nysol-take 3.0.0 → 3.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: e30036a31f3107df33aae6da18928c97c03ce52d
-  data.tar.gz: b2bc758258baffa71e8a76c75299e24458357d44
+SHA256:
+  metadata.gz: a2753f4a5688ae9282382023020a2e10ec12029e98a7aad35ef6cf21f7197053
+  data.tar.gz: ff30c45b9deec28f3f209d8171af001a4aeed53b78320845b534600f910a85fb
 SHA512:
-  metadata.gz: e1d5c04b64285de5052506231838b388a83e5258b9d015e28beece15c7129e044aefc910ffe80ec9b09c98462077e331aa36ac9dcd437c1b86e7ecf21fbda861
-  data.tar.gz: 3bb9949747aa25c85c272347bf3d84ab1d25f03b8410ba5417d97e9e288e7eb3d35eabc550ece20182e6e3dd9e51e81286d9c55b01751b12cb90c74a18d1801d
+  metadata.gz: 45950f53a25a8c36cebefe965af85b3070e75d0044a9fe8eaeeaa1aa5e0cc9c499990fb2009d7cfb8095ec8fc08090bf33295415ba852838b9788e11f5c9af01
+  data.tar.gz: 62b0116f86a64fd5e27216c02effdda7fcb3ec12d64032ccae42ffe455ee63659e98be3377cce05c5dfe211604c3b9e5fad3378d6489e2ab48f3e85c05f424f8

data/bin/mbiclique.rb

@@ -229,7 +229,6 @@ pair2tra(ei,ef1,ef2,xxtra,xxmap1,xxmap2)
 
 # 利用コマンドファイル名
 #CMD="lcm_20140215"
-#{TAKE::LcmIs::CMD} 
 
 run=""
 run << "#{type}If"

data/bin/mccomp.rb

@@ -6,7 +6,7 @@ require "nysol/mcmd"
 
 # 1.0 initial development: 2016/10/17
 # 1.1 出力のnode項目名をnf=の値にする: 2016/11/11
-$cmd="mccomp2g.rb"
+$cmd="mccomp.rb"
 $version="1.1"
 
 def help

data/bin/mitemset.rb

@@ -75,7 +75,7 @@ end
 help() if ARGV.size <= 0 or ARGV[0]=="--help"
 ver() if ARGV[0]=="--version"
 
-args=MCMD::Margs.new(ARGV,"i=,x=,O=,tid=,item=,class=,taxo=,type=,s=,S=,sx=,Sx=,g=,p=,-uniform,l=,u=,top=,T=,-replaceTaxo")
+args=MCMD::Margs.new(ARGV,"i=,x=,O=,tid=,item=,class=,taxo=,type=,s=,S=,sx=,Sx=,g=,p=,-uniform,l=,u=,top=,T=,-replaceTaxo,-q")
 
 # コマンド実行可能確認
 #exit(1) unless(MCMD::chkCmdExe(TAKE::LcmIs::CMD      , "executable"))
@@ -105,6 +105,8 @@ itemFN = itemFN["names"].join(",") if itemFN
 clsFN  = clsFN["names"].join(",")  if clsFN
 taxoFN = taxoFN["names"].join(",") if taxoFN
 
+sortInfo = args.bool("-q") 
+
 eArgs=Hash.new
 eArgs["type"   ] = args.  str("type=","F" )
 eArgs["minSup" ] = args.float("s="   ,0.05 ,0  ,1      ) # 最小サポート
@@ -160,7 +162,7 @@ end
 
 # 出力
 system("mkdir -p #{outPath}")
-lcm.output(outPath)
+lcm.output(outPath,sortInfo)
 
 MCMD::msgLog("The final results are in the directory `#{outPath}'")
 

data/bin/msequence.rb

@@ -74,7 +74,7 @@ end
 
 help() if ARGV.size <= 0 or ARGV[0]=="--help"
 ver() if ARGV[0]=="--version"
-args=MCMD::Margs.new(ARGV,"i=,c=,x=,O=,tid=,time=,item=,class=,taxo=,s=,S=,sx=,Sx=,g=,p=,-uniform,l=,u=,top=,gap=,win=,-padding,T=,-mcmdenv")
+args=MCMD::Margs.new(ARGV,"i=,c=,x=,O=,tid=,time=,item=,class=,taxo=,s=,S=,sx=,Sx=,g=,p=,-uniform,l=,u=,top=,gap=,win=,-padding,T=,-mcmdenv,-m,-c,-q")
 
 # lcm_seqコマンド実行可能確認
 #exit(1) unless(MCMD::chkCmdExe(TAKE::LcmSeq::CMD      , "executable"))
@@ -106,6 +106,9 @@ itemFN = itemFN["names"].join(",") if itemFN
 clsFN  = clsFN["names"].join(",")  if clsFN
 taxoFN = taxoFN["names"].join(",") if taxoFN
 
+sortInfo =  args.bool("-q") 
+
+
 eArgs=Hash.new
 eArgs["minSup" ] = args.float("s="   ,0.05 ,0,1    ) # 最小サポート
 eArgs["minCnt" ] = args.  int("S="   ,nil  ,1,nil  ) # 最小サポート件数
@@ -120,6 +123,13 @@ eArgs["gap"    ] = args.  int("gap=" ,nil  ,0,nil  ) # gap長上限限
 eArgs["win"    ] = args.  int("win=" ,nil  ,0,nil  ) # win size上限限
 eArgs["padding"] = args. bool("-padding") # 0item ommit
 eArgs["top"    ] = args.  int("top=" ,nil,0)
+eArgs["exM"] = args. bool("-m") # extension maximal patterns only
+eArgs["exC"] = args. bool("-c") # extension closed patterns only
+
+
+if eArgs["exM"] and eArgs["exC"] then
+	raise "-m cannot be specified with -c"
+end
 
 if eArgs["minLen"] and eArgs["maxLen"]
 	if eArgs["minLen"] > eArgs["maxLen"] then
@@ -156,7 +166,7 @@ end
 
