--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/GbffLocus.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,251 @@
+package gff;
+
+import java.util.ArrayList;
+
+import fileIO.ByteStreamWriter;
+import shared.Tools;
+
+public class GbffLocus {
+
+	public GbffLocus(ArrayList<byte[]> lines) {
+		while(num<lines.size()){
+			parseBlock(lines);
+		}
+	}
+
+	int parseBlock(ArrayList<byte[]> lines){
+		byte[] line=lines.get(num);
+		if(Tools.startsWith(line, " ")){
+			assert(false) : line;
+			num++;
+		}else if(Tools.startsWith(line, "LOCUS ")){
+			parseLocus(lines);
+		}else if(Tools.startsWith(line, "DEFINITION ")){
+			parseDefinition(lines);
+		}else if(Tools.startsWith(line, "ACCESSION ")){
+			parseAccession(lines);
+		}else if(Tools.startsWith(line, "VERSION ")){
+			parseVersion(lines);
+		}else if(Tools.startsWith(line, "DBLINK ")){
+			parseDBLink(lines);
+		}else if(Tools.startsWith(line, "KEYWORDS ")){
+			parseKeywords(lines);
+		}else if(Tools.startsWith(line, "SOURCE ")){
+			parseSource(lines);
+		}else if(Tools.startsWith(line, "REFERENCE ")){
+			parseReference(lines);
+		}else if(Tools.startsWith(line, "COMMENT ")){
+			parseComment(lines);
+		}else if(Tools.startsWith(line, "FEATURES ")){
+			parseFeatures(lines);
+		}else if(Tools.startsWith(line, "CONTIG ")){
+			parseContig(lines);
+		}else if(Tools.startsWith(line, "ORIGIN ")){
+			parseOrigin(lines);
+		}else if(Tools.startsWith(line, "PRIMARY ")){
+			parsePrimary(lines);
+		}else{
+			assert(false) : "Unhandled block type: "+new String(line);
+		}
+		return num;
+	}
+	
+	private byte[] nextLine(ArrayList<byte[]> lines){
+		byte[] line=null;
+		for(final int lim=lines.size()-1; num<lim && (line==null || line.length==0); ){
+//			System.err.println(num+", "+lim);
+			num++;
+			line=lines.get(num);
+		}
+//		System.err.println(line);
+//		assert(line!=null);
+		return line;
+	}
+	
+	private byte[] getLine(ArrayList<byte[]> lines){
+		return num>=lines.size() ? null : lines.get(num);
+	}
+	
+	/** Move pointer to next block start */
+	private int advanceBlock(ArrayList<byte[]> lines){
+		for(num++; num<lines.size(); num++){
+			byte[] line=lines.get(num);
+			if(line!=null && line.length>0 && line[0]!=' '){break;}
+		}
+		return num;
+	}
+	
+	/** Move pointer to next block start */
+	private int advanceFeature(ArrayList<byte[]> lines){
+		for(num++; num<lines.size(); num++){
+			byte[] line=lines.get(num);
+			if(line!=null && line.length>0 && (line[0]!=' ' || line[5]!=' ')){break;}
+		}
+		return num;
+	}
+	
+	private String trimBlockName(byte[] line){
+		assert(line.length>=12 && line[11]==' ') : new String(line);
+		return new String(line, 12, line.length-12);
+	}
+	
+	private String toFeatureType(byte[] line){
+		assert(line[4]==' ');
+		assert(line[5]!=' ');
+		assert(line[20]==' ');
+		int start=5, stop=6;
+		for(; stop<21 && line[stop]!=' '; stop++){}
+		return new String(line, start, stop-start);
+	}
+	
+	private int parseLocus(ArrayList<byte[]> lines){
+		byte[] line=lines.get(num);
+//		assert(Tools.startsWith(line, "LOCUS")) : new String(line);
+		if(accession==null){
+			String s=trimBlockName(line);
+			String[] split=Tools.whitespacePlus.split(s);
+			accession=split.length>0 ? split[0] : null;
+		}
+		return advanceBlock(lines);
+	}
+	
+	private int parseDefinition(ArrayList<byte[]> lines){
+		byte[] line=lines.get(num);
+		if(organism==null){
+			String s=trimBlockName(line);
+			String[] split=Tools.commaPattern.split(s);
+			organism=split.length>0 ? split[0] : null;
