X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequence.cpp;h=d6073d75da3ed630b27b626bbba8615d79b58858;hp=93ecb70f066fd8a1da6415453347aac66c57d0dd;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=4b54ce99af7db8019ea907cd7c2edf789369ada9

diff --git a/sequence.cpp b/sequence.cpp
index 93ecb70..d6073d7 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);
@@ -220,7 +216,7 @@ 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;
             } 
 			
@@ -295,9 +291,7 @@ 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 +313,7 @@ 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;  }
         
@@ -575,6 +567,15 @@ string Sequence::getUnaligned(){
 int Sequence::getNumBases(){
 	return numBases;
 }
+//********************************************************************************************************************
+
+int Sequence::getNumNs(){
+    int numNs = 0;
+	for (int i = 0; i < unaligned.length(); i++) {
+        if(toupper(unaligned[i]) == 'N') { numNs++; }
+    }
+    return numNs;
+}
 
 //********************************************************************************************************************
 
@@ -674,12 +675,12 @@ 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] = '.'; }
     }
@@ -763,6 +764,8 @@ void Sequence::trim(int length){
 	if(numBases > length){
 		unaligned = unaligned.substr(0,length);
 		numBases = length;
+        aligned = "";
+        isAligned = 0;
 	}
 	
 }