0.5.0:

	New function: reconstruction of directed acyclic graph from prior information of edge significance. For details, see library function netr_one_greedy, doc.pdf, or UPDATES in any interface.

Author: lingfeiwang

Makefile

@@ -14,8 +14,8 @@ URL_LIB_REL="$(URL_LIB)/releases"
 URL_BIN_REL="$(URL_BIN)/releases"
 URL_R_REL="$(URL_R)/releases"
 VERSION1=0
-VERSION2=4
-VERSION3=1
+VERSION2=5
+VERSION3=0
 LICENSE=AGPL-3
 LICENSE_FULL="GNU Affero General Public License, Version 3"
 LICENSE_URL="https://www.gnu.org/licenses/agpl-3.0"
@@ -152,13 +152,12 @@ Makefile.flags:
 	ldflags="$$ldflags -lgfortran"; \
 	echo "Testing local GSL" ; \
 	if [ -n "$(DIR_SRC_GSL)" ] ; then \
-		( dd=$$(pwd) && cd "$(DIR_SRC_GSL)" && ./configure && $(MAKE) && cd "$$dd" &> /dev/null ) || exit 1; \
 		echo "Testing -Wl,--whole-archive" ; \
 		ldflags2="$(DIR_SRC_GSL)/.libs/libgsl.a $(DIR_SRC_GSL)/cblas/.libs/libgslcblas.a"; \
+		$(LD) $$ldflags "-Wl,--whole-archive $$ldflags2 -Wl,--no-whole-archive" --shared -o $(TMP_FILE) &> /dev/null && \
+			ldflags2="-Wl,--whole-archive $$ldflags2 -Wl,--no-whole-archive"; \
 		$(LD) $$ldflags $$ldflags2 --shared -o $(TMP_FILE) &> /dev/null || \
-		( ldflags="-Wl,--whole-archive $$ldflags2 -Wl,--no-whole-archive" ; \
-		  $(LD) $$ldflags $$ldflags2 --shared -o $(TMP_FILE) &> /dev/null || \
-		    ( echo "Can't link to local GSL with right flag." ; exit 1; ) ) ; \
+		    ( echo "Can't link to embedded GSL with right flag." ; exit 1; ); \
 		cflags="-I $(DIR_SRC_GSL) $$cflags" ; \
 		ldflags="$$ldflags $$ldflags2" ; \
 	else \

UPDATES

@@ -1,3 +1,5 @@
+0.5.0:
+	New function: reconstruction of directed acyclic graph from prior information of edge significance. For details, see library function netr_one_greedy, doc.pdf, or UPDATES in any interface.
 0.4.1:
 	Extreme situation behavior:
 		Added error checking for few samples (<4).

base/data_struct.h

@@ -0,0 +1,27 @@
+/* Copyright 2016, 2017 Lingfei Wang
+ * 
+ * This file is part of Findr.
+ * 
+ * Findr is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * Findr is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Affero General Public License
+ * along with Findr.  If not, see <http://www.gnu.org/licenses/>.
+ */
+/* This lib contains definitions of data structures
+ */
+ 
+#ifndef _HEADER_LIB_DATA_STRUCT_H_
+#define _HEADER_LIB_DATA_STRUCT_H_
+#include "config.h"
+#include "data_struct_ll.h"
+#include "data_struct_heap.h"
+
+#endif

base/data_struct_heap.c

@@ -0,0 +1,172 @@
+/* Copyright 2016, 2017 Lingfei Wang
+ * 
+ * This file is part of Findr.
+ * 
+ * Findr is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * Findr is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Affero General Public License
+ * along with Findr.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#include "config.h"
+#include <string.h>
+#include "logger.h"
+#include "macros.h"
+#include "data_struct_heap.h"
+
+int data_heap_init(struct data_heap* h,size_t nmax)
+{
+	h->nmax=nmax;
+	h->n=0;
+	MALLOCSIZE(h->d,nmax);
+	return !h->d;
+}
+
+void data_heap_free(struct data_heap* h)
+{
+	h->nmax=0;
+	if(h->d)
+		free(h->d);
+	h->d=0;
+}
+
+void data_heap_empty(struct data_heap* h)
+{
+	h->n=0;
+}
+
+int data_heap_push(struct data_heap* h, HTYPE d)
+{
+	size_t c,p;
+	
+	if(h->nmax==h->n)
+	{
+		LOG(10,"Heap push failed: heap full.")
+		return 1;
+	}
+	h->d[h->n]=d;
+	c=h->n++;
+	while(c)
+	{
+		p=(c-1)/2;
+		if(d>h->d[p])
+			return 0;
+		h->d[c]=h->d[p];
+		h->d[p]=d;
+		c=p;
+	}
+	return 0;
+}
+
+HTYPE data_heap_pop(struct data_heap* h)
+{
+	size_t	p,c2,cm,pn;
+	HTYPE	v,ret;
+	
+	assert(h->n);
+	ret=h->d[0];
+	h->d[0]=h->d[--(h->n)];
+	if(!h->n)
+		return ret;
+	p=0;
+	pn=h->n/2;
+	while(p+1<pn)
+	{
+		cm=2*p+1;
+		c2=cm+1;
+		if(h->d[c2]<h->d[cm])
+			cm=c2;
+		if(h->d[p]<h->d[cm])
+			return ret;
+		v=h->d[p];
+		h->d[p]=h->d[cm];
+		h->d[cm]=v;
+		p=cm;
+	}
+	if(p+1==pn)
+	{
+		cm=2*p+1;
+		c2=cm+1;
+		if((c2<h->n)&&(h->d[c2]<h->d[cm]))
+			cm=c2;
+		if(h->d[p]<h->d[cm])
+			return ret;
+		v=h->d[p];
+		h->d[p]=h->d[cm];
+		h->d[cm]=v;
+	}
+	return ret;
+}
+
+int data_heapdec_push(struct data_heapdec* h, HTYPE d)
+{
+	size_t c,p;
+	
+	if(h->nmax==h->n)
+	{
+		LOG(10,"Heap push failed: heap full.")
+		return 1;
+	}
+	h->d[h->n]=d;
+	c=h->n++;
+	while(c)
+	{
+		p=(c-1)/2;
+		if(d<h->d[p])
+			return 0;
+		h->d[c]=h->d[p];
+		h->d[p]=d;
+		c=p;
+	}
+	return 0;
+}
+
+HTYPE data_heapdec_pop(struct data_heapdec* h)
+{
+	size_t	p,c2,cm,pn;
+	HTYPE	v,ret;
+	
+	assert(h->n);
+	ret=h->d[0];
+	h->d[0]=h->d[--(h->n)];
+	if(!h->n)
+		return ret;
+	p=0;
+	pn=h->n/2;
+	while(p+1<pn)
+	{
+		cm=2*p+1;
+		c2=cm+1;
+		if(h->d[c2]>h->d[cm])
+			cm=c2;
+		if(h->d[p]>h->d[cm])
+			return ret;
+		v=h->d[p];
+		h->d[p]=h->d[cm];
+		h->d[cm]=v;
+		p=cm;
+	}
+	if(p+1==pn)
+	{
+		cm=2*p+1;
+		c2=cm+1;
+		if((c2<h->n)&&(h->d[c2]>h->d[cm]))
+			cm=c2;
+		if(h->d[p]>h->d[cm])
+			return ret;
+		v=h->d[p];
+		h->d[p]=h->d[cm];
+		h->d[cm]=v;
+	}
+	return ret;
+}
+
+
+

