Load ncbi (6.1.20010709) into ncbi-tools6/branches/upstream/current.

1 files changed, 158 insertions, 2 deletions

diff --git a/network/taxon1/taxon2/tc2proc.c b/network/taxon1/taxon2/tc2proc.c
index 63e1f4c9..0a851f2c 100644
--- a/network/taxon1/taxon2/tc2proc.c
+++ b/network/taxon1/taxon2/tc2proc.c
@@ -196,6 +196,43 @@ Int4 tax1_getParent(Int4 id_tax)
     return ret_id;
 }
 
+Int4 tax1_getGenus(Int4 id_tax)
+{
+    TreeCursorPtr cursor;
+    Int4 ret_id= -1;
+
+    if(tax_tree == NULL) return -1;
+
+    if(id_tax == 1) return 0;
+
+    cursor= tree_openCursor(tax_tree, NULL, NULL);
+    if(cursor == NULL) return -1;
+
+    if(tc2_toNode(cursor, id_tax)) {
+	TXC_TreeNodePtr tnp;
+	Uint2 s;
+	Int2 rank;
+
+	do {
+	    tree_parent(cursor);
+	    tnp= tree_getNodeData(cursor, &s);
+	    if(tnp == NULL) {
+		ret_id= -1;
+		break;
+	    }
+	    ret_id= tnp->tax_id;
+	    rank= tnp->flags & 0xFF;
+	    --rank;
+	    if(rank == GenusRank) break;
+	    if((rank > 0) && (rank < GenusRank)) ret_id= -1;
+	}
+	while(ret_id > 1);
+    }
+    
+    tree_closeCursor(cursor);
+    return (ret_id > 1)? ret_id : -1;
+}
+
 int tax1_getChildren(Int4 id_tax, Int4** ids_out)
 {
     int n= 0;
@@ -528,7 +565,7 @@ Int2 tax1_getAllNames(Int4 tax_id, CharPtr **out_names, Boolean unique)
     *out_names= names= MemNew(n*sizeof(CharPtr));
     if(names != NULL) {
         for(i= 0; i < n; i++) {
-	    if(unique && (nameList[i].unique_name != NULL)) {
+	    if(unique && (nameList[i].unique_name != NULL) && (nameList[i].unique_name[0] != '\0')) {
 		names[i]= nameList[i].unique_name;
 		nameList[i].unique_name= NULL;
 	    }
@@ -839,7 +876,9 @@ static CharPtr bldLineage(TreeCursorPtr cursor)
 	if((tnp= tree_getNodeData(cursor, &s)) != NULL) {
 	    rank= tnp->flags & 0xFF;
 	    if(rank > SpeciesRank) {
-		if(lineage != NULL) MemFree(lineage);
+		if(lineage != NULL) {
+		  lineage = MemFree(lineage);
+		}
 		continue;
 	    }
 	    if(tnp->tax_id < 2) break;
@@ -1102,6 +1141,15 @@ static OrgModPtr fixModifier(Int4 tax_id, OrgModPtr omp)
     _subspec src_ss;
     _subspecPtr ss= NULL;
 
+    memset(&src_ss, 0, sizeof(_subspec));
+
+    if(omp->subtype < 2) {
+	omp->next= NULL;
+	OrgModFree(omp);
+	return NULL;
+    }
+      
+
     if((omp->subname != NULL) && (omp->subtype != 0)) {
 	src_ss.stype= omp->subtype;
 	src_ss.sname= omp->subname;
@@ -1640,5 +1688,113 @@ Int4 tax1_getTaxId4Str(CharPtr str, CharPtr* substring, Int4Ptr *Ids_out)
     }
     return 0;
 }    
+
+static int nameCmp(CharPtr s1, CharPtr s2)
+{
+    if((s1 == NULL) && (s2 == NULL)) return 0;
+    if((s1 == NULL) || (s2 == NULL)) return 1;
+
+    return strcmp(s1, s2);
+}
+
+static Int4 storedTaxId(OrgRefPtr orp)
+{
+    ValNodePtr vnp;
+    DbtagPtr dbtag;
+    ObjectIdPtr object_id;
+
+    for(vnp= orp->db; vnp != NULL; vnp= vnp->next) {
+	dbtag= vnp->data.ptrvalue;
+	if((dbtag != NULL) && (StringCmp(dbtag->db, "taxon") == 0)) {
+	    ObjectIdPtr object_id= dbtag->tag;
+	    return object_id->id;
+	}
+    }
+
+    return 0;
+}
+
+static Int4 OrgModCmp(OrgModPtr omp1, OrgModPtr omp2)
+{
+    OrgModPtr omp;
+    int found;
+
+    if(omp2 == NULL) return 0;
+    if(omp1 == NULL) return 100;
+    
+    for(;omp2 != NULL; omp2= omp2->next) {
+	found= 0;
+	for(omp= omp1; omp != NULL; omp= omp->next) {
+	    if((omp2->subtype == omp->subtype) &&
+	       (nameCmp(omp2->subname, omp->subname) == 0)) {
+		found= 1;
+		break;
+	    }
+	}
+	if(!found) return 100;
+    }
+    return 0;
+}
+
+static Int4 OrgRefCmp(OrgRefPtr orp1, OrgRefPtr orp2)
+{
+    OrgNamePtr onp1= orp1->orgname;
+    OrgNamePtr onp2= orp2->orgname;
+
+    if(onp1 == NULL) return 4;
+    if(onp2 == NULL) return -2;
+
+    if(onp1->gcode != onp2->gcode) return 2;
+    if(onp1->mgcode != onp2->mgcode) return 3;
+
+    if(nameCmp(orp1->taxname, orp2->taxname) != 0) return 10;
+
+    if(nameCmp(onp1->lineage, onp2->lineage) != 0) return 20;
+
+    if(nameCmp(orp1->common, orp2->common) != 0) return 30;
+
+    if(onp1->choice != onp2->choice) return 40;
+
+    if(nameCmp(onp1->div, onp2->div) != 0) return 50;
+
+    return OrgModCmp(onp1->mod, onp2->mod);
     
+}
+ 
+Int4 tax1e_needUpdate(OrgRefPtr inp_orgRef)
+{
+    Taxon1DataPtr res;
+    Int4 tax_id;
+    OrgRefPtr db_orgRef;
+    int is_species;
+    Boolean need_search_name= TRUE;
+    CharPtr hit_name;
+
+    tax_id= tax1_getTaxIdByOrgRef(inp_orgRef);
+    if(tax_id <= 0) return -1;
+
+    if(tax_id != storedTaxId(inp_orgRef)) return 1;
+    
+    db_orgRef= tax1_getOrgRef(tax_id, NULL, NULL, NULL /*res->embl_code*/);
+    if(db_orgRef == NULL) {
+	return -2;
+    }
+
+    return OrgRefCmp(inp_orgRef, db_orgRef);
+}
+
+Boolean tax1_isAlive(void)
+{
+    return (tax1_getTaxIdByName("dog") > 1)? TRUE : FALSE;
+}
 
+/***************************************************
+ * Get tax_id for given gi
+ * returns:
+ *       tax_id if found
+ *       0      if no data or error
+ */
+Int4 tax1_getTaxId4GI(Int4 gi)
+{
+    return tax_getTaxId4GI(gi);
+}