Package org.uniprot.uniprot

Class CommentType

java.lang.Object
org.uniprot.uniprot.CommentType
public class CommentType extends Object
Describes different types of general annotations. Equivalent to the flat file CC-line.

Java class for commentType complex type

.

The following schema fragment specifies the expected content contained within this class.


 <complexType name="commentType">
   <complexContent>
     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
       <sequence>
         <element name="molecule" type="{https://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
         <choice minOccurs="0">
           <group ref="{https://uniprot.org/uniprot}bpcCommentGroup"/>
           <sequence>
             <element name="reaction" type="{https://uniprot.org/uniprot}reactionType"/>
             <element name="physiologicalReaction" type="{https://uniprot.org/uniprot}physiologicalReactionType" maxOccurs="2" minOccurs="0"/>
           </sequence>
           <sequence>
             <element name="cofactor" type="{https://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/>
           </sequence>
           <sequence>
             <element name="subcellularLocation" type="{https://uniprot.org/uniprot}subcellularLocationType" maxOccurs="unbounded"/>
           </sequence>
           <element name="conflict">
             <complexType>
               <complexContent>
                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                   <sequence>
                     <element name="sequence" minOccurs="0">
                       <complexType>
                         <complexContent>
                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                             <attribute name="resource" use="required">
                               <simpleType>
                                 <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                                   <enumeration value="EMBL-CDS"/>
                                   <enumeration value="EMBL"/>
                                 </restriction>
                               </simpleType>
                             </attribute>
                             <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                             <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
                           </restriction>
                         </complexContent>
                       </complexType>
                     </element>
                   </sequence>
                   <attribute name="type" use="required">
                     <simpleType>
                       <restriction base="{http://www.w3.org/2001/XMLSchema}string">
                         <enumeration value="frameshift"/>
                         <enumeration value="erroneous initiation"/>
                         <enumeration value="erroneous termination"/>
                         <enumeration value="erroneous gene model prediction"/>
                         <enumeration value="erroneous translation"/>
                         <enumeration value="miscellaneous discrepancy"/>
                       </restriction>
                     </simpleType>
                   </attribute>
                   <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
                 </restriction>
               </complexContent>
             </complexType>
           </element>
           <sequence>
             <element name="link" maxOccurs="unbounded" minOccurs="0">
               <complexType>
                 <complexContent>
                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                     <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
                   </restriction>
                 </complexContent>
               </complexType>
             </element>
           </sequence>
           <sequence>
             <element name="event" type="{https://uniprot.org/uniprot}eventType" maxOccurs="4"/>
             <element name="isoform" type="{https://uniprot.org/uniprot}isoformType" maxOccurs="unbounded" minOccurs="0"/>
           </sequence>
           <sequence>
             <element name="interactant" type="{https://uniprot.org/uniprot}interactantType" maxOccurs="2" minOccurs="2"/>
             <element name="organismsDiffer" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
             <element name="experiments" type="{http://www.w3.org/2001/XMLSchema}int"/>
           </sequence>
           <element name="disease">
             <complexType>
               <complexContent>
                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                   <sequence>
                     <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
                     <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
                     <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
                     <element name="dbReference" type="{https://uniprot.org/uniprot}dbReferenceType"/>
                   </sequence>
                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                 </restriction>
               </complexContent>
             </complexType>
           </element>
         </choice>
         <element name="location" type="{https://uniprot.org/uniprot}locationType" maxOccurs="unbounded" minOccurs="0"/>
         <element name="text" type="{https://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
       </sequence>
       <attribute name="type" use="required">
         <simpleType>
           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
             <enumeration value="allergen"/>
             <enumeration value="alternative products"/>
             <enumeration value="biotechnology"/>
             <enumeration value="biophysicochemical properties"/>
             <enumeration value="catalytic activity"/>
             <enumeration value="caution"/>
             <enumeration value="cofactor"/>
             <enumeration value="developmental stage"/>
             <enumeration value="disease"/>
             <enumeration value="domain"/>
             <enumeration value="disruption phenotype"/>
             <enumeration value="activity regulation"/>
             <enumeration value="function"/>
             <enumeration value="induction"/>
             <enumeration value="miscellaneous"/>
             <enumeration value="pathway"/>
             <enumeration value="pharmaceutical"/>
             <enumeration value="polymorphism"/>
             <enumeration value="PTM"/>
             <enumeration value="RNA editing"/>
             <enumeration value="similarity"/>
             <enumeration value="subcellular location"/>
             <enumeration value="sequence caution"/>
             <enumeration value="subunit"/>
             <enumeration value="tissue specificity"/>
             <enumeration value="toxic dose"/>
             <enumeration value="online information"/>
             <enumeration value="mass spectrometry"/>
             <enumeration value="interaction"/>
           </restriction>
         </simpleType>
       </attribute>
       <attribute name="locationType" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="mass" type="{http://www.w3.org/2001/XMLSchema}float" />
       <attribute name="error" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="method" type="{http://www.w3.org/2001/XMLSchema}string" />
       <attribute name="evidence" type="{https://uniprot.org/uniprot}intListType" />
     </restriction>
   </complexContent>
 </complexType>

