Class UniProtCommentParser


  • public class UniProtCommentParser
    extends java.lang.Object
    Since:
    1.5
    Author:
    Richard Holland
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String ALTERNATIVE_PRODUCTS
      A name for a comment type.
      static java.lang.String BIOPHYSICOCHEMICAL_PROPERTIES
      A name for a comment type.
      static java.lang.String DATABASE
      A name for a comment type.
      static java.lang.String INTERACTION
      A name for a comment type.
      static java.lang.String MASS_SPECTROMETRY
      A name for a comment type.
      static java.lang.String PTM
      A name for a comment type.
      static java.lang.String SEQUENCE_CAUTION
      A name for a comment type.
    • Constructor Summary

      Constructors 
      Constructor Description
      UniProtCommentParser()
      Creates a new instance of UniProtCommentParser.
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String generate()
      Generates a comment string based on the current values of the internal fields.
      java.lang.String getAbsorptionMax()
      Getter for property absorptionMax.
      java.lang.String getAbsorptionNote()
      Getter for property absorptionNote.
      java.lang.String getCommentType()
      Getter for property commentType.
      java.lang.String getDatabaseName()
      Getter for property databaseName.
      java.util.List getEvents()
      Getter for property events.
      java.util.List getInteractions()
      Getter for property interactions.
      java.util.List getIsoforms()
      Getter for property isoforms.
      java.lang.String getKineticsNote()
      Getter for property kineticsNote.
      java.util.List getKMs()
      Getter for property KMs.
      int getMolecularWeight()
      Getter for property molecularWeight.
      java.lang.Integer getMolWeightError()
      Getter for property molWeightError.
      java.lang.String getMolWeightMethod()
      Getter for property molWeightMethod.
      int getMolWeightRangeEnd()
      Getter for property molWeightRangeEnd.
      int getMolWeightRangeStart()
      Getter for property molWeightRangeStart.
      java.lang.String getNote()
      Getter for property note.
      java.lang.String getPHDependence()
      Getter for property PHDependence.
      java.lang.String getRedoxPotential()
      Getter for property redoxPotential.
      java.util.List getSeqCautions()
      Getter for property seqCautions.
      java.lang.String getTemperatureDependence()
      Getter for property temperatureDependence.
      java.lang.String getText()
      Getter for property text.
      java.lang.String getUri()
      Getter for property uri.
      java.util.List getVMaxes()
      Getter for property VMaxes.
      static boolean isParseable​(java.lang.String c)
      Returns true if the comment may be parseable (starts with -!-).
      static boolean isParseable​(Comment c)
      Returns true if the comment may be parseable (starts with -!-).
      void parseComment​(java.lang.String c)
      Parses the comment string from the given comment and populates the internal fields appropriately.
      void parseComment​(Comment c)
      Parses the comment string from the given comment and populates the internal fields appropriately.
      void setAbsorptionMax​(java.lang.String absorptionMax)
      Setter for property absorptionMax.
      void setAbsorptionNote​(java.lang.String absorptionNote)
      Setter for property absorptionNote.
      void setCommentType​(java.lang.String commentType)
      Setter for property commentType.
      void setDatabaseName​(java.lang.String databaseName)
      Setter for property databaseName.
      void setEvents​(java.util.List events)
      Setter for property events.
      void setInteractions​(java.util.List interactions)
      Setter for property interactions.
      void setIsoforms​(java.util.List isoforms)
      Setter for property isoforms.
      void setKineticsNote​(java.lang.String kineticsNote)
      Setter for property kineticsNote.
      void setKMs​(java.util.List KMs)
      Setter for property KMs.
      void setMolecularWeight​(int molecularWeight)
      Setter for property molecularWeight.
      void setMolWeightError​(java.lang.Integer molWeightError)
      Setter for property molWeightError.
      void setMolWeightMethod​(java.lang.String molWeightMethod)
      Setter for property molWeightMethod.
      void setMolWeightRangeEnd​(int molWeightRangeEnd)
      Setter for property molWeightRangeEnd.
      void setMolWeightRangeStart​(int molWeightRangeStart)
      Setter for property molWeightRangeStart.
      void setNote​(java.lang.String note)
      Setter for property note.
      void setPHDependence​(java.lang.String PHDependence)
      Setter for property PHDependence.
      void setRedoxPotential​(java.lang.String redoxPotential)
      Setter for property redoxPotential.
      void setSeqCautions​(java.util.List seqCautions)
      Setter for property seqCautions.
      void setTemperatureDependence​(java.lang.String temperatureDependence)
      Setter for property temperatureDependence.
      void setText​(java.lang.String text)
      Setter for property text.
      void setUri​(java.lang.String uri)
      Setter for property uri.
      void setVMaxes​(java.util.List VMaxes)
      Setter for property VMaxes.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • BIOPHYSICOCHEMICAL_PROPERTIES

