nysol-take 3.0.1 → 3.0.2

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Files changed (15) hide show
  1. checksums.yaml +5 -5
  2. data/bin/mccomp.rb +1 -1
  3. data/bin/mitemset.rb +4 -2
  4. data/bin/msequence.rb +12 -2
  5. data/ext/grhfilrun/extconf.rb +3 -3
  6. data/ext/lcmrun/extconf.rb +3 -3
  7. data/ext/lcmseq0run/extconf.rb +3 -3
  8. data/ext/lcmseqrun/extconf.rb +3 -3
  9. data/ext/macerun/extconf.rb +3 -3
  10. data/ext/sspcrun/extconf.rb +3 -3
  11. data/lib/nysol/enumLcmEp.rb +18 -7
  12. data/lib/nysol/enumLcmEsp.rb +18 -4
  13. data/lib/nysol/enumLcmIs.rb +8 -3
  14. data/lib/nysol/enumLcmSeq.rb +15 -4
  15. metadata +118 -120
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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- SHA1:
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- metadata.gz: bf638296f1c835d6aec7d5b8636ab9fad33cd30e
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- data.tar.gz: 5c01613d4e66b3f62498dc8d8d5b909c12177dcb
2
+ SHA256:
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+ metadata.gz: a2753f4a5688ae9282382023020a2e10ec12029e98a7aad35ef6cf21f7197053
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+ data.tar.gz: ff30c45b9deec28f3f209d8171af001a4aeed53b78320845b534600f910a85fb
5
5
  SHA512:
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- metadata.gz: 037fb1e858907bdf772554f3f24afd96e1440999bd143726c0c116dd7351796acb73843b5e7a3be3f98ce4843641de784ce8343f1be3b50f738aadc738fd8196
7
- data.tar.gz: 1fa831a85396c424abfa2eed15e0f0c509cb43920ff353d374fe2e8ff58a841a8f7db5bdb5ffa9f0b8b5547cb23d4cc88d6615260c0a93715e1755072266c5e6
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+ metadata.gz: 45950f53a25a8c36cebefe965af85b3070e75d0044a9fe8eaeeaa1aa5e0cc9c499990fb2009d7cfb8095ec8fc08090bf33295415ba852838b9788e11f5c9af01
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+ data.tar.gz: 62b0116f86a64fd5e27216c02effdda7fcb3ec12d64032ccae42ffe455ee63659e98be3377cce05c5dfe211604c3b9e5fad3378d6489e2ab48f3e85c05f424f8
data/bin/mccomp.rb CHANGED
@@ -6,7 +6,7 @@ require "nysol/mcmd"
6
6
 
7
7
  # 1.0 initial development: 2016/10/17
8
8
  # 1.1 出力のnode項目名をnf=の値にする: 2016/11/11
9
- $cmd="mccomp2g.rb"
9
+ $cmd="mccomp.rb"
10
10
  $version="1.1"
11
11
 
12
12
  def help
data/bin/mitemset.rb CHANGED
@@ -75,7 +75,7 @@ end
75
75
  help() if ARGV.size <= 0 or ARGV[0]=="--help"
76
76
  ver() if ARGV[0]=="--version"
77
77
 
78
- 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")
78
+ 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")
79
79
 
80
80
  # コマンド実行可能確認
81
81
  #exit(1) unless(MCMD::chkCmdExe(TAKE::LcmIs::CMD , "executable"))
@@ -105,6 +105,8 @@ itemFN = itemFN["names"].join(",") if itemFN
105
105
  clsFN = clsFN["names"].join(",") if clsFN
106
106
  taxoFN = taxoFN["names"].join(",") if taxoFN
107
107
 
108
+ sortInfo = args.bool("-q")
109
+
108
110
  eArgs=Hash.new
109
111
  eArgs["type" ] = args. str("type=","F" )
110
112
  eArgs["minSup" ] = args.float("s=" ,0.05 ,0 ,1 ) # 最小サポート
@@ -160,7 +162,7 @@ end
160
162
 
161
163
  # 出力
162
164
  system("mkdir -p #{outPath}")
163
- lcm.output(outPath)
165
+ lcm.output(outPath,sortInfo)
164
166
 
