From: pschloss <pschloss>
Date: Thu, 26 Aug 2010 13:04:35 +0000 (+0000)
Subject: changes to read.otu(list/shared) - took out substr calls
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=87537e4ee46cae9b7041ae0ed4dbbc229936d37c

changes to read.otu(list/shared) - took out substr calls
---

diff --git a/groupmap.cpp b/groupmap.cpp
index 47fbc36..0e0be0e 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -61,26 +61,28 @@ string GroupMap::getGroup(string sequenceName) {
 }
 
 /************************************************************/
+
 void GroupMap::setGroup(string sequenceName, string groupN) {
 	groupmap[sequenceName] = groupN;
 }
+
 /************************************************************/
 void GroupMap::setNamesOfGroups(string seqGroup) {
-			int i, count;
-			count = 0;
-			for (i=0; i<namesOfGroups.size(); i++) {
-				if (namesOfGroups[i] != seqGroup) {
-					count++; //you have not found this group
-				}else {
-					break; //you already have it
-				}
-			}
-			if (count == namesOfGroups.size()) {
-				namesOfGroups.push_back(seqGroup); //new group
-				seqsPerGroup[seqGroup] = 0;
-				groupIndex[seqGroup] = index;
-				index++;
-			}
+	int i, count;
+	count = 0;
+	for (i=0; i<namesOfGroups.size(); i++) {
+		if (namesOfGroups[i] != seqGroup) {
+			count++; //you have not found this group
+		}else {
+			break; //you already have it
+		}
+	}
+	if (count == namesOfGroups.size()) {
+		namesOfGroups.push_back(seqGroup); //new group
+		seqsPerGroup[seqGroup] = 0;
+		groupIndex[seqGroup] = index;
+		index++;
+	}
 }
 /************************************************************/
 bool GroupMap::isValidGroup(string groupname) {
diff --git a/sharedlistvector.cpp b/sharedlistvector.cpp
index 4978031..f2d8e07 100644
--- a/sharedlistvector.cpp
+++ b/sharedlistvector.cpp
@@ -283,21 +283,42 @@ vector<SharedRAbundVector*> SharedListVector::getSharedRAbundVector() {
 		//fill vectors
 		for(int i=0;i<numBins;i++){
 			names = get(i);  
-			while (names.find_first_of(',') != -1) { 
-				name = names.substr(0,names.find_first_of(','));
-				names = names.substr(names.find_first_of(',')+1, names.length());
-				group = groupmap->getGroup(name);
-				if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
-				finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+			int nameLength = names.size();
+			string seqName = "";
+			
+			for(int j=0;j<nameLength;j++){
+				if(names[j] == ','){
+					group = groupmap->getGroup(seqName);
+					if(group == "not found") {	m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+					finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+					
+					seqName = "";
+				}
+				else{
+					seqName += names[j];
+				}
 			}
+			group = groupmap->getGroup(seqName);
+			if(group == "not found") {	m->mothurOut("Error: Sequence '" + seqName + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+			finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+			
+			
+			
+//			while (names.find_first_of(',') != -1) { 
+//				name = names.substr(0,names.find_first_of(','));
+//				names = names.substr(names.find_first_of(',')+1, names.length());
+//				group = groupmap->getGroup(name);
+//				if(group == "not found") {	m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+//				finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+//			}
 			
 			//get last name
-			group = groupmap->getGroup(names);
-			if(group == "not found") {	m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
-			finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
+//			group = groupmap->getGroup(names);
+//			if(group == "not found") {	m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine();  exit(1); }
+//			finder[group]->set(i, finder[group]->getAbundance(i) + 1, group);  //i represents what bin you are in
 			
 		}
-		
+
 		return lookup;
 	}
 	catch(exception& e) {