From: westcott <westcott>
Date: Mon, 18 Oct 2010 12:14:32 +0000 (+0000)
Subject: testing metastats compile
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=672cc1adbb2f8dac82757653cd579c093fe886c2

testing metastats compile
---

diff --git a/metastats.h b/metastats.h
index ca8943a..2f3cc62 100644
--- a/metastats.h
+++ b/metastats.h
@@ -33,7 +33,7 @@ void meanvar(double *pmatrix,int *g,int *nr,int *nc,double *storage);
 void start(double *Imatrix,int *g,int *nr,int *nc,double *testing,
 			double storage[][9]);
 
-int metastat_main (char* outputFileName, int numRows, int numCols, double threshold, int numPermutations, double** data, int);
+int metastat_main (char*, int, int, double, int, double**, int);
 
 #ifdef __cplusplus	   
 }
diff --git a/mothur b/mothur
index f090f30..ac8ea8a 100755
Binary files a/mothur and b/mothur differ
diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 46081df..26969d8 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -590,42 +590,41 @@ void PipelineCommand::createPatsPipeline(){
 		
 		//sff.info command
 		string thisCommand = "sffinfo(sff=" + sffFile + ")";
-		commands.push_back(thisCommand);
+		//commands.push_back(thisCommand);
 		
 		//trim.seqs command
 		string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
 		string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
-		thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=F, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
-		commands.push_back(thisCommand);
+		//thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=F, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
+		//commands.push_back(thisCommand);
 		
 		//unique.seqs
 		string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";
 		qualFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 		fastaFile =  m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
-		thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
-		commands.push_back(thisCommand);
+		//thisCommand = "unique.seqs(fasta=" + fastaFile + ")"; 
+		//commands.push_back(thisCommand);
 		
 		//align.seqs
 		string nameFile = m->getRootName(m->getSimpleName(fastaFile)) + "names";
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "unique" + m->getExtension(fastaFile);
-		thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
-		commands.push_back(thisCommand);
+		//thisCommand = "align.seqs(processors=" + toString(processors) + ", candidate=" + fastaFile + ", template=" + alignFile + ")";
+		//commands.push_back(thisCommand);
 		
 		//screen.seqs
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "align";
-		thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + "group=" + groupFile + ", optimize=end-minlength)";
-		commands.push_back(thisCommand);
+		//thisCommand = "screen.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", optimize=end-minlength)";
+	//	commands.push_back(thisCommand);
 		
 		//chimera.slayer
 		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "good" + m->getExtension(fastaFile);
 		nameFile = m->getRootName(m->getSimpleName(nameFile)) + "good" + m->getExtension(nameFile);
 		groupFile = m->getRootName(m->getSimpleName(groupFile)) + "good" + m->getExtension(groupFile);
-		thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
-		commands.push_back(thisCommand);
+		//thisCommand = "chimera.slayer(processors=" + toString(processors) + ", fasta=" + fastaFile + ", template=" + chimeraFile + ")";
+	//	commands.push_back(thisCommand);
 		
 		//remove.seqs
 		string accnosFile = m->getRootName(m->getSimpleName(fastaFile))  + "slayer.accnos";
-		fastaFile = m->getRootName(m->getSimpleName(fastaFile)) + "slayer.chimeras";
 		thisCommand = "remove.seqs(fasta=" + fastaFile + ", name=" + nameFile + ", group=" + groupFile + ", accnos=" + accnosFile + ", dups=T)";
 		commands.push_back(thisCommand);
 		
diff --git a/unweighted.cpp b/unweighted.cpp
index da6ad2c..edd628d 100644
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -217,7 +217,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 					int lc = t->tree[i].getLChild();
 					int rc = t->tree[i].getRChild();
 					
-					//if yes, add to total your childrens branchLengths and your childrens tempTotals
+					//if yes, add your childrens tempTotals
 					if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 						totalBL += tempTotals[lc] + tempTotals[rc]; 
 						if (t->tree[i].getBranchLength() != -1) {
@@ -225,13 +225,12 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 						}else {
 							tempTotals[i] = 0.0;
 						}
-						//tempTotals[i] = tempTotals[lc] + tempTotals[rc]; 
-					}else { //if no, your tempTotal is your childrens temp totals
+					}else { //if no, your tempTotal is your childrens temp totals + your branch length
 						tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength()); 
 					}
 				}
 			}
-			
+	cout << UniqueBL << '\t' << totalBL << endl;		
 			UW = (UniqueBL / totalBL);  
 	
 			if (isnan(UW) || isinf(UW)) { UW = 0; }
@@ -462,7 +461,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 					int lc = copyTree->tree[i].getLChild();
 					int rc = copyTree->tree[i].getRChild();
 					
-					//if yes, add to total your childrens branchLengths and your childrens tempTotals
+					//if yes, add your childrens tempTotals
 					if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
 						totalBL += tempTotals[lc] + tempTotals[rc]; 
 						if (copyTree->tree[i].getBranchLength() != -1) {
@@ -470,8 +469,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
 						}else {
 							tempTotals[i] = 0.0;
 						}
-						//tempTotals[i] = tempTotals[lc] + tempTotals[rc]; 
-					}else { //if no, your tempTotal is your childrens temp totals
+					}else { //if no, your tempTotal is your childrens temp totals + your branch length
 						tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); 
 					}
 				}