X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothurout.cpp;h=1a3bf79f50dad4e0a66e9910bb4abfe8c2cff944;hb=28bcfc4a41b8b82f66636587e0d4d355d07cbdd1;hp=dfcf25b4447d28362dae3f27a4e9cfd27e362d8e;hpb=0cefb55a2616975bd4a144fc345693695ffc9bb6;p=mothur.git

diff --git a/mothurout.cpp b/mothurout.cpp
index dfcf25b..1a3bf79 100644
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -43,7 +43,7 @@ set<string> MothurOut::getCurrentTypes()  {
         types.insert("tree");
         types.insert("flow");
         types.insert("biom");
-        types.insert("counttable");
+        types.insert("count");
         types.insert("processors");
 
 		return types;
@@ -79,7 +79,7 @@ void MothurOut::printCurrentFiles()  {
 		if (treefile != "")			{  mothurOut("tree=" + treefile); mothurOutEndLine();				}
 		if (flowfile != "")			{  mothurOut("flow=" + flowfile); mothurOutEndLine();				}
         if (biomfile != "")			{  mothurOut("biom=" + biomfile); mothurOutEndLine();				}
-        if (counttablefile != "")	{  mothurOut("counttable=" + counttablefile); mothurOutEndLine();	}
+        if (counttablefile != "")	{  mothurOut("count=" + counttablefile); mothurOutEndLine();	}
 		if (processors != "1")		{  mothurOut("processors=" + processors); mothurOutEndLine();		}
 		
 	}
@@ -1052,6 +1052,9 @@ int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 
 int MothurOut::renameFile(string oldName, string newName){
 	try {
+        
+        if (oldName == newName) { return 0; }
+        
 		ifstream inTest;
 		int exist = openInputFile(newName, inTest, "");
 		inTest.close();
@@ -1541,7 +1544,6 @@ vector<string> MothurOut::splitWhiteSpace(string input){
 //**********************************************************************************************************************
 int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
 	try {
-		
         //open input file
 		ifstream in;
 		openInputFile(namefile, in);
@@ -1572,6 +1574,23 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
             }
 		}
 		in.close();
+        
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    //are there confidence scores, if so remove them
+                    if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);	}
+                    taxMap[firstCol] = secondCol;
+                    if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
+                    pairDone = false; 
+                }
+            } 
+        }
 		
 		return taxMap.size();
 
@@ -1584,7 +1603,6 @@ int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool redund) { 
 	try {
-		
 		//open input file
 		ifstream in;
 		openInputFile(namefile, in);
@@ -1615,6 +1633,23 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool red
             }
 		}
 		in.close();
+        
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    //parse names into vector
+                    vector<string> theseNames;
+                    splitAtComma(secondCol, theseNames);
+                    for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
+                    pairDone = false; 
+                }
+            }  
+        }
 		
 		return nameMap.size();
 		
@@ -1627,7 +1662,6 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool red
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) { 
 	try {
-		
 		//open input file
 		ifstream in;
 		openInputFile(namefile, in);
@@ -1655,6 +1689,20 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip
             }
 		}
 		in.close();
+        
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    nameMap[secondCol] = firstCol;
+                    pairDone = false; 
+                }
+            } 
+        }
 		
 		return nameMap.size();
 		
@@ -1667,7 +1715,7 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) { 
 	try {
-		nameMap.clear(); nameCount.clear();
+ 		nameMap.clear(); nameCount.clear();
 		//open input file
 		ifstream in;
 		openInputFile(namefile, in);
@@ -1700,6 +1748,24 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<stri
 		}
 		in.close();
 		
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    //parse names into vector
+                    vector<string> theseNames;
+                    splitAtComma(secondCol, theseNames);
+                    for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
+                    nameCount[firstCol] = theseNames.size();
+                    pairDone = false; 
+                }
+            }
+
+        }
 		return nameMap.size();
 		
 	}
@@ -1711,7 +1777,6 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<stri
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
 	try {
-		
 		//open input file
 		ifstream in;
 		openInputFile(namefile, in);
@@ -1736,6 +1801,17 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
             }
 		}
 		in.close();
+        
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
+            }
+        }
 		
 		return nameMap.size();
 		
@@ -1747,8 +1823,7 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
 }
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) { 
-	try {
-		
+	try {        
 		//open input file
 		ifstream in;
 		openInputFile(namefile, in);
@@ -1779,6 +1854,22 @@ int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap)
 		}
 		in.close();
         
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    vector<string> temp;
+                    splitAtComma(secondCol, temp);
+                    nameMap[firstCol] = temp;
+                    pairDone = false;  
+                } 
+            }
+        }
+        
 		return nameMap.size();
 	}
 	catch(exception& e) {
@@ -1789,7 +1880,6 @@ int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap)
 /**********************************************************************************************************************/
 map<string, int> MothurOut::readNames(string namefile) { 
 	try {
-		
 		map<string, int> nameMap;
 		
 		//open input file
@@ -1820,6 +1910,20 @@ map<string, int> MothurOut::readNames(string namefile) {
             }
 		}
         in.close();
+        
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    int num = getNumNames(secondCol);
+                    nameMap[firstCol] = num;
+                    pairDone = false;  
+                } 
+            }
+        }
 		
 		return nameMap;
 		
@@ -1872,6 +1976,29 @@ int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, m
 		}
         in.close();
         
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    int num = getNumNames(secondCol);
+                    
+                    map<string, string>::iterator it = fastamap.find(firstCol);
+                    if (it == fastamap.end()) {
+                        error = 1;
+                        mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+                    }else {
+                        seqPriorityNode temp(num, it->second, firstCol);
+                        nameVector.push_back(temp);
+                    }
+                    
+                    pairDone = false;  
+                } 
+            }
+        }
 		return error;
 	}
 	catch(exception& e) {
@@ -1882,7 +2009,7 @@ int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, m
 //**********************************************************************************************************************
 set<string> MothurOut::readAccnos(string accnosfile){
 	try {
-		set<string> names;
+ 		set<string> names;
 		ifstream in;
 		openInputFile(accnosfile, in);
 		string name;
@@ -1900,6 +2027,10 @@ set<string> MothurOut::readAccnos(string accnosfile){
         }
 		in.close();	
 		
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            for (int i = 0; i < pieces.size(); i++) {  names.insert(pieces[i]);  } 
+        }
 		return names;
 	}
 	catch(exception& e) {
@@ -1927,6 +2058,11 @@ int MothurOut::readAccnos(string accnosfile, vector<string>& names){
             for (int i = 0; i < pieces.size(); i++) {  names.push_back(pieces[i]);  }
         }
 		in.close();	
+        
+        if (rest != "") {
+            vector<string> pieces = splitWhiteSpace(rest);
+            for (int i = 0; i < pieces.size(); i++) {  names.push_back(pieces[i]);  }
+        }
 		
 		return 0;
 	}