X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treemap.cpp;h=dcef7f7c19174f1aaf6a1435931c9005f986f638;hb=8f7164a88df624fd0a8d1eddbb3d744463cc9ecb;hp=5880b0c593fdd0dc96808e485921d96871e865d6;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/treemap.cpp b/treemap.cpp
index 5880b0c..dcef7f7 100644
--- a/treemap.cpp
+++ b/treemap.cpp
@@ -17,7 +17,7 @@
 }
 
 /************************************************************/
- 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);
@@ -44,6 +44,25 @@ void TreeMap::readMap() {
 		fileHandle.close();
 }
 /************************************************************/
+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 +135,7 @@ 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);
 	}
 }
@@ -134,11 +149,7 @@ 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);
 	}
 }
@@ -152,7 +163,7 @@ void TreeMap::makeSim(GroupMap* groupmap) {
 		//set names of seqs to names of groups
 		namesOfSeqs = groupmap->namesOfGroups;
 		
-		// make map where key and value are both the group name since that what the tree.groups command wants
+		// 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;
@@ -162,13 +173,36 @@ 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);
 	}
 }
+
 /************************************************************/