165
167
  MCMD::msgLog("The final results are in the directory `#{outPath}'")
166
168
 
data/bin/msequence.rb CHANGED
@@ -74,7 +74,7 @@ end
74
74
 
75
75
  help() if ARGV.size <= 0 or ARGV[0]=="--help"
76
76
  ver() if ARGV[0]=="--version"
77
- 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")
77
+ 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")
78
78
 
79
79
  # lcm_seqコマンド実行可能確認
80
80
  #exit(1) unless(MCMD::chkCmdExe(TAKE::LcmSeq::CMD , "executable"))
@@ -106,6 +106,9 @@ itemFN = itemFN["names"].join(",") if itemFN
106
106
  clsFN = clsFN["names"].join(",") if clsFN
107
107
  taxoFN = taxoFN["names"].join(",") if taxoFN
108
108
 
109
+ sortInfo = args.bool("-q")
110
+
111
+
109
112
  eArgs=Hash.new
110
113
  eArgs["minSup" ] = args.float("s=" ,0.05 ,0,1 ) # 最小サポート
111
114
  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
120
123
  eArgs["win" ] = args. int("win=" ,nil ,0,nil ) # win size上限限
121
124
  eArgs["padding"] = args. bool("-padding") # 0item ommit
122
125
  eArgs["top" ] = args. int("top=" ,nil,0)
126
+ eArgs["exM"] = args. bool("-m") # extension maximal patterns only
127
+ eArgs["exC"] = args. bool("-c") # extension closed patterns only
128
+
129
+
130
+ if eArgs["exM"] and eArgs["exC"] then
131
+ raise "-m cannot be specified with -c"
132
+ end
123
133
 
124
134
  if eArgs["minLen"] and eArgs["maxLen"]
125
135
  if eArgs["minLen"] > eArgs["maxLen"] then
@@ -156,7 +166,7 @@ end
156
166
 
157
167
  # 出力
158
168
  system("mkdir -p #{outPath}")
159
- lcm.output(outPath)
169
+ lcm.output(outPath,sortInfo)
160
170
 
161
171
  MCMD::msgLog("The final results are in the directory `#{outPath}'")
162
172
 
data/ext/grhfilrun/extconf.rb CHANGED
@@ -3,9 +3,9 @@ require "mkmf"
3
3
 
4
4
 
5
5
  cp = "$(srcdir)"
6
- $CFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
7
- $CPPFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
8
- $CXXFLAGS = " -O3 -Os -s -w -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
6
+ $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"
7
+ $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"
8
+ $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"
9
9
 
10
10
 
11
11
  create_makefile("nysol/grhfilrun")
data/ext/lcmrun/extconf.rb CHANGED
@@ -10,9 +10,9 @@ end
10
10
 
11
11
  cp = "$(srcdir)"
12
12
 
13
- $CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
14
- $CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
15
- $CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
13
+ $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"
14
+ $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"
15
+ $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"
16
16
 
17
17
  $LOCAL_LIBS += " -lstdc++ -lkgmod3"
18
18
 
data/ext/lcmseq0run/extconf.rb CHANGED
@@ -10,9 +10,9 @@ end
10
10
 
11
11
  cp = "$(srcdir)"
12
12
 
13
- $CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
14
- $CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
15
- $CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
13
+ $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"
14
+ $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"
15
+ $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"
16
16
 
17
17
  $LOCAL_LIBS += " -lstdc++ -lkgmod3"
18
18
 
data/ext/lcmseqrun/extconf.rb CHANGED
@@ -10,9 +10,9 @@ end
10
10
 
11
11
  cp = "$(srcdir)"
12
12
 
13
- $CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
14
- $CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
15
- $CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
13
+ $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"
14
+ $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"
15
+ $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"
16
16
 
17
17
  $LOCAL_LIBS += " -lstdc++ -lkgmod3"
18
18
 
data/ext/macerun/extconf.rb CHANGED
@@ -10,9 +10,9 @@ end
10
10
 
11
11
  cp = "$(srcdir)"
12
12
 
13
- $CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
14
- $CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
15
- $CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
13
+ $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"
14
+ $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"
15
+ $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"
16
16
 
