Class EmblRecord
- java.lang.Object
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- org.biojava.nbio.core.sequence.io.embl.EmblRecord
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public class EmblRecord extends java.lang.Object
this class contains the parsed data of embl file- Since:
- 5.0.0
- Author:
- Noor Aldeen Al Mbaidin
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Constructor Summary
Constructors Constructor Description EmblRecord()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.List<java.lang.String>
getAccessionNumber()
The AC (Accession number) line lists the accession numbers associated with the entry.java.lang.String
getAssemblyHeader()
The AH (Assembly Header) line provides column headings for the assembly information.java.lang.String
getAssemblyInformation()
The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.java.lang.String
getConstructedSequence()
Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.java.lang.String
getCreatedDate()
The DT line shows when an entry first appeared in the databasejava.lang.String
getDatabaseCrossReference()
The DR (Database Cross-reference) line cross-references other databases which contain information related to the entry in which the DR line appears.EmblId
getEmblId()
The ID (IDentification) line The tokens represent: 1.java.util.List<EmblReference>
getEmblReference()
The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines These lines comprise the literature citations within the database.java.lang.String
getFeatureHeader()
The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen.java.lang.String
getFeatureTable()
The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data.java.util.List<java.lang.String>
getKeyword()
The KW (KeyWord) lines provide information which can be used to generate cross-reference indexes of the sequence entries based on functional, structural, or other categories deemed important.java.lang.String
getLastUpdatedDate()
The DT (DaTe) line shows when an entry was last updated in the database.java.lang.String
getOrGanelle()
The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.java.lang.String
getOrganismClassification()
The OC (Organism Classification) lines contain the taxonomic classification Of the source organismjava.lang.String
getOrganismSpecies()
The OS (Organism Species) line specifies the preferred scientific name of the organism which was the source of the stored sequence.java.lang.String
getProjectIdentifier()
java.lang.String
getSequence()
The Sequence Data Linejava.lang.String
getSequenceDescription()
The DE (Description) lines contain general descriptive information about the sequence stored.java.lang.String
getSequenceHeader()
The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.void
setAccessionNumber(java.util.List<java.lang.String> accessionNumber)
void
setAssemblyHeader(java.lang.String assemblyHeader)
void
setAssemblyInformation(java.lang.String assemblyInformation)
void
setConstructedSequence(java.lang.String constructedSequence)
void
setCreatedDate(java.lang.String createdDate)
void
setDatabaseCrossReference(java.lang.String databaseCrossReference)
void
setEmblId(EmblId emblId)
void
setEmblReference(java.util.List<EmblReference> emblReference)
void
setFeatureHeader(java.lang.String featureHeader)
void
setFeatureTable(java.lang.String featureTable)
void
setKeyword(java.util.List<java.lang.String> keyword)
void
setLastUpdatedDate(java.lang.String lastUpdatedDate)
void
setOrGanelle(java.lang.String orGanelle)
void
setOrganismClassification(java.lang.String organismClassification)
void
setOrganismSpecies(java.lang.String organismSpecies)
void
setProjectIdentifier(java.lang.String projectIdentifier)
void
setSequence(java.lang.String sequence)
void
setSequenceDescription(java.lang.String sequenceDescription)
void
setSequenceHeader(java.lang.String sequenceHeader)
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Method Detail
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getEmblId
public EmblId getEmblId()
The ID (IDentification) line The tokens represent: 1. Primary accession number 2. Sequence version number 3. Topology: 'circular' or 'linear' 4. Molecule type 5. Data class 6. Taxonomic division 7. Sequence length- Returns:
- EmblId
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setEmblId
public void setEmblId(EmblId emblId)
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getEmblReference
public java.util.List<EmblReference> getEmblReference()
The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines These lines comprise the literature citations within the database. The citations provide access to the papers from which the data has been abstracted.- Returns:
- EmblReference
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setEmblReference
public void setEmblReference(java.util.List<EmblReference> emblReference)
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getAccessionNumber
public java.util.List<java.lang.String> getAccessionNumber()
The AC (Accession number) line lists the accession numbers associated with the entry.- Returns:
- List
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setAccessionNumber
public void setAccessionNumber(java.util.List<java.lang.String> accessionNumber)
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getProjectIdentifier
public java.lang.String getProjectIdentifier()
- Returns:
- String
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setProjectIdentifier
public void setProjectIdentifier(java.lang.String projectIdentifier)
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getOrGanelle
public java.lang.String getOrGanelle()
The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.- Returns:
- String
