373 lines
16 KiB
VB.net
373 lines
16 KiB
VB.net
#Region "Microsoft.VisualBasic::1b934dbc1d0d334500ccbc8997fed1dc, Microsoft.VisualBasic.Core\ComponentModel\Algorithm\Levenshtein\LevenshteinDistance.vb"
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' Author:
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'
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' asuka (amethyst.asuka@gcmodeller.org)
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' xie (genetics@smrucc.org)
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' xieguigang (xie.guigang@live.com)
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'
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' Copyright (c) 2018 GPL3 Licensed
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'
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'
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' GNU GENERAL PUBLIC LICENSE (GPL3)
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'
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'
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' This program is free software: you can redistribute it and/or modify
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' it under the terms of the GNU General Public License as published by
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' the Free Software Foundation, either version 3 of the License, or
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' (at your option) any later version.
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'
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' This program is distributed in the hope that it will be useful,
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' but WITHOUT ANY WARRANTY; without even the implied warranty of
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' MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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' GNU General Public License for more details.
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'
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' You should have received a copy of the GNU General Public License
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' along with this program. If not, see <http://www.gnu.org/licenses/>.
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' /********************************************************************************/
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' Summaries:
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' Module LevenshteinDistance
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'
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' Function: __createTable, __int32Equals, (+2 Overloads) ComputeDistance, CreateTable, GetVisulization
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' SaveMatch
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' Delegate Function
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'
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' Function: __computeRoute, (+2 Overloads) ComputeDistance, Similarity
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'
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'
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'
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' /********************************************************************************/
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#End Region
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Imports Microsoft.VisualBasic.CommandLine.Reflection
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Imports Microsoft.VisualBasic.ComponentModel.Algorithm
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Imports Microsoft.VisualBasic.ComponentModel.Algorithm.DynamicProgramming
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Imports Microsoft.VisualBasic.ComponentModel.DataStructures
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Imports Microsoft.VisualBasic.Linq.Extensions
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Imports Microsoft.VisualBasic.Net.Protocols
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Imports Microsoft.VisualBasic.Scripting.MetaData
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Imports Microsoft.VisualBasic.Text.Xml.Models
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Imports sys = System.Math
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Namespace Text.Levenshtein
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''' <summary>
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''' Levenshtein Edit Distance Algorithm for measure string distance
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''' </summary>
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''' <remarks>
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''' http://www.codeproject.com/Tips/697588/Levenshtein-Edit-Distance-Algorithm
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''' </remarks>
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'''
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<Package("Distance.Levenshtein",
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Description:="Implement the Levenshtein Edit Distance algorithm and result data visualization.",
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Publisher:="furkanavcu",
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Category:=APICategories.UtilityTools,
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Url:="http://www.codeproject.com/Tips/697588/Levenshtein-Edit-Distance-Algorithm")>
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<Cite(Title:="Binary codes capable of correcting deletions, insertions, and reversals",
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Pages:="707–710", StartPage:=707, Issue:="8", Volume:=10, Authors:="Levenshtein,
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Vladimir I",
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Journal:="Soviet Physics Doklady", Year:=1966)>
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Public Module LevenshteinDistance
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''' <summary>
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''' Creates distance table for data visualization
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''' </summary>
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''' <param name="reference"></param>
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''' <param name="hypotheses"></param>
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''' <param name="cost"></param>
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''' <returns></returns>
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Private Function __createTable(reference As Integer(), hypotheses As Integer(), cost As Double) As Double(,)
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Return CreateTable(Of Integer)(reference, hypotheses, DynamicProgramming.Cost(Of Integer).DefaultCost(cost), AddressOf __int32Equals)
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End Function
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Private Function __int32Equals(a As Integer, b As Integer) As Boolean
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Return a = b
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End Function
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''' <summary>
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''' 用于泛型的序列相似度比较
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''' </summary>
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''' <typeparam name="T"></typeparam>
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''' <param name="reference"></param>
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''' <param name="hypotheses"></param>
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''' <param name="cost"></param>
