Data Model version 2.1.2
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Class: Alignment


    Alignment of molecule with database reference
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link molecule to class Molecule
Main key: serial
Mandatory Attributes: dbRef
Known Subclasses: None
Children: None
Constructor: newObj = Alignment( molecule,dbRef=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
alignLength Int 0..1 Length of alignment  
alignmentProgram Text 0..1 Program used for alignment/threading.  
alignmentScore Float 0..1 Alignment score for alignment or threading program.  
dbRefAlignBegin Int 0..1 Optional. Residue number in the database reference sequence where the alignment begins.  
dbRefAlignEnd Int 0..1 Optional. Residue number in the database reference sequence where the alignment ends.  
details String 0..1 Free text, for notes, explanatory comments, etc.  
homologyRatio FloatRatio 0..1 Fractioanl homology  
nIdentical Int 0..1 Number of identical residues  
nPositive Int 0..1 Number of positive-scoring residues  
serial Int 1..1 Serial number of object. Serves as object main key. Serial numbers of deleted objects are not re-used. Serial numbers can only be set by the implementation. Values are in practice always positive, since negative values are interpreted as a signal to set the next free serial  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
dbRef ccp.api.general.DbRef.Entry 1..1 database reference used in alignment  
molSeqFragment MolSeqFragment 0..1 MolSeqFragment that alignment refers to. If not set, the alignment refers to the entire molecule  
molecule Molecule 1..1 (Parent link). parent link  
parent Molecule 1..1 link to parent object - synonym for molecule  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
alignLength
getAlignLength Int -
setAlignLength - Int
alignmentProgram
getAlignmentProgram Text -
setAlignmentProgram - Text
alignmentScore
getAlignmentScore Float -
setAlignmentScore - Float
dbRefAlignBegin
getDbRefAlignBegin Int -
setDbRefAlignBegin - Int
dbRefAlignEnd
getDbRefAlignEnd Int -
setDbRefAlignEnd - Int
details
getDetails String -
setDetails - String
homologyRatio
getHomologyRatio FloatRatio -
setHomologyRatio - FloatRatio
nIdentical
getNIdentical Int -
setNIdentical - Int
nPositive
getNPositive Int -
setNPositive - Int
serial
getSerial Int -
setSerial - Int

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
dbRef
getDbRef ccp.api.general.DbRef.Entry -
setDbRef - ccp.api.general.DbRef.Entry
molSeqFragment
getMolSeqFragment MolSeqFragment -
setMolSeqFragment - MolSeqFragment
molecule
getMolecule Molecule -
parent
getParent Molecule -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Alignment memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey Any -
get Any String
set - String, Any

Factory Methods (in package)

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Method Return Parameters
None

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2007-11-26-10:11:54_00001

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Fri Mar 28 11:18:10 2014    from data model package  ccp.api.molecule.Molecule.Alignment   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk