X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=75423855a7f583ae5ce62fc10118cf260589df6b;hb=fc1ed1ae1b022719176910ab71993bd6535810ad;hp=00ae0e664ff5fb7d289893b445be08b5fd20c89a;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index 00ae0e6..7542385 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -13,11 +13,11 @@
 
  TreeMap::TreeMap(string filename) {
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 }
 
 /************************************************************/
- TreeMap::~TreeMap(){};
+ TreeMap::~TreeMap(){}
 
 /************************************************************/
 void TreeMap::readMap() {
@@ -26,10 +26,10 @@ void TreeMap::readMap() {
 		while(fileHandle){
 			fileHandle >> seqName;			//read from first column
 			fileHandle >> seqGroup;			//read from second column
-			
+
 			namesOfSeqs.push_back(seqName);
 			setNamesOfGroups(seqGroup);
-						
+					
 			treemap[seqName].groupname = seqGroup;	//store data in map
 			
 			it2 = seqsPerGroup.find(seqGroup);
@@ -39,11 +39,45 @@ void TreeMap::readMap() {
 				seqsPerGroup[seqGroup]++;
 			}
 
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 		fileHandle.close();
 }
 /************************************************************/
+void TreeMap::addSeq(string seqName, string seqGroup) {
+	
+		namesOfSeqs.push_back(seqName);
+		setNamesOfGroups(seqGroup);
+					
+		treemap[seqName].groupname = seqGroup;	//store data in map
+			
+		it2 = seqsPerGroup.find(seqGroup);
+		if (it2 == seqsPerGroup.end()) { //if it's a new group
+			seqsPerGroup[seqGroup] = 1;
+		}else {//it's a group we already have
+			seqsPerGroup[seqGroup]++;
+		}
+}
+/************************************************************/
+void TreeMap::removeSeq(string seqName) {
+	
+	//erase name from namesOfSeqs
+	for (int i = 0; i < namesOfSeqs.size(); i++) {
+		if (namesOfSeqs[i] == seqName)  {
+			namesOfSeqs.erase(namesOfSeqs.begin()+i);
+			break;
+		}
+	}
+	
+	//decrement sequences in this group
+	string group = treemap[seqName].groupname;
+	seqsPerGroup[group]--;
+	
+	//remove seq from treemap
+	it = treemap.find(seqName);
+	treemap.erase(it);
+}
+/************************************************************/
 
 int TreeMap::getNumGroups() {
 			
@@ -116,11 +150,7 @@ bool TreeMap::isValidGroup(string groupname) {
 		return false;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the TreeMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "TreeMap", "isValidGroup");
 		exit(1);
 	}
 }
@@ -134,23 +164,19 @@ void TreeMap::print(ostream& output){
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the TreeMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "TreeMap", "print");
 		exit(1);
 	}
 }
 
 /************************************************************/
-void TreeMap::makeSim(GroupMap* groupmap) {
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
 	try {
 		//set names of groups
-		namesOfGroups = groupmap->namesOfGroups;
+		namesOfGroups = ThisnamesOfGroups;
 		
 		//set names of seqs to names of groups
-		namesOfSeqs = groupmap->namesOfGroups;
+		namesOfSeqs = ThisnamesOfGroups;
 		
 		// make map where key and value are both the group name since that what the tree.shared command wants
 		for (int i = 0; i < namesOfGroups.size(); i++) {
@@ -162,13 +188,36 @@ void TreeMap::makeSim(GroupMap* groupmap) {
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the TreeMap class Function make. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "TreeMap", "makeSim");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the TreeMap class function make. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/************************************************************/
+void TreeMap::makeSim(ListVector* list) {
+	try {
+		//set names of groups
+		namesOfGroups.clear();
+		for(int i = 0; i < list->size(); i++) {
+			namesOfGroups.push_back(list->get(i));
+		}
+		
+		//set names of seqs to names of groups
+		namesOfSeqs = namesOfGroups;
+		
+		// make map where key and value are both the group name since that what the tree.shared command wants
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
+			seqsPerGroup[namesOfGroups[i]] = 1;
+		}
+		
+		numGroups = namesOfGroups.size();
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "makeSim");
 		exit(1);
 	}
 }
+
 /************************************************************/