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API Docs / SMRUCC.genomics.Core / FastaSeq

FastaSeq

Full name SMRUCC.genomics.SequenceModel.FASTA.FastaSeq Assembly SMRUCC.genomics.Core Members 41

The FASTA format file of a bimolecular sequence.(Notice that this file is only contains on sequence.)

00 Remarks

FASTA格式的生物分子序列文件。(但是请注意:文件中只包含一条序列的情况,假若需要自定义所生成的FASTA文件的标题的格式, 请复写FastaSeq.ToString()方法)

01 Syntax

SMRUCC.genomics.SequenceModel.FASTA.FastaSeq

02 Methods

NameOverloadsSummary
.ctor 1
ToString 1 Get the title of this fasta object.(返回FASTA对象的标题,在所返回的值之中不包含有fasta标题之中的第一个字符>)
GrepTitle 1 You can using this function to convert the title from current format into another format.(使用这个方法将Fasta序列对象的标题从当前的格式转换为另外一种格式)
ToUpper 1 Convert the FastaSeq.SequenceData to upper case and then return the new created FastaSeq.
LoadNucleotideData 1 Load the fasta sequence file as a nucleotide sequence from a specific path, the function will returns a null value if the sequence contains some non-nucleotide character.
Load 1 Load a single sequence fasta file object, if the target file path is not exists on the file system or the file format is not correct, then this function will returns a null objec…
ParseFromStream 1 Parsing a fasta sequence object from a collection of string value.
TryParse 1 Try parsing a fasta sequence object from a string chunk value.
GenerateDocument 1 Generate a FASTA file data text string.
SequenceLineBreak 2 break the input sequence string into multiple lines
Equals 1 The Fasta sequence equals on both sequence data and title information.(值比较来判断是否相等)
CopyTo 1 Copy the value in current fasta object into another fasta object.(将当前的序列数据复制到目标序列数据对象之中)
Copy 1 Copy the value to a new specific type fasta object.
Reverse 1 Reverse the sequence data of the current fasta sequence object and then returns the new created fasta object.
op_Implicit 1 Convert the specific feature data in Genbank database into a fasta sequence.
Complement 1 Gets the complement sequence data of a specific fasta sequence.(获取某一条核酸序列的互补序列)
SaveTo 2 Save the current fasta sequence object into the file system.
SaveAsOneLine 1 过长的序列不每隔60个字符进行一次换行,而是直接使用一行数据进行存储
Clone 1 Copy data to a new FASTA object.(将本对象的数据拷贝至一个新的FASTA序列对象中)
AddAttribute 1
InsertAttribute 1
RemoveAttribute 1
SetAttribute 1
ToLower 1
CopyTo 1
Copy 1
GenerateDocumentText 1
Save 1

03 Properties

NameOverloadsSummary
HaveGaps 1 Does this sequence contains some gaps?(这条序列之中是否包含有空格?)
Headers 1 The attribute header of this FASTA file.
SequenceData 1 The sequence data that contains in this FASTA file.
Length 1 Get the sequence length of this Fasta object.
Title 1 The first character ">" is not included in the title string data.
locus_tag 1 split the first token of the headers inside title as the unique reference id of current sequence object.

04 Fields

NameOverloadsSummary
metadata 1 方便通过Add接口)向Attribute列表中添加数据
DefaultHeaderDelimiter 2 NCBI style header delimiter
InvalidComplementSource 1 Data type miss match: the sequence information is a protein sequence, can not get complement sequence.
defaultTitleAttributes 1

05 Members

method .ctor #
#ctor(String)
Parameters
NameTypeDescription
pathString

File path of a fasta sequence.

method ToString #
ToString

Get the title of this fasta object.(返回FASTA对象的标题,在所返回的值之中不包含有fasta标题之中的第一个字符>)

method GrepTitle #
GrepTitle(TextGrepMethod)

You can using this function to convert the title from current format into another format.(使用这个方法将Fasta序列对象的标题从当前的格式转换为另外一种格式)

Parameters
NameTypeDescription
grepTextGrepMethod

-

method ToUpper #
ToUpper

Convert the FastaSeq.SequenceData to upper case and then return the new created FastaSeq.

method LoadNucleotideData #
LoadNucleotideData(String, Boolean)

Load the fasta sequence file as a nucleotide sequence from a specific path, the function will returns a null value if the sequence contains some non-nucleotide character. (从一条序列的FASTA文件之中加载一条核酸序列,当含有非法字符的时候,会返回空文件)

Parameters
NameTypeDescription
pathString

-

strictBoolean

当拥有空格数据的时候,假若参数为真,则会返回空文件,反之不会做任何处理

method Load #
Load(String, Char())

Load a single sequence fasta file object, if the target file path is not exists on the file system or the file format is not correct, then this function will returns a null object value. (这是一个安全的函数:从文件之中加载一条Fasta序列,当目标文件file不存在或者没有序列数据的时候,会返回空值)

Parameters
NameTypeDescription
fileString

目标序列文件的文件路径

method ParseFromStream #
ParseFromStream(IEnumerable(Of String), Char())

Parsing a fasta sequence object from a collection of string value.

Remarks

(从字符串数据之中解析出Fasta序列数据)

Parameters
NameTypeDescription
streamIEnumerable(Of String)

-

method TryParse #
TryParse(String, Char)

Try parsing a fasta sequence object from a string chunk value.