 # 出力
 system("mkdir -p #{outPath}")
-lcm.output(outPath)
+lcm.output(outPath,sortInfo)
 
 MCMD::msgLog("The final results are in the directory `#{outPath}'")
 

data/bin/mtra2g.rb

@@ -340,7 +340,7 @@ eArgs["nomodel"] = true
 # クラスありパターン列挙
 if clsFN then
 	# ノードはクラス関係なく全体でfrequentな2アイテムセットを求める
-	lcm=TAKE::LcmIs.new(db);
+	lcm=TAKE::LcmIs.new(db,false);
 	eArgs["minLen"] = 1
 	eArgs["maxLen"] = 1
 	if node_support
@@ -371,7 +371,7 @@ if clsFN then
 	eArgs["minSup"] = minSup
 	eArgs["minCnt"] = minCnt
 
-	lcm=TAKE::LcmEp.new(db);
+	lcm=TAKE::LcmEp.new(db,false);
 	lcm.enumerate(eArgs)
 	# system "head #{lcm.pFile}"
 	# class%0nr,pid,pattern,size,pos%2nr,neg,posTotal,negTotal,total,support,growthRate,postProb%1nr
@@ -410,7 +410,7 @@ if clsFN then
 
 # クラスなしパターン列挙
 else
-	lcm=TAKE::LcmIs.new(db);
+	lcm=TAKE::LcmIs.new(db,false);
 	# 1 itemset
 	eArgs["minLen" ] = 1
 	eArgs["maxLen" ] = 1

data/ext/grhfilrun/extconf.rb

@@ -3,9 +3,9 @@ require "mkmf"
 
 
 cp = "$(srcdir)"
-$CFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CPPFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CXXFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
+$CFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC  -Wno-reserved-user-defined-literal  -Wc++11-narrowing -Wno-error=format-security"
+$CPPFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC  -Wno-reserved-user-defined-literal  -Wc++11-narrowing -Wno-error=format-security"
+$CXXFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC  -Wno-reserved-user-defined-literal  -Wc++11-narrowing -Wno-error=format-security"
 
 
 create_makefile("nysol/grhfilrun")

data/ext/lcmrun/extconf.rb

@@ -10,9 +10,9 @@ end
 
 cp = "$(srcdir)"
 
-$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
+$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing  -Wno-error=format-security"
+$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing  -Wno-error=format-security"
 
 $LOCAL_LIBS += " -lstdc++ -lkgmod3"
 

data/ext/lcmrun/lcmrun.cpp

@@ -5,9 +5,9 @@
 #include <sys/stat.h>
 #include <string>
 #include <ruby.h>
-
+namespace {
 #include "src/lcm.c"
-
+}
 
 #include <kgMethod.h>
 

data/ext/lcmseq0run/extconf.rb

@@ -10,9 +10,9 @@ end
 
 cp = "$(srcdir)"
 
-$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
+$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
 
 $LOCAL_LIBS += " -lstdc++ -lkgmod3"
 

data/ext/lcmseq0run/lcmseq0run.cpp

@@ -5,9 +5,9 @@
 #include <sys/stat.h>
 #include <string>
 #include <ruby.h>
-
+namespace {
 #include "src/lcm_seq_zero.c"
-
+}
 
 #include <kgMethod.h>
 

data/ext/lcmseqrun/extconf.rb

@@ -10,9 +10,9 @@ end
 
 cp = "$(srcdir)"
 
-$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
+$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
 
 $LOCAL_LIBS += " -lstdc++ -lkgmod3"
 

data/ext/lcmseqrun/lcmseqrun.cpp

@@ -5,9 +5,9 @@
 #include <sys/stat.h>
 #include <string>
 #include <ruby.h>
-
+namespace {
 #include "src/lcm_seq.c"
-
+}
 
 #include <kgMethod.h>
 

data/ext/macerun/extconf.rb

@@ -10,9 +10,9 @@ end
 
 cp = "$(srcdir)"
 
-$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
+$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
 
 $LOCAL_LIBS += " -lstdc++ -lm -lkgmod3"
 

data/ext/macerun/macerun.cpp

@@ -6,8 +6,9 @@
 #include <string>
 #include <ruby.h>
 
+namespace {
 #include "src/mace.c"
-
+}
 
 #include <kgMethod.h>
 

data/ext/sspcrun/extconf.rb

@@ -10,9 +10,9 @@ end
 
 cp = "$(srcdir)"
 
-$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
-$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
+$CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
+$CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src  -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-reserved-user-defined-literal -Wno-c++11-narrowing -Wno-error=format-security"
 
 $LOCAL_LIBS += " -lstdc++ -lkgmod3 -lm"
 

data/ext/sspcrun/sspcrun.cpp

@@ -5,12 +5,13 @@
 #include <sys/stat.h>
 #include <string>
 #include <ruby.h>
+// sspc Core
+namespace{
 #include "src/sspc.c"
+}
 #include <kgMethod.h>
 
-extern "C" {
-	void Init_sspcrun(void);
-}
+
 
 VALUE sspcrun(VALUE self,VALUE argvV){
 
@@ -41,6 +42,10 @@ VALUE sspcrun(VALUE self,VALUE argvV){
 }
 
 
+extern "C" {
+	void Init_sspcrun(void);
+}
+
 // -----------------------------------------------------------------------------
 // ruby Mcsvin クラス init
 // -----------------------------------------------------------------------------

data/lib/nysol/enumLcmEp.rb

@@ -29,7 +29,7 @@ class LcmEp
 	def calSigma(minPos,minGR,posCnt,negCnt)
 		omegaF=@@intMax.to_f/posCnt.to_f
 		beta=minPos
-		w=posCnt.to_f/negCnt.to_f
+		w=negCnt.to_f/posCnt.to_f
 #puts "omegaF=#{omegaF}"
 #puts "minPos=#{minPos}"
 #puts "beta=#{beta}"
@@ -76,11 +76,12 @@ class LcmEp
 		return pat
 	end
 