17
17
  $LOCAL_LIBS += " -lstdc++ -lm -lkgmod3"
18
18
 
data/ext/sspcrun/extconf.rb CHANGED
@@ -10,9 +10,9 @@ end
10
10
 
11
11
  cp = "$(srcdir)"
12
12
 
13
- $CFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
14
- $CPPFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
15
- $CXXFLAGS = " -O3 -Wall -I. -I#{cp}/src -DB_STATIC -D_NO_MAIN_ -DLINE -fPIC -Wno-error=format-security"
13
+ $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"
14
+ $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"
15
+ $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"
16
16
 
17
17
  $LOCAL_LIBS += " -lstdc++ -lkgmod3 -lm"
18
18
 
data/lib/nysol/enumLcmEp.rb CHANGED
@@ -29,7 +29,7 @@ class LcmEp
29
29
  def calSigma(minPos,minGR,posCnt,negCnt)
30
30
  omegaF=@@intMax.to_f/posCnt.to_f
31
31
  beta=minPos
32
- w=posCnt.to_f/negCnt.to_f
32
+ w=negCnt.to_f/posCnt.to_f
33
33
  #puts "omegaF=#{omegaF}"
34
34
  #puts "minPos=#{minPos}"
35
35
  #puts "beta=#{beta}"
@@ -166,11 +166,10 @@ class LcmEp
166
166
  if eArgs["maxSup"].class.name=="Hash"
167
167
  @maxPos = (eArgs["maxSup"][cName] * posSize.to_f + 0.99).to_i
168
168
  else
169
- p posSize
170
169
  @maxPos = (eArgs["maxSup"] * posSize.to_f + 0.99).to_i
171
170
  end
172
171
  else
173
- @maxPos = posSize.to_f
172
+ @maxPos = nil
174
173
  end
175
174
 
176
175
  @sigma[cName] = calSigma(@minPos,@minGR,posSize,negSize)
@@ -181,9 +180,14 @@ class LcmEp
181
180
  # そのときのために空ファイルを生成しておいく。
182
181
  system("touch #{lcmout}")
183
182
 
183
+ if @maxPos then
184
+ @maxPos = calSigma(@maxPos,@minGR,posSize,negSize)
185
+ end
186
+
184
187
  run=""
185
188
  run << "#{eArgs["type"]}IA"
186
- run << " -U #{@maxCnt}" if @maxCnt # windowサイズ上限
189
+ run << " -U #{@maxPos}" if @maxPos # windowサイズ上限
190
+ #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
187
191
  run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
188
192
  run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
189
193
  run << " -w #{@weightFile[cName]} #{@file} #{@sigma[cName]} #{lcmout}"
@@ -333,9 +337,16 @@ class LcmEp
333
337
  MCMD::msgLog("the number of emerging patterns enumerated is #{@size}")
334
338
  end
335
339
 
336
- def output(outpath)
337
- system "mv #{@pFile} #{outpath}/patterns.csv"
338
- system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
340
+ def output(outpath,rmsinfo)
341
+ if rmsinfo then
342
+ system "mfldname i=#{@pFile} -q o=#{outpath}/patterns.csv"
343
+ system "mfldname i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
344
+ else
345
+ system "mv #{@pFile} #{outpath}/patterns.csv"
346
+ system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
347
+ end
348
+
349
+
339
350
  end
340
351
  end
341
352
 
data/lib/nysol/enumLcmEsp.rb CHANGED
@@ -150,6 +150,10 @@ class LcmEsp
150
150
  @maxCnt = (eArgs["maxSup"] * posSize.to_f + 0.99).to_i
151
151
  end
152
152
  end
153
+ @addTP = ""
154
+ @addTP = "m" if eArgs["exM"]
155
+ @addTP = "c" if eArgs["exC"]
156
+
153
157
 
