EmblRecord (biojava 5.3.0 API)

java.lang.Object
- org.biojava.nbio.core.sequence.io.embl.EmblRecord

```
public class EmblRecord
extends Object
```
this class contains the parsed data of embl file

Since:

5.0.0

Author:

Noor Aldeen Al Mbaidin

Constructor Summary

Constructors
Constructor and Description

EmblRecord()

Constructors
Constructor and Description
`EmblRecord()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`List<String>`	`getAccessionNumber()` The AC (Accession number) line lists the accession numbers associated with the entry.
`String`	`getAssemblyHeader()` The AH (Assembly Header) line provides column headings for the assembly information.
`String`	`getAssemblyInformation()` The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.
`String`	`getConstructedSequence()` Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.
`String`	`getCreatedDate()` The DT line shows when an entry first appeared in the database
`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.
`List<EmblReference>`	`getEmblReference()` The Reference (RN, RC, RP, RX, RG, RA, RT, RL) Lines These lines comprise the literature citations within the database.
`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.
`String`	`getFeatureTable()` The FT (Feature Table) lines provide a mechanism for the annotation of the sequence data.
`List<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.
`String`	`getLastUpdatedDate()` The DT (DaTe) line shows when an entry was last updated in the database.
`String`	`getOrGanelle()` The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.
`String`	`getOrganismClassification()` The OC (Organism Classification) lines contain the taxonomic classification Of the source organism
`String`	`getOrganismSpecies()` The OS (Organism Species) line specifies the preferred scientific name of the organism which was the source of the stored sequence.
`String`	`getProjectIdentifier()`
`String`	`getSequence()` The Sequence Data Line
`String`	`getSequenceDescription()` The DE (Description) lines contain general descriptive information about the sequence stored.
`String`	`getSequenceHeader()` The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.
`void`	`setAccessionNumber(List<String> accessionNumber)`
`void`	`setAssemblyHeader(String assemblyHeader)`
`void`	`setAssemblyInformation(String assemblyInformation)`
`void`	`setConstructedSequence(String constructedSequence)`
`void`	`setCreatedDate(String createdDate)`
`void`	`setDatabaseCrossReference(String databaseCrossReference)`
`void`	`setEmblId(EmblId emblId)`
`void`	`setEmblReference(List<EmblReference> emblReference)`
`void`	`setFeatureHeader(String featureHeader)`
`void`	`setFeatureTable(String featureTable)`
`void`	`setKeyword(List<String> keyword)`
`void`	`setLastUpdatedDate(String lastUpdatedDate)`
`void`	`setOrGanelle(String orGanelle)`
`void`	`setOrganismClassification(String organismClassification)`
`void`	`setOrganismSpecies(String organismSpecies)`
`void`	`setProjectIdentifier(String projectIdentifier)`
`void`	`setSequence(String sequence)`
`void`	`setSequenceDescription(String sequenceDescription)`
`void`	`setSequenceHeader(String sequenceHeader)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - EmblRecord
```
public EmblRecord()
```
- Method Detail
  - 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
  - setEmblId
```
public void setEmblId(EmblId emblId)
```
  - getEmblReference
```
public 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
  - setEmblReference
```
public void setEmblReference(List<EmblReference> emblReference)
```
  - getAccessionNumber
```
public List<String> getAccessionNumber()
```
    The AC (Accession number) line lists the accession numbers associated with the entry.
    
    Returns:
    
    List
  - setAccessionNumber
```
public void setAccessionNumber(List<String> accessionNumber)
```
  - getProjectIdentifier
```
public String getProjectIdentifier()
```
    Returns:
    
    String
  - setProjectIdentifier
```
public void setProjectIdentifier(String projectIdentifier)
```
  - getOrGanelle
```
public String getOrGanelle()
```
    The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear sequences.
    
    Returns:
    
    String
  - setOrGanelle
```
public void setOrGanelle(String orGanelle)
```
  - getCreatedDate
```
public String getCreatedDate()
```
    The DT line shows when an entry first appeared in the database
    
    Returns:
    
    String
  - setCreatedDate
```
public void setCreatedDate(String createdDate)
```
  - getFeatureHeader
```
public 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
  - setFeatureHeader
```
public void setFeatureHeader(String featureHeader)
```
  - getFeatureTable
```
public 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
  - setFeatureTable
```
public void setFeatureTable(String featureTable)
```
  - getLastUpdatedDate
```
public String getLastUpdatedDate()
```
    The DT (DaTe) line shows when an entry was last updated in the database.
    
    Returns:
    
    String
  - setLastUpdatedDate
```
public void setLastUpdatedDate(String lastUpdatedDate)
```
  - getSequenceDescription
```
public 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
  - setSequenceDescription
```
public void setSequenceDescription(String sequenceDescription)
```
  - getKeyword
```
public List<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
  - setKeyword
```
public void setKeyword(List<String> keyword)
```
  - getOrganismSpecies
```
public 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
  - setOrganismSpecies
```
public void setOrganismSpecies(String organismSpecies)
```
  - getOrganismClassification
```
public String getOrganismClassification()
```
    The OC (Organism Classification) lines contain the taxonomic classification Of the source organism
    
    Returns:
    
    String
  - setOrganismClassification
```
public void setOrganismClassification(String organismClassification)
```
  - getDatabaseCrossReference
```
public 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
  - setDatabaseCrossReference
```
public void setDatabaseCrossReference(String databaseCrossReference)
```
  - getAssemblyHeader
```
public String getAssemblyHeader()
```
    The AH (Assembly Header) line provides column headings for the assembly information.
    
    Returns:
    
    String
  - setAssemblyHeader
```
public void setAssemblyHeader(String assemblyHeader)
```
  - getAssemblyInformation
```
public String getAssemblyInformation()
```
    The AS (Assembly Information) lines provide information on the composition of a TPA or TSA sequence.
    
    Returns:
    
    String
  - setAssemblyInformation
```
public void setAssemblyInformation(String assemblyInformation)
```
  - getConstructedSequence
```
public String getConstructedSequence()
```
    Con(structed) sequences in the CON data classes represent complete chromosomes, genomes and other long sequences constructed from segment entries.
    
    Returns:
    
    String
  - setConstructedSequence
```
public void setConstructedSequence(String constructedSequence)
```
  - getSequenceHeader
```
public String getSequenceHeader()
```
    The SQ (SeQuence header) line marks the beginning of the sequence data and Gives a summary of its content.
    
    Returns:
    
    String
  - setSequenceHeader
```
public void setSequenceHeader(String sequenceHeader)
```
  - getSequence
```
public String getSequence()
```
    The Sequence Data Line
    
    Returns:
    
    String
  - setSequence
```
public void setSequence(String sequence)
```

Class EmblRecord

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

EmblRecord

Method Detail

getEmblId

setEmblId

getEmblReference

setEmblReference

getAccessionNumber

setAccessionNumber

getProjectIdentifier

setProjectIdentifier

getOrGanelle

setOrGanelle

getCreatedDate

setCreatedDate

getFeatureHeader

setFeatureHeader

getFeatureTable

setFeatureTable

getLastUpdatedDate

setLastUpdatedDate

getSequenceDescription

setSequenceDescription

getKeyword

setKeyword

getOrganismSpecies

setOrganismSpecies

getOrganismClassification

setOrganismClassification

getDatabaseCrossReference

setDatabaseCrossReference

getAssemblyHeader

setAssemblyHeader

getAssemblyInformation

setAssemblyInformation

getConstructedSequence

setConstructedSequence

getSequenceHeader

setSequenceHeader

getSequence

setSequence