From b8af5dd65f305ff0230c43bd4648d386f72a0f12 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 20 Apr 2009 08:31:30 +0000
Subject: [PATCH] Merge of eric-test branche to the trunk

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@199 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecoPrimer                   | Bin 62448 -> 0 bytes
 src/libecoprimer/amplifiatree.c | 131 +++++++++++++++++++
 src/libecoprimer/pairtree.c     | 136 +++++++++++++++++++
 src/libecoprimer/taxstats.c     | 224 ++++++++++++++++++++++++++++++++
 4 files changed, 491 insertions(+)
 delete mode 100755 src/ecoPrimer
 create mode 100644 src/libecoprimer/amplifiatree.c
 create mode 100644 src/libecoprimer/pairtree.c
 create mode 100644 src/libecoprimer/taxstats.c

diff --git a/src/ecoPrimer b/src/ecoPrimer
deleted file mode 100755
index 13716c122e12ae6e4bfea9dcfa533af903040fa0..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/src/libecoprimer/amplifiatree.c b/src/libecoprimer/amplifiatree.c
new file mode 100644
index 0000000..3698dea
--- /dev/null
+++ b/src/libecoprimer/amplifiatree.c
@@ -0,0 +1,131 @@
+/*
+ * amplifiatree.c
+ *
+ *  Created on: 7 mars 2009
+ *      Author: coissac
+ */
+
+#include  "ecoprimer.h"
+#include <search.h>
+
+static void cleanamplifia(pamplifia_t amplifia);
+static void deleteamplifialist(pamplifialist_t list);
+static int cmpamplifia(const void* p1,const void*p2);
+
+
+static void cleanamplifiatlist(pamplifiacount_t list)
+{
+	if (list->amplifias)
+		ECOFREE(list->amplifias,
+				"Free amplifia list");
+}
+
+static void cleanamplifia(pamplifia_t amplifia)
+{
+   cleanamplifiatlist(&(amplifia->pcr));
+}
+
+static pamplifialist_t newamplifialist(pamplifialist_t parent, size_t size)
+{
+	pamplifialist_t tmp;
+
+	tmp=ECOMALLOC(sizeof(amplifialist_t)+sizeof(amplifia_t)*(size-1),
+			      "Cannot allocate new amplifia list");
+
+	tmp->amplifiaslots=size;
+	tmp->amplifiacount=0;
+	tmp->next=NULL;
+
+	if (parent)
+		parent->next=(void*)tmp;
+
+	return tmp;
+}
+
+static void deleteamplifialist(pamplifialist_t list)
+{
+	size_t i;
+
+	if (list)
+	{
+		if (list->next)
+		{
+			deleteamplifialist(list->next);
+			list->next=NULL;
+		}
+		for (i=0; i < list->amplifiacount; i++)
+			cleanamplifia((list->amplifias)+i);
+
+		ECOFREE(list,"Delete amplifia list");
+	}
+
+}
+
+static int cmpamplifia(const void* p1,const void*p2)
+{
+	pamplifia_t pr1,pr2;
+
+	pr1=(pamplifia_t)p1;
+	pr2=(pamplifia_t)p2;
+
+	if (pr1->p1 < pr2->p1) return -1;
+	if (pr1->p1 > pr2->p1) return  1;
+
+	if (pr1->asdirect1 < pr2->asdirect1) return -1;
+	if (pr1->asdirect1 > pr2->asdirect1) return  1;
+
+	if (pr1->p2 < pr2->p2) return -1;
+	if (pr1->p2 > pr2->p2) return  1;
+
+	if (pr1->asdirect2 < pr2->asdirect2) return -1;
+	if (pr1->asdirect2 > pr2->asdirect2) return  1;
+
+	return 0;
+}
+
+pamplifia_t amplifiaintree (amplifia_t key,
+		            pamplifiatree_t amplifialist)
+{
+	if (!amplifialist->tree)
+		return NULL;
+
+	return *((pamplifia_t*)tsearch((const void *)(&key),
+								&(amplifialist->tree),
