X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=groupmap.cpp;h=9b8aa3f8abc87ef9ff93520a80b3da9169d406f4;hp=481fd1decfc4516eb5e1cf618c6b4d40cffbc8a9;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc

diff --git a/groupmap.cpp b/groupmap.cpp
index 481fd1d..9b8aa3f 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -20,60 +20,293 @@
 
 /************************************************************/
  GroupMap::~GroupMap(){}
-
 /************************************************************/
 int GroupMap::readMap() {
-		string seqName, seqGroup;
+    try {
+        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);
-		}
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+    
+        while (!fileHandle.eof()) {
+            if (m->control_pressed) { fileHandle.close();  return 1; }
+        
+            fileHandle.read(buffer, 4096);
+            vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+        
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+            
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
 		fileHandle.close();
+        
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
+        
 		m->setAllGroups(namesOfGroups);
 		return error;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "readMap");
+		exit(1);
+	}
 }
 /************************************************************/
 int GroupMap::readDesignMap() {
-		string seqName, seqGroup;
+    try {
+        string seqName, seqGroup;
 		int error = 0;
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        
+        while (!fileHandle.eof()) {
+            if (m->control_pressed) { fileHandle.close();  return 1; }
+            
+            fileHandle.read(buffer, 4096);
+            vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    it = groupmap.find(seqName);
+                    
+                    if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile 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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
+		fileHandle.close();
+        
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    it = groupmap.find(seqName);
+                    
+                    if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile 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
+                    }
+                    pairDone = false; 
+                } 
+            }
 
-		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);
-		}
+        }
+        
+		m->setAllGroups(namesOfGroups);
+		return error;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "readDesignMap");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::readMap(string filename) {
+    try {
+        groupFileName = filename;
+        m->openInputFile(filename, fileHandle);
+        index = 0;
+        string seqName, seqGroup;
+		int error = 0;
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        
+        while (!fileHandle.eof()) {
+            if (m->control_pressed) { fileHandle.close();  return 1; }
+            
+            fileHandle.read(buffer, 4096);
+            vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    it = groupmap.find(seqName);
+                    
+                    if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file 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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
 		fileHandle.close();
+        
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    it = groupmap.find(seqName);
+                    
+                    if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file 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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
+        
 		m->setAllGroups(namesOfGroups);
 		return error;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "readMap");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::readDesignMap(string filename) {
+    try {
+        groupFileName = filename;
+        m->openInputFile(filename, fileHandle);
+        index = 0;
+        string seqName, seqGroup;
+		int error = 0;
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        
+        while (!fileHandle.eof()) {
+            if (m->control_pressed) { fileHandle.close();  return 1; }
+            
+            fileHandle.read(buffer, 4096);
+            vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    it = groupmap.find(seqName);
+                    
+                    if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile 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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
+		fileHandle.close();
+        
+        if (rest != "") {
+            vector<string> pieces = m->splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  seqName = pieces[i]; columnOne=false; }
+                else  { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    setNamesOfGroups(seqGroup);
+                    
+                    if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+                    m->checkName(seqName);
+                    it = groupmap.find(seqName);
+                    
+                    if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile 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
+                    }
+                    pairDone = false; 
+                } 
+            }
+        }
+        
+		m->setAllGroups(namesOfGroups);
+		return error;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "readDesignMap");
+		exit(1);
+	}
 }
-
 /************************************************************/
 int GroupMap::getNumGroups() { return namesOfGroups.size();	}
 /************************************************************/
@@ -84,6 +317,10 @@ string GroupMap::getGroup(string sequenceName) {
 	if (it != groupmap.end()) { //sequence name was in group file
 		return it->second;	
 	}else {
+        //look for it in names of groups to see if the user accidently used the wrong file
+        if (m->inUsersGroups(sequenceName, namesOfGroups)) {
+            m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ".  Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine(); 
+        }
 		return "not found";
 	}
 }
@@ -92,7 +329,7 @@ string GroupMap::getGroup(string sequenceName) {
 
 void GroupMap::setGroup(string sequenceName, string groupN) {
 	setNamesOfGroups(groupN);
-	
+	m->checkName(sequenceName);
 	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();  }
@@ -135,6 +372,22 @@ bool GroupMap::isValidGroup(string groupname) {
 	}
 }
 /************************************************************/
+int GroupMap::getCopy(GroupMap* g) {
+	try {
+        vector<string> names = g->getNamesSeqs();
+        for (int i = 0; i < names.size(); i++) {
+            if (m->control_pressed) { break; }
+            string group = g->getGroup(names[i]);
+            setGroup(names[i], group);
+        }
+        return names.size();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "getCopy");
+		exit(1);
+	}
+}
+/************************************************************/
 int GroupMap::getNumSeqs(string group) {
 	try {
 		
@@ -152,7 +405,66 @@ int GroupMap::getNumSeqs(string group) {
 		exit(1);
 	}
 }
-
+/************************************************************/
+int GroupMap::renameSeq(string oldName, string newName) {
+	try {
+		
+		map<string, string>::iterator itName;
+		
+		itName = groupmap.find(oldName);
+		
+		if (itName == groupmap.end()) {
+            m->mothurOut("[ERROR]: cannot find " + toString(oldName) + " in group file");
+            m->control_pressed = true;
+            return 0;
+        }else {
+            string group = itName->second;
+            groupmap.erase(itName);
+            groupmap[newName] = group;
+        }
+        
+        return 0;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "renameSeq");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::print(ofstream& out) {
+	try {
+		
+		for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+            out << itName->first << '\t' << itName->second << endl;
+        }
+             
+        return 0;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "print");
+		exit(1);
+	}
+}
+/************************************************************/
+int GroupMap::print(ofstream& out, vector<string> userGroups) {
+	try {
+		
+		for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
+            if (m->inUsersGroups(itName->second, userGroups)) {
+                out << itName->first << '\t' << itName->second << endl;
+            }
+        }
+        
+        return 0;
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "print");
+		exit(1);
+	}
+}
 /************************************************************/
 vector<string> GroupMap::getNamesSeqs(){
 	try {