ComparativeAlignment

Full name SMRUCC.genomics.Visualize.SyntenyVisualize.ComparativeAlignment.ComparativeAlignment Assembly SMRUCC.genomics.Visualize.SyntenyVisualize Members 4

01 Syntax

SMRUCC.genomics.Visualize.SyntenyVisualize.ComparativeAlignment.ComparativeAlignment

02 Methods

Name	Overloads	Summary
InvokeDrawing	1	If the parameter color_overrides is not null then all of the gene color will overrides the cog color as the parameter specific color.
BuildMultipleAlignmentModel	1	source is for the bbh besthit output directory, query is the query genome id or query fasta filename, ppt is a directory which stores the ptt file of the bbh genomes, query_nt i…
TCSVisualization	1	对双组分系统进行颜色赋值，其他的基因不变
BuildModel	1	Build the comparative drawing model from the ncbi ptt source.

03 Members

method InvokeDrawing #

InvokeDrawing(DrawingModel, Color, Boolean, Boolean, String)

If the parameter color_overrides is not null then all of the gene color will overrides the cog color as the parameter specific color.

Remarks

(绘制对比对图)

Parameters

Name	Type	Description
`model`	DrawingModel	-
`defaultColor`	`Color`	-
`type2Arrow`	`Boolean`	-

method BuildMultipleAlignmentModel #

BuildMultipleAlignmentModel(String, String, String, String, FastaSeq, IEnumerable(Of GeneTable))

source is for the bbh besthit output directory, query is the query genome id or query fasta filename, ppt is a directory which stores the ptt file of the bbh genomes, query_nt is using for the gcshew calculation visualize.

Parameters

Name	Type	Description
`source`	`String`	bbh结果的文件夹
`query`	`String`	query的编号
`PTT`	`String`	存放多个物种的ptt文件的文件夹

method TCSVisualization #

TCSVisualization(DrawingModel, Color, Color, Color)

对双组分系统进行颜色赋值，其他的基因不变

Parameters

Name	Type	Description
`model`	DrawingModel	-

method BuildModel #

BuildModel(DataFrameResolver, IEnumerable(Of String), IEnumerable(Of String), String, Boolean, Boolean)

Build the comparative drawing model from the ncbi ptt source. (数据框之中的每一行数据都表示同源基因，列表示为基因组)

Parameters

Name	Type	Description
`DF`	`DataFrameResolver`	生成GeneLink数据
`ColumnList`	`IEnumerable(Of String)`	假若本参数值为空，则默认取出所有的数据
`PttSource`	`IEnumerable(Of String)`	请注意，这个值的顺序是与数据框之中的列是一一对应的