1. preprocessCore
  2. Commit 57012cd9554ebf2d65b81d0995cfce1155d797b6
Browse code

standardize all exported C level functionality

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/preprocessCore@27386 bc3139a8-67e5-0310-9ffc-ced21a209358

Ben Bolstad authored on 21/09/2007 02:12:55
Showing8 changed files
DESCRIPTION
History View file @57012cd
... ... 
@@ -1,5 +1,5 @@
1 1 
 Package: preprocessCore
2 
-Version: 0.99.20
2 
+Version: 0.99.21
3 3 
 Title: A collection of pre-processing functions
4 4 
 Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
5 5 
 Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
inst/include/avg.h
History View file @57012cd
6 6 
new file mode 100644
... ... 
@@ -0,0 +1,10 @@
1 
+#ifndef AVG_H
2 
+#define AVG_H
3 
+
4 
+void ColAverage(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
5 
+void ColAverage_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
6 
+
7 
+void colaverage_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
8 
+void colaverage(double *data, int rows, int cols, double *results, double *resultsSE);
9 
+
10 
+#endif
inst/include/biweight.h
History View file @57012cd
... ... 
@@ -2,7 +2,11 @@
2 2 
 #define BIWEIGHT_H 1
3 3
4 4 
 void tukeybiweight(double *data, int rows, int cols, double *results, double *resultsSE);
5 
+void tukeybiweight_no_log(double *data, int rows, int cols, double *results, double *resultsSE);
5 6 
 void TukeyBiweight(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
7 
+void TukeyBiweight_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
8 
+void TukeyBiweight_no_log_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
9 
+
6 10 
 double Tukey_Biweight(double *x, int length);
7 11
8 12 
 #endif
inst/include/log_median.h
History View file @57012cd
... ... 
@@ -4,6 +4,7 @@
4 4
5 5
6 6 
 void LogMedian(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
7 
+void LogMedian_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
7 8
8 9 
 void logmedian(double *data, int rows, int cols, double *results, double *resultsSE);
9 10 
 void logmedian_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
inst/include/median.h
History View file @57012cd
10 11 
new file mode 100644
... ... 
@@ -0,0 +1,15 @@
1 
+#ifndef MEDIAN_H
2 
+#define MEDIAN_H 1
3 
+
4 
+
5 
+
6 
+void ColMedian(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
7 
+void ColMedian_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
8 
+
9 
+void colmedian(double *data, int rows, int cols, double *results, double *resultsSE);
10 
+void colmedian_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
11 
+
12 
+
13 
+
14 
+
15 
+#endif
inst/include/medianpolish.h
History View file @57012cd
... ... 
@@ -7,5 +7,7 @@ void median_polish_log2_no_copy(double *data, int rows, int cols, double *result
7 7 
 void median_polish_log2(double *data, int rows, int cols, double *results, double *resultsSE, double *residuals);
8 8 
 void median_polish(double *data, int rows, int cols, double *results, double *resultsSE, double *residuals);
9 9 
 void MedianPolish(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
10 
+void MedianPolish_no_log(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
11 
+
10 12
11 13 
 #endif
inst/include/preprocessCore_summarization_stubs.c
History View file @57012cd
... ... 
@@ -155,7 +155,20 @@ void LogAverage(double *data, int rows, int cols, int *cur_rows, double *results
155 155
156 156 
   if (fun == NULL)
157 157 
     fun =  (void(*)(double*, int, int, int*, double *, int, double *))R_GetCCallable("preprocessCore","LogAverage");
158 
-  fun(data,rows,cols,cur_rows,results,nprobes,resultsSE);
158 
+  fun(data, rows, cols, cur_rows, results, nprobes, resultsSE);
159 
+  return;
160 
+}
161 
+
162 
+
163 
+
164 
+void LogAverage_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes){
165 
+
166 
+
167 
+  static void(*fun)(double*, int, int, int*, double *, int) = NULL;
168 
+
169 
+  if (fun == NULL)
170 
+    fun =  (void(*)(double*, int, int, int*, double *, int))R_GetCCallable("preprocessCore","LogAverage_noSE");
171 
+  fun(data, rows, cols, cur_rows, results, nprobes);
159 172 
   return;
160 173 
 }
161 174
... ... 