-	def initialize(db)
+	def initialize(db,outtf=true)
 		@temp=MCMD::Mtemp.new
 		@db      = db         # 入力データベース
 		@file=@temp.file
 		items=@db.items
+		@outtf = outtf
 
 		# 重みファイルの作成
 		# pos,negのTransactionオブジェクトに対してLCMが扱う整数アイテムによるトランザクションファイルを生成する。
@@ -165,11 +166,10 @@ class LcmEp
 				if eArgs["maxSup"].class.name=="Hash"
 					@maxPos = (eArgs["maxSup"][cName] * posSize.to_f + 0.99).to_i
 				else
-					p posSize
 					@maxPos = (eArgs["maxSup"] * posSize.to_f + 0.99).to_i
 				end
 			else
-				@maxPos = posSize.to_f
+				@maxPos = nil
 			end
 
 			@sigma[cName] = calSigma(@minPos,@minGR,posSize,negSize)
@@ -180,9 +180,14 @@ class LcmEp
 			# そのときのために空ファイルを生成しておいく。
 			system("touch #{lcmout}")
 
+			if @maxPos then
+				@maxPos = calSigma(@maxPos,@minGR,posSize,negSize)
+			end
+
 			run=""
 			run << "#{eArgs["type"]}IA"
-			run << " -U #{@maxCnt}"         if @maxCnt # windowサイズ上限
+			run << " -U #{@maxPos}"         if @maxPos # windowサイズ上限
+			#もともと ^^ @maxCntだったがどこにも設定されていないかかったので@maxPosにしとく問題有れば変更
 			run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
 			run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
 			run << " -w #{@weightFile[cName]} #{@file} #{@sigma[cName]} #{lcmout}"
@@ -196,7 +201,6 @@ class LcmEp
 #system("cp #{@file} xxtra_#{cName}")
 #system("cp #{@weightFile[cName]} xxw_#{cName}")
 #system("echo '#{run}' >xxscp_#{cName}")
-
 			# パターンのサポートを計算しCSV出力する
 			MCMD::msgLog("output patterns to CSV file ...")
 			pFiles << @temp.file
@@ -219,28 +223,30 @@ class LcmEp
 			s = MCMD::mrecount("i=#{pFiles.last}") # 列挙されたパターンの数
 			MCMD::msgLog("the number of contrast patterns on class `#{cName}' enumerated is #{s}")
 
-			# トランザクション毎に出現するパターンを書き出す
-			MCMD::msgLog("output tid-patterns ...")
-			tFiles << @temp.file
-
-			xxw= tf.file
-			f=""
-			f << "mcut    f=#{@db.idFN}                  i=#{@db.file} |"
-			f << "muniq   k=#{@db.idFN}                  |"
-			f << "mnumber S=0 a=__tid -q                 |"
-			f << "msortf  f=__tid                        o=#{xxw};"
-			system(f)
-
-			translt = @temp.file
-			TAKE::run_lcmtrans(lcmout,"t",translt)
-
-			f=""
-			#f << "lcm_trans #{lcmout} t |" #__tid,pid
-			f << "msortf   f=__tid i=#{translt}           |"
-			f << "mjoin    k=__tid m=#{xxw} f=#{@db.idFN} |"
-			f << "msetstr  v=#{cName} a=class             |"
-			f << "mcut     f=#{@db.idFN},class,pid        o=#{tFiles.last}"
-			system(f)
+			if @outtf then
+				# トランザクション毎に出現するパターンを書き出す
+				MCMD::msgLog("output tid-patterns ...")
+				tFiles << @temp.file
+
+				xxw= tf.file
+				f=""
+				f << "mcut    f=#{@db.idFN}                  i=#{@db.file} |"
+				f << "muniq   k=#{@db.idFN}                  |"
+				f << "mnumber S=0 a=__tid -q                 |"
+				f << "msortf  f=__tid                        o=#{xxw};"
+				system(f)
+
+				translt = @temp.file
+				TAKE::run_lcmtrans(lcmout,"t",translt)
+
+				f=""
+				#f << "lcm_trans #{lcmout} t |" #__tid,pid
+				f << "msortf   f=__tid i=#{translt}           |"
+				f << "mjoin    k=__tid m=#{xxw} f=#{@db.idFN} |"
+				f << "msetstr  v=#{cName} a=class             |"
+				f << "mcut     f=#{@db.idFN},class,pid        o=#{tFiles.last}"
+				system(f)
+			end
 		}
 
 		# クラス別のパターンとtid-pidファイルを統合して最終出力
@@ -314,24 +320,33 @@ class LcmEp
 		f << "msortf  f=class,pid o=#{xxp4}"
 		system(f)
 
-		# tid-pidファイル計算
-		f=""
-		f << "mcat                                       i=#{tFiles.join(",")} |"
-		f << "msortf  f=class,pid                        |"
-		f << "mjoin   k=class,pid m=#{xxpCat} f=ppid     |" # 全クラス統一pid(ppid)結合
-		f << "msortf  f=class,ppid                       |"
-		f << "mcommon k=class,ppid K=class,pid m=#{xxp4} |" # 列挙されたパターンの選択
-		f << "mcut    f=#{@db.idFN},class,ppid:pid       |"
-		f << "msortf  f=#{@db.idFN},class,pid            o=#{@tFile}"
-		system(f)
+		if @outtf then
+			# tid-pidファイル計算
+			f=""
+			f << "mcat                                       i=#{tFiles.join(",")} |"
+			f << "msortf  f=class,pid                        |"
+			f << "mjoin   k=class,pid m=#{xxpCat} f=ppid     |" # 全クラス統一pid(ppid)結合
+			f << "msortf  f=class,ppid                       |"
+			f << "mcommon k=class,ppid K=class,pid m=#{xxp4} |" # 列挙されたパターンの選択
+			f << "mcut    f=#{@db.idFN},class,ppid:pid       |"
+			f << "msortf  f=#{@db.idFN},class,pid            o=#{@tFile}"
+			system(f)
+		end
 
