Object - Base package to handle BioMoby objects. Contains all functionality
use Object; $obj = Object->new ($id, $ns)
All methods are inherited by other objects according to ontology HAS and HASA relationships are defined using methods named from articleNames
Creates new object instances
$obj = new ($id,$ns);
Creates new object instances from XML according to XML tags.
$obj = Object->load($xml)
Returns or sets (if $newId is defined) id attribute.
$id= Object->id($newId)
Returns or sets (if $newns is defined) namespace attribute.
$namespace = Object->namespace($newns)
Returns Object datatype.
$objectName = Object->class
Returns a text representation of object's XML tree.
$string = Object->toString
Returns object as XML document.
$xml = Object->toXML
Set inner article according to articlename, class and value. For HAS articles the values are stored in an array.
Returns article value (HASA) or array of values (HAS)
$value = Object->article($articleName, $class, $value)
ISA /text_formatted
ISA /Sequence_alignment_report
ISA /PDB__Text
HASA String (JmolScript)
HASA String (Description)
ISA /Annotation
HASA String (Sequence)
HASA Integer (Score)
HASA Integer (CpG)
HASA Float (Percentaje)
HASA Float (Ratio)
ISA /Element
HASA String (Value)
HASA Integer (Key)
ISA /text_formatted
ISA /Sequence_alignment_report
ISA /Annotation
HASA Integer (TransmembraneNumber)
HASA AminoAcidSequence (TransmembraneFragment)
ISA /text_formatted
ISA /ProbMolWeightsAnnotatedAASequence
HASA AnnotationHits (AnnotationHits)
ISA /FASTA
ISA /Object
HASA Integer (From)
HASA Integer (To)
HASA Integer (Hitcount)
ISA /Object
HASA TreeDet_Annotation_XML (treedetXML)
HASA TreeDet_Annotation_HTML (treedetHTML)
HAS LutefiskAnnotation (Annotations)
ISA /text_formatted
ISA /MotifAnnotation
HASA Integer (Score)
ISA /text_formatted
ISA /text_plain
ISA /Object
HASA String (Header)
HASA String (Sequences)
HASA String (Domains)
HASA Stockholm_Text (Alignments)
ISA /Phylip_Text
ISA /Pattern
HASA Float (Fitness)
HASA Integer (Hits)
HASA Integer (SeqHits)
ISA /FASTA_NA
ISA /text_formatted
ISA /Annotation
HASA String (Enzyme_name)
HASA String (Restriction_site)
HASA Integer (5prime)
HASA Integer (3prime)
HASA Integer (5primerev)
HASA Integer (3primerev)
ISA /RNASequence
HASA String (Description)
ISA /EquicktandemAnnotatedNASequence
HASA AnnotationHits (AnnotationHits)
ISA /text_formatted
HAS TransmembraneAnnotation (Annotations)
ISA /Object
HASA String (content)
ISA /Matrix
HASA Integer (Key)
HAS ArrayFloat (Array)
ISA /text_plain
HASA String (DB)
HASA String (Evidence)
HASA String (Status)
ISA /Object
HASA Object (method)
HASA String (resultUnits)
HASA String (result)
HAS Interactor (participant)
ISA /Sequence_alignment_report
ISA /Image_Encoded
HASA text_html (legend)
ISA /MatrixFloat
HASA ArrayString (Label)
ISA /text_formatted
ISA /text_formatted
ISA /Annotation
HASA Float (MolWeight)
ISA /text_formatted
ISA /text_formatted
HAS ScoredMotifAnnotation (Annotations)
ISA /text_formatted
ISA /text_formatted
HASA String (Description)
ISA /Array
HASA Integer (Key)
HAS ElementInteger (Element)
ISA /Object
ISA /Matrix
HASA Integer (Key)
HAS ArrayInteger (Array)
HAS MotifAnnotation (Annotations)
ISA /Domain
HAS BasicAnnotation ()
HASA AnnotationHits (AnnotationHits)
ISA /text_html
ISA /text_xml
ISA /text_plain
ISA /text_formatted
HASA ArrayFloat (feature)
ISA /RestrictAnnotatedNASequence
HASA AnnotationHits (AnnotationHits)
ISA /GenericSequence
HASA String (description)
HASA String (Description)
HASA AminoAcidSequence (DeNovoPeptide)
HASA Float (Probability)
ISA /Annotation
HASA String (Type)
HASA String (Status)
HASA String (Id)
HASA String (Description)
HASA String (Evidence)
HASA String (Ref)
ISA /text_formatted
ISA /text_xml
ISA /Object
HASA ISS_Annotation_XML (issXML)
HASA NCBI_BLAST_Text (firstBlast)
HASA NCut_Matrix (ncutMatrix)
ISA /text_formatted
ISA /text_formatted
ISA /text_formatted
HAS AnnotatedDomain ()
ISA /Annotation
HASA Integer (Score)
HASA Integer (Size)
HASA Integer (Count)
ISA /text_formatted
ISA /FASTA
HAS ProbMolWeightAnnotation (Annotations)
ISA /text_formatted
ISA /Element
HASA Integer (Key)
HASA Float (Value)
ISA /text_formatted
ISA /ScoredMotifAnnotatedAASequence