+		}
+		return advanceBlock(lines);
+	}
+	
+	private int parseAccession(ArrayList<byte[]> lines){
+		byte[] line=lines.get(num);
+		if(accession==null){
+			String s=trimBlockName(line);
+			String[] split=Tools.whitespacePlus.split(s);
+			accession=split.length>0 ? split[0] : null;
+		}
+		return advanceBlock(lines);
+	}
+	
+	private int parseVersion(ArrayList<byte[]> lines){
+		byte[] line=lines.get(num);
+		String s=trimBlockName(line);
+		String[] split=Tools.whitespacePlus.split(s);
+		s=split.length>0 ? split[0] : null;
+		if(accession==null || (s!=null && s.length()>1)){
+			accession=s;
+		}
+		return advanceBlock(lines);
+	}
+	
+	private int parseDBLink(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	private int parseKeywords(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	private int parseSource(ArrayList<byte[]> lines){
+		byte[] line=lines.get(num);
+		if(species==null){
+			species=trimBlockName(line);
+		}
+		return advanceBlock(lines);
+	}
+	
+	private int parseReference(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	private int parseComment(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	private int parseFeatures(ArrayList<byte[]> lines){
+		for(byte[] line=nextLine(lines); line!=null && line[0]==' '; line=getLine(lines)){
+//			System.err.println(num+": "+new String(line));
+			String type=toFeatureType(line);
+			int idx=Tools.find(type, featureTypes);
+//			System.err.println("idx="+idx+" for '"+type+"'");
+			if(idx>=0){
+//				System.err.println("parseFeature");
+				parseFeature(lines, type);
+//				System.err.println(features.get(features.size()-1));
+			}else{
+//				System.err.println("advanceFeature");
+				advanceFeature(lines);
+			}
+		}
+		return num;
+	}
+	
+	/** Move pointer to next block start */
+	private int parseFeature(ArrayList<byte[]> lines, String type){
+		ArrayList<byte[]> flist=new ArrayList<byte[]>();
+		flist.add(lines.get(num));
+		for(num++; num<lines.size(); num++){
+			byte[] line=lines.get(num);
+			if(line!=null && line.length>0 && (line[0]!=' ' || line[5]!=' ')){
+//				assert(false) : Character.toString(line[0])+", "+Character.toString(line[5])+", "+Character.toString(line[6])+"\n"+new String(line);
+				break;
+			}
+			flist.add(line);
+		}
+		GbffFeature f=new GbffFeature(flist, type, accession);
+		if(!f.error){
+			features.add(f);
+		}else{
+//			System.err.println("Failed to parse feature "+f);
+		}
+		return num;
+	}
+	
+	private int parseContig(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	private int parseOrigin(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	private int parsePrimary(ArrayList<byte[]> lines){
+		return advanceBlock(lines);
+	}
+	
+	public void toGff(ByteStreamWriter bsw) {
+		final byte[] accessionB=accession.getBytes();
+		bsw.print(seqRegB);
+		bsw.print(accessionB);
+		if(start>0 && stop>0){
+			bsw.print(' ').print(start).print(' ').print(stop);
+		}
+		bsw.println();
+		for(GbffFeature f : features){
+			if(f.type==GbffFeature.CDS || f.type==GbffFeature.tRNA || f.type==GbffFeature.rRNA){
+				if(!f.pseudo && !f.error){
+					f.toGff(bsw);
+				}
+			}
+		}
+	}
+	
+	
+	/** Line number */
+	int num=0;
+	
+	boolean printGene=false;
+	boolean printRepeat=false; 
+	
+	public static String[] featureTypes=GbffFeature.typeStrings;
+	private static final byte[] seqRegB="##sequence-region ".getBytes();
+	
+	String accession;
+	String organism;
+	String species;
+	int start;
+	int stop;
+	ArrayList<GbffFeature> features=new ArrayList<GbffFeature>();
+}