From 2e11a0039122a506eed7fc21cc760e8699994c04 Mon Sep 17 00:00:00 2001
From: SarahsWork <sarahswork@imac.westcotts.net>
Date: Mon, 29 Apr 2013 14:55:14 -0400
Subject: [PATCH] added square format for phylipfile. made command work with
 list files containing unique and redundant sequences

---
 sensspeccommand.cpp | 61 ++++++++++++++++++++++++++++++++-------------
 sensspeccommand.h   |  3 ++-
 2 files changed, 46 insertions(+), 18 deletions(-)

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index f61232a..12786ca 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -243,16 +243,49 @@ int SensSpecCommand::execute(){
 		exit(1);
 	}
 }
+//***************************************************************************************************************
+bool SensSpecCommand::testFile(){
+	try{
+        ifstream fileHandle;
+        m->openInputFile(phylipfile, fileHandle);
+        
+        bool square = false;
+        string numTest, name;
+        fileHandle >> numTest >> name;
+
+        if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+
+        char d;
+        while((d=fileHandle.get()) != EOF){
+            if(isalnum(d)){
+                square = true;
+                break;
+            }
+            if(d == '\n'){
+                square = false;
+                break;
+            }
+        }
+        fileHandle.close();
+        
+        return square;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "SensSpecCommand", "testFile");
+		exit(1);
+	}
+}
 
 //***************************************************************************************************************
 
 int SensSpecCommand::processPhylip(){
 	try{
 		//probably need some checking to confirm that the names in the distance matrix are the same as those in the list file
-		string origCutoff = "";
+        square = testFile();
+ 		string origCutoff = "";
 		bool getCutoff = 0;
 		if(cutoff == -1.00)	{	getCutoff = 1;															}
-		else				{	origCutoff = toString(cutoff);	cutoff += (0.49 / double(precision));	}		
+		else				{	origCutoff = toString(cutoff);	cutoff += (0.49 / double(precision));	}
 		
 		map<string, int> seqMap;
 		string seqList;
@@ -265,7 +298,6 @@ int SensSpecCommand::processPhylip(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
 			if(m->control_pressed){
@@ -461,6 +493,9 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
 					else								{	trueNegatives++;	}
 				}
 			}
+            
+            if (square) { m->getline(phylipFile); } //get rest of line - redundant distances
+            m->gobble(phylipFile);
 		}
 		phylipFile.close();
 		
@@ -707,28 +742,18 @@ string SensSpecCommand::preProcessList(){
             m->openInputFile(distFile, phylipFile);
             string numTest;
             int pNumSeqs;
-			phylipFile >> numTest;
+			phylipFile >> numTest; m->gobble(phylipFile);
 			
 			if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
             else {
                 m->mothurConvert(numTest, pNumSeqs);
             }
-            phylipFile >> pNumSeqs; m->gobble(phylipFile);
             
             string seqName;
-            double distance;
-            
             for(int i=0;i<pNumSeqs;i++){
-                
                 if (m->control_pressed) { return ""; }
-                
-                phylipFile >> seqName; 
+                phylipFile >> seqName;  m->getline(phylipFile);  m->gobble(phylipFile);
                 uniqueNames.insert(seqName);
-                
-                for(int j=0;j<i;j++){
-                    phylipFile >> distance;
-                }
-                m->gobble(phylipFile);
             }
             phylipFile.close();
         }else {
@@ -778,8 +803,8 @@ string SensSpecCommand::preProcessList(){
                 m->splitAtComma(binnames, bnames);
 				
 				string newNames = "";
-                for (int i = 0; i < bnames.size(); i++) {
-					string name = bnames[i];
+                for (int j = 0; j < bnames.size(); j++) {
+					string name = bnames[j];
 					//if that name is in the .accnos file, add it
 					if (uniqueNames.count(name) != 0) {  newNames += name + ",";  }
 				}
@@ -803,6 +828,8 @@ string SensSpecCommand::preProcessList(){
 		out.close();
 
         if (wroteSomething) { return newListFile; }
+        else { m->mothurRemove(newListFile); }
+        
         return ""; 
     }
     catch(exception& e) {
diff --git a/sensspeccommand.h b/sensspeccommand.h
index 7d85a39..bfa3291 100644
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -48,7 +48,7 @@ private:
 	set<string> labels; //holds labels to be used
 
 	long int truePositives, falsePositives, trueNegatives, falseNegatives;
-	bool abort, allLines;
+	bool abort, allLines, square;
 	bool hard;
 	//string lineLabel;
 	double cutoff;
@@ -59,6 +59,7 @@ private:
 	int process(map<string, int>&, string, bool&, string&);
 	int process(set<string>&, string, bool&, string&, int);
     string preProcessList();
+    bool testFile();
 
 };
 
-- 
2.39.2