NAME

Object - Base package to handle BioMoby objects. Contains all functionality

SYNOPSIS

 use Object;
 $obj = Object->new ($id, $ns)

METHODS

All methods are inherited by other objects according to ontology HAS and HASA relationships are defined using methods named from articleNames

new

Creates new object instances

 $obj = new ($id,$ns);

load

Creates new object instances from XML according to XML tags.

 $obj = Object->load($xml)

id

Returns or sets (if $newId is defined) id attribute.

 $id= Object->id($newId)

namespace

Returns or sets (if $newns is defined) namespace attribute.

 $namespace = Object->namespace($newns)

class

Returns Object datatype.

 $objectName = Object->class

toString

Returns a text representation of object's XML tree.

 $string = Object->toString

toXML

Returns object as XML document.

 $xml = Object->toXML

article

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)

CodonUsageTable_Text

ISA /text_formatted

MSF

ISA /Sequence_alignment_report

PDB_Enriched

ISA /PDB__Text

HASA String (JmolScript)

HASA String (Description)

CpGAnnotation

ISA /Annotation

HASA String (Sequence)

HASA Integer (Score)

HASA Integer (CpG)

HASA Float (Percentaje)

HASA Float (Ratio)

ElementString

ISA /Element

HASA String (Value)

HASA Integer (Key)

Pepstats_Text

ISA /text_formatted

Clustalw_Text

ISA /Sequence_alignment_report

TransmembraneAnnotation

ISA /Annotation

HASA Integer (TransmembraneNumber)

HASA AminoAcidSequence (TransmembraneFragment)

GFF

ISA /text_formatted

PepNovoReport

ISA /ProbMolWeightsAnnotatedAASequence

HASA AnnotationHits (AnnotationHits)

FASTA_AA

ISA /FASTA

AnnotationHits

ISA /Object

HASA Integer (From)

HASA Integer (To)

HASA Integer (Hitcount)

TreeDet_Report

ISA /Object

HASA TreeDet_Annotation_XML (treedetXML)

HASA TreeDet_Annotation_HTML (treedetHTML)

LutefiskAnnotatedAASequence

ISA /AnnotatedAASequence

HAS LutefiskAnnotation (Annotations)

SwissProt_Text

ISA /text_formatted

ScoredMotifAnnotation

ISA /MotifAnnotation

HASA Integer (Score)

FASTA_Text

ISA /text_formatted

text_xhtml

ISA /text_plain

HMMPfam_Report

ISA /Object

HASA String (Header)

HASA String (Sequences)

HASA String (Domains)

HASA Stockholm_Text (Alignments)

Phylip_Interleaved_Text

ISA /Phylip_Text

MatchingPattern

ISA /Pattern

HASA Float (Fitness)

HASA Integer (Hits)

HASA Integer (SeqHits)

FASTA_NA_multi

ISA /FASTA_NA

List_Text

ISA /text_formatted

AnnotatedAASequence

ISA /CommentedAASequence

RestrictAnnotation

ISA /Annotation

HASA String (Enzyme_name)

HASA String (Restriction_site)

HASA Integer (5prime)

HASA Integer (3prime)

HASA Integer (5primerev)

HASA Integer (3primerev)

CommentedRNASequence

ISA /RNASequence

HASA String (Description)

HMM_Text

ISA /Consensus_Sequence_Text

EquicktandemReport

ISA /EquicktandemAnnotatedNASequence

HASA AnnotationHits (AnnotationHits)

Consensus_Sequence_Text

ISA /text_formatted

TransmembraneAnnotatedAASequence

ISA /AnnotatedAASequence

HAS TransmembraneAnnotation (Annotations)

text_plain

ISA /Object

HASA String (content)

MatrixFloat

ISA /Matrix

HASA Integer (Key)

HAS ArrayFloat (Array)

text_html

ISA /text_plain

InterProMotifAnnotation

ISA /ScoredMotifAnnotation

HASA String (DB)

HASA String (Evidence)

HASA String (Status)

Interaction

ISA /Object

HASA Object (method)

HASA String (resultUnits)

HASA String (result)

HAS Interactor (participant)

Stockholm_Text

ISA /Sequence_alignment_report

Typed_Image

ISA /Image_Encoded

HASA text_html (legend)

Distance_Matrix

ISA /MatrixFloat

HASA ArrayString (Label)

TFscan_Text

ISA /text_formatted

ClusterProfile_Text

ISA /text_formatted

MolWeightAnnotation

ISA /Annotation

HASA Float (MolWeight)

HSSP_Text

ISA /text_formatted

MicroArrayData_Text

ISA /text_formatted

ScoredMotifAnnotatedAASequence

ISA /AnnotatedAASequence

HAS ScoredMotifAnnotation (Annotations)

