jpayne@68: package prok;
jpayne@68: 
jpayne@68: import java.io.File;
jpayne@68: 
jpayne@68: import dna.AminoAcid;
jpayne@68: import dna.Data;
jpayne@68: import fileIO.FileFormat;
jpayne@68: import fileIO.ReadWrite;
jpayne@68: import shared.Parse;
jpayne@68: import shared.Tools;
jpayne@68: import stream.ConcurrentReadInputStream;
jpayne@68: import stream.Read;
jpayne@68: import stream.ReadInputStream;
jpayne@68: import structures.ListNum;
jpayne@68: import structures.LongHashSet;
jpayne@68: 
jpayne@68: /** Contains a lot of statics and static methods for gene-calling */
jpayne@68: public abstract class ProkObject {
jpayne@68: 	
jpayne@68: 	public static boolean parse(String arg, String a, String b){
jpayne@68: 		if(a.equalsIgnoreCase("16sstartslop") || a.equalsIgnoreCase("ssustartslop")){
jpayne@68: 			ssuStartSlop=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("23sstartslop") || a.equalsIgnoreCase("lsustartslop")){
jpayne@68: 			lsuStartSlop=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("5sstartslop")){
jpayne@68: 			r5SStartSlop=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("16sstopslop") || a.equalsIgnoreCase("ssustopslop")){
jpayne@68: 			ssuStopSlop=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("23sstopslop") || a.equalsIgnoreCase("lsustopslop")){
jpayne@68: 			lsuStopSlop=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("5sstopslop")){
jpayne@68: 			r5SStopSlop=Integer.parseInt(b);
jpayne@68: 		}else if(a.equals("plus")){
jpayne@68: 			PROCESS_PLUS_STRAND=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equals("minus")){
jpayne@68: 			PROCESS_MINUS_STRAND=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("min16SIdentity") || a.equalsIgnoreCase("min16SId")) {
jpayne@68: 			min16SIdentity=Float.parseFloat(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("min18SIdentity") || a.equalsIgnoreCase("min18SId")) {
jpayne@68: 			min18SIdentity=Float.parseFloat(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("min23SIdentity") || a.equalsIgnoreCase("min23SId")) {
jpayne@68: 			min23SIdentity=Float.parseFloat(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("min5SIdentity") || a.equalsIgnoreCase("min5SId")) {
jpayne@68: 			min5SIdentity=Float.parseFloat(b);
jpayne@68: 		}			
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("align16s") || a.equalsIgnoreCase("load16SSequence")){
jpayne@68: 			load16SSequence=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("align23s") || a.equalsIgnoreCase("load23SSequence")){
jpayne@68: 			load23SSequence=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("align18s") || a.equalsIgnoreCase("load18SSequence")){
jpayne@68: 			load18SSequence=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("align5s") || a.equalsIgnoreCase("load5SSequence")){
jpayne@68: 			load5SSequence=Parse.parseBoolean(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else if(a.equalsIgnoreCase("load16skmers") || a.equalsIgnoreCase("load18skmers") || a.equalsIgnoreCase("loadssukmers")){
jpayne@68: 			loadSSUkmers=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("load23skmers") || a.equalsIgnoreCase("load28skmers") || a.equalsIgnoreCase("loadlsukmers")){
jpayne@68: 			loadLSUkmers=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("load5skmers")){
jpayne@68: 			load5Skmers=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("loadtrnakmers")){
jpayne@68: 			loadtRNAkmers=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("klongtrna")){
jpayne@68: 			kLongTRna=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("longkmers")){
jpayne@68: 			loadSSUkmers=loadLSUkmers=load5Skmers=loadtRNAkmers=Parse.parseBoolean(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("klong5s")){
jpayne@68: 			kLong5S=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("klong16s") || a.equalsIgnoreCase("klong18s") || a.equalsIgnoreCase("klongssu")){
jpayne@68: 			kLongSSU=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("klong23s") || a.equalsIgnoreCase("klong28s") || a.equalsIgnoreCase("klonglsu")){
jpayne@68: 			kLongLSU=Integer.parseInt(b);
jpayne@68: 		}else if(a.equalsIgnoreCase("klongtrna")){
jpayne@68: 			kLongTRna=Integer.parseInt(b);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		else{
jpayne@68: 			return false;
jpayne@68: 		}
jpayne@68: 		return true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static boolean processType(int type){
