added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 873e5d1788162611db706617d9cf17f73df6a48b..58274b3ec365c573eacc9644a446c209f35f63ff 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -168,8 +168,9 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
                                        
                                        //initialize groupcounts
                                        if (groupmap != NULL) {
-                                               for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
-                                                       tree[index].groupCount[groupmap->namesOfGroups[j]] = 0;
+                                               vector<string> mGroups = groupmap->getNamesOfGroups();
+                                               for (int j = 0; j < mGroups.size(); j++) {
+                                                       tree[index].groupCount[mGroups[j]] = 0;
                                                }
                                                
                                                //find out the sequences group
@@ -234,8 +235,9 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
                                if (groupmap != NULL) {
                                        
                                        map<string, bool> containsGroup; 
-                                       for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
-                                               containsGroup[groupmap->namesOfGroups[j]] = false;
+                                       vector<string> mGroups = groupmap->getNamesOfGroups();
+                                       for (int j = 0; j < mGroups.size(); j++) {
+                                               containsGroup[mGroups[j]] = false;
                                        }
                                        
                                        for (int k = 0; k < names.size(); k++) {
@@ -273,9 +275,10 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
                                        //initialize groupcounts
                                        if (groupmap != NULL) {
                                                map<string, bool> containsGroup; 
-                                               for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
-                                                       tree[index].groupCount[groupmap->namesOfGroups[j]] = 0;
-                                                       containsGroup[groupmap->namesOfGroups[j]] = false;
+                                               vector<string> mGroups = groupmap->getNamesOfGroups();
+                                               for (int j = 0; j < mGroups.size(); j++) {
+                                                       tree[index].groupCount[mGroups[j]] = 0;
+                                                       containsGroup[mGroups[j]] = false;
                                                }
                                                
                                                
@@ -349,9 +352,9 @@ void PhyloSummary::print(ofstream& out){
                if (groupmap != NULL) {
                        //so the labels match the counts below, since the map sorts them automatically...
                        //sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
-                       
-                       for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
-                               out << groupmap->namesOfGroups[i] << '\t';
+                       vector<string> mGroups = groupmap->getNamesOfGroups();
+                       for (int i = 0; i < mGroups.size(); i++) {
+                               out << mGroups[i] << '\t';
                        }
                }
                
@@ -372,7 +375,8 @@ void PhyloSummary::print(ofstream& out){
                        //for (itGroup = tree[0].groupCount.begin(); itGroup != tree[0].groupCount.end(); itGroup++) {
                        //      out << itGroup->second << '\t';
                        //}
-                       for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[0].groupCount[groupmap->namesOfGroups[i]] << '\t'; } 
+                       vector<string> mGroups = groupmap->getNamesOfGroups();
+                       for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; } 
                }
                out << endl;
                
@@ -409,7 +413,8 @@ void PhyloSummary::print(int i, ofstream& out){
                                        //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
                                        //      out << itGroup->second << '\t';
                                        //}
-                                       for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {  out << tree[it->second].groupCount[groupmap->namesOfGroups[i]] << '\t'; } 
+                                       vector<string> mGroups = groupmap->getNamesOfGroups();
+                                       for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; } 
                                }
                                out << endl;
                                
@@ -453,8 +458,8 @@ void PhyloSummary::readTreeStruct(ifstream& in){
                        
                        //initialize groupcounts
                        if (groupmap != NULL) {
-                               for (int j = 0; j < groupmap->namesOfGroups.size(); j++) {
-                                       tree[i].groupCount[groupmap->namesOfGroups[j]] = 0;
+                               for (int j = 0; j < (groupmap->getNamesOfGroups()).size(); j++) {
+                                       tree[i].groupCount[(groupmap->getNamesOfGroups())[j]] = 0;
                                }
                        }