Package org.biojavax.bio.seq.io
Class UniProtCommentParser
java.lang.Object
org.biojavax.bio.seq.io.UniProtCommentParser
- Since:
- 1.5
- Author:
- Richard Holland
-
Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A class to describe events for alternative product comments.static class
A class to describe protein-protein interactions.static class
A class to describe isoforms for alternative product comments.static class
A class to describe seq caution entries. -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
A name for a comment type.static final String
A name for a comment type.static final String
A name for a comment type.static final String
A name for a comment type.static final String
A name for a comment type.static final String
A name for a comment type.static final String
A name for a comment type. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongenerate()
Generates a comment string based on the current values of the internal fields.Getter for property absorptionMax.Getter for property absorptionNote.Getter for property commentType.Getter for property databaseName.Getter for property events.Getter for property interactions.Getter for property isoforms.Getter for property kineticsNote.getKMs()
Getter for property KMs.int
Getter for property molecularWeight.Getter for property molWeightError.Getter for property molWeightMethod.int
Getter for property molWeightRangeEnd.int
Getter for property molWeightRangeStart.getNote()
Getter for property note.Getter for property PHDependence.Getter for property redoxPotential.Getter for property seqCautions.Getter for property temperatureDependence.getText()
Getter for property text.getUri()
Getter for property uri.Getter for property VMaxes.static boolean
Returns true if the comment may be parseable (starts with -!static boolean
Returns true if the comment may be parseable (starts with -!void
Parses the comment string from the given comment and populates the internal fields appropriately.void
Parses the comment string from the given comment and populates the internal fields appropriately.void
setAbsorptionMax
(String absorptionMax) Setter for property absorptionMax.void
setAbsorptionNote
(String absorptionNote) Setter for property absorptionNote.void
setCommentType
(String commentType) Setter for property commentType.void
setDatabaseName
(String databaseName) Setter for property databaseName.void
Setter for property events.void
setInteractions
(List interactions) Setter for property interactions.void
setIsoforms
(List isoforms) Setter for property isoforms.void
setKineticsNote
(String kineticsNote) Setter for property kineticsNote.void
Setter for property KMs.void
setMolecularWeight
(int molecularWeight) Setter for property molecularWeight.void
setMolWeightError
(Integer molWeightError) Setter for property molWeightError.void
setMolWeightMethod
(String molWeightMethod) Setter for property molWeightMethod.void
setMolWeightRangeEnd
(int molWeightRangeEnd) Setter for property molWeightRangeEnd.void
setMolWeightRangeStart
(int molWeightRangeStart) Setter for property molWeightRangeStart.void
Setter for property note.void
setPHDependence
(String PHDependence) Setter for property PHDependence.void
setRedoxPotential
(String redoxPotential) Setter for property redoxPotential.void
setSeqCautions
(List seqCautions) Setter for property seqCautions.void
setTemperatureDependence
(String temperatureDependence) Setter for property temperatureDependence.void
Setter for property text.void
Setter for property uri.void
Setter for property VMaxes.
-
Field Details
-
BIOPHYSICOCHEMICAL_PROPERTIES
A name for a comment type.- See Also:
-
DATABASE
A name for a comment type.- See Also:
-
MASS_SPECTROMETRY
A name for a comment type.- See Also:
-
ALTERNATIVE_PRODUCTS
A name for a comment type.- See Also:
-
INTERACTION
A name for a comment type.- See Also:
-
PTM
A name for a comment type.- See Also:
-
SEQUENCE_CAUTION
A name for a comment type.- See Also:
-
-
Constructor Details
-
UniProtCommentParser
public UniProtCommentParser()Creates a new instance of UniProtCommentParser.
-
-
Method Details
-
parseComment
Parses the comment string from the given comment and populates the internal fields appropriately. If the comment is not a UniProt comment (does not start with -!-) then an exception is thrown.- Parameters:
c
- the comment to parse.- Throws:
ParseException
- if the comment was not parseable.
-
parseComment
Parses the comment string from the given comment and populates the internal fields appropriately. If the comment is not a UniProt comment (does not start with -!-) then an exception is thrown.- Parameters:
c
- the comment to parse.- Throws:
ParseException
- if the comment was not parseable.
-
isParseable
Returns true if the comment may be parseable (starts with -!-).- Parameters:
c
- the comment to check.- Returns:
- true if it starts with -!-, false otherwise.
-
isParseable
Returns true if the comment may be parseable (starts with -!-).- Parameters:
c
- the comment to check.- Returns:
- true if it starts with -!-, false otherwise.
-
generate
Generates a comment string based on the current values of the internal fields.- Returns:
- the comment string representing the current settings.
