jpayne@68: package sketch;
jpayne@68: 
jpayne@68: import java.io.PrintStream;
jpayne@68: import java.util.HashMap;
jpayne@68: 
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import shared.Shared;
jpayne@68: import stream.ConcurrentReadInputStream;
jpayne@68: import stream.FASTQ;
jpayne@68: import stream.Read;
jpayne@68: import structures.ListNum;
jpayne@68: import tax.GiToTaxid;
jpayne@68: import tax.TaxTree;
jpayne@68: 
jpayne@68: public class SSUMap {
jpayne@68: 	
jpayne@68: 	public static synchronized void load(PrintStream outstream){
jpayne@68: 		if(r16SFile!=null && r16SMap==null){
jpayne@68: 			r16SMap=load(r16SFile, TaxTree.default16SFile(), outstream);
jpayne@68: 		}
jpayne@68: 		if(r18SFile!=null && r18SMap==null){
jpayne@68: 			r18SMap=load(r18SFile, TaxTree.default18SFile(), outstream);
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static synchronized HashMap<Integer, byte[]> load(String ssuFile, String defaultFile, PrintStream outstream){
jpayne@68: 		HashMap<Integer, byte[]> map=null;
jpayne@68: 		if(ssuFile!=null){
jpayne@68: 			final boolean oldAminoIn=Shared.AMINO_IN;
jpayne@68: 			final boolean oldInterleaved=FASTQ.FORCE_INTERLEAVED;
jpayne@68: 			Shared.AMINO_IN=false;//SSUs are nucleotide, which can cause a crash, esp. with IUPAC symbols
jpayne@68: 			FASTQ.FORCE_INTERLEAVED=false;
jpayne@68: 
jpayne@68: 			String fname=ssuFile;
jpayne@68: 			if("auto".equalsIgnoreCase(fname)){fname=defaultFile;}
jpayne@68: 			final FileFormat ffssu=FileFormat.testInput(fname, FileFormat.FA, null, true, false);
jpayne@68: 			map=loadSSU(ffssu, outstream);
jpayne@68: 
jpayne@68: 			Shared.AMINO_IN=oldAminoIn;
jpayne@68: 			FASTQ.FORCE_INTERLEAVED=oldInterleaved;
jpayne@68: 		}
jpayne@68: 		return map;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static HashMap<Integer, byte[]> loadSSU(FileFormat ff, PrintStream outstream){
jpayne@68: 		ConcurrentReadInputStream cris=makeCris(ff, outstream);
jpayne@68: 		HashMap<Integer, byte[]> map=new HashMap<Integer, byte[]>(1000000);
jpayne@68: 		
jpayne@68: 		//Grab the first ListNum of reads
jpayne@68: 		ListNum<Read> ln=cris.nextList();
jpayne@68: 
jpayne@68: 		//Check to ensure pairing is as expected
jpayne@68: 		if(ln!=null && !ln.isEmpty()){
jpayne@68: //			if(verbose){outstream.println("Fetched "+ln.size()+" reads.");}
jpayne@68: 			Read r=ln.get(0);
jpayne@68: 			assert(ff.samOrBam() || (r.mate!=null)==cris.paired());
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		//As long as there is a nonempty read list...
jpayne@68: 		while(ln!=null && ln.size()>0){
jpayne@68: 			if(verbose){outstream.println("Fetched "+ln.size()+" reads.");}
jpayne@68: 			for(Read r : ln){
jpayne@68: 				final int tid=GiToTaxid.getID(r.id);
jpayne@68: 				if(tid>=0 && r.length()>1000){
jpayne@68: 					byte[] old=map.get(tid);
jpayne@68: 					if(old==null || old.length<r.length()){map.put(tid, r.bases);}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
jpayne@68: 
jpayne@68: 			//Fetch a new list
jpayne@68: 			ln=cris.nextList();
jpayne@68: 		}
jpayne@68: 
jpayne@68: 		//Notify the input stream that the final list was used
jpayne@68: 		if(ln!=null){
jpayne@68: 			cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
jpayne@68: 		}
jpayne@68: 		errorState|=ReadWrite.closeStream(cris);
jpayne@68: 		
jpayne@68: 		return map;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static ConcurrentReadInputStream makeCris(FileFormat ff, PrintStream outstream){
jpayne@68: 		if(verbose){outstream.println("makeCris");}
jpayne@68: 		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null);
jpayne@68: 		cris.start(); //Start the stream
jpayne@68: 		if(verbose){outstream.println("Loading "+ff.name());}
jpayne@68: 		boolean paired=cris.paired();
jpayne@68: 		assert(!paired);
jpayne@68: //		if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
jpayne@68: 		return cris;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static boolean hasMap(){return r16SMap!=null || r18SMap!=null;}
jpayne@68: 	public static int r16SCount(){return r16SMap==null ? 0 : r16SMap.size();}
jpayne@68: 	public static int r18SCount(){return r18SMap==null ? 0 : r18SMap.size();}
jpayne@68: 	
jpayne@68: 	public static String r16SFile=null;
jpayne@68: 	public static String r18SFile=null;
jpayne@68: 	public static HashMap<Integer, byte[]> r16SMap=null;
jpayne@68: 	public static HashMap<Integer, byte[]> r18SMap=null;
jpayne@68: 	static boolean verbose=false;
jpayne@68: 	static boolean errorState=false;
jpayne@68: 	
jpayne@68: }