jpayne@68: 		return (type==CDS ? callCDS : type==r16S ? call16S : type==r23S ? call23S : type==r18S ? call18S : type==r5S ? call5S : type==tRNA ? calltRNA : true);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int startSlop(int type) {
jpayne@68: 		int slop=(type==r16S ? ssuStartSlop : type==r23S ? lsuStartSlop : type==r18S ? ssuStartSlop : type==r5S ? r5SStartSlop : 9999);
jpayne@68: 		return slop;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int stopSlop(int type) {
jpayne@68: 		int slop=(type==r16S ? ssuStopSlop : type==r23S ? lsuStopSlop : type==r18S ? ssuStopSlop : type==r5S ? r5SStopSlop : 9999);
jpayne@68: 		return slop;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static float minID(int type) {
jpayne@68: 		float minIdentity=(type==r16S ? min16SIdentity : type==r23S ? min23SIdentity : type==r18S ? min18SIdentity : type==r5S ? min5SIdentity : 0);
jpayne@68: 		return minIdentity;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static Read[] consensusReads(int type) {
jpayne@68: 		Read[] consensusReads=(type==r16S ? r16SSequence : type==r23S ? r23SSequence : type==r18S ? r18SSequence : type==r5S ? r5SSequence : null);
jpayne@68: 		return consensusReads;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static LongHashSet kmerSet(int type) {
jpayne@68: 		LongHashSet set=(type==tRNA ? trnaKmers : type==r16S ? ssuKmers : type==r23S ? lsuKmers : type==r5S ? r5SKmers : type==r18S ? ssuKmers : null);
jpayne@68: 		return set;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int kLongLen(int type) {
jpayne@68: 		int kLongLen=(type==tRNA ? kLongTRna : type==r16S ? kLongSSU : type==r23S ? kLongLSU : type==r5S ? kLong5S : type==r18S ? kLongSSU : -1);
jpayne@68: 		return kLongLen;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static int flagToType(int flag) {
jpayne@68: 		return Integer.numberOfTrailingZeros(flag)+1;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static byte typeToFlag(int type) {
jpayne@68: 		assert(type<=6);
jpayne@68: 		return (byte)(1<<(type-1));
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static boolean callType(int type){//TODO: Turn these functions into array lookups
jpayne@68: 		if(type==CDS){return callCDS;}
jpayne@68: 		else if(type==tRNA){return calltRNA;}
jpayne@68: 		else if(type==r16S){return call16S;}
jpayne@68: 		else if(type==r23S){return call23S;}
jpayne@68: 		else if(type==r5S){return call5S;}
jpayne@68: 		else if(type==r18S){return call18S;}
jpayne@68: 		assert(false) : type;
jpayne@68: 		return false;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------          Long Kmers          ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static synchronized void loadLongKmers(){
jpayne@68: //		assert(ssuKmers==null);
jpayne@68: //		assert(false) : load5Skmers+", "+kLong5s;
jpayne@68: 		if(loadedLongKmers){return;}
jpayne@68: 		if(loadSSUkmers){ssuKmers=loadLongKmersByType(kLongSSU, "ssu");}
jpayne@68: 		if(loadLSUkmers){lsuKmers=loadLongKmersByType(kLongLSU, "lsu");}
jpayne@68: 		if(load5Skmers){r5SKmers=loadLongKmersByType(kLong5S, "5S");}
jpayne@68: 		if(loadtRNAkmers){trnaKmers=loadLongKmersByType(kLongTRna, "tRNA");}
jpayne@68: 		loadedLongKmers=true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: //	private static LongHashSet loadLongKmers(StatsContainer sc, int k, String prefix){
jpayne@68: //		String fname=Data.findPath("?"+prefix+"_"+k+"mers.fa");
jpayne@68: //		if(!new File(fname).exists()){
jpayne@68: //			fname=fname+".gz";
jpayne@68: //			if(!new File(fname).exists()){
jpayne@68: //				System.err.println("Can't find "+fname);
jpayne@68: //				return null;
jpayne@68: //			}
jpayne@68: //		}
jpayne@68: //		LongHashSet set=loadLongKmers(fname, k);
jpayne@68: //		sc.kmerSet=set;
jpayne@68: //		sc.kLongLen=k;
jpayne@68: //		return set;
jpayne@68: //	}
jpayne@68: 	
jpayne@68: 	private static LongHashSet loadLongKmersByType(int k, String prefix){
jpayne@68: 		String fname=Data.findPath("?"+prefix+"_"+k+"mers.fa", true);
jpayne@68: 		if(!new File(fname).exists()){
jpayne@68: 			fname=fname+".gz";
jpayne@68: 			if(!new File(fname).exists()){
jpayne@68: 				System.err.println("Can't find "+fname);
jpayne@68: 				return null;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		LongHashSet set=loadLongKmers(fname, k);
jpayne@68: 		return set;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static LongHashSet loadLongKmers(String fname, int k){//TODO: Consider making this a LongHashSet.  No reason not to...