@@ -169,12 +182,23 @@ void tukeybiweight(double *data, int rows, int cols, double *results, double *re
169 182 
     fun = (void(*)(double *, int, int, double *, double *))R_GetCCallable("preprocessCore","tukeybiweight");
170 183 
   fun(data, rows, cols, results, resultsSE);
171 184 
   return;
185 
+}
172 186
187 
+void tukeybiweight_no_log(double *data, int rows, int cols, double *results, double *resultsSE){
173 188
189 
+  static void(*fun)(double *, int, int, double *, double *) = NULL;
174 190
191 
+  if (fun == NULL)
192 
+    fun = (void(*)(double *, int, int, double *, double *))R_GetCCallable("preprocessCore","tukeybiweight_no_log");
193 
+  fun(data, rows, cols, results, resultsSE);
194 
+  return;
175 195 
 }
176 196
177 197
198 
+
199 
+
200 
+
201 
+
178 202 
 void TukeyBiweight(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE){
179 203
180 204
... ... 
@@ -184,12 +208,35 @@ void TukeyBiweight(double *data, int rows, int cols, int *cur_rows, double *resu
184 208 
     fun = (void(*)(double *, int, int, int *, double *, int, double *))R_GetCCallable("preprocessCore","TukeyBiweight");
185 209 
   fun(data, rows, cols, cur_rows,results, nprobes, resultsSE);
186 210 
   return;
211 
+}
212 
+
213 
+void TukeyBiweight_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes){
214 
+
215 
+
216 
+  static void(*fun)(double *, int, int, int *, double *, int) = NULL;
217 
+
218 
+  if (fun == NULL)
219 
+    fun = (void(*)(double *, int, int, int *, double *, int))R_GetCCallable("preprocessCore","TukeyBiweight_noSE");
220 
+  fun(data, rows, cols, cur_rows,results, nprobes);
221 
+  return;
222 
+}
223 
+
224 
+
225 
+void TukeyBiweight_no_log_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes){
187 226
188 227
228 
+  static void(*fun)(double *, int, int, int *, double *, int) = NULL;
229 
+
230 
+  if (fun == NULL)
231 
+    fun = (void(*)(double *, int, int, int *, double *, int))R_GetCCallable("preprocessCore","TukeyBiweight_no_log_noSE");
232 
+  fun(data, rows, cols, cur_rows,results, nprobes);
233 
+  return;
189 234 
 }
190 235
191 236
192 237
238 
+
239 
+
193 240 
 double Tukey_Biweight(double *x, int length){
194 241
195 242 
   static double(*fun)(double *, int) = NULL;
... ... 
@@ -310,6 +357,19 @@ void MedianPolish(double *data, int rows, int cols, int *cur_rows, double *resul
310 357 
 }
311 358
312 359
360 
+void MedianPolish_no_log(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE){
361 
+
362 
+
363 
+  static void(*fun)(double *, int, int, int *, double *, int, double *) = NULL;
364 
+
365 
+  if (fun == NULL)
366 
+    fun = (void(*)(double *, int, int, int *, double *, int, double *))R_GetCCallable("preprocessCore","MedianPolish_no_log");
367 
+
368 
+  fun(data,rows,cols,cur_rows,results,nprobes,resultsSE);
369 
+  return;
370 
+
371 
+}
372 
+
313 373
314 374
315 375
... ... 