HASA AnnotationHits (AnnotationHits)
ISA /Array
HASA Integer (Key)
HAS ElementString (Element)
ISA /Object
HASA Newick_Text (tree)
HASA ClusterProfile_Text (profiles)
HASA MicroArrayData_Text (microarraydata)
ISA /DNASequence
HASA String (Description)
ISA /GenericSequence
ISA /text_plain
HAS MolWeightAnnotation (Annotations)
ISA /text_formatted
HAS AntigenicAnnotation (Annotations)
HAS EquicktandemAnnotation (Annotations)
ISA /Annotation
HASA AminoAcidSequence (LutefiskPeptide)
HASA Integer (Rank)
HASA Float (Prc)
HASA Float (PevzScr)
HASA Float (Quality)
HASA Float (IntScr)
HASA Float (X-corr)
ISA /Object
HASA String (Header)
HASA String (Sequences)
HASA String (Domains)
HASA Stockholm_Text (Alignments)
HASA String (Histogram)
HASA String (Statistics)
ISA /VirtualSequence
HASA String (SequenceString)
ISA /GFF
ISA /Object
HASA String (shortlabel)
HASA String (term)
HASA String (definition)
ISA /Object
ISA /Matrix
HASA Integer (Key)
HAS ArrayString (Array)
ISA /text_formatted
ISA /Object
HASA String (Method)
HASA String (Domain_ID)
HASA String (Domain_acc)
HASA String (Description)
HASA Integer (Start)
HASA Integer (End)
HASA Float (Score)
HASA Float (Evalue)
ISA /Object
HAS RestrictAnnotation (Annotations)
ISA /text_formatted
ISA /Element
HASA Integer (Key)
HASA Integer (Value)
ISA /text_formatted
HAS InterProMotifAnnotation (Annotations)
ISA /Sequence_alignment_report
ISA /text_formatted
ISA /AntigenicAnnotatedAASequence
HASA AnnotationHits (AnnotationHits)
ISA /Sequence_alignment_report
ISA /Object
HASA String (role)
ISA /text_formatted
ISA /text_formatted
ISA /text_formatted
ISA /FASTA_AA
ISA /Annotation
HASA Integer (Max_score_pos)
HASA Float (Score)
ISA /text_xml
ISA /text_formatted
ISA /Object
HASA Integer (Start)
HASA Integer (End)
ISA /Annotation
HASA Float (Score)
HASA AminoAcidSequence (MaturePeptide)
ISA /text_formatted
ISA /Object
ISA /Object
ISA /GenericSequence
ISA /ScoredMotifAnnotatedAASequence
HASA AnnotationHits (AnnotationHits)
ISA /text_formatted
HAS SigcleaveAnnotation (Annotations)
ISA /TransmembraneAnnotatedAASequence
HASA AnnotationHits (AnnotationHits)
ISA /text_formatted
ISA /text_xml
ISA /text_xml
ISA /Object
ISA /GFF
ISA /Object
HASA String (Category)
HASA String (Term)
HASA DateTime (Date)
ISA /text_formatted
ISA /text_formatted
ISA /MatrixFloat
HASA ArrayString (labelOfRows)
HASA ArrayString (labelOfColumns)
HASA String (ListAcc)
ISA /text_formatted
HASA Integer (TotalHits)
ISA /Annotation
HASA String (ID)
HASA String (AC)
ISA /text_xml
HASA Float (tm)
HASA Integer (position)
ISA /Object
HASA Integer (Length)
ISA /Object
HASA String (content)
ISA /Object
HASA Float (MW)
HASA Float (MWTolerance)
HASA Float (FragIonTolerance)
HASA Float (IonOffset)
HASA Integer (ChargeState)
HASA Float (CysResMass)
HASA Float (IonsWindow)
HASA Float (ExtThreshold)
HASA Integer (ExtNumber)
HASA Integer (Gaps)
HASA Float (PeakWidth)
HASA Float (DataThreshold)
HASA Float (IonsResidue)
HASA Float (CterminalMass)
HASA Float (NterminalMass)
HASA Float (NterminalTagMass)
HASA Float (CterminalTagMass)
HASA String (SequenceTag)
HAS LutefiskAnnotatedAASequence (AnnotatedSequence)
ISA /Object
HASA Newick_Text (tree)
HASA ClusterProfile_Text (profiles)
HASA MicroArrayData_Text (microarraydata)
ISA /MolWeightsAnnotatedAASequence
HASA Float (Score)
HASA Float (Hit)
HASA Float (Accuracy_ratio)
HASA String (Name)
ISA /Object
HASA FeatureAASequence (Tiny)
HASA FeatureAASequence (Small)
HASA FeatureAASequence (Aliphatic)
HASA FeatureAASequence (Aromatic)
HASA FeatureAASequence (Non-polar)
HASA FeatureAASequence (Polar)
HASA FeatureAASequence (Charged)
HASA FeatureAASequence (Positive)
HASA FeatureAASequence (Negative)
HASA FeatureAASequence (Hydropathy_KD)
HASA FeatureAASequence (Hydropathy_OHM)
HASA FeatureAASequence (Consensus)
ISA /Array
HASA Integer (Key)
HAS ElementFloat (Element)
HAS FeatureAnnotation (Annotations)
ISA /text_formatted
ISA /SigcleaveAnnotatedAASequence
HASA AnnotationHits (AnnotationHits)
ISA /text_formatted
ISA /text_html
ISA /Object
ISA /Object
HASA String (rawdata)
HASA String (mimeType)
ISA /text_xml
ISA /text_formatted
ISA /text_formatted
HAS CpGAnnotation (Annotations)
ISA /PDB_Enriched
HASA text_html (Report)
ISA /text_formatted