added kruskwalliscommand to Xcode project and fixed parameter issues.

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 612b2364d617432d64819413b8d8eb03d9865a64..fb2495c13fe8c09095221fbff3fb79c29c9d129a 100644 (file)
--- 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;
     }
@@ -110,6 +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;
@@ -135,6 +260,8 @@ 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 +275,30 @@ 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;
     }