jpayne@68: package gff;
jpayne@68: 
jpayne@68: import java.util.ArrayList;
jpayne@68: 
jpayne@68: import fileIO.ByteStreamWriter;
jpayne@68: import shared.Tools;
jpayne@68: 
jpayne@68: public class GbffLocus {
jpayne@68: 
jpayne@68: 	public GbffLocus(ArrayList<byte[]> lines) {
jpayne@68: 		while(num<lines.size()){
jpayne@68: 			parseBlock(lines);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	int parseBlock(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=lines.get(num);
jpayne@68: 		if(Tools.startsWith(line, " ")){
jpayne@68: 			assert(false) : line;
jpayne@68: 			num++;
jpayne@68: 		}else if(Tools.startsWith(line, "LOCUS ")){
jpayne@68: 			parseLocus(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "DEFINITION ")){
jpayne@68: 			parseDefinition(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "ACCESSION ")){
jpayne@68: 			parseAccession(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "VERSION ")){
jpayne@68: 			parseVersion(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "DBLINK ")){
jpayne@68: 			parseDBLink(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "KEYWORDS ")){
jpayne@68: 			parseKeywords(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "SOURCE ")){
jpayne@68: 			parseSource(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "REFERENCE ")){
jpayne@68: 			parseReference(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "COMMENT ")){
jpayne@68: 			parseComment(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "FEATURES ")){
jpayne@68: 			parseFeatures(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "CONTIG ")){
jpayne@68: 			parseContig(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "ORIGIN ")){
jpayne@68: 			parseOrigin(lines);
jpayne@68: 		}else if(Tools.startsWith(line, "PRIMARY ")){
jpayne@68: 			parsePrimary(lines);
jpayne@68: 		}else{
jpayne@68: 			assert(false) : "Unhandled block type: "+new String(line);
jpayne@68: 		}
jpayne@68: 		return num;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private byte[] nextLine(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=null;
jpayne@68: 		for(final int lim=lines.size()-1; num<lim && (line==null || line.length==0); ){
jpayne@68: //			System.err.println(num+", "+lim);
jpayne@68: 			num++;
jpayne@68: 			line=lines.get(num);
jpayne@68: 		}
jpayne@68: //		System.err.println(line);
jpayne@68: //		assert(line!=null);
jpayne@68: 		return line;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private byte[] getLine(ArrayList<byte[]> lines){
jpayne@68: 		return num>=lines.size() ? null : lines.get(num);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Move pointer to next block start */
jpayne@68: 	private int advanceBlock(ArrayList<byte[]> lines){
jpayne@68: 		for(num++; num<lines.size(); num++){
jpayne@68: 			byte[] line=lines.get(num);
jpayne@68: 			if(line!=null && line.length>0 && line[0]!=' '){break;}
jpayne@68: 		}
jpayne@68: 		return num;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Move pointer to next block start */
jpayne@68: 	private int advanceFeature(ArrayList<byte[]> lines){
jpayne@68: 		for(num++; num<lines.size(); num++){
jpayne@68: 			byte[] line=lines.get(num);
jpayne@68: 			if(line!=null && line.length>0 && (line[0]!=' ' || line[5]!=' ')){break;}
jpayne@68: 		}
jpayne@68: 		return num;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private String trimBlockName(byte[] line){
jpayne@68: 		assert(line.length>=12 && line[11]==' ') : new String(line);
jpayne@68: 		return new String(line, 12, line.length-12);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private String toFeatureType(byte[] line){
jpayne@68: 		assert(line[4]==' ');
jpayne@68: 		assert(line[5]!=' ');
jpayne@68: 		assert(line[20]==' ');
jpayne@68: 		int start=5, stop=6;
jpayne@68: 		for(; stop<21 && line[stop]!=' '; stop++){}
jpayne@68: 		return new String(line, start, stop-start);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseLocus(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=lines.get(num);
jpayne@68: //		assert(Tools.startsWith(line, "LOCUS")) : new String(line);
jpayne@68: 		if(accession==null){
jpayne@68: 			String s=trimBlockName(line);
jpayne@68: 			String[] split=Tools.whitespacePlus.split(s);
jpayne@68: 			accession=split.length>0 ? split[0] : null;
jpayne@68: 		}
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseDefinition(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=lines.get(num);
jpayne@68: 		if(organism==null){
jpayne@68: 			String s=trimBlockName(line);
