RESTRICTION_SITE_MODIFIED
Qualifier name for modified sequence produced when applying a potential restriction sitestatic java.lang.String
POTENTIAL_RESTRICTION_SITE_OFFSET
Hidden qualifier name for offset relative to annotation where modified sequence introduced when applying a potential restriction site beginsstatic java.lang.String
POTENTIAL_RESTRICTION_SITE_ORIGINAL
Qualifier name for original sequence before applying a potential restriction sitestatic java.lang.String
RECOGNITION_PATTERN
Name to use for SequenceAnnotationQualifiers that specify the recognition pattern of a restriction enzyme.static java.lang.String
REFERENCED_DOCUMENT_LABEL_PREFIX
If a qualifier starts with eitherWEAK_REFERENCED_DOCUMENT_PREFIX
orSTRONG_REFERENCED_DOCUMENT_PREFIX
then in may optionally contain a label to display to the user assoicated with the link by appending this suffix after the URN of the document followed by the text to display to the user.static java.lang.String
STRONG_REFERENCED_DOCUMENT_PREFIX
If a qualifier value starts with this prefix, and the remainder of the qualifier value is aURN.toString()
of a document, then it is assumed to be a strong reference to that document.static java.lang.String
TRANSLATED_REGION_INTERVALS_NAME
Deprecated.these are no longer createdstatic java.lang.String
VARIANT_AMINO_ACIDS
Qualifier used to represent how aSequenceAnnotation.TYPE_POLYMORPHISM
has changed from its original value.static java.lang.String
VARIANT_CHANGE
Qualifier used to represent how aSequenceAnnotation.TYPE_POLYMORPHISM
has changed from its original value.static java.lang.String
VARIANT_CHANGE_ARROW
Used to represent the separating arrow between the original and variant sequence for aVARIANT_CHANGE
qualifier.static java.lang.String
VARIANT_ID
Qualifier used to represent the database ID of a variant (for example the value may be a dbSNP ID of the form rs1234).static java.lang.String
VARIANT_NO_CHANGE
Qualifier value representing a change with no actual change to bases.static java.lang.String
VARIANT_NUCLEOTIDES
Qualifier used to represent how aSequenceAnnotation.TYPE_POLYMORPHISM
has changed from its original value.static java.lang.String
VARIANT_REFERENCE_AMINO_ACIDS
Qualifier used to represent what the reference sequence was over the interval covered by the annotationstatic java.lang.String
VARIANT_REFERENCE_NUCLEOTIDES
Qualifier used to represent what the reference sequence was over the interval covered by the annotationstatic java.lang.String
WEAK_REFERENCED_DOCUMENT_PREFIX
If a qualifier value starts with this prefix, and the remainder of the qualifier value is aURN.toString()
of a document, then it is assumed to be a weak reference to that document.
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Constructor Summary
Constructors Constructor Description SequenceAnnotationQualifier(SequenceAnnotationQualifier qualifier)
creates a copy of the given SequenceAnnotationQualifier.SequenceAnnotationQualifier(java.lang.String name, URN urn, boolean strong, java.lang.String label)
create a new SequenceAnnotationQualifier which contains a reference to another document.SequenceAnnotationQualifier(java.lang.String name, java.lang.String value)
create a new SequenceAnnotationQualifier
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static java.lang.String
createFormattedPotentialRestrictionSiteQualifier(java.lang.String originalSequence, java.lang.String modifiedSequence, int offsetRelativeToAnnotation, int patternLength, boolean original)
Create a formatted potential restriction site value for Modified or Original qualifierboolean
equals(java.lang.Object obj)
java.lang.String
getDisplayedValue(boolean allowHtml)
Returns the value with html tags stripped or angle brackets escaped depending on whether html is allowed.java.lang.String
getName()
Get the name of this qualifier.java.lang.String
getValue()
Get the value of this qualifier.int
hashCode()
boolean
isHidden()
Returns true if this qualifier is hidden from the user interface.boolean
isValueHtml()
Scans through the string to check if there appears to be valid angle brackets in it (an equal number, in the right order).java.lang.String
toString()
Returns a human readable string with information about this qualifier; the exact format of the string is not guaranteed and should not be relied on, because it may change at any time.
