Class UniProtCommentParser

java.lang.Object
org.biojavax.bio.seq.io.UniProtCommentParser

public class UniProtCommentParser extends Object
Since:
1.5
Author:
Richard Holland
  • Field Details

  • Constructor Details

    • UniProtCommentParser

      Creates a new instance of UniProtCommentParser.
  • Method Details

    • 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

      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

      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

      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

      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

      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

      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

      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

      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

      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

      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

      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.