X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=75423855a7f583ae5ce62fc10118cf260589df6b;hb=d945488119ad368b180537f36ed40298ff170f39;hp=bee0d11ed21323ee9dff1bc38c860a3042231150;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index bee0d11..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);
@@ -39,15 +39,49 @@ 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() {
 			
-	return seqsPerGroup.size();	
+	return namesOfGroups.size();	
 		
 }
 /************************************************************/
@@ -72,7 +106,13 @@ string TreeMap::getGroup(string sequenceName) {
 }
 /************************************************************/
 void TreeMap::setIndex(string seq, int index) {
-	treemap[seq].vectorIndex = index;
+	it = treemap.find(seq);
+	if (it != treemap.end()) { //sequence name was in group file
+		treemap[seq].vectorIndex = index;	
+	}else {
+		treemap[seq].vectorIndex = index;
+		treemap[seq].groupname = "not found";
+	}
 }
 /************************************************************/
 int TreeMap::getIndex(string seq) {
@@ -100,7 +140,20 @@ void TreeMap::setNamesOfGroups(string seqGroup) {
 				namesOfGroups.push_back(seqGroup); //new group
 			}
 }
-
+/************************************************************/
+bool TreeMap::isValidGroup(string groupname) {
+	try {
+		for (int i = 0; i < namesOfGroups.size(); i++) {
+			if (groupname == namesOfGroups[i]) { return true; }
+		}
+		
+		return false;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "isValidGroup");
+		exit(1);
+	}
+}
 /***********************************************************************/
 
 void TreeMap::print(ostream& output){
@@ -111,13 +164,60 @@ 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";
+		m->errorOut(e, "TreeMap", "print");
+		exit(1);
+	}
+}
+
+/************************************************************/
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
+	try {
+		//set names of groups
+		namesOfGroups = ThisnamesOfGroups;
+		
+		//set names of seqs to names of groups
+		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++) {
+			treemap[namesOfGroups[i]].groupname = namesOfGroups[i];
+			seqsPerGroup[namesOfGroups[i]] = 1;
+		}
+		
+		numGroups = namesOfGroups.size();
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeMap", "makeSim");
 		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";
+}
+/************************************************************/
+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);
 	}
 }
 
 /************************************************************/
+