+						        cmpamplifia
+							  ));
+}
+
+pamplifia_t insertamplifia(amplifia_t key,
+		           pamplifiatree_t list)
+{
+	pamplifia_t current;
+	pamplifia_t found;
+
+	if (list->last->amplifiacount==list->last->amplifiaslots)
+	{
+		list->last->next=newamplifialist(list,100);
+		list->last=list->last->next;
+	}
+
+	current = list->last->amplifias + list->last->amplifiacount;
+	*current=key;
+
+	found = *((pamplifia_t*)tsearch((const void *)current,
+			                    &(list->tree),
+			                    cmpamplifia));
+	if (found==current)
+		list->last->amplifiacount++;
+
+	return found;
+}
+
+pamplifiatree_t initamplifiatree(pamplifiatree_t tree)
+{
+	if (!tree)
+		tree = ECOMALLOC(sizeof(amplifiatree_t),"Cannot allocate amplifia tree");
+
+	tree->first=newamplifialist(NULL,500);
+	tree->last=tree->first;
+
+	tree->tree=NULL;
+}
diff --git a/src/libecoprimer/pairtree.c b/src/libecoprimer/pairtree.c
new file mode 100644
index 0000000..7155104
--- /dev/null
+++ b/src/libecoprimer/pairtree.c
@@ -0,0 +1,136 @@
+/*
+ * pairtree.c
+ *
+ *  Created on: 7 mars 2009
+ *      Author: coissac
+ */
+
+#include  "ecoprimer.h"
+#include <search.h>
+
+static void cleanpair(ppair_t pair);
+static void deletepairlist(ppairlist_t list);
+static int cmppair(const void* p1,const void*p2);
+
+
+static void cleanamplifiatlist(pamplifiacount_t list)
+{
+	if (list->amplifias)
+		ECOFREE(list->amplifias,
+				"Free amplifia list");
+}
+
+static void cleanpair(ppair_t pair)
+{
+   cleanamplifiatlist(&(pair->pcr));
+}
+
+static ppairlist_t newpairlist(ppairlist_t parent, size_t size)
+{
+	ppairlist_t tmp;
+
+	tmp=ECOMALLOC(sizeof(pairlist_t)+sizeof(pair_t)*(size-1),
+			      "Cannot allocate new pair list");
+
+	tmp->pairslots=size;
+	tmp->paircount=0;
+	tmp->next=NULL;
+
+	if (parent)
+		parent->next=(void*)tmp;
+
+
+	return tmp;
+}
+
+static void deletepairlist(ppairlist_t list)
+{
+	size_t i;
+
+	if (list)
+	{
+		if (list->next)
+		{
+			deletepairlist(list->next);
+			list->next=NULL;
+		}
+		for (i=0; i < list->paircount; i++)
+			cleanpair((list->pairs)+i);
+
+		ECOFREE(list,"Delete pair list");
+	}
+
+}
+
+static int cmppair(const void* p1,const void*p2)
+{
+	ppair_t pr1,pr2;
+
+	pr1=(ppair_t)p1;
+	pr2=(ppair_t)p2;
+
+	if (pr1->p1 < pr2->p1) return -1;
+	if (pr1->p1 > pr2->p1) return  1;
+
+	if (pr1->asdirect1 < pr2->asdirect1) return -1;
+	if (pr1->asdirect1 > pr2->asdirect1) return  1;
+
+	if (pr1->p2 < pr2->p2) return -1;
+	if (pr1->p2 > pr2->p2) return  1;
+
+	if (pr1->asdirect2 < pr2->asdirect2) return -1;
+	if (pr1->asdirect2 > pr2->asdirect2) return  1;
+
+	return 0;
+}
+
+ppair_t pairintree (pair_t key,
+		            ppairtree_t pairlist)
+{
+	if (!pairlist->tree)
+		return NULL;
+
+	return *((ppair_t*)tsearch((const void *)(&key),
+								&(pairlist->tree),
+						        cmppair
+							  ));
+}
+
+ppair_t insertpair(pair_t key,
+		           ppairtree_t list)
+{
+	ppair_t current;
+	ppair_t found;
+
+	if (list->last->paircount==list->last->pairslots)
+	{