 		@size = MCMD::mrecount("i=#{@pFile}") # 列挙されたパターンの数
 		MCMD::msgLog("the number of emerging patterns enumerated is #{@size}")
 	end
 
-  def output(outpath)
-		system "mv #{@pFile} #{outpath}/patterns.csv"
-		system "mv #{@tFile} #{outpath}/tid_pats.csv"
+  def output(outpath,rmsinfo)
+  	if rmsinfo then
+			system "mfldname i=#{@pFile} -q o=#{outpath}/patterns.csv"
+			system "mfldname i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
+		else
+			system "mv #{@pFile} #{outpath}/patterns.csv"
+			system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
+		end
+
+
 	end
 end
 

data/lib/nysol/enumLcmEsp.rb

@@ -49,11 +49,12 @@ class LcmEsp
 	#	return lcmq*minSup.to_f*negCnt.to_f/minGR.to_f/(1-lcmq)
 	#end
 
-	def initialize(db)
+	def initialize(db,outtf=true)
 		@temp=MCMD::Mtemp.new
 		@db      = db         # 入力データベース
 		@file=@temp.file
 		items=@db.items
+		@outtf = outtf
 
 		# 重みファイルの作成
 		# pos,negのTransactionオブジェクトに対してLCMが扱う整数アイテムによるトランザクションファイルを生成する。
@@ -149,6 +150,10 @@ class LcmEsp
  					@maxCnt = (eArgs["maxSup"] * posSize.to_f + 0.99).to_i
 				end
 			end
+			@addTP = ""		
+			@addTP = "m" if eArgs["exM"]
+			@addTP = "c" if eArgs["exC"]
+
 
 			@sigma[cName] = calSigma(@minPos,@minGR,posSize,negSize)
 
@@ -157,8 +162,12 @@ class LcmEsp
 			# 頻出パターンがなかった場合、lcm出力ファイルが生成されないので
 			# そのときのために空ファイルを生成しておいく。
 			system("touch #{lcmout}")
+			
+			if @maxCnt then
+				@maxCnt = calSigma(@maxCnt,@minGR,posSize,negSize)
+			end
 
-			run="CIA"
+			run="CIA#{@addTP}"
 			run << " -U #{@maxCnt}"         if @maxCnt # windowサイズ上限
 			run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
 			run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
@@ -195,27 +204,29 @@ class LcmEsp
 			s = MCMD::mrecount("i=#{pFiles.last}") # 列挙されたパターンの数
 			MCMD::msgLog("the number of contrast patterns on class `#{cName}' enumerated is #{s}")
 
-			# トランザクション毎に出現するシーケンスを書き出す
-			MCMD::msgLog("output tid-patterns ...")
-			tFiles << @temp.file
-
-			xxw= tf.file
-			f=""
-			f << "mcut    f=#{@db.idFN} i=#{@db.file} |"
-			f << "muniq   k=#{@db.idFN} |"
-			f << "mnumber S=0 a=__tid -q|"
-			f << "msortf  f=__tid       o=#{xxw}"
-			system(f)
-			translt = @temp.file
-			TAKE::run_lcmtrans(lcmout,"t",translt)
-
-			f=""
-			#f << "lcm_trans #{lcmout} t |" #__tid,pid
-			f << "msortf   f=__tid i=#{translt}          |"
-			f << "mjoin    k=__tid m=#{xxw} f=#{@db.idFN} |"
-			f << "msetstr  v=#{cName} a=class             |"
-			f << "mcut     f=#{@db.idFN},class,pid        o=#{tFiles.last}"
-			system(f)
+			if @outtf then
+				# トランザクション毎に出現するシーケンスを書き出す
+				MCMD::msgLog("output tid-patterns ...")
+				tFiles << @temp.file
+
+				xxw= tf.file
+				f=""
+				f << "mcut    f=#{@db.idFN} i=#{@db.file} |"
+				f << "muniq   k=#{@db.idFN} |"
+				f << "mnumber S=0 a=__tid -q|"
+				f << "msortf  f=__tid       o=#{xxw}"
+				system(f)
+				translt = @temp.file
+				TAKE::run_lcmtrans(lcmout,"t",translt)
+
+				f=""
+				#f << "lcm_trans #{lcmout} t |" #__tid,pid
+				f << "msortf   f=__tid i=#{translt}          |"
+				f << "mjoin    k=__tid m=#{xxw} f=#{@db.idFN} |"
+				f << "msetstr  v=#{cName} a=class             |"
+				f << "mcut     f=#{@db.idFN},class,pid        o=#{tFiles.last}"
+				system(f)
+			end
 		}
 
 		# クラス別のパターンとtid-pidファイルを統合して最終出力
@@ -258,24 +269,32 @@ class LcmEsp
 		f << "msortf  f=class,pid o=#{xxp4}"
 		system(f)
 
-		# tid-pidファイル計算
-		f=""
-		f << "mcat                                       i=#{tFiles.join(",")} |"
-		f << "msortf  f=class,pid                        |"
-		f << "mjoin   k=class,pid m=#{xxpCat} f=ppid     |" # 全クラス統一pid(ppid)結合
-		f << "msortf  f=class,ppid                       |"
-		f << "mcommon k=class,ppid K=class,pid m=#{xxp4} |" # 列挙されたパターンの選択
-		f << "mcut    f=#{@db.idFN},class,ppid:pid       |"
-		f << "msortf  f=#{@db.idFN},class,pid            o=#{@tFile}"
-		system(f)
+		if @outtf then
+			# tid-pidファイル計算
+			f=""
+			f << "mcat                                       i=#{tFiles.join(",")} |"
+			f << "msortf  f=class,pid                        |"
+			f << "mjoin   k=class,pid m=#{xxpCat} f=ppid     |" # 全クラス統一pid(ppid)結合
+			f << "msortf  f=class,ppid                       |"
+			f << "mcommon k=class,ppid K=class,pid m=#{xxp4} |" # 列挙されたパターンの選択
+			f << "mcut    f=#{@db.idFN},class,ppid:pid       |"
+			f << "msortf  f=#{@db.idFN},class,pid            o=#{@tFile}"
+			system(f)
+		end
 