        public static final java.lang.String BIOPHYSICOCHEMICAL_PROPERTIES
        A name for a comment type.
        See Also:
        Constant Field Values
      • DATABASE

        public static final java.lang.String DATABASE
        A name for a comment type.
        See Also:
        Constant Field Values
      • MASS_SPECTROMETRY

        public static final java.lang.String MASS_SPECTROMETRY
        A name for a comment type.
        See Also:
        Constant Field Values
      • ALTERNATIVE_PRODUCTS

        public static final java.lang.String ALTERNATIVE_PRODUCTS
        A name for a comment type.
        See Also:
        Constant Field Values
      • INTERACTION

        public static final java.lang.String INTERACTION
        A name for a comment type.
        See Also:
        Constant Field Values
      • PTM

        public static final java.lang.String PTM
        A name for a comment type.
        See Also:
        Constant Field Values
      • SEQUENCE_CAUTION

        public static final java.lang.String SEQUENCE_CAUTION
        A name for a comment type.
        See Also:
        Constant Field Values
    • Constructor Detail

      • UniProtCommentParser

        public UniProtCommentParser()
        Creates a new instance of UniProtCommentParser.
    • Method Detail

      • parseComment

        public void parseComment​(Comment c)
                          throws ParseException
        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

        public void parseComment​(java.lang.String c)
                          throws ParseException
        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

        public static boolean isParseable​(Comment c)
        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

        public static boolean isParseable​(java.lang.String c)
        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

        public java.lang.String generate()
                                  throws ParseException
        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

        public java.lang.String getCommentType()
        Getter for property commentType.
        Returns:
        Value of property commentType.
      • setCommentType

        public void setCommentType​(java.lang.String commentType)
        Setter for property commentType.
        Parameters:
        commentType - New value of property commentType.
      • getText

        public java.lang.String getText()
        Getter for property text.
        Returns:
        Value of property text.
      • setText

        public void setText​(java.lang.String text)
        Setter for property text.
        Parameters:
        text - New value of property text.
      • getDatabaseName

        public java.lang.String getDatabaseName()
        Getter for property databaseName.
        Returns:
        Value of property databaseName.
      • setDatabaseName

        public void setDatabaseName​(java.lang.String databaseName)
        Setter for property databaseName.
        Parameters:
        databaseName - New value of property databaseName.
      • getNote

        public java.lang.String getNote()
        Getter for property note.
        Returns:
        Value of property note.
      • setNote

        public void setNote​(java.lang.String note)
        Setter for property note.
        Parameters:
        note - New value of property note.
      • getUri

        public java.lang.String getUri()
        Getter for property uri.
        Returns:
        Value of property uri.
      • setUri

        public void setUri​(java.lang.String uri)
        Setter for property uri.
        Parameters:
        uri - New value of property uri.
      • getMolecularWeight

        public int getMolecularWeight()
        Getter for property molecularWeight.
        Returns:
        Value of property molecularWeight.
      • setMolecularWeight

        public void setMolecularWeight​(int molecularWeight)
        Setter for property molecularWeight.
        Parameters:
        molecularWeight - New value of property molecularWeight.
      • getMolWeightError

        public java.lang.Integer getMolWeightError()
        Getter for property molWeightError.
        Returns:
        Value of property molWeightError.
      • setMolWeightError

        public void setMolWeightError​(java.lang.Integer molWeightError)
        Setter for property molWeightError.
        Parameters:
        molWeightError - New value of property molWeightError.
      • getMolWeightRangeStart

        public int getMolWeightRangeStart()
        Getter for property molWeightRangeStart.
        Returns:
        Value of property molWeightRangeStart.
      • setMolWeightRangeStart

        public void setMolWeightRangeStart​(int molWeightRangeStart)
        Setter for property molWeightRangeStart.
        Parameters:
        molWeightRangeStart - New value of property molWeightRangeStart.
      • getMolWeightRangeEnd

        public int getMolWeightRangeEnd()
        Getter for property molWeightRangeEnd.
        Returns:
        Value of property molWeightRangeEnd.
      • setMolWeightRangeEnd

