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package dna;
/**
* @author Brian Bushnell
* @date Jan 4, 2013
*
*/
public class Scaffold implements Comparable<Scaffold> {
public Scaffold(String name_, String assembly_, int length_){
name=name_;
assembly=assembly_;
length=length_;
}
/** Assumes SAM format.
* e.g.<br> @SQ SN:scaffold_0 LN:1785514 AS:build 9 */
public Scaffold(byte[] s){
this(new String(s).split("\t"));
}
/** Assumes SAM format.
* e.g.<br> @SQ SN:scaffold_0 LN:1785514 AS:build 9 */
public Scaffold(String s){
this(s.split("\t"));
}
/** Assumes SAM format */
public Scaffold(String[] split) {
assert(split.length>2 && split[0].equals("@SQ"));
for(String s : split){
if(s.equals("@SQ")){
//Do nothing
}else if(s.startsWith("SN:")){
assert(name==null);
name=new String(s.substring(3)); //Data.forceIntern(s.substring(3));
}else if(s.startsWith("LN:")){
length=Integer.parseInt(s.substring(3));
}else if(s.startsWith("AS:")){
assembly=Data.forceIntern(s.substring(3));
}
}
assert(length>-1);
assert(name!=null);
}
public Scaffold(String name_, int length_) {
name=name_;
length=length_;
}
@Override
public int hashCode(){
return name.hashCode();
}
@Override
public int compareTo(Scaffold other){
return name.compareTo(other.name);
}
@Override
public String toString(){
return "@SQ\tSN:"+name+"\tLN:"+length+(assembly==null ? "" : "\tAS:"+assembly);
}
public String name;
public String assembly;
public int length=-1;
public long basehits=0;
public long readhits=0;
/** For calculating FPKM */
public long fraghits=0;
public long readhitsMinus=0;
/** {A,C,G,T,N} */
public long[] basecount;
public float gc;
/** For attaching things */
public Object obj1;
/** For attaching more things */
public Object obj2;
}
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