@@ -482,6 +542,17 @@ void LogMedian(double *data, int rows, int cols, int *cur_rows, double *results,
482 542
483 543 
 }
484 544
545 
+void LogMedian_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE){
546 
+
547 
+  static void(*fun)(double *, int, int, int *, double *, int, double *) = NULL;
548 
+
549 
+  if (fun == NULL)
550 
+    fun = (void(*)(double *, int, int, int *, double *, int, double *))R_GetCCallable("preprocessCore","LogMedian_noSE");
551 
+  fun(data, rows, cols, cur_rows, results, nprobes, resultsSE);
552 
+  return;
553 
+
554 
+}
555 
+
485 556
486 557 
 void logmedian(double *data, int rows, int cols, double *results, double *resultsSE){
487 558
... ... 
@@ -505,3 +576,105 @@ void logmedian_no_copy(double *data, int rows, int cols, double *results, double
505 576 
   return;
506 577
507 578 
 }
579 
+
580 
+
581 
+
582 
+
583 
+
584 
+
585 
+
586 
+void colaverage_no_copy(double *data, int rows, int cols, double *results, double *resultsSE){
587 
+
588 
+  static void(*fun)(double*, int, int, double *, double *) = NULL;
589 
+
590 
+  if (fun == NULL)
591 
+    fun =  (void(*)(double*, int, int, double *, double *))R_GetCCallable("preprocessCore","colaverage_no_copy");
592 
+
593 
+  fun(data,rows,cols,results,resultsSE);
594 
+  return;
595 
+}
596 
+
597 
+void colaverage(double *data, int rows, int cols, double *results, double *resultsSE){
598 
+
599 
+  static void(*fun)(double*, int, int, double *, double *) = NULL;
600 
+
601 
+  if (fun == NULL)
602 
+    fun =  (void(*)(double*, int, int, double *, double *))R_GetCCallable("preprocessCore","colaverage");
603 
+
604 
+  fun(data,rows,cols,results,resultsSE);
605 
+  return;
606 
+}
607 
+
608 
+
609 
+
610 
+void ColAverage(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE){
611 
+
612 
+  static void(*fun)(double*, int, int, int*, double *, int, double *) = NULL;
613 
+
614 
+  if (fun == NULL)
615 
+    fun =  (void(*)(double*, int, int, int*, double *, int, double *))R_GetCCallable("preprocessCore","ColAverage");
616 
+
617 
+  fun(data, rows, cols, cur_rows, results, nprobes, resultsSE);
618 
+  return;
619 
+}
620 
+
621 
+void ColAverage_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes){
622 
+
623 
+  static void(*fun)(double*, int, int, int*, double *, int) = NULL;
624 
+
625 
+  if (fun == NULL)
626 
+    fun =  (void(*)(double*, int, int, int*, double *, int))R_GetCCallable("preprocessCore","ColAverage_noSE");
627 
+
628 
+  fun(data, rows, cols, cur_rows, results, nprobes);
629 
+  return;
630 
+}
631 
+
632 
+
633 
+
634 
+
635 
+void colmedian_no_copy(double *data, int rows, int cols, double *results, double *resultsSE){
636 
+
637 
+  static void(*fun)(double*, int, int, double *, double *) = NULL;
638 
+
639 
+  if (fun == NULL)
640 
+    fun =  (void(*)(double*, int, int, double *, double *))R_GetCCallable("preprocessCore","colmedian_no_copy");
641 
+
642 
+  fun(data,rows,cols,results,resultsSE);
643 
+  return;
644 
+}
645 
+
646 
+void colmedian(double *data, int rows, int cols, double *results, double *resultsSE){
647 
+
648 
+  static void(*fun)(double*, int, int, double *, double *) = NULL;
649 
+
650 
+  if (fun == NULL)
651 
+    fun =  (void(*)(double*, int, int, double *, double *))R_GetCCallable("preprocessCore","colmedian");
652 
+
653 
+  fun(data,rows,cols,results,resultsSE);
654 
+  return;
655 
+}
656 
+
657 
+
658 
+
659 
+void ColMedian(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE){
660 
+
661 
+  static void(*fun)(double*, int, int, int*, double *, int, double *) = NULL;
662 
+
663 
+  if (fun == NULL)
664 
+    fun =  (void(*)(double*, int, int, int*, double *, int, double *))R_GetCCallable("preprocessCore","ColMedian");
665 
+
666 
+  fun(data, rows, cols, cur_rows, results, nprobes, resultsSE);
667 
+  return;
668 
+}
669 
+
670 
+void ColMedian_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes){
671 
+
672 
+  static void(*fun)(double*, int, int, int*, double *, int) = NULL;
673 
+
674 
+  if (fun == NULL)
675 
+    fun =  (void(*)(double*, int, int, int*, double *, int))R_GetCCallable("preprocessCore","ColMedian_noSE");
676 
+
677 
+  fun(data, rows, cols, cur_rows, results, nprobes);
678 
+  return;
679 
+}
680 
+
src/init_package.c
History View file @57012cd
... ... 