Remarks

(尝试从一个字符串之中解析出一个fasta序列数据)

Parameters
NameTypeDescription
sString

The string text value which is in the Fasta format.(FASTA格式的序列文本)

method GenerateDocument #
GenerateDocument(Int32, Boolean, Boolean, String)

Generate a FASTA file data text string.

Remarks

(将这个FASTA对象转换为文件格式以方便进行存储)

Parameters
NameTypeDescription
overridesInt32

是否使用FastaSeq.ToString()方法进行标题的复写,假若为假,则默认使用Attributes属性进行标题的生成, 因为在继承类之中可能会复写ToString函数以生成不同的标题格式,则可以使用这个参数来决定是否使用复写的格式。

lineBreakBoolean

大于0的数值会换行,小于或者等于0的数值不会换行

method SequenceLineBreak #
SequenceLineBreak(Int32, String)

break the input sequence string into multiple lines

Parameters
NameTypeDescription
lineBreakInt32

-

sequenceString

-

Returns

this function will returns empty string always if the given input sequence is empty or nothing.

method Equals #
Equals(Object)

The Fasta sequence equals on both sequence data and title information.(值比较来判断是否相等)

Parameters
NameTypeDescription
objObject

-

method CopyTo #
CopyTo``1(``0)

Copy the value in current fasta object into another fasta object.(将当前的序列数据复制到目标序列数据对象之中)

Type Parameters
NameDescription
TFasta

Fasta sequence object type.(目标序列数据类型)

Parameters
NameTypeDescription
FastaObject``0

The target fasta object will be copied to, if the value is null of this fasta object, then this function will generate a new fasta sequence object.(假若值为空,则会创建一个新的序列对象)

method Copy #
Copy``1

Copy the value to a new specific type fasta object.

Type Parameters
NameDescription
T

Type information of the target fasta object.

method Reverse #
Reverse

Reverse the sequence data of the current fasta sequence object and then returns the new created fasta object.

method op_Implicit #
op_Implicit(Feature)

Convert the specific feature data in Genbank database into a fasta sequence.

Parameters
NameTypeDescription
featureFeature

只是从这个特性对象之中得到蛋白质序列

method Complement #
Complement(FastaSeq)

Gets the complement sequence data of a specific fasta sequence.(获取某一条核酸序列的互补序列)

Parameters
NameTypeDescription
FASTAFastaSeq

The target fasta sequence object should be a nucleotide sequence, or this function will returns a null value. (目标FASTA对象必须为核酸序列,否则返回空值)

method SaveTo overload 2 #
SaveTo(String, Encoding)

Save the current fasta sequence object into the file system.

Parameters
NameTypeDescription
PathString

-

encodingEncoding

-

method SaveTo #
SaveTo(Int32, String, Encoding)

Save the current fasta sequence object into the file system. smaller than 1 will means no line break in the saved fasta sequence.

Parameters
NameTypeDescription
PathInt32

-

encodingString

-

method SaveAsOneLine #
SaveAsOneLine(String, Encoding)

过长的序列不每隔60个字符进行一次换行,而是直接使用一行数据进行存储

Parameters
NameTypeDescription
PathString

-

encodingEncoding

-

method Clone #
Clone

Copy data to a new FASTA object.(将本对象的数据拷贝至一个新的FASTA序列对象中)

property HaveGaps #
HaveGaps

Does this sequence contains some gaps?(这条序列之中是否包含有空格?)

property Headers #
Headers

The attribute header of this FASTA file. The fasta header usually have some format which can be parsed by some specific loader and gets some well organized information about the sequence. The format of the header is usually different between each biological database.

Remarks

(这个FASTA文件的属性头,标题的格式通常在不同的数据库之间是具有很大差异的)

property SequenceData #
SequenceData

The sequence data that contains in this FASTA file.

Remarks

(包含在这个FASTA文件之中的序列数据)

property Length #
Length

Get the sequence length of this Fasta object.

Remarks

(获取序列的长度)

property Title #
Title

The first character ">" is not included in the title string data.

Remarks

(标题之中是不包含有FASTA数据的第一个>字符的)

property locus_tag #
locus_tag

split the first token of the headers inside title as the unique reference id of current sequence object.

Returns

sequence id

field metadata #
metadata

方便通过Add接口向Attribute列表中添加数据

field DefaultHeaderDelimiter #
DefaultHeaderDelimiter

NCBI style header delimiter

field InvalidComplementSource #
InvalidComplementSource

Data type miss match: the sequence information is a protein sequence, can not get complement sequence.

field defaultTitleAttributes #
defaultTitleAttributes
field DefaultHeaderDelimiter overload 2 #
DefaultHeaderDelimiter
method AddAttribute #
AddAttribute(String)
method InsertAttribute #
InsertAttribute(String, Int32)
method RemoveAttribute #
RemoveAttribute(Int32)
method SetAttribute #
SetAttribute(Int32, String)
method ToLower #
ToLower()
method SequenceLineBreak overload 2 #
SequenceLineBreak(StringBuilder, Int32, String)
method CopyTo #
CopyTo(TFasta)
method Copy #
Copy()
method GenerateDocumentText #
GenerateDocumentText(IAbstractFastaToken)
method Save #
Save(String, Encodings)