 		@size = MCMD::mrecount("i=#{@pFile}") # 列挙されたパターンの数
 		MCMD::msgLog("the number of emerging sequence patterns enumerated is #{@size}")
 	end
 
-  def output(outpath)
-		system "mv #{@pFile} #{outpath}/patterns.csv"
-		system "mv #{@tFile} #{outpath}/tid_pats.csv"
+  def output(outpath,rmsinfo)
+  	if rmsinfo then
+			system "mfldname i=#{@pFile} -q o=#{outpath}/patterns.csv"
+			system "mfldname i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
+		else
+			system "mv #{@pFile} #{outpath}/patterns.csv"
+			system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
+		end
+
 	end
 end
 

data/lib/nysol/enumLcmIs.rb

@@ -53,11 +53,12 @@ class LcmIs
 		return pat
 	end
 
-	def initialize(db)
+	def initialize(db,outtf=true)
 		@temp=MCMD::Mtemp.new
 		@db = db # 入力データベース
 		@file=@temp.file
 		items=@db.items
+		@outtf = outtf
 
 		# アイテムをシンボルから番号に変換する。
 		f=""
@@ -96,13 +97,6 @@ class LcmIs
 			end
 		end
 
-		# lcmのパラメータ設定と実行
-		#run=""
-		#run << "#{CMD} #{@type}If"
-		#run << " -U #{@maxCnt}"         if @maxCnt # windowサイズ上限
-		#run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
-		#run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
-
 		run=""
 		run << "#{@type}If"
 		run << " -U #{@maxCnt}"         if @maxCnt # windowサイズ上限
@@ -235,39 +229,46 @@ class LcmIs
 		@size = MCMD::mrecount("i=#{@pFile}") # 列挙されたパターンの数
 		MCMD::msgLog("the number of patterns enumerated is #{@size}")
 
-		# トランザクション毎に出現するシーケンスを書き出す
-		MCMD::msgLog("output tid-patterns ...")
-		@tFile = @temp.file
+		if @outtf then
+			# トランザクション毎に出現するシーケンスを書き出す
+			MCMD::msgLog("output tid-patterns ...")
+			@tFile = @temp.file
 
-		xxw1= tf.file
-		f=""
-		f << "mcut    f=#{@db.idFN} i=#{@db.file} |"
-		f << "muniq   k=#{@db.idFN}  |"
-		f << "mnumber S=0 a=__tid -q |"
-		f << "msortf  f=__tid       o=#{xxw1}"
-		system(f)
+			xxw1= tf.file
+			f=""
+			f << "mcut    f=#{@db.idFN} i=#{@db.file} |"
+			f << "muniq   k=#{@db.idFN}  |"
+			f << "mnumber S=0 a=__tid -q |"
+			f << "msortf  f=__tid       o=#{xxw1}"
+			system(f)
 
-		xxw2= tf.file
-		f=""
-		f << "mcut    f=pid i=#{@pFile} |"
-		f << "msortf  f=pid o=#{xxw2}"
-		system(f)
+			xxw2= tf.file
+			f=""
+			f << "mcut    f=pid i=#{@pFile} |"
+			f << "msortf  f=pid o=#{xxw2}"
+			system(f)
 
-		xxw3 = tf.file
-		TAKE::run_lcmtrans(lcmout,"t",xxw3)
-		f=""
-#		f << "lcm_trans #{lcmout} t |" #__tid,pid
-		f << "msortf   f=pid  i=#{xxw3}                 |"
-		f << "mcommon  k=pid m=#{xxw2}                 |"
-		f << "msortf   f=__tid                         |"
-		f << "mjoin    k=__tid m=#{xxw1} f=#{@db.idFN} |"
-		f << "mcut     f=#{@db.idFN},pid               o=#{@tFile}"
-		system(f)
+			xxw3 = tf.file
+			TAKE::run_lcmtrans(lcmout,"t",xxw3)
+			f=""
+			#f << "lcm_trans #{lcmout} t |" #__tid,pid
+			f << "msortf   f=pid  i=#{xxw3}                 |"
+			f << "mcommon  k=pid m=#{xxw2}                 |"
+			f << "msortf   f=__tid                         |"
+			f << "mjoin    k=__tid m=#{xxw1} f=#{@db.idFN} |"
+			f << "mcut     f=#{@db.idFN},pid               o=#{@tFile}"
+			system(f)
+		end
 	end
 
-  def output(outpath)
-		system "mv #{@pFile} #{outpath}/patterns.csv"
-		system "mv #{@tFile} #{outpath}/tid_pats.csv"
+  def output(outpath,rmsinfo)
+  	if rmsinfo then
+			system "mfldnmae i=#{@pFile} -q o=#{outpath}/patterns.csv"
+			system "mfldnmae i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
+		else
+			system "mv #{@pFile} #{outpath}/patterns.csv"
+			system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
+		end
 	end
 end
 

data/lib/nysol/enumLcmSeq.rb

@@ -13,11 +13,12 @@ module TAKE
 class LcmSeq
 	attr_reader :size  # 列挙されたパターン数
 
-	def initialize(db)
+	def initialize(db,outtf=true)
 		@temp=MCMD::Mtemp.new
 		@db = db # 入力データベース
 		@file=@temp.file
 		items=@db.items
+		@outtf = outtf
 