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''' <param name="equals">泛型化的元素等价性的比较方法</param>
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''' <returns></returns>
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Public Function CreateTable(Of T)(reference As T(), hypotheses As T(), cost As Cost(Of T), equals As GenericLambda(Of T).IEquals) As Double(,)
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Dim distTable As Double(,) = New Double(reference.Length, hypotheses.Length) {}
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For i As Integer = 0 To reference.Length - 1
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distTable(i, 0) = i * cost.insert(reference(i))
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Next
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For j As Integer = 0 To hypotheses.Length - 1
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distTable(0, j) = j * cost.delete(hypotheses(j))
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Next
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distTable(reference.Length, 0) = cost.insert(Nothing)
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distTable(0, hypotheses.Length) = cost.delete(Nothing)
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'd[i,j] <- min( d[i-1,j] + delete.fun(source.vec[i-1]),
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'd[i,j-1] + insert.fun(target.vec[j-1]),
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'd[i-1,j-1] + substitute.fun(source.vec[i-1], target.vec[j-1]) );
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For i As Integer = 1 To reference.Length
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For j As Integer = 1 To hypotheses.Length
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If equals(reference(i - 1), hypotheses(j - 1)) Then
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' if the letters are same
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distTable(i, j) = distTable(i - 1, j - 1)
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Else ' if not add 1 to its neighborhoods and assign minumun of its neighborhoods
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Dim n As Double = sys.Min(
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distTable(i - 1, j - 1) + cost.substitute(reference(i - 1), hypotheses(j - 1)),
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distTable(i - 1, j) + cost.delete(reference(i - 1)))
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distTable(i, j) = sys.Min(n, distTable(i, j - 1) + cost.insert(hypotheses(j - 1)))
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End If
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Next
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Next
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Return distTable
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End Function
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''' <summary>
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''' 泛型序列的相似度的比较计算方法，这个函数返回的是距离
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''' </summary>
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''' <typeparam name="T"></typeparam>
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''' <param name="reference"></param>
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''' <param name="hypotheses"></param>
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''' <param name="equals"></param>
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''' <param name="cost"></param>
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''' <returns></returns>
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Public Function ComputeDistance(Of T)(reference As T(), hypotheses As T(), equals As GenericLambda(Of T).IEquals, Optional cost As Double = 0.7) As Double
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If hypotheses Is Nothing Then hypotheses = New T() {}
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If reference Is Nothing Then reference = New T() {}
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Dim distTable#(,) = CreateTable(Of T)(reference, hypotheses, DynamicProgramming.Cost(Of T).DefaultCost(cost), equals)
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Dim i As Integer = reference.Length, j As Integer = hypotheses.Length
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Return distTable(i, j)
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End Function
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''' <summary>
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''' 泛型序列的相似度的比较计算方法，这个会返回所有的数据
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''' </summary>
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''' <typeparam name="T"></typeparam>
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''' <param name="reference"></param>
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''' <param name="hypotheses"></param>
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''' <param name="equals"></param>
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''' <param name="asChar">这个只是用于进行显示输出的</param>
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''' <param name="cost"></param>
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''' <returns></returns>
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Public Function ComputeDistance(Of T)(reference As T(), hypotheses As T(), equals As GenericLambda(Of T).IEquals, asChar As ToChar(Of T), Optional cost As Double = 0.7) As DistResult
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If hypotheses Is Nothing Then hypotheses = New T() {}
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If reference Is Nothing Then reference = New T() {}
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Dim distTable#(,) = CreateTable(Of T)(reference, hypotheses, DynamicProgramming.Cost(Of T).DefaultCost(cost), equals)
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Dim i As Integer = reference.Length,
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j As Integer = hypotheses.Length
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Dim sHyp As String = New String(hypotheses.Select(Function(x) asChar(x)).ToArray)
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Dim sRef As String = New String(reference.Select(Function(x) asChar(x)).ToArray)
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Dim result As New DistResult With {
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.Hypotheses = sHyp,
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.Reference = sRef
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}
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Return __computeRoute(sHyp, result, i, j, distTable)
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End Function
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<ExportAPI("ToHTML", Info:="View distance evolve route of the Levenshtein Edit Distance calculation.")>
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Public Function GetVisulization(res As DistResult) As String
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Return res.HTMLVisualize
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End Function
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<ExportAPI("Write.Xml.DistResult")>
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Public Function SaveMatch(result As DistResult, SaveTo As String) As Boolean
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Return result.GetXml.SaveTo(SaveTo)
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End Function
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Public Delegate Function ToChar(Of T)(x As T) As Char
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''' <summary>
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''' Implement the Levenshtein Edit Distance algorithm between string.