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setOrGanelle
public void setOrGanelle(java.lang.String orGanelle)
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getCreatedDate
public java.lang.String getCreatedDate()
The DT line shows when an entry first appeared in the database- Returns:
- String
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setCreatedDate
public void setCreatedDate(java.lang.String createdDate)
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getFeatureHeader
public java.lang.String getFeatureHeader()
The FH (Feature Header) lines are present only to improve readability of an entry when it is printed or displayed on a terminal screen.- Returns:
- String
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setFeatureHeader
public void setFeatureHeader(java.lang.String featureHeader)
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getFeatureTable
public java.lang.String getFeatureTable()
The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data. Regions or sites in the sequence which are of interest are listed in the table.- Returns:
- String
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setFeatureTable
public void setFeatureTable(java.lang.String featureTable)
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getLastUpdatedDate
public java.lang.String getLastUpdatedDate()
The DT (DaTe) line shows when an entry was last updated in the database.- Returns:
- String
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setLastUpdatedDate
public void setLastUpdatedDate(java.lang.String lastUpdatedDate)
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getSequenceDescription
public java.lang.String getSequenceDescription()
The DE (Description) lines contain general descriptive information about the sequence stored. This may include the designations of genes for which the sequence codes, the region of the genome from which it is derived, or other information which helps to identify the sequence.- Returns:
- String
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setSequenceDescription
public void setSequenceDescription(java.lang.String sequenceDescription)
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getKeyword
public java.util.List<java.lang.String> getKeyword()
The KW (KeyWord) lines provide information which can be used to generate cross-reference indexes of the sequence entries based on functional, structural, or other categories deemed important.- Returns:
- List
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setKeyword
public void setKeyword(java.util.List<java.lang.String> keyword)
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getOrganismSpecies
public java.lang.String getOrganismSpecies()
The OS (Organism Species) line specifies the preferred scientific name of the organism which was the source of the stored sequence. In most cases this is done by giving the Latin genus and species designations, followed (in parentheses) by the preferred common name in English where known.- Returns:
- String
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setOrganismSpecies
public void setOrganismSpecies(java.lang.String organismSpecies)
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getOrganismClassification
public java.lang.String getOrganismClassification()
The OC (Organism Classification) lines contain the taxonomic classification Of the source organism- Returns:
- String
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setOrganismClassification
public void setOrganismClassification(java.lang.String organismClassification)
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getDatabaseCrossReference
public java.lang.String getDatabaseCrossReference()
The DR (Database Cross-reference) line cross-references other databases which contain information related to the entry in which the DR line appears.- Returns:
- String
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setDatabaseCrossReference
public void setDatabaseCrossReference(java.lang.String databaseCrossReference)
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getAssemblyHeader
public java.lang.String getAssemblyHeader()
The AH (Assembly Header) line provides column headings for the assembly information.- Returns:
- String
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setAssemblyHeader
public void setAssemblyHeader(java.lang.String assemblyHeader)
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getAssemblyInformation
public java.lang.String getAssemblyInformation()
The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.- Returns:
- String
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setAssemblyInformation
public void setAssemblyInformation(java.lang.String assemblyInformation)
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getConstructedSequence
public java.lang.String getConstructedSequence()
Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.- Returns:
- String
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setConstructedSequence
public void setConstructedSequence(java.lang.String constructedSequence)
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getSequenceHeader
public java.lang.String getSequenceHeader()
The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.- Returns:
- String
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setSequenceHeader
public void setSequenceHeader(java.lang.String sequenceHeader)
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getSequence
public java.lang.String getSequence()
The Sequence Data Line- Returns:
- String
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setSequence
public void setSequence(java.lang.String sequence)
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