changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 92a43e965044c06c2fdcaca78d50779440b301ab..612b2364d617432d64819413b8d8eb03d9865a64 100644 (file)
--- 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();    }