 		# アイテムをシンボルから番号に変換する。
 		f=""
@@ -64,6 +65,12 @@ class LcmSeq
 			File.open(xxtop,"r"){|fpr| @minCnt=fpr.gets().to_i}
 			@minCnt=1 if @minCnt<0
 		end
+		
+		@addTP = ""		
+		@addTP = "m" if eArgs["exM"]
+		@addTP = "c" if eArgs["exC"]
+			
+
 
 		# lcm_seq出力ファイル
 		lcmout = tf.file
@@ -72,7 +79,7 @@ class LcmSeq
 		system("touch #{lcmout}")
 
 		# lcm_seqのパラメータ設定と実行
-		run="CIf"
+		run="CIf#{@addTP}"
 		run << " -U #{@maxCnt}"         if @maxCnt # windowサイズ上限
 		run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
 		run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
@@ -107,36 +114,43 @@ class LcmSeq
 		f << "msortf   f=support%nr                                                   o=#{@pFile}"
 		system(f)
 
-		# トランザクション毎に出現するシーケンスを書き出す
-		MCMD::msgLog("output tid-patterns ...")
-		@tFile = @temp.file
-
-		xxw = tf.file #Mtemp.new.name
-		f=""
-		f << "mcut    f=#{@db.idFN} i=#{@db.file} |"
-		f << "muniq   k=#{@db.idFN}  |"
-		f << "mnumber S=0 a=__tid -q |"
-		f << "msortf  f=__tid       o=#{xxw}"
-		system(f)
-
-		translt = @temp.file
-		TAKE::run_lcmtrans(lcmout,"t",translt)
-
-		f=""
-#		f << "lcm_trans #{lcmout} t |" #__tid,pid
-		f << "msortf   f=__tid i=#{translt}           |"
-		f << "mjoin    k=__tid m=#{xxw} f=#{@db.idFN} |"
-		f << "mcut     f=#{@db.idFN},pid              |"
-		f << "msortf   f=#{@db.idFN},pid              o=#{@tFile}"
-		system(f)
+		if @outtf then
+			# トランザクション毎に出現するシーケンスを書き出す
+			MCMD::msgLog("output tid-patterns ...")
+			@tFile = @temp.file
+
+			xxw = tf.file #Mtemp.new.name
+			f=""
+			f << "mcut    f=#{@db.idFN} i=#{@db.file} |"
+			f << "muniq   k=#{@db.idFN}  |"
+			f << "mnumber S=0 a=__tid -q |"
+			f << "msortf  f=__tid       o=#{xxw}"
+			system(f)
+
+			translt = @temp.file
+			TAKE::run_lcmtrans(lcmout,"t",translt)
+
+			f=""
+			#		f << "lcm_trans #{lcmout} t |" #__tid,pid
+			f << "msortf   f=__tid i=#{translt}           |"
+			f << "mjoin    k=__tid m=#{xxw} f=#{@db.idFN} |"
+			f << "mcut     f=#{@db.idFN},pid              |"
+			f << "msortf   f=#{@db.idFN},pid              o=#{@tFile}"
+			system(f)
+		end
 
 		@size = MCMD::mrecount("i=#{@pFile}") # 列挙されたパターンの数
 		MCMD::msgLog("the number of contrast patterns enumerated is #{@size}")
 	end
 
-  def output(outpath)
-		system "mv #{@pFile} #{outpath}/patterns.csv"
-		system "mv #{@tFile} #{outpath}/tid_pats.csv"
+  def output(outpath,rmsinfo)
+  	if rmsinfo then
+			system "mfldnmae i=#{@pFile} -q o=#{outpath}/patterns.csv"
+			system "mfldnmae i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
+		else
+			system "mv #{@pFile} #{outpath}/patterns.csv"
+			system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
+		end
 	end
 end
 

