merged upstream changes to this fork

Mothur.xcodeproj/xcuserdata/SarahsWork.xcuserdatad/xcschemes/Mothur.xcscheme

@@ -14,7 +14,7 @@
             <BuildableReference
                BuildableIdentifier = "primary"
                BlueprintIdentifier = "8DD76FA90486AB0100D96B5E"
-               BuildableName = "Mothur"
+               BuildableName = "mothur"
                BlueprintName = "Mothur"
                ReferencedContainer = "container:Mothur.xcodeproj">
             </BuildableReference>
@@ -32,7 +32,7 @@
          <BuildableReference
             BuildableIdentifier = "primary"
             BlueprintIdentifier = "8DD76FA90486AB0100D96B5E"
-            BuildableName = "Mothur"
+            BuildableName = "mothur"
             BlueprintName = "Mothur"
             ReferencedContainer = "container:Mothur.xcodeproj">
          </BuildableReference>
@@ -50,7 +50,7 @@
          <BuildableReference
             BuildableIdentifier = "primary"
             BlueprintIdentifier = "8DD76FA90486AB0100D96B5E"
-            BuildableName = "Mothur"
+            BuildableName = "mothur"
             BlueprintName = "Mothur"
             ReferencedContainer = "container:Mothur.xcodeproj">
          </BuildableReference>
@@ -68,7 +68,7 @@
          <BuildableReference
             BuildableIdentifier = "primary"
             BlueprintIdentifier = "8DD76FA90486AB0100D96B5E"
-            BuildableName = "Mothur"
+            BuildableName = "mothur"
             BlueprintName = "Mothur"
             ReferencedContainer = "container:Mothur.xcodeproj">
          </BuildableReference>

aligncommand.h

@@ -1,6 +1,5 @@
 #ifndef ALIGNCOMMAND_H
 #define ALIGNCOMMAND_H
-
 /*
  *  aligncommand.h
  *  Mothur
@@ -10,7 +9,6 @@
  *
  */
 
-#include "mothur.h"
 #include "command.hpp"
 #include "database.hpp"
 #include "alignment.hpp"

alignment.cpp

@@ -15,7 +15,7 @@
 
 /**************************************************************************************************/
 
-Alignment::Alignment() {	/*	do nothing	*/	}
+Alignment::Alignment() {	m = MothurOut::getInstance(); /*	do nothing	*/	}
 
 /**************************************************************************************************/
 
@@ -53,7 +53,8 @@ void Alignment::resize(int A) {
 
 void Alignment::traceBack(){			//	This traceback routine is used by the dynamic programming algorithms
 	try {	
-									//	to fill the values of seqAaln and seqBaln
+		BBaseMap.clear();
+        ABaseMap.clear(); //	to fill the values of seqAaln and seqBaln
 		seqAaln = "";
 		seqBaln = "";
 		int row = lB-1;
@@ -65,31 +66,51 @@ void Alignment::traceBack(){			//	This traceback routine is used by the dynamic
 		//	matrix
 
 		if(currentCell.prevCell == 'x'){	seqAaln = seqBaln = "NOALIGNMENT";		}//If there's an 'x' in the bottom-
-		else{												//	right corner bail out because it means nothing got aligned
+		else{	//	right corner bail out because it means nothing got aligned
+            int count = 0;
 			while(currentCell.prevCell != 'x'){				//	while the previous cell isn't an 'x', keep going...
 
 				if(currentCell.prevCell == 'u'){			//	if the pointer to the previous cell is 'u', go up in the
 					seqAaln = '-' + seqAaln;				//	matrix.  this indicates that we need to insert a gap in
 					seqBaln = seqB[row] + seqBaln;			//	seqA and a base in seqB
+                    BBaseMap[row] = count;
 					currentCell = alignment[--row][column];
 				}
 				else if(currentCell.prevCell == 'l'){		//	if the pointer to the previous cell is 'l', go to the left
 					seqBaln = '-' + seqBaln;				//	in the matrix.  this indicates that we need to insert a gap
 					seqAaln = seqA[column] + seqAaln;		//	in seqB and a base in seqA
+                    ABaseMap[column] = count;
 					currentCell = alignment[row][--column];
 				}
 				else{
 					seqAaln = seqA[column] + seqAaln;		//	otherwise we need to go diagonally up and to the left,
 					seqBaln = seqB[row] + seqBaln;			//	here we add a base to both alignments
+                    BBaseMap[row] = count;
+                    ABaseMap[column] = count;
 					currentCell = alignment[--row][--column];
 				}
+                count++;
 			}
 		}
 
-		pairwiseLength = seqAaln.length();
+
+        pairwiseLength = seqAaln.length();
 		seqAstart = 1;	seqAend = 0;
 		seqBstart = 1;	seqBend = 0;
-
+        //flip maps since we now know the total length
+        map<int, int> newAMap;
+        for (map<int, int>::iterator it = ABaseMap.begin(); it != ABaseMap.end(); it++) {
+            int spot = it->second;
+            newAMap[pairwiseLength-spot-1] = it->first-1;
+        }
+        ABaseMap = newAMap;
+        map<int, int> newBMap;
+        for (map<int, int>::iterator it = BBaseMap.begin(); it != BBaseMap.end(); it++) {
+            int spot = it->second;
+            newBMap[pairwiseLength-spot-1] = it->first-1;
+        }
+		BBaseMap = newBMap;
+
 		for(int i=0;i<seqAaln.length();i++){
 			if(seqAaln[i] != '-' && seqBaln[i] == '-')		{	seqAstart++;	}
 			else if(seqAaln[i] == '-' && seqBaln[i] != '-')	{	seqBstart++;	}
@@ -156,7 +177,16 @@ int Alignment::getCandidateEndPos(){
 int Alignment::getTemplateStartPos(){
 	return seqBstart;									//	this is called to report the quality of the alignment
 }
+/**************************************************************************************************/
+
+map<int, int> Alignment::getSeqAAlnBaseMap(){
+	return ABaseMap;									
+}
+/**************************************************************************************************/
 
+map<int, int> Alignment::getSeqBAlnBaseMap(){
+	return BBaseMap;									
+}
 /**************************************************************************************************/
 
 int Alignment::getTemplateEndPos(){

alignment.hpp

@@ -30,6 +30,8 @@ class Alignment {
 //	float getAlignmentScore();
 	string getSeqAAln();
 	string getSeqBAln();
+    map<int, int> getSeqAAlnBaseMap();
+    map<int, int> getSeqBAlnBaseMap();
 	int getCandidateStartPos();
 	int getCandidateEndPos();
 	int getTemplateStartPos();
@@ -49,6 +51,8 @@ class Alignment {
 	int pairwiseLength;
 	int nRows, nCols, lA, lB;
 	vector<vector<AlignmentCell> > alignment;
+    map<int, int> ABaseMap;
+    map<int, int> BBaseMap;
 	MothurOut* m;
 };
 

bayesian.cpp

@@ -27,7 +27,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
 		if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
 
 		/************calculate the probablity that each word will be in a specific taxonomy*************/
-		string tfileroot = baseTName.substr(0,baseTName.find_last_of(".")+1);
+		string tfileroot = m->getFullPathName(baseTName.substr(0,baseTName.find_last_of(".")+1));
 		string tempfileroot = m->getRootName(m->getSimpleName(baseName));
 		string phyloTreeName = tfileroot + "tree.train";
 		string phyloTreeSumName = tfileroot + "tree.sum";
@@ -230,7 +230,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
 				delete phyloTree;
 
 				phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
-				
+                
 				//save probabilities
 				if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
 			}