| Helper Class |
Generally useful static methods.
Inheritance HierarchyNamespace: Bio.Util
Assembly: Bio.Core (in Bio.Core.dll) Version: 2.0.0.1 (2.0.0.1)
SyntaxThe Helper type exposes the following members.
Methods| Name | Description | |
|---|---|---|
  | ASCIIEncoding |
Simple method to take a byte array and convert it to ASCII string.
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| BigMul |
Helper method for large multiplication - this function is missing
from the portable profile.
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| CheckCondition(Boolean) |
Confirms that a condition is true. Raise an exception if it is not.
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| CheckCondition(Boolean, FuncString) |
Confirms that a condition is true. Raise an exception if it is not.
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| CheckCondition(Boolean, String) |
Confirms that a condition is true. Raise an exception if it is not.
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| CheckCondition(Boolean, String, Object) |
Confirms that a condition is true. Raise an exception if it is not.
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| CheckConditionT(Boolean) |
Confirms that a condition is true. Raise an exception of type T if it is not.
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| CheckConditionT(Boolean, FuncString) |
Confirms that a condition is true. Raise an exception if it is not.
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| CheckConditionT(Boolean, String) |
Confirms that a condition is true. Raise an exception of type T if it is not.
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| CheckConditionT(Boolean, String, Object) |
Confirms that a condition is true. Raise an exception if it is not.
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| Copy(Array, Array, Int64) |
Copies source array to destination array.
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| Copy(Array, Int64, Array, Int64, Int64) |
Copies source array to destination array.
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| CreateDelimitedString |
Creates a delimited string containing the object's string values.
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| CreateTabString |
Creates a tab-delimited string containing the object's string values.
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| FileEndsWithZippedExtension |
Determine if file ends with extension ".gz"
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| GenerateAlphabetCheckFailureException |
Create a useful error message when a sequence fails validation.
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| GetCrossReferenceLink |
Returns a string which represents specified CrossReferenceLink.
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| GetGenBankAccession |
Returns a string which represents specified GenBankAccession.
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| GetHexString |
Gets the HexString from the specified byte array.
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| GetInt16 |
Returns 16 bit signed integer from the byte array stored as little-endian.
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| GetInt32 |
Returns 32 bit signed integer from the byte array stored as little-endian.
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| GetLittleEndianByteArray(Int16) |
Gets a byte array which represents value of 16 bit singed integer in LittleEndian format.
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| GetLittleEndianByteArray(Int32) |
Gets a byte array which represents value of 32 bit singed integer in LittleEndian format.
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| GetLittleEndianByteArray(Single) |
Gets byte array which represents value of float in LittleEndian format.
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| GetLittleEndianByteArray(UInt16) |
Gets a byte array which represents value of 16 bit unsinged integer in LittleEndian format.
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| GetLittleEndianByteArray(UInt32) |
Gets a byte array which represents value of 32 bit unsigned integer in LittleEndian format.
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| GetMatePairedReadType |
Gets the mate paired read type.
That is for F/1/X1 it provides R/2/Y1.
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| GetNormalRandom(Double, Double) |
Returns random numbers according to an approximate normal distribution
with an average and standard deviation set by the caller.
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| GetNormalRandom(Double, Double, Int32) |
Returns random numbers according to an approximate normal distribution
with an average and standard deviation set by the caller. This is done iteratively
using the central limit theorem.
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| GetPairedReadId |
Concatenates the specified original sequence id, paired read type and library name to paired read id format.
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| GetProjectIdentifier |
Returns a string which represents specified ProjectIdentifier.
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| GetReadIdExcludingOtherInfo |
Returns the id exluding the otherinformation part from it.
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| GetReverseComplement |
Get reverse complement of sequence string.
Handles only unambiguous DNA sequence strings.
Note: This method is a light-weight implementation of sequence.ReverseComplement.
This only works for unambiguous DNA sequences, which is characteristic of the input for de-novo.
