X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=e8c96b3a42b88b6dbd4a003fe3a2454d2bbb4cb3;hb=ab750bdf95b4eb92186e4ce333edbd77396cda23;hp=a6bd54982e9ca509463f5d40822d1ae232e83bb1;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index a6bd549..e8c96b3 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -14,18 +14,16 @@
 FilterSeqsCommand::FilterSeqsCommand(){
 	globaldata = GlobalData::getInstance();
 	
-	if(globaldata->getFastaFile() != "")		{	readSeqs =  new ReadFasta(globaldata->inputFileName);	}
-	else if(globaldata->getNexusFile() != "")	{	readSeqs = new ReadNexus(globaldata->inputFileName);	}
-	else if(globaldata->getClustalFile() != "") {	readSeqs = new ReadClustal(globaldata->inputFileName);	}
-	else if(globaldata->getPhylipFile() != "")	{	readSeqs = new ReadPhylip(globaldata->inputFileName);	}
-	
-	readSeqs->read();
-	db = readSeqs->getDB();
-	numSeqs = db->size();
-	
-	alignmentLength = db->get(0).getAlignLength();
-
-	filter = string(alignmentLength, '1');
+	if(globaldata->getFastaFile() == "")		{	cout << "You must enter a fasta formatted file" << endl;	}
+	trump = globaldata->getTrump()[0];
+//	vertical = 
+//	readSeqs->read();
+//	db = readSeqs->getDB();
+//	numSeqs = db->size();
+//	
+//	alignmentLength = db->get(0).getAlignLength();
+//
+//	filter = string(alignmentLength, '1');
 }
 
 /**************************************************************************************/
@@ -46,87 +44,98 @@ void FilterSeqsCommand::doHard() {
 	else{
 		filter = hardFilter;
 	}
-	
+
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doTrump() {
+void FilterSeqsCommand::doTrump(Sequence seq) {
 
-	char trump = globaldata->getTrump()[0];
 	
-	for(int i = 0; i < numSeqs; i++) {
-		string curAligned = db->get(i).getAligned();;
-
-		for(int j = 0; j < alignmentLength; j++) {
-			if(curAligned[j] == trump){
-				filter[j] = '0';
-			}
-		}
-	}
+//	for(int i = 0; i < numSeqs; i++) {
+//		string curAligned = db->get(i).getAligned();;
+//
+//		for(int j = 0; j < alignmentLength; j++) {
+//			if(curAligned[j] == trump){
+//				filter[j] = '0';
+//			}
+//		}
+//	}
 
