X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequence.cpp;h=efeb88ce65183135c2a0aaef36d8d3a1c8f432cc;hp=4c631a23451d4d9723aec3a29bed423737b243ba;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=75cff1a83a64cd46e9dd603e02597a2bb6a76119

diff --git a/sequence.cpp b/sequence.cpp
index 4c631a2..efeb88c 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -21,9 +21,7 @@ Sequence::Sequence(string newName, string sequence) {
 		initialize();	
 		name = newName;
         
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-        }
+        m->checkName(name);
 		
 		//setUnaligned removes any gap characters for us
 		setUnaligned(sequence);
@@ -41,9 +39,7 @@ Sequence::Sequence(string newName, string sequence, string justUnAligned) {
 		initialize();	
 		name = newName;
         
-        for (int i = 0; i < name.length(); i++) {
-            if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-        }
+        m->checkName(name);
 		
 		//setUnaligned removes any gap characters for us
 		setUnaligned(sequence);
@@ -80,7 +76,8 @@ Sequence::Sequence(istringstream& fastaString){
 				}
 			}
 			
-			while (!fastaString.eof())	{	char c = fastaString.get();  if (c == 10 || c == 13){ break;	}	} // get rest of line if there's any crap there
+			//while (!fastaString.eof())	{	char c = fastaString.get();  if (c == 10 || c == 13){ break;	}	} // get rest of line if there's any crap there
+            comment = getCommentString(fastaString);
 			
 			int numAmbig = 0;
 			sequence = getSequenceString(fastaString, numAmbig);
@@ -124,7 +121,8 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
 				}
 			}
 			
-			while (!fastaString.eof())	{	char c = fastaString.get();  if (c == 10 || c == 13){ break;	}	} // get rest of line if there's any crap there
+			//while (!fastaString.eof())	{	char c = fastaString.get();  if (c == 10 || c == 13){ break;	}	} // get rest of line if there's any crap there
+            comment = getCommentString(fastaString);
 			
 			int numAmbig = 0;
 			sequence = getSequenceString(fastaString, numAmbig);
@@ -170,8 +168,8 @@ Sequence::Sequence(ifstream& fastaFile){
 				}
 			}
 			
-			//read real sequence
-			while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){  break;	}	} // get rest of line if there's any crap there
+			//while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){  break;	}	} // get rest of line if there's any crap there
+            comment = getCommentString(fastaFile);
 			
 			int numAmbig = 0;
 			sequence = getSequenceString(fastaFile, numAmbig);
@@ -220,9 +218,11 @@ Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
 			//read info after sequence name
 			while (!fastaFile.eof())	{	
                 char c = fastaFile.get(); 
-                if (c == 10 || c == 13){  break;	}	
+                if (c == 10 || c == 13 || c == -1){   break;	}
                 extraInfo += c;
-            } 
+            }
+            
+            comment = extraInfo;
 			
 			int numAmbig = 0;
 			sequence = getSequenceString(fastaFile, numAmbig);
@@ -265,8 +265,8 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
 				}
 			}
 			
-			//read real sequence
-			while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	 break;	}	} // get rest of line if there's any crap there
+			//while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	 break;	}	} // get rest of line if there's any crap there
+            comment = getCommentString(fastaFile);
 			
 			int numAmbig = 0;
 			sequence = getSequenceString(fastaFile, numAmbig);
@@ -295,9 +295,7 @@ string Sequence::getSequenceName(ifstream& fastaFile) {
             
 			name = name.substr(1); 
             
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
             
         }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
@@ -319,9 +317,7 @@ string Sequence::getSequenceName(istringstream& fastaFile) {
             
 			name = name.substr(1); 
             
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
             
         }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
@@ -368,17 +364,19 @@ string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
 string Sequence::getCommentString(ifstream& fastaFile) {
 	try {
 		char letter;
-		string sequence = "";
+		string temp = "";
 		
 		while(fastaFile){
 			letter=fastaFile.get();
-			if((letter == '\r') || (letter == '\n')){  
+			if((letter == '\r') || (letter == '\n') || letter == -1){
 				m->gobble(fastaFile);  //in case its a \r\n situation
 				break;
-			}
+			}else {
+                temp += letter;
+            }
 		}
 		
-		return sequence;
+		return temp;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Sequence", "getCommentString");
@@ -422,17 +420,19 @@ string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
 string Sequence::getCommentString(istringstream& fastaFile) {
 	try {
 		char letter;
-		string sequence = "";
+		string temp = "";
 		
 		while(fastaFile){
 			letter=fastaFile.get();
-			if((letter == '\r') || (letter == '\n')){  
+			if((letter == '\r') || (letter == '\n') || letter == -1){  
 				m->gobble(fastaFile);  //in case its a \r\n situation
 				break;
-			}
+			}else {
+                temp += letter;
+            }
 		}
 		
-		return sequence;
+		return temp;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Sequence", "getCommentString");
@@ -447,6 +447,7 @@ void Sequence::initialize(){
 	unaligned = "";
 	aligned = "";
 	pairwise = "";
+    comment = "";
 	
 	numBases = 0;
 	alignmentLength = 0;
@@ -589,7 +590,7 @@ int Sequence::getNumNs(){
 
 void Sequence::printSequence(ostream& out){
 
-	out << ">" << name << endl;
+	out << ">" << name << comment << endl;
 	if(isAligned){
 		out << aligned << endl;
 	}
@@ -683,12 +684,12 @@ int Sequence::filterToPos(int start){
     
     if (start > aligned.length()) { start = aligned.length(); m->mothurOut("[ERROR]: start to large.\n"); }
     
-	for(int j = 0; j < start-1; j++) {
+	for(int j = 0; j < start; j++) {
 		aligned[j] = '.';
 	}
 	
     //things like ......----------AT become ................AT
-    for(int j = start-1; j < aligned.length(); j++) {
+    for(int j = start; j < aligned.length(); j++) {
         if (isalpha(aligned[j])) { break; }
         else { aligned[j] = '.'; }
     }