X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=needlemanoverlap.cpp;h=1c2ef223539c65a95ca1dac66a823d226b6108b8;hp=b14d8e3d10e42ee9c7a21f5595315b29ad172ff5;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=3abb236c602eb168ee112f080b563ebe2c705029

diff --git a/needlemanoverlap.cpp b/needlemanoverlap.cpp
index b14d8e3..1c2ef22 100644
--- a/needlemanoverlap.cpp
+++ b/needlemanoverlap.cpp
@@ -24,8 +24,8 @@
 
 /**************************************************************************************************/
 
-NeedlemanOverlap::NeedlemanOverlap(float gO, float m, float mm, int r) ://	note that we don't have a gap extend
-gap(gO), match(m), mismatch(mm), Alignment(r) {							//	the gap openning penalty is assessed for
+NeedlemanOverlap::NeedlemanOverlap(float gO, float f, float mm, int r) ://	note that we don't have a gap extend
+gap(gO), match(f), mismatch(mm), Alignment(r) {							//	the gap openning penalty is assessed for
 	try {																	//	every gapped position
 		for(int i=1;i<nCols;i++){
 			alignment[0][i].prevCell = 'l';					//	initialize first row by pointing all poiters to the left
@@ -39,11 +39,9 @@ gap(gO), match(m), mismatch(mm), Alignment(r) {							//	the gap openning penalt
 	
 	}
 	catch(exception& e) {
-		errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
+		m->errorOut(e, "NeedlemanOverlap", "NeedlemanOverlap");
 		exit(1);
 	}
-																
-																		
 }
 /**************************************************************************************************/
 
@@ -53,18 +51,21 @@ NeedlemanOverlap::~NeedlemanOverlap(){	/*	do nothing	*/	}
 
 void NeedlemanOverlap::align(string A, string B){
 	try {
+	
 		seqA = ' ' + A;	lA = seqA.length();		//	algorithm requires a dummy space at the beginning of each string
 		seqB = ' ' + B;	lB = seqB.length();		//	algorithm requires a dummy space at the beginning of each string
 
-		if (lA > nRows) { mothurOut("Your one of your candidate sequences is longer than you longest template sequence."); mothurOutEndLine();  }
+		if (lA > nRows) { m->mothurOut("One of your candidate sequences is longer than you longest template sequence. Your longest template sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + "."); m->mothurOutEndLine();  }
 		
 		for(int i=1;i<lB;i++){					//	This code was largely translated from Perl code provided in Ex 3.1 
+		
 			for(int j=1;j<lA;j++){				//	of the O'Reilly BLAST book.  I found that the example output had a
+	
 				//	number of errors
 				float diagonal;
 				if(seqB[i] == seqA[j])	{	diagonal = alignment[i-1][j-1].cValue + match;		}
 				else					{	diagonal = alignment[i-1][j-1].cValue + mismatch;	}
-				
+			
 				float up	= alignment[i-1][j].cValue + gap;
 				float left	= alignment[i][j-1].cValue + gap;
 				
@@ -90,17 +91,110 @@ void NeedlemanOverlap::align(string A, string B){
 				}
 			}
 		}
+
 		Overlap over;						
 		over.setOverlap(alignment, lA, lB, 0);		//	Fix gaps at the beginning and end of the sequences
 		traceBack();								//	Traceback the alignment to populate seqAaln and seqBaln
-		
+	
 	}
 	catch(exception& e) {
-		errorOut(e, "NeedlemanOverlap", "align");
+		m->errorOut(e, "NeedlemanOverlap", "align");
 		exit(1);
 	}
 
 }
+/**************************************************************************************************/
 
