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package align2;
import java.util.HashSet;
import fileIO.TextFile;
import stream.Read;
/**
* @author Brian Bushnell
* @date Mar 14, 2013
*
*/
public class Blacklist {
public static boolean inWhitelist(Read r){
return r==null ? false : (inWhitelist2(r) || inWhitelist2(r.mate));
}
private static boolean inWhitelist2(Read r){
if(r==null || !r.mapped() || whitelist==null || whitelist.isEmpty()){return false;}
byte[] name=r.getScaffoldName(false);
return (name!=null && whitelist.contains(new String(name)));
}
public static boolean inBlacklist(Read r){
if(r==null){return false;}
boolean a=inBlacklist2(r);
boolean b=inBlacklist2(r.mate);
if(!a && !b){return false;}
if(a){
return b || r.mate==null || !r.mate.mapped();
}
return b && !r.mapped();
}
private static boolean inBlacklist2(Read r){
if(r==null || !r.mapped() || blacklist==null || blacklist.isEmpty()){return false;}
byte[] name=r.getScaffoldName(false);
return (name!=null && blacklist.contains(new String(name)));
}
public static void addToBlacklist(String fname){
addToSet(fname, true);
}
public static void addToWhitelist(String fname){
addToSet(fname, false);
}
public static synchronized int addToSet(String fname, boolean black){
final HashSet<String> set;
int added=0, overwritten=0;
if(black){
if(blacklist==null){blacklist=new HashSet<String>(4001);}
set=blacklist;
}else{
if(whitelist==null){whitelist=new HashSet<String>(4001);}
set=whitelist;
}
TextFile tf=new TextFile(fname, false);
String line=tf.nextLine();
if(line==null){return 0;}
final boolean fasta=(line.charAt(0)=='>');
System.err.println("Detected "+(black ? "black" : "white")+"list file "+fname+" as "+(fasta ? "" : "non-")+"fasta-formatted.");
while(line!=null){
String key=null;
if(fasta){
if(line.charAt(0)=='>'){key=new String(line.substring(1));}
}else{
key=line;
}
if(key!=null){
boolean b=set.add(key);
added++;
if(!b){
if(overwritten==0){
System.err.println("Duplicate "+(black ? "black" : "white")+"list key "+key);
System.err.println("Subsequent duplicates from this file will not be mentioned.");
}
overwritten++;
}
}
line=tf.nextLine();
}
if(overwritten>0){
System.err.println("Added "+overwritten+" duplicate keys.");
}
return added-overwritten;
}
public static boolean hasBlacklist(){return blacklist!=null && !blacklist.isEmpty();}
public static boolean hasWhitelist(){return whitelist!=null && !whitelist.isEmpty();}
public static void clearBlacklist(){blacklist=null;}
public static void clearWhitelist(){whitelist=null;}
private static HashSet<String> blacklist=null;
private static HashSet<String> whitelist=null;
}
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