  • Field Details

  • Constructor Details

    • CommentType

      public CommentType()

  • Method Details

    • getMolecule

      public MoleculeType getMolecule()
      Gets the value of the molecule property.
      Returns:
      possible object is MoleculeType

    • setMolecule

      public void setMolecule(MoleculeType value)
      Sets the value of the molecule property.
      Parameters:
      value - allowed object is MoleculeType

    • getAbsorption

      public CommentType.Absorption getAbsorption()
      Gets the value of the absorption property.
      Returns:
      possible object is CommentType.Absorption

    • setAbsorption

      public void setAbsorption(CommentType.Absorption value)
      Sets the value of the absorption property.
      Parameters:
      value - allowed object is CommentType.Absorption

    • getKinetics

      public CommentType.Kinetics getKinetics()
      Gets the value of the kinetics property.
      Returns:
      possible object is CommentType.Kinetics

    • setKinetics

      public void setKinetics(CommentType.Kinetics value)
      Sets the value of the kinetics property.
      Parameters:
      value - allowed object is CommentType.Kinetics

    • getPhDependence

      public CommentType.PhDependence getPhDependence()
      Gets the value of the phDependence property.
      Returns:
      possible object is CommentType.PhDependence

    • setPhDependence

      public void setPhDependence(CommentType.PhDependence value)
      Sets the value of the phDependence property.
      Parameters:
      value - allowed object is CommentType.PhDependence

    • getRedoxPotential

      public CommentType.RedoxPotential getRedoxPotential()
      Gets the value of the redoxPotential property.
      Returns:
      possible object is CommentType.RedoxPotential

    • setRedoxPotential

      public void setRedoxPotential(CommentType.RedoxPotential value)
      Sets the value of the redoxPotential property.
      Parameters:
      value - allowed object is CommentType.RedoxPotential

    • getTemperatureDependence

      public CommentType.TemperatureDependence getTemperatureDependence()
      Gets the value of the temperatureDependence property.
      Returns:
      possible object is CommentType.TemperatureDependence

    • setTemperatureDependence

      public void setTemperatureDependence(CommentType.TemperatureDependence value)
      Sets the value of the temperatureDependence property.
      Parameters:
      value - allowed object is CommentType.TemperatureDependence

    • getReaction

      public ReactionType getReaction()
      Gets the value of the reaction property.
      Returns:
      possible object is ReactionType

    • setReaction

      public void setReaction(ReactionType value)
      Sets the value of the reaction property.
      Parameters:
      value - allowed object is ReactionType

    • getPhysiologicalReaction

      public List<PhysiologicalReactionType> getPhysiologicalReaction()
      Gets the value of the physiologicalReaction property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the physiologicalReaction property.

      For example, to add a new item, do as follows: 

       getPhysiologicalReaction().add(newItem);

      Objects of the following type(s) are allowed in the list PhysiologicalReactionType

      Returns:
      The value of the physiologicalReaction property.

    • getCofactor

      public List<CofactorType> getCofactor()
      Gets the value of the cofactor property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the cofactor property.

      For example, to add a new item, do as follows: 

       getCofactor().add(newItem);

      Objects of the following type(s) are allowed in the list CofactorType

      Returns:
      The value of the cofactor property.

    • getSubcellularLocation

      public List<SubcellularLocationType> getSubcellularLocation()
      Gets the value of the subcellularLocation property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the subcellularLocation property.

      For example, to add a new item, do as follows: 

       getSubcellularLocation().add(newItem);

      Objects of the following type(s) are allowed in the list SubcellularLocationType

      Returns:
      The value of the subcellularLocation property.

    • getConflict

      public CommentType.Conflict getConflict()
      Used in 'sequence caution' annotations.
      Returns:
      possible object is CommentType.Conflict

    • setConflict

      public void setConflict(CommentType.Conflict value)
      Sets the value of the conflict property.
      Parameters:
      value - allowed object is CommentType.Conflict
      See Also:

    • getLink

      public List<CommentType.Link> getLink()
      Used in 'online information' annotations. Gets the value of the link property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the link property.

