X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collect.cpp;h=9a89020efe91f8bdd2733a3de553611e86ee6da3;hp=379424c9155d7dcee7e0535644652ef852f19481;hb=615301e57c25e241356a9c2380648d117709458d;hpb=5a86e9e5a5a9e061e17b3ae64fb8881f14e53b8a

diff --git a/collect.cpp b/collect.cpp
index 379424c..9a89020 100644
--- a/collect.cpp
+++ b/collect.cpp
@@ -24,7 +24,9 @@ int Collect::getCurve(float percentFreq = 0.01){
                 }   
 				
 				//convert freq percentage to number
-				int increment = numSeqs * percentFreq;
+				int increment = 1;
+				if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+				else { increment = percentFreq;  }
 																						                                                                        
                 for(int i=0;i<numSeqs;i++){
 						
@@ -68,40 +70,42 @@ int Collect::getCurve(float percentFreq = 0.01){
 /***********************************************************************/
 int Collect::getSharedCurve(float percentFreq = 0.01){
 try {
-				globaldata = GlobalData::getInstance();
                 vector<SharedRAbundVector*> lookup; 
 				vector<SharedRAbundVector*> subset;
 
                 //create and initialize vector of sharedvectors, one for each group
-                for (int i = 0; i < globaldata->Groups.size(); i++) { 
+				vector<string> mGroups = m->getGroups();
+                for (int i = 0; i < mGroups.size(); i++) { 
                         SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
                         temp->setLabel(sharedorder->getLabel());
-                        temp->setGroup(globaldata->Groups[i]);
-                        temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
-                        lookup.push_back(temp);
+                        temp->setGroup(mGroups[i]);
+						lookup.push_back(temp);
                 }
-
+	
                 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
         
                 //initialize labels for output
                 //makes  'uniqueAB         uniqueAC  uniqueBC' if your groups are A, B, C
                 getGroupComb();
-                groupLabel = ""; 
-                for (int s = 0; s < groupComb.size(); s++) {
-                        groupLabel = groupLabel + label + groupComb[s] + "\t";
-                }
-				
-				//for multi displays
-				string groupLabelAll = groupLabel + label + "all\t";
 				
                 for(int i=0;i<displays.size();i++){
                         ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
+						bool hasLciHci = displays[i]->hasLciHci();
+						groupLabel = "";
+						for (int s = 0; s < groupComb.size(); s++) {
+							if (hasLciHci) {  groupLabel = groupLabel + label + groupComb[s] + "\t" + label + groupComb[s] + "lci\t" + label + groupComb[s] + "hci\t"; }
+							else{  groupLabel = groupLabel + label + groupComb[s] + "\t";  }
+						}
+
+						string groupLabelAll = groupLabel + label + "all\t"; 
 						if ((displays[i]->isCalcMultiple() == true) && (displays[i]->getAll() == true)) {   displays[i]->init(groupLabelAll); }
 						else {  displays[i]->init(groupLabel);  }           
                 }
                 
 				//convert freq percentage to number
-				int increment = numSeqs * percentFreq;
+				int increment = 1;
+				if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+				else { increment = percentFreq;  }
 				
                 //sample all the members
                 for(int i=0;i<numSeqs;i++){
@@ -111,7 +115,7 @@ 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()) {
@@ -127,17 +131,27 @@ try {
 								//how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
 
                                 int n = 1;
+								bool pair = true;
                                 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
                                         for (int l = n; l < lookup.size(); l++) {
 												subset.clear(); //clear out old pair of sharedrabunds
 												//add new pair of sharedrabund vectors
 												subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-                                                ccd->updateSharedData(subset, i+1, globaldata->Groups.size());
+											
+												//load subset with rest of lookup for those calcs that need everyone to calc for a pair
+												for (int w = 0; w < lookup.size(); w++) {
+													if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
+												}
+						
+                                                ccd->updateSharedData(subset, i+1, m->getNumGroups(), pair);
                                         }
                                         n++;
                                 }
+							
 								//if this is a calculator that can do multiples then do them
-								ccd->updateSharedData(lookup, i+1, globaldata->Groups.size()); 
+								pair = false;
+								ccd->updateSharedData(lookup, i+1, m->getNumGroups(), pair); 
+							
                         }
                         totalNumSeq = i+1;
                 }
@@ -146,19 +160,27 @@ try {
                 if(numSeqs % increment != 0){
                         //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
                         int n = 1;
+						bool pair = true;
                         for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
                                 for (int l = n; l < lookup.size(); l++) {
 										subset.clear(); //clear out old pair of sharedrabunds
 										//add new pair of sharedrabund vectors
 										subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-										ccd->updateSharedData(subset, totalNumSeq, globaldata->Groups.size());
+									
+										//load subset with rest of lookup for those calcs that need everyone to calc for a pair
+										for (int w = 0; w < lookup.size(); w++) {
+											if ((w != k) && (w != l)) { subset.push_back(lookup[w]); }
+										}
+									
+										ccd->updateSharedData(subset, totalNumSeq, m->getNumGroups(), pair);
                                 }
                                 n++;
                         }
 						//if this is a calculator that can do multiples then do them
-						ccd->updateSharedData(lookup, totalNumSeq, globaldata->Groups.size()); 
+						pair = false;
+						ccd->updateSharedData(lookup, totalNumSeq, m->getNumGroups(), pair); 
                 }
-                
+	 
                 //resets output files
                 for(int i=0;i<displays.size();i++){
                         displays[i]->reset();
@@ -187,9 +209,10 @@ void Collect::getGroupComb() {
 	numGroupComb = 0;
                 
 	int n = 1;
-	for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
-		for (int l = n; l < globaldata->Groups.size(); l++) {
-			group = globaldata->Groups[i] + globaldata->Groups[l];
+	vector<string> mGroups = m->getGroups();
+	for (int i = 0; i < (m->getNumGroups() - 1); i++) {
+		for (int l = n; l < m->getNumGroups(); l++) {
+			group = mGroups[i] + mGroups[l];
 			groupComb.push_back(group);        
 			numGroupComb++;
 		}