Package org.biojava.nbio.core.sequence.io.embl

Class EmblRecord

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 Details

  • Method Details

    • 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:

    • 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:

    • 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:

    • 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:

    • setOrGanelle

      public void setOrGanelle(String orGanelle)

    • getCreatedDate

      public String getCreatedDate()
      The DT line shows when an entry first appeared in the database
      Returns:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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:

    • setDatabaseCrossReference

      public void setDatabaseCrossReference(String databaseCrossReference)

    • getAssemblyHeader

      public String getAssemblyHeader()
      The AH (Assembly Header) line provides column headings for the assembly information.
      Returns:

    • 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:

    • 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:

    • setSequenceHeader

      public void setSequenceHeader(String sequenceHeader)

    • getSequence

      public String getSequence()
      The Sequence Data Line
      Returns:

    • setSequence

      public void setSequence(String sequence)