154
158
  @sigma[cName] = calSigma(@minPos,@minGR,posSize,negSize)
155
159
 
@@ -158,8 +162,12 @@ class LcmEsp
158
162
  # 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
159
163
  # そのときのために空ファイルを生成しておいく。
160
164
  system("touch #{lcmout}")
165
+
166
+ if @maxCnt then
167
+ @maxCnt = calSigma(@maxCnt,@minGR,posSize,negSize)
168
+ end
161
169
 
162
- run="CIA"
170
+ run="CIA#{@addTP}"
163
171
  run << " -U #{@maxCnt}" if @maxCnt # windowサイズ上限
164
172
  run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
165
173
  run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
@@ -278,9 +286,15 @@ class LcmEsp
278
286
  MCMD::msgLog("the number of emerging sequence patterns enumerated is #{@size}")
279
287
  end
280
288
 
281
- def output(outpath)
282
- system "mv #{@pFile} #{outpath}/patterns.csv"
283
- system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
289
+ def output(outpath,rmsinfo)
290
+ if rmsinfo then
291
+ system "mfldname i=#{@pFile} -q o=#{outpath}/patterns.csv"
292
+ system "mfldname i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
293
+ else
294
+ system "mv #{@pFile} #{outpath}/patterns.csv"
295
+ system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
296
+ end
297
+
284
298
  end
285
299
  end
286
300
 
data/lib/nysol/enumLcmIs.rb CHANGED
@@ -261,9 +261,14 @@ class LcmIs
261
261
  end
262
262
  end
263
263
 
264
- def output(outpath)
265
- system "mv #{@pFile} #{outpath}/patterns.csv"
266
- system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
264
+ def output(outpath,rmsinfo)
265
+ if rmsinfo then
266
+ system "mfldnmae i=#{@pFile} -q o=#{outpath}/patterns.csv"
267
+ system "mfldnmae i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
268
+ else
269
+ system "mv #{@pFile} #{outpath}/patterns.csv"
270
+ system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
271
+ end
267
272
  end
268
273
  end
269
274
 
data/lib/nysol/enumLcmSeq.rb CHANGED
@@ -65,6 +65,12 @@ class LcmSeq
65
65
  File.open(xxtop,"r"){|fpr| @minCnt=fpr.gets().to_i}
66
66
  @minCnt=1 if @minCnt<0
67
67
  end
68
+
69
+ @addTP = ""
70
+ @addTP = "m" if eArgs["exM"]
71
+ @addTP = "c" if eArgs["exC"]
72
+
73
+
68
74
 
69
75
  # lcm_seq出力ファイル
70
76
  lcmout = tf.file
@@ -73,7 +79,7 @@ class LcmSeq
73
79
  system("touch #{lcmout}")
74
80
 
75
81
  # lcm_seqのパラメータ設定と実行
76
- run="CIf"
82
+ run="CIf#{@addTP}"
77
83
  run << " -U #{@maxCnt}" if @maxCnt # windowサイズ上限
78
84
  run << " -l #{eArgs['minLen']}" if eArgs["minLen"] # パターンサイズ下限
79
85
  run << " -u #{eArgs['maxLen']}" if eArgs['maxLen'] # パターンサイズ上限
@@ -137,9 +143,14 @@ class LcmSeq
137
143
  MCMD::msgLog("the number of contrast patterns enumerated is #{@size}")
138
144
  end
139
145
 
140
- def output(outpath)
141
- system "mv #{@pFile} #{outpath}/patterns.csv"
142
- system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
146
+ def output(outpath,rmsinfo)
147
+ if rmsinfo then
148
+ system "mfldnmae i=#{@pFile} -q o=#{outpath}/patterns.csv"
149
+ system "mfldnmae i=#{@tFile} -q o=#{outpath}/tid_pats.csv" if @outtf
150
+ else
151
+ system "mv #{@pFile} #{outpath}/patterns.csv"
152
+ system "mv #{@tFile} #{outpath}/tid_pats.csv" if @outtf
153
+ end
143
154
  end
144
155
  end
145
156
 