NCut_Clusters

ISA /text_formatted

FSSP_Text

ISA /text_formatted

CommentedNASequence

ISA /NucleotideSequence

HASA String (Description)

ArrayInteger

ISA /Array

HASA Integer (Key)

HAS ElementInteger (Element)

Element

ISA /Object

MatrixInteger

ISA /Matrix

HASA Integer (Key)

HAS ArrayInteger (Array)

MotifAnnotatedAASequence

ISA /AnnotatedAASequence

HAS MotifAnnotation (Annotations)

AnnotatedDomain

ISA /Domain

HAS BasicAnnotation ()

CpGReport

ISA /CpGAnnotatedNASequence

HASA AnnotationHits (AnnotationHits)

DGPI_Report

ISA /text_html

TreeDet_Annotation_XML

ISA /text_xml

text_xml

ISA /text_plain

EMBL_Text

ISA /text_formatted

FeatureAASequence

ISA /CommentedAASequence

HASA ArrayFloat (feature)

RestrictReport

ISA /RestrictAnnotatedNASequence

HASA AnnotationHits (AnnotationHits)

PropertySequence

ISA /GenericSequence

HASA String (description)

CommentedAASequence

ISA /AminoAcidSequence

HASA String (Description)

ProbMolWeightAnnotation

ISA /MolWeightAnnotation

HASA AminoAcidSequence (DeNovoPeptide)

HASA Float (Probability)

FeatureAnnotation

ISA /Annotation

HASA String (Type)

HASA String (Status)

HASA String (Id)

HASA String (Description)

HASA String (Evidence)

HASA String (Ref)

FSOLV_Text

ISA /text_formatted

BLAST_XML

ISA /text_xml

ISS_Report

ISA /Object

HASA ISS_Annotation_XML (issXML)

HASA NCBI_BLAST_Text (firstBlast)

HASA NCut_Matrix (ncutMatrix)

MEME_Text

ISA /text_formatted

PDB__Text

ISA /text_formatted

Phylip_tree_Text

ISA /text_formatted

DomainAnnotatedSequence

ISA /CommentedAASequence

HAS AnnotatedDomain ()

EquicktandemAnnotation

ISA /Annotation

HASA Integer (Score)

HASA Integer (Size)

HASA Integer (Count)

CodcmpReport_Text

ISA /text_formatted

FASTA_NA

ISA /FASTA

ProbMolWeightsAnnotatedAASequence

ISA /AnnotatedAASequence

HAS ProbMolWeightAnnotation (Annotations)

mmCIF_Text

ISA /text_formatted

ElementFloat

ISA /Element

HASA Integer (Key)

HASA Float (Value)

FASTA_pep

ISA /text_formatted

DNASequence

ISA /NucleotideSequence

PatmatdbReport

ISA /ScoredMotifAnnotatedAASequence

HASA AnnotationHits (AnnotationHits)

ArrayString

ISA /Array

HASA Integer (Key)

HAS ElementString (Element)

Clustering

ISA /Object

HASA Newick_Text (tree)

HASA ClusterProfile_Text (profiles)

HASA MicroArrayData_Text (microarraydata)

CommentedDNASequence

ISA /DNASequence

HASA String (Description)

NucleotideSequence

ISA /GenericSequence

text_formatted

ISA /text_plain

MolWeightsAnnotatedAASequence

ISA /AnnotatedAASequence

HAS MolWeightAnnotation (Annotations)

GenBank_Text

ISA /text_formatted

AntigenicAnnotatedAASequence

ISA /AnnotatedAASequence

HAS AntigenicAnnotation (Annotations)

EquicktandemAnnotatedNASequence

ISA /AnnotatedNASequence

HAS EquicktandemAnnotation (Annotations)

LutefiskAnnotation

ISA /Annotation

HASA AminoAcidSequence (LutefiskPeptide)

HASA Integer (Rank)

HASA Float (Prc)

HASA Float (PevzScr)

HASA Float (Quality)

HASA Float (IntScr)

HASA Float (X-corr)

HMMSearch_Report

ISA /Object

HASA String (Header)

HASA String (Sequences)

HASA String (Domains)

HASA Stockholm_Text (Alignments)

HASA String (Histogram)

HASA String (Statistics)

GenericSequence

ISA /VirtualSequence

HASA String (SequenceString)

GFF2

ISA /GFF

InteractionMethod

ISA /Object

HASA String (shortlabel)

HASA String (term)

HASA String (definition)

Array

ISA /Object

MatrixString

ISA /Matrix

HASA Integer (Key)

HAS ArrayString (Array)

Phylip_treefile_Text

ISA /text_formatted

Domain

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)

