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package dna;
import shared.LineParser1;
import shared.LineParserS1;
/**
* @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 */
@Deprecated
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);
}
/** Should be faster. Assumes SAM format.
* e.g.<br> @SQ SN:scaffold_0 LN:1785514 AS:build 9 */
public Scaffold(LineParser1 lp) {
assert(lp.startsWith("@SQ"));
for(int i=1, terms=lp.terms(); i<terms; i++){
if(lp.termStartsWith("SN:", i)){
assert(name==null);
lp.incrementA(3);
name=lp.parseStringFromCurrentField();
name=Data.forceIntern(name);
}else if(lp.termStartsWith("LN:", i)){
assert(length<=0);
lp.incrementA(3);
length=lp.parseIntFromCurrentField();
}else if(lp.termStartsWith("AS:", i)){
assert(assembly==null);
lp.incrementA(3);
assembly=lp.parseStringFromCurrentField();
}
}
assert(length>-1);
assert(name!=null);
}
/** Should be faster. Assumes SAM format.
* e.g.<br> @SQ SN:scaffold_0 LN:1785514 AS:build 9 */
public Scaffold(LineParserS1 lp) {
assert(lp.startsWith("@SQ"));
for(int i=1; i<lp.terms(); i++){
if(lp.termStartsWith("SN:", i)){
assert(name==null);
lp.incrementA(3);
name=lp.parseStringFromCurrentField();
name=Data.forceIntern(name);
}else if(lp.termStartsWith("LN:", i)){
assert(length<=0);
lp.incrementA(3);
length=lp.parseIntFromCurrentField();
}else if(lp.termStartsWith("AS:", i)){
assert(assembly==null);
lp.incrementA(3);
assembly=lp.parseStringFromCurrentField();
}
}
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 static String name(LineParser1 lp) {
assert(lp.startsWith("@SQ"));
for(int i=1; i<lp.terms(); i++){
if(lp.termStartsWith("SN:", i)){
lp.incrementA(3);
String name=lp.parseStringFromCurrentField();
return name;
}
}
assert(false);
return null;
}
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 obj0;
/** For attaching things for strand1 */
public Object obj1;
}
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