X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=92a43e965044c06c2fdcaca78d50779440b301ab;hb=ffc44592ff7ae94f14f9e21f87198e33d323cd1d;hp=f6705e53db2048691b95050f3005bdccecf21347;hpb=8c616f2509abd2fb9485a38607c1b439d243b85c;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index f6705e5..92a43e9 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,6 +44,7 @@ int GroupMap::readMap() {
 			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+		m->setAllGroups(namesOfGroups);
 		return error;
 }
 /************************************************************/
@@ -69,9 +70,38 @@ int GroupMap::readDesignMap() {
 			m->gobble(fileHandle);
 		}
 		fileHandle.close();
+		m->setAllGroups(namesOfGroups);
 		return error;
 }
-
+/************************************************************/
+int GroupMap::readDesignMap(string filename) {
+    groupFileName = filename;
+	m->openInputFile(filename, fileHandle);
+	index = 0;
+    string seqName, seqGroup;
+    int error = 0;
+    
+    while(fileHandle){
+        fileHandle >> seqName;	m->gobble(fileHandle);		//read from first column
+        fileHandle >> seqGroup;			//read from second column
+        
+        if (m->control_pressed) {  fileHandle.close();  return 1; }
+        
+        setNamesOfGroups(seqGroup);
+        
+        it = groupmap.find(seqName);
+        
+        if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 group named " + seqName + ", group names must be unique. Please correct."); m->mothurOutEndLine();  }
+        else {
+            groupmap[seqName] = seqGroup;	//store data in map
+            seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
+        }
+        m->gobble(fileHandle);
+    }
+    fileHandle.close();
+    m->setAllGroups(namesOfGroups);
+    return error;
+}
 /************************************************************/
 int GroupMap::getNumGroups() { return namesOfGroups.size();	}
 /************************************************************/
@@ -89,7 +119,15 @@ string GroupMap::getGroup(string sequenceName) {
 /************************************************************/
 
 void GroupMap::setGroup(string sequenceName, string groupN) {
-	groupmap[sequenceName] = groupN;
+	setNamesOfGroups(groupN);
+	
+	it = groupmap.find(sequenceName);
+	
+	if (it != groupmap.end()) {  m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
+	else {
+		groupmap[sequenceName] = groupN;	//store data in map
+		seqsPerGroup[groupN]++;  //increment number of seqs in that group
+	}
 }
 
 /************************************************************/
@@ -161,4 +199,25 @@ vector<string> GroupMap::getNamesSeqs(){
 	}
 }
 /************************************************************/
+vector<string> GroupMap::getNamesSeqs(vector<string> picked){
+	try {
+		
+		vector<string> names;
+		
+		for (it = groupmap.begin(); it != groupmap.end(); it++) {
+			//if you are belong to one the the groups in the picked vector add you
+			if (m->inUsersGroups(it->second, picked)) {
+				names.push_back(it->first);
+			}
+		}
+		
+		return names;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "getNamesSeqs");
+		exit(1);
+	}
+}
+
+/************************************************************/