      For example, to add a new item, do as follows: 

       getLink().add(newItem);

      Objects of the following type(s) are allowed in the list CommentType.Link

      Returns:
      The value of the link property.

    • getEvent

      public List<EventType> getEvent()
      Gets the value of the event property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the event property.

      For example, to add a new item, do as follows: 

       getEvent().add(newItem);

      Objects of the following type(s) are allowed in the list EventType

      Returns:
      The value of the event property.

    • getIsoform

      public List<IsoformType> getIsoform()
      Gets the value of the isoform property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the isoform property.

      For example, to add a new item, do as follows: 

       getIsoform().add(newItem);

      Objects of the following type(s) are allowed in the list IsoformType

      Returns:
      The value of the isoform property.

    • getInteractant

      public List<InteractantType> getInteractant()
      Gets the value of the interactant property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the interactant property.

      For example, to add a new item, do as follows: 

       getInteractant().add(newItem);

      Objects of the following type(s) are allowed in the list InteractantType

      Returns:
      The value of the interactant property.

    • isOrganismsDiffer

      public Boolean isOrganismsDiffer()
      Gets the value of the organismsDiffer property.
      Returns:
      possible object is Boolean

    • setOrganismsDiffer

      public void setOrganismsDiffer(Boolean value)
      Sets the value of the organismsDiffer property.
      Parameters:
      value - allowed object is Boolean

    • getExperiments

      public Integer getExperiments()
      Gets the value of the experiments property.
      Returns:
      possible object is Integer

    • setExperiments

      public void setExperiments(Integer value)
      Sets the value of the experiments property.
      Parameters:
      value - allowed object is Integer

    • getDisease

      public CommentType.Disease getDisease()
      Used in 'disease' annotations.
      Returns:
      possible object is CommentType.Disease

    • setDisease

      public void setDisease(CommentType.Disease value)
      Sets the value of the disease property.
      Parameters:
      value - allowed object is CommentType.Disease
      See Also:

    • getLocation

      public List<LocationType> getLocation()
      Used in 'mass spectrometry' and 'sequence caution' annotations. Gets the value of the location property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the location property.

      For example, to add a new item, do as follows: 

       getLocation().add(newItem);

      Objects of the following type(s) are allowed in the list LocationType

      Returns:
      The value of the location property.

    • getText

      public List<EvidencedStringType> getText()
      Gets the value of the text property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the text property.

      For example, to add a new item, do as follows: 

       getText().add(newItem);

      Objects of the following type(s) are allowed in the list EvidencedStringType

      Returns:
      The value of the text property.

    • getType

      public String getType()
      Describes the type of a general annotation. Equivalent to the flat file CC comment topics (except for "DATABASE" which is translated to "online information").
      Returns:
      possible object is String

    • setType

      public void setType(String value)
      Sets the value of the type property.
      Parameters:
      value - allowed object is String
      See Also:

    • getLocationType

      public String getLocationType()
      Describes the type of sequence location in 'RNA editing' annotations. Common values are "Not_applicable" and "Undetermined".
      Returns:
      possible object is String

    • setLocationType

      public void setLocationType(String value)
      Sets the value of the locationType property.
      Parameters:
      value - allowed object is String
      See Also:

    • getName

      public String getName()
      Describes an optional name for an 'online information'.
      Returns:
      possible object is String

    • setName

      public void setName(String value)
      Sets the value of the name property.
      Parameters:
      value - allowed object is String
      See Also:

    • getMass

      public Float getMass()
      Describes the molecular mass in 'mass spectrometry' annotations.
      Returns:
      possible object is Float

    • setMass

      public void setMass(Float value)
      Sets the value of the mass property.
      Parameters:
      value - allowed object is Float
      See Also:

    • getError

      public String getError()
      Describes the error of the mass measurement in 'mass spectrometry' annotations.
      Returns:
      possible object is String

    • setError

      public void setError(String value)
      Sets the value of the error property.
      Parameters:
      value - allowed object is String
      See Also:

    • getMethod

      public String getMethod()
      Describes the experimental method in 'mass spectrometry' annotations.
      Returns:
      possible object is String

    • setMethod

      public void setMethod(String value)
      Sets the value of the method property.
      Parameters:
      value - allowed object is String
      See Also:

    • getEvidence

      public List<Integer> getEvidence()
      Gets the value of the evidence property.

      This accessor method returns a reference to the live list, not a snapshot. Therefore any modification you make to the returned list will be present inside the JAXB object. This is why there is not a set method for the evidence property.

      For example, to add a new item, do as follows: 

       getEvidence().add(newItem);

      Objects of the following type(s) are allowed in the list Integer

      Returns:
      The value of the evidence property.