jpayne@68: package prok;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: import java.util.Arrays;
jpayne@68: 
jpayne@68: import dna.AminoAcid;
jpayne@68: import gff.GffLine;
jpayne@68: import stream.Read;
jpayne@68: import structures.IntList;
jpayne@68: 
jpayne@68: /**
jpayne@68:  * Tracks information about a scaffold for AnalyzeGenes.
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Sep 24, 2018
jpayne@68:  *
jpayne@68:  */
jpayne@68: class ScafData {
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------        Initialization        ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	ScafData(Read r){
jpayne@68: 		this(r.id, r.bases, new byte[r.length()]);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	ScafData(String name_, byte[] bases_, byte[] frames_){
jpayne@68: 		name=name_;
jpayne@68: 		bases=bases_;
jpayne@68: 		frames=frames_;
jpayne@68: 		cdsLines[0]=new ArrayList<GffLine>();
jpayne@68: 		cdsLines[1]=new ArrayList<GffLine>();
jpayne@68: 		rnaLines[0]=new ArrayList<GffLine>();
jpayne@68: 		rnaLines[1]=new ArrayList<GffLine>();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------           Methods            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	void clear(){
jpayne@68: 		Arrays.fill(frames, (byte)0);
jpayne@68: 		starts.clear();
jpayne@68: 		stops.clear();
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void reverseComplement(){
jpayne@68: 		AminoAcid.reverseComplementBasesInPlace(bases);
jpayne@68: 		strand=1^strand;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void addCDS(GffLine gline){
jpayne@68: 		assert(gline.strand>=0) : gline+"\n"+gline.strand;
jpayne@68: 		cdsLines[gline.strand].add(gline);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	void addRNA(GffLine gline){
jpayne@68: 		assert(gline.strand>=0) : gline+"\n"+gline.strand;
jpayne@68: 		rnaLines[gline.strand].add(gline);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	byte[] fetch(int start, int stop){
jpayne@68: 		assert(start>=0 && stop<bases.length);
jpayne@68: 		assert(start<stop);
jpayne@68: 		return Arrays.copyOfRange(bases, start, stop+1);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	int strand(){return strand;}
jpayne@68: 
jpayne@68: 	public int length() {return bases==null ? 0 : bases.length;}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------            Fields            ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	final String name;
jpayne@68: 	final byte[] bases;
jpayne@68: 	final byte[] frames;
jpayne@68: 	final IntList starts=new IntList(8);
jpayne@68: 	final IntList stops=new IntList(8);
jpayne@68: 	private int strand=0;
jpayne@68: 	
jpayne@68: 	/** gLines[strand] holds the GffLines for that strand */
jpayne@68: 	@SuppressWarnings("unchecked")
jpayne@68: 	ArrayList<GffLine>[] cdsLines=new ArrayList[2];
jpayne@68: 	@SuppressWarnings("unchecked")
jpayne@68: 	ArrayList<GffLine>[] rnaLines=new ArrayList[2];
jpayne@68: }