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doVertical() {
-
-	vector<int> counts(alignmentLength, 0);
-	
-	for(int i = 0; i < numSeqs; i++) {
-		string curAligned = db->get(i).getAligned();;
-		
-		for(int j = 0; j < alignmentLength; j++) {
-			if(curAligned[j] == '-' || curAligned[j] == '.'){
-				counts[j]++;
-			}
-		}
-	}
-	for(int i=0;i<alignmentLength;i++){
-		if(counts[i] == numSeqs)	{	filter[i] = '0';		}
-	}
+void FilterSeqsCommand::doVertical(Sequence seq) {
+
+//	vector<int> counts(alignmentLength, 0);
+//	
+//	for(int i = 0; i < numSeqs; i++) {
+//		string curAligned = db->get(i).getAligned();;
+//		
+//		for(int j = 0; j < alignmentLength; j++) {
+//			if(curAligned[j] == '-' || curAligned[j] == '.'){
+//				counts[j]++;
+//			}
+//		}
+//	}
+//	for(int i=0;i<alignmentLength;i++){
+//		if(counts[i] == numSeqs)	{	filter[i] = '0';		}
+//	}
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doSoft() {
-
-	int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
-
-	vector<int> a(alignmentLength, 0);
-	vector<int> t(alignmentLength, 0);
-	vector<int> g(alignmentLength, 0);
-	vector<int> c(alignmentLength, 0);
-	vector<int> x(alignmentLength, 0);
-	
-	for(int i=0;i<numSeqs;i++){
-		string curAligned = db->get(i).getAligned();;
-
-		for(int j=0;j<alignmentLength;j++){
-			if(toupper(curAligned[j]) == 'A')										{	a[j]++;	}
-			else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[i]) == 'U')	{	t[j]++;	}
-			else if(toupper(curAligned[j]) == 'G')									{	g[j]++;	}
-			else if(toupper(curAligned[j]) == 'C')									{	c[j]++;	}
-		}
-	}
-
-	for(int i=0;i<alignmentLength;i++){
-		if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
-			filter[i] = '0';			
-		}
-	}
+void FilterSeqsCommand::doSoft(Sequence seq) {
+
+//	int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
+//
+//	vector<int> a(alignmentLength, 0);
+//	vector<int> t(alignmentLength, 0);
+//	vector<int> g(alignmentLength, 0);
+//	vector<int> c(alignmentLength, 0);
+//	vector<int> x(alignmentLength, 0);
+//	
+//	for(int i=0;i<numSeqs;i++){
+//		string curAligned = db->get(i).getAligned();;
+//
+//		for(int j=0;j<alignmentLength;j++){
+//			if(toupper(curAligned[j]) == 'A')										{	a[j]++;	}
+//			else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[i]) == 'U')	{	t[j]++;	}
+//			else if(toupper(curAligned[j]) == 'G')									{	g[j]++;	}
+//			else if(toupper(curAligned[j]) == 'C')									{	c[j]++;	}
+//		}
+//	}
+//
+//	for(int i=0;i<alignmentLength;i++){
+//		if(a[i] < softThreshold && t[i] < softThreshold && g[i] < softThreshold && c[i] < softThreshold){
+//			filter[i] = '0';			
+//		}
+//	}
 }
 
 /**************************************************************************************/
 
 int FilterSeqsCommand::execute() {	
 	try {
-						
-		if(globaldata->getHard().compare("") != 0)		{	doHard();		}	//	has to be applied first!
-		if(globaldata->getTrump().compare("") != 0)		{	doTrump();		}
-		if(globaldata->getVertical() == "T")			{	doVertical();	}
-		if(globaldata->getSoft().compare("") != 0)		{	doSoft();		}
-
+		ifstream inFASTA;
+		openInputFile(globaldata->getFastaFile(), inFASTA);
+		
+		Sequence testSeq(inFASTA);
+		alignmentLength = testSeq.getAlignLength();
+		inFASTA.seekg(0);
+		int numSeqs = 0;
+		
+		if(globaldata->getHard().compare("") != 0)	{	doHard();								}
+		else										{	filter = string(alignmentLength, '1');	}
+		while(!inFASTA.eof()){
+			Sequence seq(inFASTA);
+			if(globaldata->getTrump().compare("") != 0)	{	doTrump(seq);		}
+			if(isTrue(globaldata->getVertical()) == 1)	{	doVertical(seq);	}
+//			if(globaldata->getSoft().compare("") != 0)	{	doSoft(seq);		}			
+			numSeqs++;
+		}
+		
 		ofstream outfile;
 		string filterFile = getRootName(globaldata->inputFileName) + "filter";
 		openOutputFile(filterFile, outfile);
@@ -137,17 +146,17 @@ int FilterSeqsCommand::execute() {
 		string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
 		openOutputFile(filteredFasta, outfile);
 
-		for(int i=0;i<numSeqs;i++){
-			string curAligned = db->get(i).getAligned();
-			outfile << '>' << db->get(i).getName() << endl;
-			for(int j=0;j<alignmentLength;j++){
-				if(filter[j] == '1'){
-					outfile << curAligned[j];
-				}
-			}
-			outfile << endl;
-		}
-		outfile.close();
+//		for(int i=0;i<numSeqs;i++){
+//			string curAligned = db->get(i).getAligned();
+//			outfile << '>' << db->get(i).getName() << endl;
+//			for(int j=0;j<alignmentLength;j++){
+//				if(filter[j] == '1'){
+//					outfile << curAligned[j];
+//				}
+//			}
+//			outfile << endl;
+//		}
+//		outfile.close();
 		
 		int filteredLength = 0;
 		for(int i=0;i<alignmentLength;i++){