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Field Detail
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GENETIC_CODE_NAME
public static final java.lang.String GENETIC_CODE_NAME
Name to use for SequenceAnnotationQualifiers that specify a genetic code- See Also:
- Constant Field Values
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EXTRACTED_REGION_INTERVALS_NAME
public static final java.lang.String EXTRACTED_REGION_INTERVALS_NAME
Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents an extraction (annotations of typeSequenceAnnotation.TYPE_EXTRACTED_REGION
The value of the qualifier is parsable usingSequenceAnnotationInterval(String)
.- See Also:
- Constant Field Values
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EXTRACTED_REGION_ORIGINAL_CIRCULAR_SEQUENCE_LENGTH
public static final java.lang.String EXTRACTED_REGION_ORIGINAL_CIRCULAR_SEQUENCE_LENGTH
Name to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents an extraction (annotations of typeSequenceAnnotation.TYPE_EXTRACTED_REGION
from a circular sequence, in which case, this qualifier contains the length of the original circular sequence.- See Also:
- Constant Field Values
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TRANSLATED_REGION_INTERVALS_NAME
@Deprecated public static final java.lang.String TRANSLATED_REGION_INTERVALS_NAME
Deprecated.these are no longer createdName to use for a SequenceAnnotationQualifier to specify that the SequenceAnnotation represents a translation.- See Also:
- Constant Field Values
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RECOGNITION_PATTERN
public static final java.lang.String RECOGNITION_PATTERN
Name to use for SequenceAnnotationQualifiers that specify the recognition pattern of a restriction enzyme. The corresponding value must be in rebase format, e.g. "(4/8)" indicates a cut 4 and 8 bases from the recognition sequence start, respectively, in the sense and antisense strand- See Also:
- Constant Field Values
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EDITING_HISTORY_ORIGINAL_BASES
public static final java.lang.String EDITING_HISTORY_ORIGINAL_BASES
Record the bases that were originally in the location covered by an annotation of typeSequenceAnnotation.TYPE_EDITING_HISTORY_DELETION
,SequenceAnnotation.TYPE_EDITING_HISTORY_INSERTION
orSequenceAnnotation.TYPE_EDITING_HISTORY_REPLACEMENT
. .- See Also:
- Constant Field Values
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NCBI_TRANSL_TABLE
public static final java.lang.String NCBI_TRANSL_TABLE
Qualifier name used by NCBI for the translation table number of a CDS- See Also:
- Constant Field Values
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NCBI_TRANSL_EXCEPT
public static final java.lang.String NCBI_TRANSL_EXCEPT
Qualifier name used by NCBI for exceptions to standard translation- Since:
- API 4.1011 (Geneious 10.1.1)
- See Also:
- Constant Field Values
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NCBI_AUTOMATIC_TRANSLATION
public static final java.lang.String NCBI_AUTOMATIC_TRANSLATION
The qualifier name that NCBI uses to provide the translation of aSequenceAnnotation.TYPE_CDS
annotation, taking into account qualifiers that Geneious may not. For exampleNCBI_TRANSL_EXCEPT
- Since:
- API 4.1011 (Geneious 10.1.1)
- See Also:
- Constant Field Values
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ORIGINAL_NCBI_AUTOMATIC_TRANSLATION
public static final java.lang.String ORIGINAL_NCBI_AUTOMATIC_TRANSLATION
When editing an annotation containing aNCBI_AUTOMATIC_TRANSLATION
property, Geneious renames this property toORIGINAL_NCBI_AUTOMATIC_TRANSLATION
- Since:
- API 4.1103 (Geneious 11.0.3)
- See Also:
- Constant Field Values
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NCBI_CODON_START
public static final java.lang.String NCBI_CODON_START
Qualifier name used by NCBI for the frame of a CDS (may be 1, 2 or 3).- Since:
- API 4.54 (Geneious 5.5.4)
- See Also:
SequenceAnnotation.getCodonStart()
, Constant Field Values
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VARIANT_ID
public static final java.lang.String VARIANT_ID
Qualifier used to represent the database ID of a variant (for example the value may be a dbSNP ID of the form rs1234). If the value is a recognised format thengetDisplayedValue(boolean)
may hyperlink to the appropriate database- Since:
- API 4.600 (Geneious 6.0.0)
- See Also:
- Constant Field Values
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VARIANT_CHANGE
public static final java.lang.String VARIANT_CHANGE
Qualifier used to represent how aSequenceAnnotation.TYPE_POLYMORPHISM
has changed from its original value.
