X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=92a43e965044c06c2fdcaca78d50779440b301ab;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=598e301648978ab642274edb69ffa41bbea6f205;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index 598e301..92a43e9 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -12,8 +12,9 @@
 /************************************************************/
 
  GroupMap::GroupMap(string filename) {
+	m = MothurOut::getInstance();
 	groupFileName = filename;
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 	index = 0;
 }
 
@@ -24,26 +25,84 @@
 int GroupMap::readMap() {
 		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 groupfile contains more than 1 sequence named " + seqName + ", sequence 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::readDesignMap() {
+		string seqName, seqGroup;
+		int error = 0;
+
 		while(fileHandle){
-			fileHandle >> seqName;			//read from first column
+			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; mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); mothurOutEndLine();  }
+			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
 			}
-			gobble(fileHandle);
+			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();	}
 /************************************************************/
 
@@ -58,26 +117,36 @@ 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
+	}
 }
+
 /************************************************************/
 void GroupMap::setNamesOfGroups(string seqGroup) {
-			int i, count;
-			count = 0;
-			for (i=0; i<namesOfGroups.size(); i++) {
-				if (namesOfGroups[i] != seqGroup) {
-					count++; //you have not found this group
-				}else {
-					break; //you already have it
-				}
-			}
-			if (count == namesOfGroups.size()) {
-				namesOfGroups.push_back(seqGroup); //new group
-				seqsPerGroup[seqGroup] = 0;
-				groupIndex[seqGroup] = index;
-				index++;
-			}
+	int i, count;
+	count = 0;
+	for (i=0; i<namesOfGroups.size(); i++) {
+		if (namesOfGroups[i] != seqGroup) {
+			count++; //you have not found this group
+		}else {
+			break; //you already have it
+		}
+	}
+	if (count == namesOfGroups.size()) {
+		namesOfGroups.push_back(seqGroup); //new group
+		seqsPerGroup[seqGroup] = 0;
+		groupIndex[seqGroup] = index;
+		index++;
+	}
 }
 /************************************************************/
 bool GroupMap::isValidGroup(string groupname) {
@@ -89,7 +158,7 @@ bool GroupMap::isValidGroup(string groupname) {
 		return false;
 	}
 	catch(exception& e) {
-		errorOut(e, "GroupMap", "isValidGroup");
+		m->errorOut(e, "GroupMap", "isValidGroup");
 		exit(1);
 	}
 }
@@ -107,7 +176,7 @@ int GroupMap::getNumSeqs(string group) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "GroupMap", "getNumSeqs");
+		m->errorOut(e, "GroupMap", "getNumSeqs");
 		exit(1);
 	}
 }
@@ -125,9 +194,30 @@ vector<string> GroupMap::getNamesSeqs(){
 		return names;
 	}
 	catch(exception& e) {
-		errorOut(e, "GroupMap", "getNamesSeqs");
+		m->errorOut(e, "GroupMap", "getNamesSeqs");
 		exit(1);
 	}
 }
 /************************************************************/
+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);
+	}
+}
+
+/************************************************************/