+		list->last->next=newpairlist(list->last,100);
+		list->last=list->last->next;
+	}
+
+	current = list->last->pairs + list->last->paircount;
+	*current=key;
+
+	found = *((ppair_t*)tsearch((const void *)current,
+			                    &(list->tree),
+			                    cmppair));
+	if (found==current)
+		list->last->paircount++;
+
+	return found;
+}
+
+ppairtree_t initpairtree(ppairtree_t tree)
+{
+
+	if (!tree)
+		tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree");
+
+	tree->first=newpairlist(NULL,300);
+	tree->last=tree->first;
+
+	tree->tree=NULL;
+	tree->count=0;
+
+	return tree;
+}
diff --git a/src/libecoprimer/taxstats.c b/src/libecoprimer/taxstats.c
new file mode 100644
index 0000000..5cf82b8
--- /dev/null
+++ b/src/libecoprimer/taxstats.c
@@ -0,0 +1,224 @@
+/*
+ * taxstats.c
+ *
+ *  Created on: 12 mars 2009
+ *      Author: coissac
+ */
+
+#include <search.h>
+#include  "ecoprimer.h"
+
+static int cmptaxon(const void *t1, const void* t2);
+
+static int cmptaxon(const void *t1, const void* t2)
+{
+	const size_t taxid1=(size_t)t1;
+	const size_t taxid2=(size_t)t2;
+
+	// fprintf(stderr,"==> counted taxid1 : %d\n",taxid1);
+	// fprintf(stderr,"==> counted taxid2 : %d\n",taxid2);
+
+	if (taxid1 < taxid2)
+		return -1;
+	if (taxid1 > taxid2)
+		return +1;
+	return 0;
+}
+
+int32_t counttaxon(int32_t taxid)
+{
+	static void* taxontree=NULL;
+	static int32_t taxoncount=0;
+
+	// fprintf(stderr,"counted taxid : %d taxontree %p\n",taxid,taxontree);
+
+	if (taxid==-1)
+	{
+		if (taxontree)
+			ECOFREE(taxontree,"Free taxon tree");
+		taxontree=NULL;
+		taxoncount=0;
+		return 0;
+	}
+	
+
+	if ((taxid > 0) && ((!taxontree) || (!tfind((void*)((size_t)taxid),&taxontree,cmptaxon))))
+	{
+		tsearch((void*)((size_t)taxid),&taxontree,cmptaxon);
+		taxoncount++;
+	}
+
+	return taxoncount;
+}
+
+int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
+					   poptions_t options)
+{
+
+	uint32_t i;
+	ecotx_t  *taxon;
+	ecotx_t  *tmptaxon;
+
+	counttaxon(-1);
+
+    for (i=0;i<seqdbsize;i++)
+	{
+    	taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]);
+	    seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
+
+		tmptaxon = eco_findtaxonatrank(taxon,
+									   options->taxonrankidx);
+
+	    // fprintf(stderr,"Taxid : %d %p\n",taxon->taxid,tmptaxon);
+
+		if (tmptaxon)
+		{
+			// fprintf(stderr,"orig : %d trans : %d\n",taxon->taxid,
+			// 		                                tmptaxon->taxid);
+
+			seqdb[i]->ranktaxonid=tmptaxon->taxid;
+			if (seqdb[i]->isexample)
+				options->intaxa = counttaxon(tmptaxon->taxid);
+		}
+		else
+			seqdb[i]->ranktaxonid=-1;
+	}
+
+	counttaxon(-1);
+
+    for (i=0;i<seqdbsize;i++)
+		{
+			if (seqdb[i]->ranktaxonid>=0 && !seqdb[i]->isexample)
+				options->outtaxa = counttaxon(seqdb[i]->ranktaxonid);
+		}
+
+    return options->outtaxa + options->intaxa;
+}
+
+
+float taxonomycoverage(ppair_t pair, poptions_t options)
+{
+	int32_t seqcount;
+	int32_t i;
+	int32_t incount=0;
+	int32_t outcount=0;
+
+
+	seqcount=pair->pcr.ampcount;