For substitution style variants, this should be of the form "A"+VARIANT_CHANGE_ARROW+"TT" to represent a change from A to TT.
For insertion style variants, this should be of the form "+AA" to represent an insertion of AA.
For deletion style variants, this should be of the form "-GC" to represent a deletion of GC.
For tandem repeat style variants, this may instead be of the form "(GT)5"+VARIANT_CHANGE_ARROW+"(GT)7" to represent an increase from 5 copies of GT to 7 copies of GT.- Since:
- API 4.615 (Geneious 6.1.5)
- See Also:
- Constant Field Values
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VARIANT_NO_CHANGE
public static final java.lang.String VARIANT_NO_CHANGE
Qualifier value representing a change with no actual change to bases. This is sometimes added to sequences when parsing VCF files.- Since:
- API 4.202300 (Genious 2023.0.0)
- See Also:
- Constant Field Values
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VARIANT_CHANGE_ARROW
public static final java.lang.String VARIANT_CHANGE_ARROW
Used to represent the separating arrow between the original and variant sequence for aVARIANT_CHANGE
qualifier.- Since:
- API 4.615 (Geneious 6.1.5)
- See Also:
- Constant Field Values
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VARIANT_NUCLEOTIDES
public static final java.lang.String VARIANT_NUCLEOTIDES
Qualifier used to represent how aSequenceAnnotation.TYPE_POLYMORPHISM
has changed from its original value.- Since:
- API 4.615 (Geneious 6.1.5)
- See Also:
- Constant Field Values
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VARIANT_AMINO_ACIDS
public static final java.lang.String VARIANT_AMINO_ACIDS
Qualifier used to represent how aSequenceAnnotation.TYPE_POLYMORPHISM
has changed from its original value.- Since:
- API 4.615 (Geneious 6.1.5)
- See Also:
- Constant Field Values
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VARIANT_REFERENCE_NUCLEOTIDES
public static final java.lang.String VARIANT_REFERENCE_NUCLEOTIDES
Qualifier used to represent what the reference sequence was over the interval covered by the annotation- Since:
- API 4.615 (Geneious 6.1.5)
- See Also:
- Constant Field Values
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VARIANT_REFERENCE_AMINO_ACIDS
public static final java.lang.String VARIANT_REFERENCE_AMINO_ACIDS
Qualifier used to represent what the reference sequence was over the interval covered by the annotation- Since:
- API 4.900 (Geneious 9.0.0)
- See Also:
- Constant Field Values
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COLOR
public static final java.lang.String COLOR
Qualifier name used to override the color of an individual annotation. The qualifier value should be an html style hex color (e.g. #FF0000 for red or #00FF00 for green)- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
- Constant Field Values
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ALL_LOCATIONS
public static final java.lang.String ALL_LOCATIONS
The name of the qualifier used to display all matching locations for repeat annotations. The value should be formatted as a semicolon separated list of positions, where each position may be prefixed by a name and a colon. Each position should be suffixed by a + or - to indicate the strand. For a value that meets these requirements, the sequence viewer will create clickable hyperlinks to jump to the each position.- Since:
- API 4.900 (Geneious 9.0.0)
- See Also:
- Constant Field Values
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JUNCTION_SOURCE
public static final java.lang.String JUNCTION_SOURCE
The name of the qualifier used to display the source location of a variant junction. The value should be formatted as a numeric 1-based index of a location in the sequence, suffixed by a + or - to indicate the strand. The value may be prefixed by a name and a colon to indicate a sequence other than the current sequence. For a value that meets these requirements, the sequence viewer will create a clickable hyperlink to jump to the position.- Since:
- API 4.900 (Geneious 9.0.0)
- See Also:
JUNCTION_DESTINATION
,SequenceAnnotation.TYPE_JUNCTION
, Constant Field Values
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JUNCTION_DESTINATION
public static final java.lang.String JUNCTION_DESTINATION
The name of the qualifier used to display the destination location of a variant junction. The value should be formatted as a numeric 1-based index of a location in the sequence, suffixed by a + or - to indicate the strand. The value may be prefixed by a name and a colon to indicate a sequence other than the current sequence. For a value that meets these requirements, the sequence viewer will create a clickable hyperlink to jump to the position.- Since:
