Removes distance storage in sens.spec

source/commands/sensspeccommand.cpp

@@ -290,7 +290,7 @@ int SensSpecCommand::execute(){
 
 //***************************************************************************************************************
 
-int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool& getCutoff, string& origCutoff){
+int SensSpecCommand::process(ListVector*& list, bool& getCutoff, string& origCutoff){
 
 	try {
 
@@ -316,7 +316,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
 		trueNegatives = 0;
 		falseNegatives = 0;
 
-		map<string, double> distanceMap;
+		set<string> distanceMap;
 
 		//could segfault out if there are sequences in phylip-formatted distance
 		//matrix that aren't in the list file
@@ -338,8 +338,6 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
 
 				phylipFile >> seqNameVector[i];
 
-				//otuIndices[i] = seqMap[seqName];
-
 				for(int j=0;j<i;j++){
 					phylipFile >> distance;
 
@@ -352,7 +350,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
 							seqNamePair = seqNameVector[j] + '-' + seqNameVector[i];
 						}
 
-						distanceMap[seqNamePair] = distance;
+						distanceMap.insert(seqNamePair);
 					}
 				}
 
@@ -381,12 +379,12 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
 					} else {
 						seqNamePair = seqNameB + '-' + seqNameA;
 					}
-					distanceMap[seqNamePair] = distance;
+                    distanceMap.insert(seqNamePair);
 				}
 			}
 			columnFile.close();
 		}
-
+        cout << m->getRAMUsed()/(double)GIG << endl;
 		for(int otu=0;otu<numOTUs;otu++){
 			if (m->control_pressed) { return 0; }
 
@@ -421,7 +419,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
 						seqNamePair = otuVector[j] + '-' + otuVector[i];
 					}
 
-					map<string, double>::iterator it = distanceMap.find(seqNamePair);
+					set<string>::iterator it = distanceMap.find(seqNamePair);
 
 					if(it != distanceMap.end()){
 						truePositives++;
@@ -457,8 +455,6 @@ int SensSpecCommand::processListFile(){
 		if(cutoff == -1.00)	{	getCutoff = 1;                                          }
 		else 				{	origCutoff = toString(m->ceilDist(cutoff, precision));	}
 
-		map<string, int> seqMap;
-
 		InputData input(listFile, "list");
 		ListVector* list = input.getListVector();
 		string lastLabel = list->getLabel();
@@ -477,7 +473,7 @@ int SensSpecCommand::processListFile(){
 
 				//process
 				// int numSeqs = fillSeqMap(seqMap, list);
-				process(seqMap, list, getCutoff, origCutoff);
+				process(list, getCutoff, origCutoff);
 			}
 
 			if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
@@ -492,7 +488,7 @@ int SensSpecCommand::processListFile(){
 
 				//process
 				//int numSeqs = fillSeqMap(seqMap, list);
-				process(seqMap, list, getCutoff, origCutoff);
+				process(list, getCutoff, origCutoff);
 
 				//restore real lastlabel to save below
 				list->setLabel(saveLabel);
@@ -523,7 +519,7 @@ int SensSpecCommand::processListFile(){
 
 			//process
 			//int numSeqs = fillSeqMap(seqMap, list);
-			process(seqMap, list, getCutoff, origCutoff);
+			process(list, getCutoff, origCutoff);
 
 			delete list;
 		}

source/commands/sensspeccommand.h

@@ -52,7 +52,7 @@ class SensSpecCommand : public Command {
 	double cutoff;
 	int precision;
 
-	int process(map<string, int>&, ListVector*&, bool&, string&);
+	int process(ListVector*&, bool&, string&);
 };
 
 #endif