jpayne@68: 			String[] split=Tools.commaPattern.split(s);
jpayne@68: 			organism=split.length>0 ? split[0] : null;
jpayne@68: 		}
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseAccession(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=lines.get(num);
jpayne@68: 		if(accession==null){
jpayne@68: 			String s=trimBlockName(line);
jpayne@68: 			String[] split=Tools.whitespacePlus.split(s);
jpayne@68: 			accession=split.length>0 ? split[0] : null;
jpayne@68: 		}
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseVersion(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=lines.get(num);
jpayne@68: 		String s=trimBlockName(line);
jpayne@68: 		String[] split=Tools.whitespacePlus.split(s);
jpayne@68: 		s=split.length>0 ? split[0] : null;
jpayne@68: 		if(accession==null || (s!=null && s.length()>1)){
jpayne@68: 			accession=s;
jpayne@68: 		}
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseDBLink(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseKeywords(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseSource(ArrayList<byte[]> lines){
jpayne@68: 		byte[] line=lines.get(num);
jpayne@68: 		if(species==null){
jpayne@68: 			species=trimBlockName(line);
jpayne@68: 		}
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseReference(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseComment(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseFeatures(ArrayList<byte[]> lines){
jpayne@68: 		for(byte[] line=nextLine(lines); line!=null && line[0]==' '; line=getLine(lines)){
jpayne@68: //			System.err.println(num+": "+new String(line));
jpayne@68: 			String type=toFeatureType(line);
jpayne@68: 			int idx=Tools.find(type, featureTypes);
jpayne@68: //			System.err.println("idx="+idx+" for '"+type+"'");
jpayne@68: 			if(idx>=0){
jpayne@68: //				System.err.println("parseFeature");
jpayne@68: 				parseFeature(lines, type);
jpayne@68: //				System.err.println(features.get(features.size()-1));
jpayne@68: 			}else{
jpayne@68: //				System.err.println("advanceFeature");
jpayne@68: 				advanceFeature(lines);
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return num;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Move pointer to next block start */
jpayne@68: 	private int parseFeature(ArrayList<byte[]> lines, String type){
jpayne@68: 		ArrayList<byte[]> flist=new ArrayList<byte[]>();
jpayne@68: 		flist.add(lines.get(num));
jpayne@68: 		for(num++; num<lines.size(); num++){
jpayne@68: 			byte[] line=lines.get(num);
jpayne@68: 			if(line!=null && line.length>0 && (line[0]!=' ' || line[5]!=' ')){
jpayne@68: //				assert(false) : Character.toString(line[0])+", "+Character.toString(line[5])+", "+Character.toString(line[6])+"\n"+new String(line);
jpayne@68: 				break;
jpayne@68: 			}
jpayne@68: 			flist.add(line);
jpayne@68: 		}
jpayne@68: 		GbffFeature f=new GbffFeature(flist, type, accession);
jpayne@68: 		if(!f.error){
jpayne@68: 			features.add(f);
jpayne@68: 		}else{
jpayne@68: //			System.err.println("Failed to parse feature "+f);
jpayne@68: 		}
jpayne@68: 		return num;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseContig(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parseOrigin(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int parsePrimary(ArrayList<byte[]> lines){
jpayne@68: 		return advanceBlock(lines);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void toGff(ByteStreamWriter bsw) {
jpayne@68: 		final byte[] accessionB=accession.getBytes();
jpayne@68: 		bsw.print(seqRegB);
jpayne@68: 		bsw.print(accessionB);
jpayne@68: 		if(start>0 && stop>0){
jpayne@68: 			bsw.print(' ').print(start).print(' ').print(stop);
jpayne@68: 		}
jpayne@68: 		bsw.println();
jpayne@68: 		for(GbffFeature f : features){
jpayne@68: 			if(f.type==GbffFeature.CDS || f.type==GbffFeature.tRNA || f.type==GbffFeature.rRNA){
jpayne@68: 				if(!f.pseudo && !f.error){
jpayne@68: 					f.toGff(bsw);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	/** Line number */
jpayne@68: 	int num=0;
jpayne@68: 	
jpayne@68: 	boolean printGene=false;
jpayne@68: 	boolean printRepeat=false; 
jpayne@68: 	
jpayne@68: 	public static String[] featureTypes=GbffFeature.typeStrings;
jpayne@68: 	private static final byte[] seqRegB="##sequence-region ".getBytes();
jpayne@68: 	
jpayne@68: 	String accession;
jpayne@68: 	String organism;
jpayne@68: 	String species;
jpayne@68: 	int start;
jpayne@68: 	int stop;
jpayne@68: 	ArrayList<GbffFeature> features=new ArrayList<GbffFeature>();
jpayne@68: }