base/data_struct_heap.h

@@ -0,0 +1,77 @@
+/* Copyright 2016, 2017 Lingfei Wang
+ * 
+ * This file is part of Findr.
+ * 
+ * Findr is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * Findr is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Affero General Public License
+ * along with Findr.  If not, see <http://www.gnu.org/licenses/>.
+ */
+/* This lib contains definition of heap data structure
+ */
+ 
+#ifndef _HEADER_LIB_DATA_STRUCT_HEAP_H_
+#define _HEADER_LIB_DATA_STRUCT_HEAP_H_
+#include "config.h"
+#include <stdlib.h>
+#include <assert.h>
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+
+#define HTYPE	size_t
+
+//Incremental heap
+struct data_heap
+{
+	size_t nmax;
+	size_t n;
+	HTYPE* restrict	d;
+};
+
+int data_heap_init(struct data_heap* h,size_t nmax);
+void data_heap_free(struct data_heap* h);
+void data_heap_empty(struct data_heap* h);
+int data_heap_push(struct data_heap* h, HTYPE d);
+HTYPE data_heap_pop(struct data_heap* h);
+// int data_heap_popto(struct data_heap* h, HTYPE* d);
+static inline HTYPE data_heap_get(const struct data_heap* h,size_t n);
+static inline HTYPE data_heap_top(const struct data_heap* h);
+
+//Decremental heap
+#define data_heapdec data_heap
+#define data_heapdec_init data_heap_init
+#define data_heapdec_free data_heap_free
+#define data_heapdec_empty data_heap_empty
+int data_heapdec_push(struct data_heapdec* h, HTYPE d);
+HTYPE data_heapdec_pop(struct data_heapdec* h);
+#define data_heapdec_get data_heap_get
+#define data_heapdec_top data_heap_top
+
+
+static inline HTYPE data_heap_get(const struct data_heap* h,size_t n)
+{
+	assert(h->n>n);
+	return h->d[n];
+}
+
+static inline HTYPE data_heap_top(const struct data_heap* h)
+{
+	return data_heap_get(h,0);
+}
+
+#ifdef __cplusplus
+}
+#endif
+#endif

base/data_struct_ll.c

@@ -0,0 +1,57 @@
+/* Copyright 2016, 2017 Lingfei Wang
+ * 
+ * This file is part of Findr.
+ * 
+ * Findr is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ * 
+ * Findr is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Affero General Public License
+ * along with Findr.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#include "config.h"
+#include <string.h>
+#include "macros.h"
+#include "data_struct_ll.h"
+
+int data_ll_init(struct data_ll* ll,size_t nmax)
+{
+	assert(ll);
+	ll->nmax=nmax;
+	ll->n=0;
+	MALLOCSIZE(ll->d,2*nmax);
+	if(!ll->d)
+	{
+		LOG(1,"Not enough memory.")
+		return 1;
+	}
+	memset(ll->d,-1,2*nmax*sizeof(*ll->d));
+	return 0;
+}
+
+void data_ll_free(struct data_ll* ll)
+{
+	assert(ll);
+	if(ll->d)
+	{
+		free(ll->d);
+		ll->d=0;
+	}
+	ll->nmax=0;
+}
+
+void data_ll_empty(struct data_ll* ll)
+{
+	assert(ll);
+	ll->n=0;
+	memset(ll->d,-1,2*ll->nmax*sizeof(*ll->d));
+}
+
+
+