Package org.biojavax.bio.seq.io

Class UniProtCommentParser

    • 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​(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​(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 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 String getCommentType()
        Getter for property commentType.
        Returns:
        Value of property commentType.

      • setCommentType

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

      • getText

        public String getText()
        Getter for property text.
        Returns:
        Value of property text.

      • setText

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

      • getDatabaseName

        public String getDatabaseName()
        Getter for property databaseName.
        Returns:
        Value of property databaseName.

      • setDatabaseName

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

      • getNote

        public String getNote()
        Getter for property note.
        Returns:
        Value of property note.

      • setNote

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

      • getUri

        public String getUri()
        Getter for property uri.
        Returns:
        Value of property uri.

      • setUri

        public void setUri​(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 Integer getMolWeightError()
        Getter for property molWeightError.
        Returns:
        Value of property molWeightError.

      • setMolWeightError

        public void setMolWeightError​(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 String getMolWeightMethod()
        Getter for property molWeightMethod.
        Returns:
        Value of property molWeightMethod.

      • setMolWeightMethod

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

      • getInteractions

        public List getInteractions()
        Getter for property interactions.
        Returns:
        Value of property interactions.

      • setInteractions

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

      • getSeqCautions

        public List getSeqCautions()
        Getter for property seqCautions.
        Returns:
        Value of property seqCautions.

      • setSeqCautions

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

      • getEvents

        public List getEvents()
        Getter for property events.
        Returns:
        Value of property events.

      • setEvents

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

      • getIsoforms

        public List getIsoforms()
        Getter for property isoforms.
        Returns:
        Value of property isoforms.

      • setIsoforms

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

      • getAbsorptionMax

        public String getAbsorptionMax()
        Getter for property absorptionMax.
        Returns:
        Value of property absorptionMax.

      • setAbsorptionMax

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

      • getAbsorptionNote

        public String getAbsorptionNote()
        Getter for property absorptionNote.
        Returns:
        Value of property absorptionNote.

      • setAbsorptionNote

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

      • getKMs

        public List getKMs()
        Getter for property KMs.
        Returns:
        Value of property KMs.

      • setKMs

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

      • getVMaxes

        public List getVMaxes()
        Getter for property VMaxes.
        Returns:
        Value of property VMaxes.

      • setVMaxes

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

      • getKineticsNote

        public String getKineticsNote()
        Getter for property kineticsNote.
        Returns:
        Value of property kineticsNote.

      • setKineticsNote

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

      • getPHDependence

        public String getPHDependence()
        Getter for property PHDependence.
        Returns:
        Value of property PHDependence.

      • setPHDependence

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

      • getRedoxPotential

        public String getRedoxPotential()
        Getter for property redoxPotential.
        Returns:
        Value of property redoxPotential.

      • setRedoxPotential

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

      • getTemperatureDependence

        public String getTemperatureDependence()
        Getter for property temperatureDependence.
        Returns:
        Value of property temperatureDependence.

      • setTemperatureDependence

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