- API 4.900 (Geneious 9.0.0)
- See Also:
JUNCTION_SOURCE
,SequenceAnnotation.TYPE_JUNCTION
, Constant Field Values
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HIDDEN_PREFIX
public static final java.lang.String HIDDEN_PREFIX
Qualifiers that have a name that begins with this prefix will be hidden from the user interface- See Also:
- Constant Field Values
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HIDDEN_QUALIFIER_EXCLUDE_FROM_ANNOTATION_RESULT_COUNTER
public static final java.lang.String HIDDEN_QUALIFIER_EXCLUDE_FROM_ANNOTATION_RESULT_COUNTER
Qualifier name used to determine whether the annotation generator should not count this annotation as a generated result from aSequenceAnnotationGenerator
in order to report an accurate number of results that are relevant to the operation. This qualifier is only applicable to annotations that are NOT part of aSequenceTrack
. The value of this qualifier must be either "true" or "false" case-insensitive. If unset, the assumed value is "false".- Since:
- API 4.202120 (Geneious 2021.2.0)
- See Also:
- Constant Field Values
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HIDDEN_QUALIFIER_FORCE_FADED
public static final java.lang.String HIDDEN_QUALIFIER_FORCE_FADED
The value of this qualifier denotes whether or not this annotation should always be shown as faded when drawn on the sequence viewer. It should be a value of either "True" or "False"- Since:
- API 4.202100 (Geneious 2021.0.0)
- See Also:
- Constant Field Values
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HIDDEN_QUALIFIER_FORCE_BOLD
public static final java.lang.String HIDDEN_QUALIFIER_FORCE_BOLD
The value of this qualifier denotes whether or not this annotation should always be shown as bold when drawn on the sequence viewer. It should be a value of either "True" or "False"- Since:
- API 4.202100 (Geneious 2021.0.0)
- See Also:
- Constant Field Values
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HIDDEN_QUALIFIER_BACKGROUND_COLOR
public static final java.lang.String HIDDEN_QUALIFIER_BACKGROUND_COLOR
Qualifier name used to override the background color of an individual annotation. The qualifier value should be an html style hex color (e.g. #FF0000 for red or #00FF00 for green)- Since:
- API 4.202100 (Geneious 2021.0.0)
- See Also:
- Constant Field Values
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HIDDEN_QUALIFIER_HIGH_VIEW_PRIORITY
public static final java.lang.String HIDDEN_QUALIFIER_HIGH_VIEW_PRIORITY
Qualifier name used to prioritise showing an annotation even when zoomed out. This doesn't guarantee that the annotation will be shown, but makes it much more likely. It should be a value of either "True" or "False"- Since:
- API 4.202100 (Geneious 2021.0.0)
- See Also:
- Constant Field Values
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HIDE_QUALIFIER_IN_SEQUENCE_VIEWER_TOOLTIP
public static final java.lang.String HIDE_QUALIFIER_IN_SEQUENCE_VIEWER_TOOLTIP
The value of this qualifier denotes the name of another qualifier which should not appear in the tooltips displayed in the Sequence Viewer. An annotation can have multiple of these qualifiers to hide multiple qualifiers from the sequence viewer tooltip.- Since:
- API 4.202020 (Geneious 2020.2.0)
- See Also:
- Constant Field Values
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HIDDEN_QUALIFIER_FOR_ACTIVELY_LINKED_PARENTS
public static final java.lang.String HIDDEN_QUALIFIER_FOR_ACTIVELY_LINKED_PARENTS
The name of a qualifier that can be added to annotations on documents which are actively linked to their descendants (seeOperationRecordDocument.hasAnyActiveLinks()
). When a document containing an annotation with this qualifier is regenerated because its parent has changed, then despite all other data on the document being discarded, if this annotation (or an annotation unambiguously identified as the same annotation) still exists on the new version of the document, then this qualifier will be copied to that new annotation. Qualifiers of this type will be hidden from the user interface. They are intended for programatic use only.- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
SequenceAnnotation.HIDDEN_TYPE_FOR_ACTIVELY_LINKED_PARENTS
, Constant Field Values