metadata CHANGED
@@ -1,31 +1,30 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: nysol-take
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.0.1
4
+ version: 3.0.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - NYSOL
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2017-10-26 00:00:00.000000000 Z
11
+ date: 2025-05-27 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: nysol
15
15
  requirement: !ruby/object:Gem::Requirement
16
16
  requirements:
17
- - - ~>
17
+ - - "~>"
18
18
  - !ruby/object:Gem::Version
19
19
  version: 3.0.0
20
20
  type: :runtime
21
21
  prerelease: false
22
22
  version_requirements: !ruby/object:Gem::Requirement
23
23
  requirements:
24
- - - ~>
24
+ - - "~>"
25
25
  - !ruby/object:Gem::Version
26
26
  version: 3.0.0
27
- description: |2
28
- nysol TAKE tools
27
+ description: " nysol TAKE tools\n"
29
28
  email: info@nysol.jp
30
29
  executables:
31
30
  - mclique.rb
@@ -54,165 +53,165 @@ extensions:
54
53
  - ext/macerun/extconf.rb
55
54
  extra_rdoc_files: []
56
55
  files:
57
- - ext/lcmrun/extconf.rb
58
- - ext/lcmrun/lcmrun.cpp
59
- - ext/lcmseqrun/extconf.rb
60
- - ext/lcmseqrun/lcmseqrun.cpp
61
- - ext/lcmseq0run/extconf.rb
62
- - ext/lcmseq0run/lcmseq0run.cpp
56
+ - bin/mbiclique.rb
57
+ - bin/mbipolish.rb
58
+ - bin/mccomp.rb
59
+ - bin/mclique.rb
60
+ - bin/mclique2g.rb
61
+ - bin/mcliqueInfo.rb
62
+ - bin/mfriends.rb
63
+ - bin/mgdiff.rb
64
+ - bin/mhifriend.rb
65
+ - bin/mhipolish.rb
66
+ - bin/mitemset.rb
67
+ - bin/mpal.rb
68
+ - bin/mpolishing.rb
69
+ - bin/msequence.rb
70
+ - bin/mtra2g.rb
71
+ - bin/mtra2gc.rb
63
72
  - ext/grhfilrun/extconf.rb
64
73
  - ext/grhfilrun/grhfilrun.c
65
- - ext/sspcrun/extconf.rb
66
- - ext/sspcrun/sspcrun.cpp
67
- - ext/macerun/extconf.rb
68
- - ext/macerun/macerun.cpp
74
+ - ext/grhfilrun/src/_sspc.c
75
+ - ext/grhfilrun/src/aheap.c
76
+ - ext/grhfilrun/src/aheap.h
77
+ - ext/grhfilrun/src/base.c
78
+ - ext/grhfilrun/src/base.h
79
+ - ext/grhfilrun/src/fstar.c
80
+ - ext/grhfilrun/src/fstar.h
81
+ - ext/grhfilrun/src/grhfil.c
82
+ - ext/grhfilrun/src/itemset.c
83
+ - ext/grhfilrun/src/itemset.h
84
+ - ext/grhfilrun/src/problem.c
85
+ - ext/grhfilrun/src/problem.h
86
+ - ext/grhfilrun/src/queue.c
87
+ - ext/grhfilrun/src/queue.h
88
+ - ext/grhfilrun/src/sample.c
89
+ - ext/grhfilrun/src/sspc.c
90
+ - ext/grhfilrun/src/sspc2.c
91
+ - ext/grhfilrun/src/stdlib2.c
92
+ - ext/grhfilrun/src/stdlib2.h
93
+ - ext/grhfilrun/src/trsact.c
94
+ - ext/grhfilrun/src/trsact.h
95
+ - ext/grhfilrun/src/vec.c
96
+ - ext/grhfilrun/src/vec.h
97
+ - ext/lcmrun/extconf.rb
98
+ - ext/lcmrun/lcmrun.cpp
69
99
  - ext/lcmrun/src/aheap.c
