added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 7ce90733b72b02d6f05175d14b61f73599b58d2c..fb2495c13fe8c09095221fbff3fb79c29c9d129a 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -162,6 +162,79 @@ int GroupMap::readDesignMap() {
        }
 }
 /************************************************************/
+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"); }
+                    
+                    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"); }
+                    
+                    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;