X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=f4cc6d82fbe5d97779d4d80dbba9ee9a483940ab;hb=37a2c0b7dc68bfa53c8f38a713259929c4c46a9f;hp=f92253d4b39d8cd444d60018843b70a27187e676;hpb=a5a908953ab2ebb9386a895e5ddddf0135ad1f99;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index f92253d..f4cc6d8 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -3,13 +3,11 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "filterseqscommand.h"
-#include <iostream>
-#include <fstream>
 
 /**************************************************************************************/
 void FilterSeqsCommand::doTrump() {
@@ -99,8 +97,24 @@ void FilterSeqsCommand::doFilter() {
 int FilterSeqsCommand::execute() {	
 	try {
 		globaldata = GlobalData::getInstance();
-		db = globaldata->gSequenceDB;
+		filename = globaldata->inputFileName;
 		
+		if(globaldata->getFastaFile() != "") {
+			readSeqs =  new ReadFasta(filename); }
+		else if(globaldata->getNexusFile() != "") {
+			readSeqs = new ReadNexus(filename); }
+		else if(globaldata->getClustalFile() != "") {
+			readSeqs = new ReadClustal(filename); }
+		else if(globaldata->getPhylipFile() != "") {
+			readSeqs = new ReadPhylip(filename); }
+			
+		readSeqs->read();
+		db = readSeqs->getDB();
+		
+		//for(int i = 0; i < db->size(); i++) {
+//			cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getAligned() << "\n\n";
+//		}
+
 		for(int i = 0; i < db->get(0).getLength(); i++) 
 			columnsToRemove.push_back(false);
 		
@@ -109,7 +123,6 @@ int FilterSeqsCommand::execute() {
 			doTrump();
 		else if(globaldata->getSoft().compare("") != 0)
 			doSoft();
-			
 		else if(globaldata->getFilter().compare("") != 0) 
 			doFilter();
 		
@@ -121,6 +134,8 @@ int FilterSeqsCommand::execute() {
 //			else
 //				cout << "false\n";
 //		}
+
+
 		//Creating the new SequenceDB 
 		SequenceDB newDB;
 		for(int i = 0; i < db->size(); i++) {
@@ -136,11 +151,16 @@ int FilterSeqsCommand::execute() {
 			newDB.add(newSeq);
 		}
 		
+		string newFileName = getRootName(filename) + "filter.fa";
 		ofstream outfile;
-		outfile.open("filtertest.txt");
+		outfile.open(newFileName.c_str());
 		newDB.print(outfile);
 		outfile.close();
 			
+		globaldata->clear();
+		//delete db;
+		//delete newDB;
+		
 		return 0;
 	}
 	catch(exception& e) {
@@ -151,5 +171,4 @@ int FilterSeqsCommand::execute() {
 		cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}
-}
-/**************************************************************************************/
+}
\ No newline at end of file