Matrix

ISA /Object

RestrictAnnotatedNASequence

ISA /AnnotatedNASequence

HAS RestrictAnnotation (Annotations)

DTA_Text

ISA /text_formatted

ElementInteger

ISA /Element

HASA Integer (Key)

HASA Integer (Value)

PrositeDoc_Text

ISA /text_formatted

InterProMotifAnnotatedAASequence

ISA /AnnotatedAASequence

HAS InterProMotifAnnotation (Annotations)

PIR_Text

ISA /Sequence_alignment_report

BLAST__Text

ISA /text_formatted

AntigenicReport

ISA /AntigenicAnnotatedAASequence

HASA AnnotationHits (AnnotationHits)

Phylip_Text

ISA /Sequence_alignment_report

Interactor

ISA /Object

HASA String (role)

NCBI_BLAST_Text

ISA /text_formatted

PHD_Text

ISA /text_formatted

DCCP_Text

ISA /text_formatted

FASTA_AA_multi

ISA /FASTA_AA

AntigenicAnnotation

ISA /Annotation

HASA Integer (Max_score_pos)

HASA Float (Score)

DASGFF

ISA /text_xml

Clustalw_Evaluated_Text

ISA /text_formatted

Annotation

ISA /Object

HASA Integer (Start)

HASA Integer (End)

SigcleaveAnnotation

ISA /Annotation

HASA Float (Score)

HASA AminoAcidSequence (MaturePeptide)

NCut_Text

ISA /text_formatted

DateTime

ISA /Object

String

ISA /Object

AminoAcidSequence

ISA /GenericSequence

PatmatmotifsReport

ISA /ScoredMotifAnnotatedAASequence

HASA AnnotationHits (AnnotationHits)

Newick_Text

ISA /text_formatted

SigcleaveAnnotatedAASequence

ISA /AnnotatedAASequence

HAS SigcleaveAnnotation (Annotations)

TransmembraneReport

ISA /TransmembraneAnnotatedAASequence

HASA AnnotationHits (AnnotationHits)

Sequence_alignment_report

ISA /text_formatted

FunCUT_Annotation_XML

ISA /text_xml

ISS_Annotation_XML

ISA /text_xml

Integer

ISA /Object

GFF3

ISA /GFF

BasicAnnotation

ISA /Object

HASA String (Category)

HASA String (Term)

HASA DateTime (Date)

DSSP_Text

ISA /text_formatted

Enzymatic_Text

ISA /text_formatted

NCut_Matrix

ISA /MatrixFloat

HASA ArrayString (labelOfRows)

HASA ArrayString (labelOfColumns)

HASA String (ListAcc)

FASTA

ISA /text_formatted

PPSearchReport

ISA /MotifAnnotatedAASequence

HASA Integer (TotalHits)

MotifAnnotation

ISA /Annotation

HASA String (ID)

HASA String (AC)

IntAct_XML

ISA /text_xml

TTS

ISA /CommentedDNASequence

HASA Float (tm)

HASA Integer (position)

VirtualSequence

ISA /Object

HASA Integer (Length)

AnnotatedNASequence

ISA /CommentedNASequence

Pattern

ISA /Object

HASA String (content)

LutefiskReport

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)

HierarchicalClustering

ISA /Object

HASA Newick_Text (tree)

HASA ClusterProfile_Text (profiles)

HASA MicroArrayData_Text (microarraydata)

EmowseAnnotatedAASequence

ISA /MolWeightsAnnotatedAASequence

HASA Float (Score)

HASA Float (Hit)

HASA Float (Accuracy_ratio)

HASA String (Name)

PepinfoReport

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)

ArrayFloat

ISA /Array

HASA Integer (Key)

HAS ElementFloat (Element)

FeatureAnnotatedAASequence

ISA /AnnotatedAASequence

HAS FeatureAnnotation (Annotations)

Meta_Alignment_Text

ISA /text_formatted

SigcleaveReport

ISA /SigcleaveAnnotatedAASequence

HASA AnnotationHits (AnnotationHits)

Pepcoil_Text

ISA /text_formatted

TreeDet_Annotation_HTML

ISA /text_html

RNASequence

ISA /NucleotideSequence

Float

ISA /Object

Image_Encoded

ISA /Object

HASA String (rawdata)

HASA String (mimeType)

CathDomainDescription_XML

ISA /text_xml

RefSeq_Text

ISA /text_formatted

SequenceDescription_Text

ISA /text_formatted

CpGAnnotatedNASequence

ISA /AnnotatedNASequence

HAS CpGAnnotation (Annotations)

Structure_Alignment_Report

ISA /PDB_Enriched

HASA text_html (Report)

PMUT_Text

ISA /text_formatted