100
+ - ext/lcmrun/src/aheap.h
70
101
  - ext/lcmrun/src/base.c
102
+ - ext/lcmrun/src/base.h
71
103
  - ext/lcmrun/src/itemset.c
104
+ - ext/lcmrun/src/itemset.h
72
105
  - ext/lcmrun/src/lcm.c
73
106
  - ext/lcmrun/src/problem.c
74
- - ext/lcmrun/src/queue.c
75
- - ext/lcmrun/src/sgraph.c
76
- - ext/lcmrun/src/stdlib2.c
77
- - ext/lcmrun/src/trsact.c
78
- - ext/lcmrun/src/vec.c
79
- - ext/lcmrun/src/aheap.h
80
- - ext/lcmrun/src/base.h
81
- - ext/lcmrun/src/itemset.h
82
107
  - ext/lcmrun/src/problem.h
108
+ - ext/lcmrun/src/queue.c
83
109
  - ext/lcmrun/src/queue.h
110
+ - ext/lcmrun/src/sgraph.c
84
111
  - ext/lcmrun/src/sgraph.h
112
+ - ext/lcmrun/src/stdlib2.c
85
113
  - ext/lcmrun/src/stdlib2.h
114
+ - ext/lcmrun/src/trsact.c
86
115
  - ext/lcmrun/src/trsact.h
116
+ - ext/lcmrun/src/vec.c
87
117
  - ext/lcmrun/src/vec.h
88
- - ext/lcmseqrun/src/aheap.c
89
- - ext/lcmseqrun/src/base.c
90
- - ext/lcmseqrun/src/itemset.c
91
- - ext/lcmseqrun/src/itemset_zero.c
92
- - ext/lcmseqrun/src/lcm_seq.c
93
- - ext/lcmseqrun/src/lcm_seq_zero.c
94
- - ext/lcmseqrun/src/problem.c
95
- - ext/lcmseqrun/src/problem_zero.c
96
- - ext/lcmseqrun/src/queue.c
97
- - ext/lcmseqrun/src/stdlib2.c
98
- - ext/lcmseqrun/src/trsact.c
99
- - ext/lcmseqrun/src/vec.c
100
- - ext/lcmseqrun/src/aheap.h
101
- - ext/lcmseqrun/src/base.h
102
- - ext/lcmseqrun/src/itemset.h
103
- - ext/lcmseqrun/src/problem.h
104
- - ext/lcmseqrun/src/queue.h
105
- - ext/lcmseqrun/src/stdlib2.h
106
- - ext/lcmseqrun/src/trsact.h
107
- - ext/lcmseqrun/src/vec.h
118
+ - ext/lcmseq0run/extconf.rb
119
+ - ext/lcmseq0run/lcmseq0run.cpp
108
120
  - ext/lcmseq0run/src/aheap.c
121
+ - ext/lcmseq0run/src/aheap.h
109
122
  - ext/lcmseq0run/src/base.c
123
+ - ext/lcmseq0run/src/base.h
110
124
  - ext/lcmseq0run/src/itemset.c
125
+ - ext/lcmseq0run/src/itemset.h
111
126
  - ext/lcmseq0run/src/itemset_zero.c
112
127
  - ext/lcmseq0run/src/lcm_seq.c
113
128
  - ext/lcmseq0run/src/lcm_seq_zero.c
114
129
  - ext/lcmseq0run/src/problem.c
130
+ - ext/lcmseq0run/src/problem.h
115
131
  - ext/lcmseq0run/src/problem_zero.c
116
132
  - ext/lcmseq0run/src/queue.c
117
- - ext/lcmseq0run/src/stdlib2.c
118
- - ext/lcmseq0run/src/trsact.c
119
- - ext/lcmseq0run/src/vec.c
120
- - ext/lcmseq0run/src/aheap.h
121
- - ext/lcmseq0run/src/base.h
122
- - ext/lcmseq0run/src/itemset.h
123
- - ext/lcmseq0run/src/problem.h
124
133
  - ext/lcmseq0run/src/queue.h
134
+ - ext/lcmseq0run/src/stdlib2.c
125
135
  - ext/lcmseq0run/src/stdlib2.h
136
+ - ext/lcmseq0run/src/trsact.c
126
137
  - ext/lcmseq0run/src/trsact.h
138
+ - ext/lcmseq0run/src/vec.c
127
139
  - ext/lcmseq0run/src/vec.h