@@ -99,7 +99,8 @@ void R_init_preprocessCore(DllInfo *info){
99 99 
   R_RegisterCCallable("preprocessCore", "median_polish_log2", (DL_FUNC)&median_polish_log2);
100 100 
   R_RegisterCCallable("preprocessCore", "median_polish", (DL_FUNC)&median_polish);
101 101 
   R_RegisterCCallable("preprocessCore", "MedianPolish", (DL_FUNC)&MedianPolish);
102 
-
102 
+  R_RegisterCCallable("preprocessCore", "MedianPolish_no_log", (DL_FUNC)&MedianPolish_no_log);
103 
+
103 104
104 105 
   R_RegisterCCallable("preprocessCore","AverageLog", (DL_FUNC)&AverageLog);
105 106 
   R_RegisterCCallable("preprocessCore","averagelog_no_copy", (DL_FUNC)&averagelog_no_copy);
... ... 
@@ -119,6 +120,7 @@ void R_init_preprocessCore(DllInfo *info){
119 120 
   R_RegisterCCallable("preprocessCore","LogMedian", (DL_FUNC)&LogMedian);
120 121 
   R_RegisterCCallable("preprocessCore","logmedian_no_copy", (DL_FUNC)&logmedian_no_copy);
121 122 
   R_RegisterCCallable("preprocessCore","logmedian", (DL_FUNC)&logmedian);
123 
+  R_RegisterCCallable("preprocessCore","LogMedian_noSE", (DL_FUNC)&LogMedian_noSE);
122 124
123 125 
   R_RegisterCCallable("preprocessCore","ColMedian", (DL_FUNC)&ColMedian);
124 126 
   R_RegisterCCallable("preprocessCore","colmedian_no_copy", (DL_FUNC)&colmedian_no_copy);
... ... 
@@ -130,9 +132,12 @@ void R_init_preprocessCore(DllInfo *info){
130 132 
   R_RegisterCCallable("preprocessCore","LogAverage_noSE", (DL_FUNC)&LogAverage_noSE);
131 133
132 134 
   R_RegisterCCallable("preprocessCore","tukeybiweight", (DL_FUNC)&tukeybiweight);
135 
+  R_RegisterCCallable("preprocessCore","tukeybiweight_no_log", (DL_FUNC)&tukeybiweight_no_log);
133 136 
   R_RegisterCCallable("preprocessCore","TukeyBiweight", (DL_FUNC)&TukeyBiweight);
137 
+  R_RegisterCCallable("preprocessCore","TukeyBiweight_noSE", (DL_FUNC)&TukeyBiweight_noSE);
138 
+  R_RegisterCCallable("preprocessCore","TukeyBiweight_no_log_noSE", (DL_FUNC)&TukeyBiweight_no_log_noSE);
134 139 
   R_RegisterCCallable("preprocessCore","Tukey_Biweight", (DL_FUNC)&Tukey_Biweight);
135 
-
140 
+
136 141
137 142 
   R_RegisterCCallable("preprocessCore","lm_wfit", (DL_FUNC)&lm_wfit);
138 143