X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;fp=groupmap.cpp;h=612b2364d617432d64819413b8d8eb03d9865a64;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=92a43e965044c06c2fdcaca78d50779440b301ab;hpb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index 92a43e9..612b236 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -23,84 +23,138 @@
 
 /************************************************************/
 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);
+                    
+                    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();
+        
 		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;
-
-		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);
-		}
+        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);
+                    
+                    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();
+        
 		m->setAllGroups(namesOfGroups);
 		return error;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "readDesignMap");
+		exit(1);
+	}
 }
 /************************************************************/
 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);
+    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;
         
-        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
+        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);
+                    
+                    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->gobble(fileHandle);
+		fileHandle.close();
+        
+		m->setAllGroups(namesOfGroups);
+		return error;
     }
-    fileHandle.close();
-    m->setAllGroups(namesOfGroups);
-    return error;
+	catch(exception& e) {
+		m->errorOut(e, "GroupMap", "readDesignMap");
+		exit(1);
+	}
 }
 /************************************************************/
 int GroupMap::getNumGroups() { return namesOfGroups.size();	}