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WEAK_REFERENCED_DOCUMENT_PREFIX
public static final java.lang.String WEAK_REFERENCED_DOCUMENT_PREFIX
If a qualifier value starts with this prefix, and the remainder of the qualifier value is aURN.toString()
of a document, then it is assumed to be a weak reference to that document. a weak reference means that if the referenced document is deleted, the link will remain, referring to a document that no longer exists. To specify the name of the link as displayed to the user, useREFERENCED_DOCUMENT_LABEL_PREFIX
- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
STRONG_REFERENCED_DOCUMENT_PREFIX
,REFERENCED_DOCUMENT_LABEL_PREFIX
, Constant Field Values
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STRONG_REFERENCED_DOCUMENT_PREFIX
public static final java.lang.String STRONG_REFERENCED_DOCUMENT_PREFIX
If a qualifier value starts with this prefix, and the remainder of the qualifier value is aURN.toString()
of a document, then it is assumed to be a strong reference to that document. a strong reference means that if the referenced document is deleted, the document will not really be deleted but be kept in a hidden area of the database and will always be available as long as the referencing document still exists. Similarly, exporting a document (in Geneious format) with a strong refernece will export the referenced document with it. To specify the name of the link as displayed to the user, useREFERENCED_DOCUMENT_LABEL_PREFIX
- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
WEAK_REFERENCED_DOCUMENT_PREFIX
,REFERENCED_DOCUMENT_LABEL_PREFIX
, Constant Field Values
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REFERENCED_DOCUMENT_LABEL_PREFIX
public static final java.lang.String REFERENCED_DOCUMENT_LABEL_PREFIX
If a qualifier starts with eitherWEAK_REFERENCED_DOCUMENT_PREFIX
orSTRONG_REFERENCED_DOCUMENT_PREFIX
then in may optionally contain a label to display to the user assoicated with the link by appending this suffix after the URN of the document followed by the text to display to the user. For example STRONG_REFERENCED_DOCUMENT_PREFIX+urn.toString()+ REFERENCED_DOCUMENT_LABEL_PREFIX+"Forward Primer"- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
STRONG_REFERENCED_DOCUMENT_PREFIX
,WEAK_REFERENCED_DOCUMENT_PREFIX
, Constant Field Values
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DIFFERENTIAL_EXPRESSION_METHOD
public static final java.lang.String DIFFERENTIAL_EXPRESSION_METHOD
Qualifier name for the differential expression method used- Since:
- API 4.1010 (Geneious 10.1.0)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_P_VALUE
public static final java.lang.String DIFFERENTIAL_EXPRESSION_P_VALUE
Qualifier name for differential expression p-value- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_ADJUSTED_P_VALUE
public static final java.lang.String DIFFERENTIAL_EXPRESSION_ADJUSTED_P_VALUE
Qualifier name for differential expression adjust p-value- Since:
- API 4.1010 (Geneious 10.1.0)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_ABSOLUTE_CONFIDENCE_QUALIFIER
public static final java.lang.String DIFFERENTIAL_EXPRESSION_ABSOLUTE_CONFIDENCE_QUALIFIER
Qualifier name for differential expression absolute confidence- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_CONFIDENCE_QUALIFIER
public static final java.lang.String DIFFERENTIAL_EXPRESSION_CONFIDENCE_QUALIFIER
Qualifier name for differential expression confidence- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_RATIO_QUALIFIER
public static final java.lang.String DIFFERENTIAL_EXPRESSION_RATIO_QUALIFIER
Qualifier name for differential expression expression ratio- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_LOG2_RATIO_QUALIFIER
public static final java.lang.String DIFFERENTIAL_EXPRESSION_LOG2_RATIO_QUALIFIER
Qualifier name for differential expression log base 2 ratio- Since:
- API 4.810 (Geneious 8.1.0)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_LOG_FOLD_STANDARD_ERROR_QUALIFIER
public static final java.lang.String DIFFERENTIAL_EXPRESSION_LOG_FOLD_STANDARD_ERROR_QUALIFIER
Qualifier name for differential expression log fold standard error- Since:
- API 4.1010 (Geneious 10.1.0)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_BASE_MEAN
public static final java.lang.String DIFFERENTIAL_EXPRESSION_BASE_MEAN
Qualifier name for differential expression base mean- Since:
- API 4.1010 (Geneious 10.1.0)
- See Also:
- Constant Field Values