- Throws:
ParseException
- if the current settings do not allow the creation of a correct comment string.
-
getCommentType
Getter for property commentType.- Returns:
- Value of property commentType.
-
setCommentType
Setter for property commentType.- Parameters:
commentType
- New value of property commentType.
-
getText
Getter for property text.- Returns:
- Value of property text.
-
setText
Setter for property text.- Parameters:
text
- New value of property text.
-
getDatabaseName
Getter for property databaseName.- Returns:
- Value of property databaseName.
-
setDatabaseName
Setter for property databaseName.- Parameters:
databaseName
- New value of property databaseName.
-
getNote
Getter for property note.- Returns:
- Value of property note.
-
setNote
Setter for property note.- Parameters:
note
- New value of property note.
-
getUri
Getter for property uri.- Returns:
- Value of property uri.
-
setUri
Setter for property uri.- Parameters:
uri
- New value of property uri.
-
getMolecularWeight
Getter for property molecularWeight.- Returns:
- Value of property molecularWeight.
-
setMolecularWeight
Setter for property molecularWeight.- Parameters:
molecularWeight
- New value of property molecularWeight.
-
getMolWeightError
Getter for property molWeightError.- Returns:
- Value of property molWeightError.
-
setMolWeightError
Setter for property molWeightError.- Parameters:
molWeightError
- New value of property molWeightError.
-
getMolWeightRangeStart
Getter for property molWeightRangeStart.- Returns:
- Value of property molWeightRangeStart.
-
setMolWeightRangeStart
Setter for property molWeightRangeStart.- Parameters:
molWeightRangeStart
- New value of property molWeightRangeStart.
-
getMolWeightRangeEnd
Getter for property molWeightRangeEnd.- Returns:
- Value of property molWeightRangeEnd.
-
setMolWeightRangeEnd
Setter for property molWeightRangeEnd.- Parameters:
molWeightRangeEnd
- New value of property molWeightRangeEnd.
-
getMolWeightMethod
Getter for property molWeightMethod.- Returns:
- Value of property molWeightMethod.
-
setMolWeightMethod
Setter for property molWeightMethod.- Parameters:
molWeightMethod
- New value of property molWeightMethod.
-
getInteractions
Getter for property interactions.- Returns:
- Value of property interactions.
-
setInteractions
Setter for property interactions.- Parameters:
interactions
- New value of property interactions.
-
getSeqCautions
Getter for property seqCautions.- Returns:
- Value of property seqCautions.
-
setSeqCautions
Setter for property seqCautions.- Parameters:
seqCautions
- New value of property seqCautions.
-
getEvents
Getter for property events.- Returns:
- Value of property events.
-
setEvents
Setter for property events.- Parameters:
events
- New value of property events.
-
getIsoforms
Getter for property isoforms.- Returns:
- Value of property isoforms.
-
setIsoforms
Setter for property isoforms.- Parameters:
isoforms
- New value of property isoforms.
-
getAbsorptionMax
Getter for property absorptionMax.- Returns:
- Value of property absorptionMax.
-
setAbsorptionMax
Setter for property absorptionMax.- Parameters:
absorptionMax
- New value of property absorptionMax.
-
getAbsorptionNote
Getter for property absorptionNote.- Returns:
- Value of property absorptionNote.
-
setAbsorptionNote
Setter for property absorptionNote.- Parameters:
absorptionNote
- New value of property absorptionNote.
-
getKMs
Getter for property KMs.- Returns:
- Value of property KMs.
-
setKMs
Setter for property KMs.- Parameters:
KMs
- New value of property KMs.
-
getVMaxes
Getter for property VMaxes.- Returns:
- Value of property VMaxes.
-
setVMaxes
Setter for property VMaxes.- Parameters:
VMaxes
- New value of property VMaxes.
-
getKineticsNote
Getter for property kineticsNote.- Returns:
- Value of property kineticsNote.
-
setKineticsNote
Setter for property kineticsNote.- Parameters:
kineticsNote
- New value of property kineticsNote.
-
getPHDependence
Getter for property PHDependence.- Returns:
- Value of property PHDependence.
-
setPHDependence
Setter for property PHDependence.- Parameters:
PHDependence
- New value of property PHDependence.
-
getRedoxPotential
Getter for property redoxPotential.- Returns:
- Value of property redoxPotential.
-
setRedoxPotential
Setter for property redoxPotential.- Parameters:
redoxPotential
- New value of property redoxPotential.
-
getTemperatureDependence
Getter for property temperatureDependence.- Returns:
- Value of property temperatureDependence.
-
setTemperatureDependence
Setter for property temperatureDependence.- Parameters:
temperatureDependence
- New value of property temperatureDependence.
-