FastaFile

namespace: SMRUCC.genomics.SequenceModel.FASTA

A FASTA file that contains multiple sequence data.
(一个包含有多条序列数据的FASTA文件)

Methods

#ctor

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.#ctor(System.Collections.Generic.IEnumerable{SMRUCC.genomics.SequenceModel.FASTA.FastaToken})

构造函数会自动移除空值对象

Parameter Name Remarks
data -

AppendToFile

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.AppendToFile(System.String)
Parameter Name Remarks
file

The target FASTA file that to append this FASTA sequences.(将要拓展这些FASTA序列的目标FASTA文件)
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Distinct

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.Distinct

Get a new fasta2 object which is been clear the duplicated records in the collection.
(获取去除集合中的重复的记录新列表,原有列表中数据未被改变)

FlushData

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.FlushData

Clear the sequence data in this fasta file.

Generate

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.Generate

在写入数据到文本文件之前需要将目标对象转换为文本字符串

LoadNucleotideData

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.LoadNucleotideData(System.String,System.Boolean)

加载一个FASTA序列文件并检查其中是否全部为核酸序列数据,假若不是,则会将该序列移除

Parameter Name Remarks
path -

Match

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.Match(System.String,System.Text.RegularExpressions.RegexOptions)

使用正则表达式来搜索在序列中含有特定模式的序列对象

Parameter Name Remarks
regxText -

ParseDocument

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.ParseDocument(System.String)

Try parsing a fasta file object from the text file content doc

Parameter Name Remarks
doc The file data content in the fasta file, not the path of the fasta file!

Query

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.Query(System.String,Microsoft.VisualBasic.CompareMethod)
Parameter Name Remarks
KeyWord A key string that to search in this fasta file.
CaseSensitive For text compaired method that not case sensitive, otherwise in the method od binary than case sensitive.

QueryAny

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.QueryAny(System.String,Microsoft.VisualBasic.CompareMethod)
Parameter Name Remarks
KeyWord A key string that to search in this fasta file.
CaseSensitive For text compaired method that not case sensitive, otherwise in the method od binary than case sensitive.

Read

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.Read(System.String,System.Boolean)

Load the fasta file from the local filesystem.

Parameter Name Remarks
File -
Explicit 当参数为真的时候,目标文件不存在则会抛出错误,反之则会返回一个空文件

Save

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.Save(System.Int32,System.String,System.Text.Encoding)

Save the fasta file into the local filesystem.

Parameter Name Remarks
Path -
encoding 不同的程序会对这个由要求,例如meme程序在linux系统之中要求序列文件为unicode编码格式而windows版本的meme程序则要求ascii格式

SaveData``1

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SMRUCC.genomics.SequenceModel.FASTA.FastaFile.SaveData``1(System.Collections.Generic.IEnumerable{``0},System.String,System.Text.Encoding)

可以使用这个方法来作为通用的继承与fasta对象的集合的序列的数据保存工作

Parameter Name Remarks
data -
path -
encoding -

Properties

FilePath

本FASTA数据文件对象的文件位置