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''' </summary>
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''' <param name="reference">The reference string ASCII cache.</param>
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''' <param name="hypotheses"></param>
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''' <param name="cost"></param>
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''' <returns></returns>
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<ExportAPI("ComputeDistance", Info:="Implement the Levenshtein Edit Distance algorithm.")>
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Public Function ComputeDistance(reference As Integer(), hypotheses As String, Optional cost As Double = 0.7) As DistResult
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If hypotheses Is Nothing Then hypotheses = ""
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If reference Is Nothing Then reference = New Integer() {}
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Dim distTable#(,) = __createTable(reference,
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hypotheses.Select(Function(ch) Asc(ch)).ToArray,
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cost)
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Dim i As Integer = reference.Length,
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j As Integer = hypotheses.Length
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Dim result As New DistResult With {
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.Hypotheses = hypotheses,
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.Reference = Nothing
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}
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Return __computeRoute(hypotheses, result, i, j, distTable)
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End Function
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Const a As Integer = Asc("a"c)
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Public Function Similarity(Of T)(query As T(), subject As T(), Optional penalty As Double = 0.75) As Double
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If query.IsNullOrEmpty OrElse subject.IsNullOrEmpty Then
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Return 0
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End If
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Dim distinct As T() =
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(New [Set](query) + New [Set](subject)) _
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.ToArray _
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.Select(Function(x) DirectCast(x, T)) _
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.ToArray
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Dim dict = (From index As Integer
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In distinct.Sequence(offSet:=a)
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Select ch = ChrW(index),
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obj = distinct(index - a)) _
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.ToDictionary(Function(x) x.obj,
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Function(x) x.ch)
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Dim ref As String = New String(query.Select(Function(x) dict(x)).ToArray)
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Dim sbj As String = New String(subject.Select(Function(x) dict(x)).ToArray)
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If String.IsNullOrEmpty(ref) OrElse String.IsNullOrEmpty(sbj) Then
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Return 0
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End If
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Dim result As DistResult = ComputeDistance(ref, sbj, penalty)
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If result Is Nothing Then
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Return 0
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Else
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Return result.Score
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End If
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End Function
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''' <summary>
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''' 计算lev编辑的变化路径
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''' </summary>
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''' <param name="hypotheses"></param>
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''' <param name="result"></param>
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''' <param name="i"></param>
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''' <param name="j"></param>
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''' <param name="distTable"></param>
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''' <returns></returns>
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Private Function __computeRoute(hypotheses$,
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result As DistResult,
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i%, j%,
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distTable#(,)) As DistResult
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Dim css As New List(Of Coordinate)
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Dim evolve As List(Of Char) = New List(Of Char)
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Dim edits As New List(Of Char)
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While True
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Call css.Add({i - 1, j})
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If i = 0 AndAlso j = 0 Then
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Dim evolveRoute As Char() = evolve.ToArray
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Call Array.Reverse(evolveRoute)
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Call css.Add({i, j})
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result.DistTable = distTable _
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.ToVectorList _
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.Select(Function(vec) New Streams.Array.Double With {
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.Values = vec
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}) _
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.ToArray
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result.DistEdits = New String(evolveRoute)
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result.Path = css.ToArray
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result.Matches = New String(edits.ToArray.Reverse.ToArray)
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Exit While
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ElseIf i = 0 AndAlso j > 0 Then ' delete
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Call evolve.Add("d"c)
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Call css.Add({i - 1, j})
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Call edits.Add("-"c)
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j -= 1
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ElseIf i > 0 AndAlso j = 0 Then
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Call evolve.Add("i"c) ' insert
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Call css.Add({i - 1, j})
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Call edits.Add("-"c)
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i -= 1
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Else
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If distTable(i - 1, j - 1) <= distTable(i - 1, j) AndAlso
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distTable(i - 1, j - 1) <= distTable(i, j - 1) Then
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Call css.Add({i - 1, j})
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If distTable(i - 1, j - 1) = distTable(i, j) Then
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Call evolve.Add("m"c) ' match
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Call edits.Add(hypotheses(j - 1))
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Else
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Call evolve.Add("s"c) ' substitue
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Call edits.Add("-"c)
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End If
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i -= 1
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j -= 1
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ElseIf distTable(i - 1, j) < distTable(i, j - 1) Then
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Call css.Add({i - 1, j})
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Call evolve.Add("i") ' insert
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Call edits.Add("-"c)
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i -= 1
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ElseIf distTable(i, j - 1) < distTable(i - 1, j) Then
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Call css.Add({i - 1, j})
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Call evolve.Add("d") ' delete
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Call edits.Add("-"c)
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j -= 1
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End If
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End If
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If css.Count > 1024 AndAlso css.Count - evolve.Count > 128 Then
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' Call $"{reference} ==> {hypotheses} stack could not be solve, operation abort!".__DEBUG_ECHO
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Return Nothing
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End If
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End While
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Return result
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End Function
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''' <summary>
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''' The edit distance between two strings is defined as the minimum number of
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''' edit operations required to transform one string into another.
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''' (请注意，这函数是大小写敏感的。如果需要大小写不敏感，在使用前，请先将函数的两个字符串参数都转换为小写形式)
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''' </summary>
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''' <param name="reference"></param>
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''' <param name="hypotheses"></param>
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''' <param name="cost"></param>
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''' <returns></returns>
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<ExportAPI("ComputeDistance", Info:="Implement the Levenshtein Edit Distance algorithm.")>
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Public Function ComputeDistance(reference$, hypotheses$, Optional cost# = 0.7) As DistResult
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If hypotheses Is Nothing Then hypotheses = ""
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If reference Is Nothing Then reference = ""
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Dim distTable As Double(,) = __createTable(
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reference.Select(Function(ch) AscW(ch)).ToArray,
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hypotheses.Select(Function(ch) AscW(ch)).ToArray,
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cost)
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Dim i As Integer = reference.Length,
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j As Integer = hypotheses.Length
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Dim result As New DistResult With {
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.Hypotheses = hypotheses,
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.Reference = reference
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}
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Return __computeRoute(hypotheses, result, i, j, distTable)
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End Function
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End Module
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End Namespace
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