140
+ - ext/lcmseqrun/extconf.rb
141
+ - ext/lcmseqrun/lcmseqrun.cpp
142
+ - ext/lcmseqrun/src/aheap.c
143
+ - ext/lcmseqrun/src/aheap.h
144
+ - ext/lcmseqrun/src/base.c
145
+ - ext/lcmseqrun/src/base.h
146
+ - ext/lcmseqrun/src/itemset.c
147
+ - ext/lcmseqrun/src/itemset.h
148
+ - ext/lcmseqrun/src/itemset_zero.c
149
+ - ext/lcmseqrun/src/lcm_seq.c
150
+ - ext/lcmseqrun/src/lcm_seq_zero.c
151
+ - ext/lcmseqrun/src/problem.c
152
+ - ext/lcmseqrun/src/problem.h
153
+ - ext/lcmseqrun/src/problem_zero.c
154
+ - ext/lcmseqrun/src/queue.c
155
+ - ext/lcmseqrun/src/queue.h
156
+ - ext/lcmseqrun/src/stdlib2.c
157
+ - ext/lcmseqrun/src/stdlib2.h
158
+ - ext/lcmseqrun/src/trsact.c
159
+ - ext/lcmseqrun/src/trsact.h
160
+ - ext/lcmseqrun/src/vec.c
161
+ - ext/lcmseqrun/src/vec.h
162
+ - ext/lcmtransrun/extconf.rb
163
+ - ext/lcmtransrun/lcmtransrun.cpp
164
+ - ext/macerun/extconf.rb
165
+ - ext/macerun/macerun.cpp
166
+ - ext/macerun/src/aheap.c
167
+ - ext/macerun/src/aheap.h
168
+ - ext/macerun/src/itemset.c
169
+ - ext/macerun/src/itemset.h
170
+ - ext/macerun/src/mace.c
171
+ - ext/macerun/src/problem.c
172
+ - ext/macerun/src/problem.h
173
+ - ext/macerun/src/queue.c
174
+ - ext/macerun/src/queue.h
175
+ - ext/macerun/src/sgraph.c
176
+ - ext/macerun/src/sgraph.h
177
+ - ext/macerun/src/stdlib2.c
178
+ - ext/macerun/src/stdlib2.h
179
+ - ext/macerun/src/vec.c
180
+ - ext/macerun/src/vec.h
181
+ - ext/sspcrun/extconf.rb
128
182
  - ext/sspcrun/src/_sspc.c
129
183
  - ext/sspcrun/src/aheap.c
184
+ - ext/sspcrun/src/aheap.h
130
185
  - ext/sspcrun/src/base.c
186
+ - ext/sspcrun/src/base.h
131
187
  - ext/sspcrun/src/fstar.c
188
+ - ext/sspcrun/src/fstar.h
132
189
  - ext/sspcrun/src/grhfil.c
133
190
  - ext/sspcrun/src/itemset.c
191
+ - ext/sspcrun/src/itemset.h
134
192
  - ext/sspcrun/src/problem.c
193
+ - ext/sspcrun/src/problem.h
135
194
  - ext/sspcrun/src/queue.c
195
+ - ext/sspcrun/src/queue.h
136
196
  - ext/sspcrun/src/sample.c
137
197
  - ext/sspcrun/src/sspc.c
138
198
  - ext/sspcrun/src/sspc2.c
139
199
  - ext/sspcrun/src/stdlib2.c
140
- - ext/sspcrun/src/trsact.c
141
- - ext/sspcrun/src/vec.c
142
- - ext/sspcrun/src/aheap.h
143
- - ext/sspcrun/src/base.h
144
- - ext/sspcrun/src/fstar.h
145
- - ext/sspcrun/src/itemset.h
146
- - ext/sspcrun/src/problem.h
147
- - ext/sspcrun/src/queue.h
148
200
  - ext/sspcrun/src/stdlib2.h
201
+ - ext/sspcrun/src/trsact.c
149
202
  - ext/sspcrun/src/trsact.h
203
+ - ext/sspcrun/src/vec.c
150
204
  - ext/sspcrun/src/vec.h
151
- - ext/macerun/src/aheap.c
152
- - ext/macerun/src/itemset.c
153
- - ext/macerun/src/mace.c
154
- - ext/macerun/src/problem.c
155
- - ext/macerun/src/queue.c
