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/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
import java.util.HashMap;
import java.util.Iterator;
public class CheckSequence {
String error = new String("");
String alphabet;
CheckSequence() {
ProAlign.log("CheckSequence");
}
boolean isDna(HashMap seqs) {
Iterator seqKeys = seqs.keySet().iterator();
String name, seq;
int acgt = 0, total = 0;
while(seqKeys.hasNext()) {
name = (String) seqKeys.next();
seq = (String) seqs.get(name);
for(int i=0; i<seq.length(); i++) {
if(seq.charAt(i)=='A') {
acgt++;
} else if(seq.charAt(i)=='C') {
acgt++;
} else if(seq.charAt(i)=='G') {
acgt++;
} else if(seq.charAt(i)=='T') {
acgt++;
} else if(seq.charAt(i)=='U') {
acgt++;
}
total++;
}
}
if(((double) acgt/(double) total)>0.9d) {
return true;
}
return false;
}
boolean isFromAlphabet(HashMap seqs,String alphabet) {
boolean isFine = true;
Iterator seqKeys = seqs.keySet().iterator();
String name, seq;
while(seqKeys.hasNext()) {
name = (String) seqKeys.next();
seq = (String) seqs.get(name);
for(int i=0; i<seq.length(); i++) {
if(alphabet.indexOf(seq.charAt(i))<0) {
isFine = false;
error += "\n "+name+": '"+seq.charAt(i)+
"' is not from alphabet '"+alphabet+"'!";
ProAlign.log.print("\n "+name+": '"+seq.charAt(i)+
"' is not from alphabet '"+alphabet+"'!");
}
}
}
return isFine;
}
String getError() {
return error;
}
}
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