+
+	counttaxon(-1);
+	for (i=0; i < seqcount; i++)
+		if (pair->pcr.amplifias[i].sequence->isexample)
+			incount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
+
+	counttaxon(-1);
+	for (i=0; i < seqcount; i++)
+		if (!pair->pcr.amplifias[i].sequence->isexample)
+			outcount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
+
+
+	pair->intaxa=incount;
+	pair->outtaxa=outcount;
+	return (float)incount/options->intaxa;
+}
+
+
+static int cmpamp(const void *ampf1, const void* ampf2)
+{
+	int i;
+	int j = 0;
+	int incr = 1;
+	char cd1;
+	char cd2;
+	int chd = 0;
+	int len = 0;
+	
+	pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
+	pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
+	
+	
+	if (pampf1->strand != pampf2->strand)
+	{
+		incr = -1;
+		j = pampf1->length - 1;
+		if (pampf2->strand)
+		{
+			pampf1 = (pamptotaxon_t) ampf2;
+			pampf2 = (pamptotaxon_t) ampf1;
+			chd = 1;
+		}
+	}
+	
+	len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
+	
+	for (i = 0; i < len; i++, j += incr)
+	{
+		cd1 = pampf1->amplifia[i];
+		if (incr == -1)
+			cd2 = ecoComplementChar(pampf2->amplifia[j]);
+		else
+			cd2 = pampf2->amplifia[j];
+		
+		if (cd1 < cd2) return chd ? 1: -1;
+		if (cd2 < cd1) return chd ? -1: 1;
+	}
+	
+	if (pampf1->length > pampf2->length) return chd ? -1: 1;
+	if (pampf2->length > pampf1->length) return chd ? 1: -1;
+	
+	return 0;
+}
+
+void twalkaction (const void *node, VISIT order, int level)
+{
+	const size_t taxid=(size_t)node;
+	counttaxon(taxid);
+}
+
+void taxonomyspecificity (ppair_t pair)
+{
+	uint32_t i;
+	uint32_t ampfindex = 0;
+	int32_t taxid;
+	void *ampftree = NULL;
+	pamptotaxon_t pcurrentampf;
+	pamptotaxon_t *ptmp;
+	
+	pamptotaxon_t ampfwithtaxtree = ECOMALLOC(sizeof(amptotaxon_t) * pair->pcr.ampcount,"Cannot allocate amplifia tree");
+	
+	for (i = 0; i < pair->pcr.ampcount; i++)
+	{
+		/*populate taxon ids tree against each unique amplifia
+		i.e set of taxon ids for each amplifia*/
+		ampfwithtaxtree[ampfindex].amplifia = pair->pcr.amplifias[i].amplifia;
+		ampfwithtaxtree[ampfindex].strand = pair->pcr.amplifias[i].strand;
+		ampfwithtaxtree[ampfindex].length = pair->pcr.amplifias[i].length;
+		pcurrentampf = &ampfwithtaxtree[ampfindex];
+		taxid = pair->pcr.amplifias[i].sequence->ranktaxonid;
+		ptmp = tfind((const void*)pcurrentampf, &ampftree, cmpamp);
+		if (ptmp == NULL)
+		{
+			pcurrentampf = &ampfwithtaxtree[ampfindex];
+			tsearch((void*)pcurrentampf,&ampftree,cmpamp);
+			ampfindex++;
+		}
+		else
+			pcurrentampf = *ptmp;
+		
+		if (tfind((void*)((size_t)taxid), &(pcurrentampf->taxontree), cmptaxon) == NULL)
+		{
+			pcurrentampf->taxoncount++;
+			tsearch((void*)((size_t)taxid),&(pcurrentampf->taxontree),cmptaxon);
+		}
+	}
+	
+	counttaxon(-1);
+	for (i = 0; i < ampfindex; i++)
+	{
+		if (ampfwithtaxtree[i].taxoncount > 1)
+			twalk(ampfwithtaxtree[i].taxontree, twalkaction);
+	}
+	
+	pair->notwellidentifiedtaxa = counttaxon(-2);
+	ECOFREE (ampfwithtaxtree, "Free amplifia table");
+}
\ No newline at end of file