metadata

@@ -1,31 +1,30 @@
 --- !ruby/object:Gem::Specification
 name: nysol-take
 version: !ruby/object:Gem::Version
-  version: 3.0.0
+  version: 3.0.2
 platform: ruby
 authors:
 - NYSOL
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-07-06 00:00:00.000000000 Z
+date: 2025-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nysol
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 3.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 3.0.0
-description: |2
-      nysol TAKE tools
+description: "    nysol TAKE tools\n"
 email: info@nysol.jp
 executables:
 - mclique.rb
@@ -54,165 +53,165 @@ extensions:
 - ext/macerun/extconf.rb
 extra_rdoc_files: []
 files:
-- ext/lcmrun/extconf.rb
-- ext/lcmrun/lcmrun.cpp
-- ext/lcmseqrun/extconf.rb
-- ext/lcmseqrun/lcmseqrun.cpp
-- ext/lcmseq0run/extconf.rb
-- ext/lcmseq0run/lcmseq0run.cpp
+- bin/mbiclique.rb
+- bin/mbipolish.rb
+- bin/mccomp.rb
+- bin/mclique.rb
+- bin/mclique2g.rb
+- bin/mcliqueInfo.rb
+- bin/mfriends.rb
+- bin/mgdiff.rb
+- bin/mhifriend.rb
+- bin/mhipolish.rb
+- bin/mitemset.rb
+- bin/mpal.rb
+- bin/mpolishing.rb
+- bin/msequence.rb
+- bin/mtra2g.rb
+- bin/mtra2gc.rb
 - ext/grhfilrun/extconf.rb
 - ext/grhfilrun/grhfilrun.c
-- ext/sspcrun/extconf.rb
-- ext/sspcrun/sspcrun.cpp
-- ext/macerun/extconf.rb
-- ext/macerun/macerun.cpp
+- ext/grhfilrun/src/_sspc.c
+- ext/grhfilrun/src/aheap.c
+- ext/grhfilrun/src/aheap.h
+- ext/grhfilrun/src/base.c
+- ext/grhfilrun/src/base.h
+- ext/grhfilrun/src/fstar.c
+- ext/grhfilrun/src/fstar.h
+- ext/grhfilrun/src/grhfil.c
+- ext/grhfilrun/src/itemset.c
+- ext/grhfilrun/src/itemset.h
+- ext/grhfilrun/src/problem.c
+- ext/grhfilrun/src/problem.h
+- ext/grhfilrun/src/queue.c
+- ext/grhfilrun/src/queue.h
+- ext/grhfilrun/src/sample.c
+- ext/grhfilrun/src/sspc.c
+- ext/grhfilrun/src/sspc2.c
+- ext/grhfilrun/src/stdlib2.c
+- ext/grhfilrun/src/stdlib2.h
+- ext/grhfilrun/src/trsact.c
+- ext/grhfilrun/src/trsact.h
+- ext/grhfilrun/src/vec.c
+- ext/grhfilrun/src/vec.h
+- ext/lcmrun/extconf.rb
+- ext/lcmrun/lcmrun.cpp
 - ext/lcmrun/src/aheap.c
+- ext/lcmrun/src/aheap.h
 - ext/lcmrun/src/base.c
+- ext/lcmrun/src/base.h
 - ext/lcmrun/src/itemset.c
+- ext/lcmrun/src/itemset.h
 - ext/lcmrun/src/lcm.c
 - ext/lcmrun/src/problem.c
-- ext/lcmrun/src/queue.c
-- ext/lcmrun/src/sgraph.c
-- ext/lcmrun/src/stdlib2.c
-- ext/lcmrun/src/trsact.c
-- ext/lcmrun/src/vec.c
-- ext/lcmrun/src/aheap.h
-- ext/lcmrun/src/base.h
-- ext/lcmrun/src/itemset.h
 - ext/lcmrun/src/problem.h
+- ext/lcmrun/src/queue.c
 - ext/lcmrun/src/queue.h
+- ext/lcmrun/src/sgraph.c
 - ext/lcmrun/src/sgraph.h
+- ext/lcmrun/src/stdlib2.c
 - ext/lcmrun/src/stdlib2.h
+- ext/lcmrun/src/trsact.c
 - ext/lcmrun/src/trsact.h
+- ext/lcmrun/src/vec.c
 - ext/lcmrun/src/vec.h
-- ext/lcmseqrun/src/aheap.c
-- ext/lcmseqrun/src/base.c
-- ext/lcmseqrun/src/itemset.c
-- ext/lcmseqrun/src/itemset_zero.c
-- ext/lcmseqrun/src/lcm_seq.c
-- ext/lcmseqrun/src/lcm_seq_zero.c
-- ext/lcmseqrun/src/problem.c
-- ext/lcmseqrun/src/problem_zero.c
-- ext/lcmseqrun/src/queue.c
-- ext/lcmseqrun/src/stdlib2.c
-- ext/lcmseqrun/src/trsact.c
-- ext/lcmseqrun/src/vec.c
-- ext/lcmseqrun/src/aheap.h
-- ext/lcmseqrun/src/base.h
-- ext/lcmseqrun/src/itemset.h
-- ext/lcmseqrun/src/problem.h
-- ext/lcmseqrun/src/queue.h
-- ext/lcmseqrun/src/stdlib2.h
-- ext/lcmseqrun/src/trsact.h
-- ext/lcmseqrun/src/vec.h
+- ext/lcmseq0run/extconf.rb
+- ext/lcmseq0run/lcmseq0run.cpp
 - ext/lcmseq0run/src/aheap.c
+- ext/lcmseq0run/src/aheap.h
 - ext/lcmseq0run/src/base.c
+- ext/lcmseq0run/src/base.h
 - ext/lcmseq0run/src/itemset.c
+- ext/lcmseq0run/src/itemset.h
 - ext/lcmseq0run/src/itemset_zero.c
 - ext/lcmseq0run/src/lcm_seq.c
 - ext/lcmseq0run/src/lcm_seq_zero.c
 - ext/lcmseq0run/src/problem.c
+- ext/lcmseq0run/src/problem.h
 - ext/lcmseq0run/src/problem_zero.c
 - ext/lcmseq0run/src/queue.c
-- ext/lcmseq0run/src/stdlib2.c
-- ext/lcmseq0run/src/trsact.c
-- ext/lcmseq0run/src/vec.c
-- ext/lcmseq0run/src/aheap.h
-- ext/lcmseq0run/src/base.h
-- ext/lcmseq0run/src/itemset.h
-- ext/lcmseq0run/src/problem.h
 - ext/lcmseq0run/src/queue.h
+- ext/lcmseq0run/src/stdlib2.c
 - ext/lcmseq0run/src/stdlib2.h