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DIFFERENTIAL_EXPRESSION_WALD_STAT
public static final java.lang.String DIFFERENTIAL_EXPRESSION_WALD_STAT
Qualifier name for differential expression Wald statistic- Since:
- API 4.1010 (Geneious 10.1.0)
- See Also:
- Constant Field Values
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EXPRESSION_RPKM
public static final java.lang.String EXPRESSION_RPKM
Qualifier name for expression RPKM (reads per kilobase million)- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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EXPRESSION_FPKM
public static final java.lang.String EXPRESSION_FPKM
Qualifier name for expression FPKM (fragments per kilobase million)- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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EXPRESSION_TPM
public static final java.lang.String EXPRESSION_TPM
Qualifier name for expression TPM (transcripts per million)- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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EXPRESSION_RAW_READ_COUNT
public static final java.lang.String EXPRESSION_RAW_READ_COUNT
Qualifier name for expression raw read count- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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EXPRESSION_RAW_FRAGMENT_COUNT
public static final java.lang.String EXPRESSION_RAW_FRAGMENT_COUNT
Qualifier name for expression raw fragment count- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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EXPRESSION_RAW_TRANSCRIPT_COUNT
public static final java.lang.String EXPRESSION_RAW_TRANSCRIPT_COUNT
Qualifier name for expression raw transcript count- Since:
- API 4.801 (Geneious 8.0.1)
- See Also:
- Constant Field Values
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METHYLATION_QUALIFIER
public static final java.lang.String METHYLATION_QUALIFIER
Qualifier name for methylation of a restriction enzyme- Since:
- API 4.201910 (Geneious Prime 2019.1.0)
- See Also:
- Constant Field Values
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POTENTIAL_RESTRICTION_SITE_MODIFIED
public static final java.lang.String POTENTIAL_RESTRICTION_SITE_MODIFIED
Qualifier name for modified sequence produced when applying a potential restriction site- Since:
- API 4.1100 (Geneious 11.0.0)
- See Also:
createFormattedPotentialRestrictionSiteQualifier(String, String, int, int, boolean)
, Constant Field Values
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POTENTIAL_RESTRICTION_SITE_ORIGINAL
public static final java.lang.String POTENTIAL_RESTRICTION_SITE_ORIGINAL
Qualifier name for original sequence before applying a potential restriction site- Since:
- API 4.1100 (Geneious 11.0.0)
- See Also:
createFormattedPotentialRestrictionSiteQualifier(String, String, int, int, boolean)
, Constant Field Values
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POTENTIAL_RESTRICTION_SITE_OFFSET
public static final java.lang.String POTENTIAL_RESTRICTION_SITE_OFFSET
Hidden qualifier name for offset relative to annotation where modified sequence introduced when applying a potential restriction site begins- Since:
- API 4.1100 (Geneious 11.0.0)
- See Also:
createFormattedPotentialRestrictionSiteQualifier(String, String, int, int, boolean)
, Constant Field Values
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Constructor Detail
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SequenceAnnotationQualifier
public SequenceAnnotationQualifier(java.lang.String name, java.lang.String value)
create a new SequenceAnnotationQualifier- Parameters:
name
- the name of the qualifier; must not be null, but may be ""value
- the value of the qualifier; must not be null, but may be ""- Throws:
java.lang.IllegalArgumentException
- if name or value is null
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SequenceAnnotationQualifier
public SequenceAnnotationQualifier(SequenceAnnotationQualifier qualifier)
creates a copy of the given SequenceAnnotationQualifier. Since this class is immutable, use of this method should almost never be necessary.- Parameters:
qualifier
- the qualifier to copy
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SequenceAnnotationQualifier
public SequenceAnnotationQualifier(java.lang.String name, URN urn, boolean strong, java.lang.String label)
create a new SequenceAnnotationQualifier which contains a reference to another document. In the sequence viewer the reference will appear as a clickable hyperlink to the document.- Parameters:
name
- the name of the qualifier; must not be null, but may be ""urn
- the URN of the document this qualifier links to; must not be nullstrong
- whether this is a strong link rather than a weak link. SeeWEAK_REFERENCED_DOCUMENT_PREFIX
andSTRONG_REFERENCED_DOCUMENT_PREFIX
label
- the label for the link. May be null. SeeREFERENCED_DOCUMENT_LABEL_PREFIX
- Throws:
java.lang.IllegalArgumentException
- if name or urn is null- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
WEAK_REFERENCED_DOCUMENT_PREFIX
,STRONG_REFERENCED_DOCUMENT_PREFIX
,REFERENCED_DOCUMENT_LABEL_PREFIX
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Method Detail
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createFormattedPotentialRestrictionSiteQualifier
public static java.lang.String createFormattedPotentialRestrictionSiteQualifier(java.lang.String originalSequence, java.lang.String modifiedSequence, int offsetRelativeToAnnotation, int patternLength, boolean original)
Create a formatted potential restriction site value for Modified or Original qualifier- Parameters:
originalSequence
- original sequence (should be same length as modifiedSequence)modifiedSequence
- modified sequence (should be same length as originalSequence)offsetRelativeToAnnotation
- position relative to the annotation (negative) where the first modified base appearspatternLength
- length of the restriction site pattern (length of the annotation)original
- if true, originalSequence will be formatted; if false, modifiedSequence will be formatted- Returns:
- the HTML-formatted sequence. If sequences differ in length, this will be a substring of length equal to the shorter of the two
- Since:
- API 4.1100 (Geneious 11.0.0)
- See Also:
POTENTIAL_RESTRICTION_SITE_MODIFIED
,POTENTIAL_RESTRICTION_SITE_ORIGINAL
,POTENTIAL_RESTRICTION_SITE_OFFSET
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toString
public java.lang.String toString()
Returns a human readable string with information about this qualifier; the exact format of the string is not guaranteed and should not be relied on, because it may change at any time. The current implementation truncates the value to at most 50 characters and appends ...- Overrides:
toString
in classjava.lang.Object
- Returns:
- A human readable string with information about this qualifier.
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getName
public java.lang.String getName()
Get the name of this qualifier.- Returns:
- the name of this qualifier. Never null.
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getValue
public java.lang.String getValue()
Get the value of this qualifier.- Returns:
- the value of this qualifier. Never null.
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equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in classjava.lang.Object
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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isHidden
public boolean isHidden()
Returns true if this qualifier is hidden from the user interface. (i.e. its name starts withHIDDEN_PREFIX
- Returns:
- true if this qualifier is hidden from the user interface. (i.e. its name starts with
HIDDEN_PREFIX
- Since:
- API 4.50 (Geneious 5.5.0)
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getDisplayedValue
public java.lang.String getDisplayedValue(boolean allowHtml)
Returns the value with html tags stripped or angle brackets escaped depending on whether html is allowed.
Also handles special cases wheregetValue()
starts withSTRONG_REFERENCED_DOCUMENT_PREFIX
orWEAK_REFERENCED_DOCUMENT_PREFIX
. If allowHtml is true and the qualifier is called db_xref then its value may also be hyperlinked to the appropriate database website- Parameters:
allowHtml
- true to allow the value to be formatted as html.- Returns:
- the value of this qualifier in a form for displaying to a user
- Since:
- API 4.60 (Geneious 5.6.0)
- See Also:
isValueHtml()
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isValueHtml
public boolean isValueHtml()
Scans through the string to check if there appears to be valid angle brackets in it (an equal number, in the right order). If the value is over 1,000 characters long, the scan will stop at 1,000 and return true if there have been some valid angle brackets before that cut off.- Returns:
- true if the value of this qualifier appears to be html
- Since:
- API 4.800 (Geneious 8.0.0)
- See Also:
getDisplayedValue(boolean)
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