Class DataFrameSnp
java.lang.Object
org.snpsift.annotate.mem.dataFrame.DataFrame
org.snpsift.annotate.mem.dataFrame.DataFrameSnp
- All Implemented Interfaces:
Serializable
The DataFrameSnp class extends the DataFrame class and represents a specific type of data frame
that deals with single nucleotide polymorphisms (SNPs). Each instance of DataFrameSnp is associated
with a specific alternative allele ('A', 'C', 'G', or 'T') based on the provided variant category.
This class provides methods to retrieve the alternative allele and to check if a given entry matches
specific position and allele values.
Limitations:
- The class assumes that the variant category provided during instantiation is one of the SNP categories
(SNP_A, SNP_C, SNP_G, SNP_T). If an invalid category is provided, a RuntimeException is thrown.
- The eq method assumes that the alternative allele (alt) is always in uppercase. If the provided alt
parameter in the eq method is not in uppercase, a RuntimeException is thrown.
- See Also:
-
Field Summary
Fields inherited from class org.snpsift.annotate.mem.dataFrame.DataFrame
MAX_ROWS_TO_SHOW -
Constructor Summary
ConstructorsConstructorDescriptionDataFrameSnp(VariantTypeCounter variantTypeCounter, VariantCategory variantCategory) -
Method Summary
Methods inherited from class org.snpsift.annotate.mem.dataFrame.DataFrame
add, check, columnNames, createColumn, createColumns, find, get, getColumn, getRow, hasEntry, resize, set, sizeBytes, toString