Added get.line command.

[mothur.git] / collect.cpp

diff --git a/collect.cpp b/collect.cpp
index 2ed5ca7f10eeefdb860ae9fc7b5859b5eb239c0e..1c8128aef4ba42ec11fc2a7edbaa8cd42aa97ced 100644 (file)
--- a/collect.cpp
+++ b/collect.cpp
@@ -64,7 +64,8 @@ void Collect::getSharedCurve(int increment = 1){
 try {
                globaldata = GlobalData::getInstance();
                vector<SharedRAbundVector*> lookup; 
-
+               vector<string> chosenGroups = globaldata->sharedGroups;
+               
                //create and initialize vector of sharedvectors, one for each group
                for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
                        SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
@@ -78,7 +79,7 @@ try {
        
                //initialize labels for output
                //makes  'uniqueAB       uniqueAC  uniqueBC' if your groups are A, B, C
-               getGroupComb();
+               getGroupComb(chosenGroups);
                groupLabel = "";
                for (int s = 0; s < groupComb.size(); s++) {
                        groupLabel = groupLabel + label + groupComb[s] + "\t";
@@ -94,7 +95,6 @@ try {
                        //get first sample
                        individual chosen = sharedorder->get(i);
                        int abundance; 
-                                       
                        //set info for sharedvector in chosens group
                        for (int j = 0; j < lookup.size(); j++) { 
                                if (chosen.group == lookup[j]->getGroup()) {
@@ -103,7 +103,7 @@ try {
                                         break;
                                }
                        }
-                       
+
                        //calculate at 0 and the given increment
                        if((i == 0) || (i+1) % increment == 0){
                                //randomize group order
@@ -116,8 +116,8 @@ try {
                                        }
                                        n++;
                                }
-                       }
                        totalNumSeq = i+1;
+                       }
                }
                
                //calculate last line if you haven't already
@@ -150,7 +150,7 @@ try {
 
 /**************************************************************************************/
 
-void Collect::getGroupComb() {
+void Collect::getGroupComb(vector<string> chosen) {
                string group;
                
                numGroupComb = 0;
@@ -158,13 +158,28 @@ void Collect::getGroupComb() {
                int n = 1;
                for (int i = 0; i < (globaldata->gGroupmap->getNumGroups() - 1); i++) {
                        for (int l = n; l < globaldata->gGroupmap->getNumGroups(); l++) {
-                               group = globaldata->gGroupmap->namesOfGroups[i] + globaldata->gGroupmap->namesOfGroups[l];
-                               groupComb.push_back(group);     
-                               numGroupComb++;
+                               string g1 = globaldata->gGroupmap->namesOfGroups[i];
+                               string g2 = globaldata->gGroupmap->namesOfGroups[l];
+                               if(validGroup(chosen, g1) && validGroup(chosen, g2)) { 
+                                       group = g1 + g2;
+                                       groupComb.push_back(group);     
+                                       numGroupComb++;
+                               }
                        }
                        n++;
                }
-
 }
 
 /**************************************************************************************/
+
+bool Collect::validGroup(vector<string> chosen, string group) {
+       if(chosen.size() == 0)
+               return true;
+       for(int i = 0; i < chosen.size(); i++)
+               if(chosen.at(i).compare(group) == 0)
+                       return true;
+       return false;
+}
+                                       
+
+