+- ext/lcmseq0run/src/trsact.c
 - ext/lcmseq0run/src/trsact.h
+- ext/lcmseq0run/src/vec.c
 - ext/lcmseq0run/src/vec.h
+- ext/lcmseqrun/extconf.rb
+- ext/lcmseqrun/lcmseqrun.cpp
+- ext/lcmseqrun/src/aheap.c
+- ext/lcmseqrun/src/aheap.h
+- ext/lcmseqrun/src/base.c
+- ext/lcmseqrun/src/base.h
+- ext/lcmseqrun/src/itemset.c
+- ext/lcmseqrun/src/itemset.h
+- ext/lcmseqrun/src/itemset_zero.c
+- ext/lcmseqrun/src/lcm_seq.c
+- ext/lcmseqrun/src/lcm_seq_zero.c
+- ext/lcmseqrun/src/problem.c
+- ext/lcmseqrun/src/problem.h
+- ext/lcmseqrun/src/problem_zero.c
+- ext/lcmseqrun/src/queue.c
+- ext/lcmseqrun/src/queue.h
+- ext/lcmseqrun/src/stdlib2.c
+- ext/lcmseqrun/src/stdlib2.h
+- ext/lcmseqrun/src/trsact.c
+- ext/lcmseqrun/src/trsact.h
+- ext/lcmseqrun/src/vec.c
+- ext/lcmseqrun/src/vec.h
+- ext/lcmtransrun/extconf.rb
+- ext/lcmtransrun/lcmtransrun.cpp
+- ext/macerun/extconf.rb
+- ext/macerun/macerun.cpp
+- ext/macerun/src/aheap.c
+- ext/macerun/src/aheap.h
+- ext/macerun/src/itemset.c
+- ext/macerun/src/itemset.h
+- ext/macerun/src/mace.c
+- ext/macerun/src/problem.c
+- ext/macerun/src/problem.h
+- ext/macerun/src/queue.c
+- ext/macerun/src/queue.h
+- ext/macerun/src/sgraph.c
+- ext/macerun/src/sgraph.h
+- ext/macerun/src/stdlib2.c
+- ext/macerun/src/stdlib2.h
+- ext/macerun/src/vec.c
+- ext/macerun/src/vec.h
+- ext/sspcrun/extconf.rb
 - ext/sspcrun/src/_sspc.c
 - ext/sspcrun/src/aheap.c
+- ext/sspcrun/src/aheap.h
 - ext/sspcrun/src/base.c
+- ext/sspcrun/src/base.h
 - ext/sspcrun/src/fstar.c
+- ext/sspcrun/src/fstar.h
 - ext/sspcrun/src/grhfil.c
 - ext/sspcrun/src/itemset.c
+- ext/sspcrun/src/itemset.h
 - ext/sspcrun/src/problem.c
+- ext/sspcrun/src/problem.h
 - ext/sspcrun/src/queue.c
+- ext/sspcrun/src/queue.h
 - ext/sspcrun/src/sample.c
 - ext/sspcrun/src/sspc.c
 - ext/sspcrun/src/sspc2.c
 - ext/sspcrun/src/stdlib2.c
-- ext/sspcrun/src/trsact.c
-- ext/sspcrun/src/vec.c
-- ext/sspcrun/src/aheap.h
-- ext/sspcrun/src/base.h
-- ext/sspcrun/src/fstar.h
-- ext/sspcrun/src/itemset.h
-- ext/sspcrun/src/problem.h
-- ext/sspcrun/src/queue.h
 - ext/sspcrun/src/stdlib2.h
+- ext/sspcrun/src/trsact.c
 - ext/sspcrun/src/trsact.h
+- ext/sspcrun/src/vec.c
 - ext/sspcrun/src/vec.h
-- ext/macerun/src/aheap.c
-- ext/macerun/src/itemset.c
-- ext/macerun/src/mace.c
-- ext/macerun/src/problem.c
-- ext/macerun/src/queue.c
-- ext/macerun/src/sgraph.c
-- ext/macerun/src/stdlib2.c
-- ext/macerun/src/vec.c
-- ext/macerun/src/aheap.h
-- ext/macerun/src/itemset.h
-- ext/macerun/src/problem.h
-- ext/macerun/src/queue.h
-- ext/macerun/src/sgraph.h
-- ext/macerun/src/stdlib2.h
-- ext/macerun/src/vec.h
-- ext/grhfilrun/src/_sspc.c
-- ext/grhfilrun/src/aheap.c
-- ext/grhfilrun/src/base.c
-- ext/grhfilrun/src/fstar.c
-- ext/grhfilrun/src/grhfil.c
-- ext/grhfilrun/src/itemset.c
-- ext/grhfilrun/src/problem.c
-- ext/grhfilrun/src/queue.c
-- ext/grhfilrun/src/sample.c
-- ext/grhfilrun/src/sspc.c
-- ext/grhfilrun/src/sspc2.c
-- ext/grhfilrun/src/stdlib2.c
-- ext/grhfilrun/src/trsact.c
-- ext/grhfilrun/src/vec.c
-- ext/grhfilrun/src/aheap.h
-- ext/grhfilrun/src/base.h
-- ext/grhfilrun/src/fstar.h
-- ext/grhfilrun/src/itemset.h
-- ext/grhfilrun/src/problem.h
-- ext/grhfilrun/src/queue.h
-- ext/grhfilrun/src/stdlib2.h
-- ext/grhfilrun/src/trsact.h
-- ext/grhfilrun/src/vec.h
-- ext/lcmtransrun/extconf.rb
-- ext/lcmtransrun/lcmtransrun.cpp
+- ext/sspcrun/sspcrun.cpp
 - lib/nysol/enumLcmEp.rb
 - lib/nysol/enumLcmEsp.rb
 - lib/nysol/enumLcmIs.rb
 - lib/nysol/enumLcmSeq.rb
 - lib/nysol/items.rb
 - lib/nysol/seqDB.rb
+- lib/nysol/take.rb
 - lib/nysol/taxonomy.rb
 - lib/nysol/traDB.rb
-- lib/nysol/take.rb
-- bin/mclique.rb
-- bin/mbiclique.rb
-- bin/mbipolish.rb
-- bin/mclique2g.rb
-- bin/mcliqueInfo.rb
-- bin/mgdiff.rb
-- bin/mitemset.rb
-- bin/mpolishing.rb
-- bin/msequence.rb
-- bin/mfriends.rb
-- bin/mccomp.rb
-- bin/mhifriend.rb
-- bin/mhipolish.rb
-- bin/mpal.rb
-- bin/mtra2gc.rb
-- bin/mtra2g.rb
 homepage: http://www.nysol.jp/
 licenses: []
 metadata: {}
@@ -222,17 +221,16 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 3.0.3.1
 signing_key: 
 specification_version: 4
 summary: nysol TAKE tools