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| GetSequenceRange |
Get a range of sequence.
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| GetSequenceSegment |
Returns a string which represents specified SequenceSegment.
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| GetSingle |
Returns float from the byte array.
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| GetStrandTopology(String) |
Returns a SequenceStrandTopology corresponds to the specified string.
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| GetStrandTopology(SequenceStrandTopology) |
Returns a string which represents specified SequenceStrandTopology.
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| GetStrandType(String) |
Returns a SequenceStrandType corresponds to the specified string.
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| GetStrandType(SequenceStrandType) |
Returns a string which represents specified SequenceStrandType.
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| GetString |
Gets string representing specified delta alignment.
This method is used in comparative Utilities to write delta alignments to file.
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| GetUInt16 |
Returns 16 bit unsigned integer from the byte array stored as little-endian.
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| GetUInt32 |
Returns 32 bit unsigned integer from the byte array stored as little-endian.
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| GetUInt64 |
Returns 32 bit unsigned integer from the byte array stored as little-endian.
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| IsBAM |
Identifies if a file extension is a
valid extension for BAM formats.
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| IsFasta |
Identifies if a file extension is a
valid extension for FASTA formats.
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| IsFastQ |
Identifies if a file extension is a
valid extension for FastQ formats.
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| IsGenBank |
Identifies if a file extension is a
valid extension for GenBank formats.
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| IsValidPatternValue(String, String, String) |
Validates specified value with the specified regular expression pattern.
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| IsValidPatternValue(String, String, Regex) |
Validates specified value with the specified regular expression.
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| IsValidRange |
Validates int value.
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| IsValidRegexValue(String, String) |
Validates specified value with the specified regular expression.
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| IsValidRegexValue(Regex, String) |
Validates specified value with the specified regular expression.
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| IsZippedFasta |
Identifies if a file extension is a
valid extension for FASTA formats that is gzipped.
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| IsZippedFastQ |
Identifies if a file extension is a
valid extension for a gzipped FastQ formats.
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| KeysEqualTKey, TValue1, TValue2 |
Efficiently (log n) test if two dictionaries have the same key set.
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| RemoveSequencePolyTail |
Get a Sequence Poly Tail.
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| SplitSequence |
Split sequence for Iron poython.
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| StringContainsIllegalCharacters |
Determines if the string contains any characters specified in the list.
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| StringHasMatch |
See if test string is identical to any of the passed list of strings.
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| StringMultiply |
String Multiply. Build a string by concatenating copies of the input string.
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| ValidatePairedSequenceId |
Validates the specified sequence id is in the format of paired read or not.
If so then gets the original sequence id, paired read type and library name from the paired sequence id.
For Example:
if the sequence id is "seq1.F:10K!324;abcd;345" then this method will return true and
originalSequenceId - "seq1"
pairedReadType - "F"
libraryName - "10K"
if the sequence id is not in the format of "originalSequenceId.{F,R}:LibraryName"
or "originalSequenceId.{F,R}:LibraryName!otherInfo" then this method will return false.
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| WrapAroundLeftShift |
Shifts the bits of an int around in a wrapped way. It is useful for creating hashcodes of collections.
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Fields| Name | Description | |
|---|---|---|
 | AlphabetsToShowInToString |
Stores the number of alphabets to show in ToString function of a class.
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| GenBankMetadataKey |
Key to get GenBankMetadata object from Metadata of a sequence which is parsed from GenBankParser.
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| PairedReadDelimiter |
Delimitar "!" used to seperate the PairedRead information with other info in the sequence id.
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| SAMAlignedSequenceHeaderKey |
Key to get SAMAlignedSequenceHeader object from Metadata of a aligned sequence which is parsed from SAMParser.
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| SAMAlignmentHeaderKey |
Key to get SAMAlignmentHeader object from Metadata of a sequence alignment which is parsed from SAMParser.
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| ZippedFileExtension |
The .gz extension to indicate gzipped files
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See Also