added boneh, efron, and solow calculators

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 6170d0043252b8283728db25b59a4adc5b7930b2..f4cc6d82fbe5d97779d4d80dbba9ee9a483940ab 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -14,7 +14,7 @@ void FilterSeqsCommand::doTrump() {
        trump = globaldata->getTrump();
        for(int i = 0; i < db->size(); i++) {
                Sequence cur = db->get(i);
-               string curAligned = cur.getUnaligned();
+               string curAligned = cur.getAligned();
                for(int j = 0; j < curAligned.length(); j++) {
                        string curChar = curAligned.substr(j, 1);
                        if(curChar.compare(trump) == 0) 
@@ -37,7 +37,7 @@ void FilterSeqsCommand::doSoft() {
        
        for(int i = 0; i < db->size(); i++) {
                Sequence cur = db->get(i);
-               string curAligned = cur.getUnaligned();
+               string curAligned = cur.getAligned();
                
                for(int j = 0; j < curAligned.length(); j++) {
                        string curChar = curAligned.substr(j, 1);
@@ -112,7 +112,7 @@ int FilterSeqsCommand::execute() {
                db = readSeqs->getDB();
                
                //for(int i = 0; i < db->size(); i++) {
-//                     cout << db->get(i).getLength() << "\n" << db->get(i).getName() << ": " << db->get(i).getUnaligned() << "\n\n";
+//                     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++) 
@@ -140,7 +140,7 @@ int FilterSeqsCommand::execute() {
                SequenceDB newDB;
                for(int i = 0; i < db->size(); i++) {
                        Sequence curSeq = db->get(i);
-                       string curAligned = curSeq.getUnaligned();
+                       string curAligned = curSeq.getAligned();
                        string curName = curSeq.getName();
                        string newAligned = "";
                        for(int j = 0; j < curAligned.length(); j++)