156
- - ext/macerun/src/sgraph.c
157
- - ext/macerun/src/stdlib2.c
158
- - ext/macerun/src/vec.c
159
- - ext/macerun/src/aheap.h
160
- - ext/macerun/src/itemset.h
161
- - ext/macerun/src/problem.h
162
- - ext/macerun/src/queue.h
163
- - ext/macerun/src/sgraph.h
164
- - ext/macerun/src/stdlib2.h
165
- - ext/macerun/src/vec.h
166
- - ext/grhfilrun/src/_sspc.c
167
- - ext/grhfilrun/src/aheap.c
168
- - ext/grhfilrun/src/base.c
169
- - ext/grhfilrun/src/fstar.c
170
- - ext/grhfilrun/src/grhfil.c
171
- - ext/grhfilrun/src/itemset.c
172
- - ext/grhfilrun/src/problem.c
173
- - ext/grhfilrun/src/queue.c
174
- - ext/grhfilrun/src/sample.c
175
- - ext/grhfilrun/src/sspc.c
176
- - ext/grhfilrun/src/sspc2.c
177
- - ext/grhfilrun/src/stdlib2.c
178
- - ext/grhfilrun/src/trsact.c
179
- - ext/grhfilrun/src/vec.c
180
- - ext/grhfilrun/src/aheap.h
181
- - ext/grhfilrun/src/base.h
182
- - ext/grhfilrun/src/fstar.h
183
- - ext/grhfilrun/src/itemset.h
184
- - ext/grhfilrun/src/problem.h
185
- - ext/grhfilrun/src/queue.h
186
- - ext/grhfilrun/src/stdlib2.h
187
- - ext/grhfilrun/src/trsact.h
188
- - ext/grhfilrun/src/vec.h
189
- - ext/lcmtransrun/extconf.rb
190
- - ext/lcmtransrun/lcmtransrun.cpp
205
+ - ext/sspcrun/sspcrun.cpp
191
206
  - lib/nysol/enumLcmEp.rb
192
207
  - lib/nysol/enumLcmEsp.rb
193
208
  - lib/nysol/enumLcmIs.rb
194
209
  - lib/nysol/enumLcmSeq.rb
195
210
  - lib/nysol/items.rb
196
211
  - lib/nysol/seqDB.rb
212
+ - lib/nysol/take.rb
197
213
  - lib/nysol/taxonomy.rb
198
214
  - lib/nysol/traDB.rb
199
- - lib/nysol/take.rb
200
- - bin/mclique.rb
201
- - bin/mbiclique.rb
202
- - bin/mbipolish.rb
203
- - bin/mclique2g.rb
204
- - bin/mcliqueInfo.rb
205
- - bin/mgdiff.rb
206
- - bin/mitemset.rb
207
- - bin/mpolishing.rb
208
- - bin/msequence.rb
209
- - bin/mfriends.rb
210
- - bin/mccomp.rb
211
- - bin/mhifriend.rb
212
- - bin/mhipolish.rb
213
- - bin/mpal.rb
214
- - bin/mtra2gc.rb
215
- - bin/mtra2g.rb
216
215
  homepage: http://www.nysol.jp/
217
216
  licenses: []
218
217
  metadata: {}
@@ -222,17 +221,16 @@ require_paths:
222
221
  - lib
223
222
  required_ruby_version: !ruby/object:Gem::Requirement
224
223
  requirements:
225
- - - '>='
224
+ - - ">="
226
225
  - !ruby/object:Gem::Version
227
226
  version: '0'
228
227
  required_rubygems_version: !ruby/object:Gem::Requirement
229
228
  requirements:
230
- - - '>='
229
+ - - ">="
231
230
  - !ruby/object:Gem::Version
232
231
  version: '0'
233
232
  requirements: []
234
- rubyforge_project:
235
- rubygems_version: 2.0.14
233
+ rubygems_version: 3.0.3.1
236
234
  signing_key:
237
235
  specification_version: 4
238
236
  summary: nysol TAKE tools