        public void setMolWeightRangeEnd​(int molWeightRangeEnd)
        Setter for property molWeightRangeEnd.
        Parameters:
        molWeightRangeEnd - New value of property molWeightRangeEnd.
      • getMolWeightMethod

        public java.lang.String getMolWeightMethod()
        Getter for property molWeightMethod.
        Returns:
        Value of property molWeightMethod.
      • setMolWeightMethod

        public void setMolWeightMethod​(java.lang.String molWeightMethod)
        Setter for property molWeightMethod.
        Parameters:
        molWeightMethod - New value of property molWeightMethod.
      • getInteractions

        public java.util.List getInteractions()
        Getter for property interactions.
        Returns:
        Value of property interactions.
      • setInteractions

        public void setInteractions​(java.util.List interactions)
        Setter for property interactions.
        Parameters:
        interactions - New value of property interactions.
      • getSeqCautions

        public java.util.List getSeqCautions()
        Getter for property seqCautions.
        Returns:
        Value of property seqCautions.
      • setSeqCautions

        public void setSeqCautions​(java.util.List seqCautions)
        Setter for property seqCautions.
        Parameters:
        seqCautions - New value of property seqCautions.
      • getEvents

        public java.util.List getEvents()
        Getter for property events.
        Returns:
        Value of property events.
      • setEvents

        public void setEvents​(java.util.List events)
        Setter for property events.
        Parameters:
        events - New value of property events.
      • getIsoforms

        public java.util.List getIsoforms()
        Getter for property isoforms.
        Returns:
        Value of property isoforms.
      • setIsoforms

        public void setIsoforms​(java.util.List isoforms)
        Setter for property isoforms.
        Parameters:
        isoforms - New value of property isoforms.
      • getAbsorptionMax

        public java.lang.String getAbsorptionMax()
        Getter for property absorptionMax.
        Returns:
        Value of property absorptionMax.
      • setAbsorptionMax

        public void setAbsorptionMax​(java.lang.String absorptionMax)
        Setter for property absorptionMax.
        Parameters:
        absorptionMax - New value of property absorptionMax.
      • getAbsorptionNote

        public java.lang.String getAbsorptionNote()
        Getter for property absorptionNote.
        Returns:
        Value of property absorptionNote.
      • setAbsorptionNote

        public void setAbsorptionNote​(java.lang.String absorptionNote)
        Setter for property absorptionNote.
        Parameters:
        absorptionNote - New value of property absorptionNote.
      • getKMs

        public java.util.List getKMs()
        Getter for property KMs.
        Returns:
        Value of property KMs.
      • setKMs

        public void setKMs​(java.util.List KMs)
        Setter for property KMs.
        Parameters:
        KMs - New value of property KMs.
      • getVMaxes

        public java.util.List getVMaxes()
        Getter for property VMaxes.
        Returns:
        Value of property VMaxes.
      • setVMaxes

        public void setVMaxes​(java.util.List VMaxes)
        Setter for property VMaxes.
        Parameters:
        VMaxes - New value of property VMaxes.
      • getKineticsNote

        public java.lang.String getKineticsNote()
        Getter for property kineticsNote.
        Returns:
        Value of property kineticsNote.
      • setKineticsNote

        public void setKineticsNote​(java.lang.String kineticsNote)
        Setter for property kineticsNote.
        Parameters:
        kineticsNote - New value of property kineticsNote.
      • getPHDependence

        public java.lang.String getPHDependence()
        Getter for property PHDependence.
        Returns:
        Value of property PHDependence.
      • setPHDependence

        public void setPHDependence​(java.lang.String PHDependence)
        Setter for property PHDependence.
        Parameters:
        PHDependence - New value of property PHDependence.
      • getRedoxPotential

        public java.lang.String getRedoxPotential()
        Getter for property redoxPotential.
        Returns:
        Value of property redoxPotential.
      • setRedoxPotential

        public void setRedoxPotential​(java.lang.String redoxPotential)
        Setter for property redoxPotential.
        Parameters:
        redoxPotential - New value of property redoxPotential.
      • getTemperatureDependence

        public java.lang.String getTemperatureDependence()
        Getter for property temperatureDependence.
        Returns:
        Value of property temperatureDependence.
      • setTemperatureDependence

        public void setTemperatureDependence​(java.lang.String temperatureDependence)
        Setter for property temperatureDependence.
        Parameters:
        temperatureDependence - New value of property temperatureDependence.