X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=groupmap.cpp;h=7ce90733b72b02d6f05175d14b61f73599b58d2c;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=612b2364d617432d64819413b8d8eb03d9865a64;hpb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;p=mothur.git

diff --git a/groupmap.cpp b/groupmap.cpp
index 612b236..7ce9073 100644
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -44,6 +44,7 @@ int GroupMap::readMap() {
                 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 groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -57,6 +58,30 @@ int GroupMap::readMap() {
         }
 		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 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;
     }
@@ -88,6 +113,8 @@ int GroupMap::readDesignMap() {
                 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 designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -101,6 +128,31 @@ int GroupMap::readDesignMap() {
         }
 		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 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;
     }
@@ -135,6 +187,8 @@ int GroupMap::readDesignMap(string filename) {
                 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 designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
@@ -148,6 +202,30 @@ int GroupMap::readDesignMap(string filename) {
         }
 		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 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;
     }