X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=68450fb15a7b140803aab2d54d8c5bc84e7ce688;hb=7e354c9abb09ea3cf5b500a16cc7f6dd79ccb6f5;hp=95d51f329f30d8a639d0772844e54be5246e5005;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 95d51f3..68450fb 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -36,7 +36,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
 			
 			//check for required parameters
 			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
+			if (fastafile == "not found") { mothurOut("fasta is a required parameter for the filter.seqs command."); mothurOutEndLine(); abort = true; }
 			else if (fastafile == "not open") { abort = true; }	
 
 			//check for optional parameter and set defaults
@@ -56,106 +56,43 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
 			
 			numSeqs = 0;
 			
+			if (abort == false) {
+			
+				if (soft != 0)			{  F.setSoft(soft);		}
+				if (trump != '*')		{  F.setTrump(trump);	}
+			
+			}
+						
 		}
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function FilterSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 //**********************************************************************************************************************
 
 void FilterSeqsCommand::help(){
 	try {
-		cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
-		cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical.  " << "\n";
-		cout << "The fasta parameter is required." << "\n";
-		cout << "The trump parameter .... The default is ..." << "\n";
-		cout << "The soft parameter .... The default is ...." << "\n";
-		cout << "The hard parameter .... The default is ...." << "\n";
-		cout << "The vertical parameter .... The default is T." << "\n";
-		cout << "The filter.seqs command should be in the following format: " << "\n";
-		cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
-		cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
-		cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta)." << "\n" << "\n";
+		mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
+		mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard and vertical. \n");
+		mothurOut("The fasta parameter is required.\n");
+		mothurOut("The trump parameter .... The default is ...\n");
+		mothurOut("The soft parameter .... The default is ....\n");
+		mothurOut("The hard parameter .... The default is ....\n");
+		mothurOut("The vertical parameter .... The default is T.\n");
+		mothurOut("The filter.seqs command should be in the following format: \n");
+		mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
+		mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+		mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "FilterSeqsCommand", "help");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doHard() {
-	
-	ifstream fileHandle;
-	openInputFile(hard, fileHandle);
-	
-	fileHandle >> filter;
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doTrump(Sequence seq) {
-	
-	string curAligned = seq.getAligned();
-
-	for(int j = 0; j < alignmentLength; j++) {
-		if(curAligned[j] == trump){
-			filter[j] = '0';
-		}
-	}
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doVertical() {
-
-	for(int i=0;i<alignmentLength;i++){
-		if(gap[i] == numSeqs)	{	filter[i] = '0';	}
-	}
-	
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doSoft() {
-	
-	int threshold = int (soft * numSeqs);
-	
-	for(int i=0;i<alignmentLength;i++){
-		if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){	filter[i] = 0;	}
-	}
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::getFreqs(Sequence seq) {
-
-	string curAligned = seq.getAligned();;
-	
-	for(int j=0;j<alignmentLength;j++){
-		if(toupper(curAligned[j]) == 'A')										{	a[j]++;		}
-		else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U')	{	t[j]++;		}
-		else if(toupper(curAligned[j]) == 'G')									{	g[j]++;		}
-		else if(toupper(curAligned[j]) == 'C')									{	c[j]++;		}
-		else if(curAligned[j] == '-' || curAligned[j] == '.')					{	gap[j]++;	}
-	}
-	
 }
 
 /**************************************************************************************/
@@ -172,31 +109,33 @@ int FilterSeqsCommand::execute() {
 		alignmentLength = testSeq.getAlignLength();
 		inFASTA.seekg(0);
 		
+		F.setLength(alignmentLength);
+		
 		if(soft != 0 || isTrue(vertical)){
-			a.assign(alignmentLength, 0);
-			t.assign(alignmentLength, 0);
-			g.assign(alignmentLength, 0);
-			c.assign(alignmentLength, 0);
-			gap.assign(alignmentLength, 0);
+			F.initialize();
 		}
 		
-		if(hard.compare("") != 0)	{	doHard();		}
-		else						{	filter = string(alignmentLength, '1');	}
+		if(hard.compare("") != 0)	{	F.doHard(hard);		}
+		else						{	F.setFilter(string(alignmentLength, '1'));	}
 
 		if(trump != '*' || isTrue(vertical) || soft != 0){
 			while(!inFASTA.eof()){	//read through and create the filter...
 				Sequence seq(inFASTA);
-				if(trump != '*'){	doTrump(seq);	}
-				if(isTrue(vertical) || soft != 0){	getFreqs(seq);	}
+				if(trump != '*'){	F.doTrump(seq);	}
+				if(isTrue(vertical) || soft != 0){	F.getFreqs(seq);	}
 				numSeqs++;
 				cout.flush();
 			}
 		
 		}
 		inFASTA.close();
+		F.setNumSeqs(numSeqs);
+		
 		
-		if(isTrue(vertical) == 1)	{	doVertical();	}
-		if(soft != 0)	{	doSoft();		}			
+		if(isTrue(vertical) == 1)	{	F.doVertical();	}
+		if(soft != 0)				{	F.doSoft();		}
+		
+		filter = F.getFilter();
 
 		ofstream outFilter;
 		string filterFile = getRootName(fastafile) + "filter";
@@ -204,15 +143,15 @@ int FilterSeqsCommand::execute() {
 		outFilter << filter << endl;
 		outFilter.close();
 		
-
-		openInputFile(fastafile, inFASTA);
+		ifstream inFasta2;
+		openInputFile(fastafile, inFasta2);
 		string filteredFasta = getRootName(fastafile) + "filter.fasta";
 		ofstream outFASTA;
 		openOutputFile(filteredFasta, outFASTA);
 
 		numSeqs = 0;
-		while(!inFASTA.eof()){
-			Sequence seq(inFASTA);
+		while(!inFasta2.eof()){
+			Sequence seq(inFasta2);
 			string align = seq.getAligned();
 			string filterSeq = "";
 	
@@ -224,10 +163,10 @@ int FilterSeqsCommand::execute() {
 
 			outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
 			numSeqs++;
-			gobble(inFASTA);
+			gobble(inFasta2);
 		}
 		outFASTA.close();
-		inFASTA.close();
+		inFasta2.close();
 		
 		
 		int filteredLength = 0;
@@ -235,21 +174,17 @@ int FilterSeqsCommand::execute() {
 			if(filter[i] == '1'){	filteredLength++;	}
 		}
 		
-		cout << endl;
-		cout << "Length of filtered alignment: " << filteredLength << endl;
-		cout << "Number of columns removed: " << alignmentLength-filteredLength << endl;
-		cout << "Length of the original alignment: " << alignmentLength << endl;
-		cout << "Number of sequences used to construct filter: " << numSeqs << endl;
+		mothurOutEndLine();
+		mothurOut("Length of filtered alignment: " + toString(filteredLength)); mothurOutEndLine();
+		mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); mothurOutEndLine();
+		mothurOut("Length of the original alignment: " + toString(alignmentLength)); mothurOutEndLine();
+		mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); mothurOutEndLine();
 		
 		return 0;
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "FilterSeqsCommand", "execute");
 		exit(1);
 	}
 }