Interface SequenceListDocument
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- All Known Subinterfaces:
EditableSequenceListDocument
,ExtendedEditableSequenceListDocument
- All Known Implementing Classes:
DefaultSequenceListDocument
,PdbDocument
public interface SequenceListDocument
A document containing 0 or more nucleotide and 0 or more protein sequences. It is valid for the document to contain no sequences of either type. To construct a sequence list, it is recommended you use aDefaultSequenceListDocument
or to construct sequence lists that are too large to fit in memory, use aSequenceListOnDisk.Builder
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List<AminoAcidSequenceDocument>
getAminoAcidSequences()
Gets the amino acid sequences in this document.java.util.List<NucleotideSequenceDocument>
getNucleotideSequences()
Gets the nucleotide sequences in this document.
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Method Detail
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getNucleotideSequences
java.util.List<NucleotideSequenceDocument> getNucleotideSequences()
Gets the nucleotide sequences in this document. Client code should not attempt to make any changes to the returned list or any of the sequences in the returned list even if the sequences areEditableSequenceDocuments
. To add/delete/reorder sequences useEditableSequenceListDocument
. To modify individual sequences in the list, useExtendedEditableSequenceListDocument.replaceNucleotideSequence(int, NucleotideSequenceDocument)
Note that using the editing methods will require loading the entire sequence list into memory, which might not be possible on large sequence lists. SeeDefaultSequenceListDocument.replaceContents
for a discussion on efficiently handling editing large sequence lists.- Returns:
- the nucleotide sequences contained in this document. This list may be empty but will not be null.
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getAminoAcidSequences
java.util.List<AminoAcidSequenceDocument> getAminoAcidSequences()
Gets the amino acid sequences in this document. Client code should not attempt to make any changes to the returned list or any of the sequences in the returned list even if the sequences areEditableSequenceDocuments
. To add/delete/reorder sequences useEditableSequenceListDocument
. To modify individual sequences in the list, useExtendedEditableSequenceListDocument.replaceAminoAcidSequence(int, AminoAcidSequenceDocument)
- Returns:
- the amino acid sequences contained in this document. This list may be empty but will not be null.
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