+void NeedlemanOverlap::alignPrimer(string A, string B){
+	try {
+        
+		seqA = ' ' + A;	lA = seqA.length();		//	algorithm requires a dummy space at the beginning of each string
+		seqB = ' ' + B;	lB = seqB.length();		//	algorithm requires a dummy space at the beginning of each string
+        
+		if (lA > nRows) { m->mothurOut("One of your candidate sequences is longer than you longest template sequence. Your longest template sequence is " + toString(nRows) + ". Your candidate is " + toString(lA) + "."); m->mothurOutEndLine();  }
+		
+		for(int i=1;i<lB;i++){					//	This code was largely translated from Perl code provided in Ex 3.1
+            
+			for(int j=1;j<lA;j++){				//	of the O'Reilly BLAST book.  I found that the example output had a
+                
+				//	number of errors
+				float diagonal;
+				if(isEquivalent(seqB[i],seqA[j]))	{	diagonal = alignment[i-1][j-1].cValue + match;		}
+				else                                {	diagonal = alignment[i-1][j-1].cValue + mismatch;	}
+                
+				float up	= alignment[i-1][j].cValue + gap;
+				float left	= alignment[i][j-1].cValue + gap;
+				
+				if(diagonal >= up){
+					if(diagonal >= left){
+						alignment[i][j].cValue = diagonal;
+						alignment[i][j].prevCell = 'd';
+					}
+					else{
+						alignment[i][j].cValue = left;
+						alignment[i][j].prevCell = 'l';
+					}
+				}
+				else{
+					if(up >= left){
+						alignment[i][j].cValue = up;
+						alignment[i][j].prevCell = 'u';
+					}
+					else{
+						alignment[i][j].cValue = left;
+						alignment[i][j].prevCell = 'l';
+					}
+				}
+			}
+		}
+        
+		Overlap over;
+		over.setOverlap(alignment, lA, lB, 0);		//	Fix gaps at the beginning and end of the sequences
+		traceBack();								//	Traceback the alignment to populate seqAaln and seqBaln
+        
+	}
+	catch(exception& e) {
+		m->errorOut(e, "NeedlemanOverlap", "alignPrimer");
+		exit(1);
+	}
+    
+}
+//********************************************************************/
+bool NeedlemanOverlap::isEquivalent(char oligo, char seq){
+	try {
+		
+        bool same = true;
+					
+        oligo = toupper(oligo);
+        seq = toupper(seq);
+        
+        if(oligo != seq){
+            if(oligo == 'A' && (seq != 'A' && seq != 'M' && seq != 'R' && seq != 'W' && seq != 'D' && seq != 'H' && seq != 'V'))       {	same = false;	}
+            else if(oligo == 'C' && (seq != 'C' && seq != 'Y' && seq != 'M' && seq != 'S' && seq != 'B' && seq != 'H' && seq != 'V'))       {	same = false;	}
+            else if(oligo == 'G' && (seq != 'G' && seq != 'R' && seq != 'K' && seq != 'S' && seq != 'B' && seq != 'D' && seq != 'V'))       {	same = false;	}
+            else if(oligo == 'T' && (seq != 'T' && seq != 'Y' && seq != 'K' && seq != 'W' && seq != 'B' && seq != 'D' && seq != 'H'))       {	same = false;	}
+            else if((oligo == '.' || oligo == '-'))           {	same = false;	}
+            else if((oligo == 'N' || oligo == 'I') && (seq == 'N'))                         {	same = false;	}
+            else if(oligo == 'R' && (seq != 'A' && seq != 'G'))                        {	same = false;	}
+            else if(oligo == 'Y' && (seq != 'C' && seq != 'T'))                        {	same = false;	}
+            else if(oligo == 'M' && (seq != 'C' && seq != 'A'))                        {	same = false;	}
+            else if(oligo == 'K' && (seq != 'T' && seq != 'G'))                        {	same = false;	}
+            else if(oligo == 'W' && (seq != 'T' && seq != 'A'))                        {	same = false;	}
+            else if(oligo == 'S' && (seq != 'C' && seq != 'G'))                        {	same = false;	}
+            else if(oligo == 'B' && (seq != 'C' && seq != 'T' && seq != 'G'))       {	same = false;	}
+            else if(oligo == 'D' && (seq != 'A' && seq != 'T' && seq != 'G'))       {	same = false;	}
+            else if(oligo == 'H' && (seq != 'A' && seq != 'T' && seq != 'C'))       {	same = false;	}
+            else if(oligo == 'V' && (seq != 'A' && seq != 'C' && seq != 'G'))       {	same = false;	}
+        }
+
+		
+		
+		return same;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TrimOligos", "countDiffs");
+		exit(1);
+	}
+}
 /**************************************************************************************************/