jpayne@68: 		FileFormat ff=FileFormat.testInput(fname, FileFormat.FA, null, false, false);
jpayne@68: 		ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null);
jpayne@68: 		cris.start(); //Start the stream
jpayne@68: //		if(verbose){outstream.println("Started cris");}
jpayne@68: 		
jpayne@68: 		LongHashSet set=new LongHashSet(1000);
jpayne@68: 		ListNum<Read> ln=cris.nextList();
jpayne@68: 		while(ln!=null && ln.size()>0){
jpayne@68: 			processList(ln, set, k);
jpayne@68: 			cris.returnList(ln);
jpayne@68: 			ln=cris.nextList();
jpayne@68: 		}
jpayne@68: 		if(ln!=null){cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());}
jpayne@68: 		ReadWrite.closeStream(cris);
jpayne@68: 		return set;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static LongHashSet processList(ListNum<Read> ln, LongHashSet set, int k){
jpayne@68: 		final long mask=~((-1L)<<(2*k));
jpayne@68: 		for(Read r : ln){
jpayne@68: 			final byte[] bases=r.bases;
jpayne@68: 			long kmer=0;
jpayne@68: 			int len=0;
jpayne@68: 			for(byte b : bases){
jpayne@68: 				final int num=AminoAcid.baseToNumber[b];
jpayne@68: 				if(num>=0){
jpayne@68: 					len++;
jpayne@68: 					kmer=((kmer<<2)|num)&mask;
jpayne@68: 					if(len>=k){
jpayne@68: 						set.add(kmer);
jpayne@68: 					}
jpayne@68: 				}else{
jpayne@68: 					len=0;
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return set;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	/*----------------      Consensus Sequence      ----------------*/
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static synchronized void loadConsensusSequenceFromFile(boolean removeMito, boolean removeChloro){
jpayne@68: 		if(loadedConsensusSequence){return;}
jpayne@68: //		assert(r16SSequence==null);
jpayne@68: 		if(load16SSequence){r16SSequence=loadConsensusSequenceType("16S", removeMito, removeChloro);}
jpayne@68: 		if(load18SSequence){r18SSequence=loadConsensusSequenceType("18S", removeMito, removeChloro);}
jpayne@68: 		if(load23SSequence){r23SSequence=loadConsensusSequenceType("23S", removeMito, removeChloro);}
jpayne@68: 		if(load5SSequence){r5SSequence=loadConsensusSequenceType("5S", removeMito, removeChloro);}
jpayne@68: 		if(loadtRNASequence){trnaSequence=loadConsensusSequenceType("tRNA", removeMito, removeChloro);}
jpayne@68: 		loadedConsensusSequence=true;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static Read[] loadConsensusSequenceType(String prefix, boolean removeMito, boolean removeChloro){
jpayne@68: 		String fname=null;
jpayne@68: 		fname=Data.findPath("?"+prefix+"_consensus_sequence.fq", false);
jpayne@68: 		if(fname!=null && (fname.endsWith(".jar") || new File(fname).exists())){
jpayne@68: 			fname=Tools.fixExtension(fname);
jpayne@68: 		}else{
jpayne@68: 			fname=Data.findPath("?"+prefix+"_consensus_sequence.fa", true);
jpayne@68: 			fname=Tools.fixExtension(fname);
jpayne@68: 			if(!fname.endsWith(".jar") && !new File(fname).exists()){
jpayne@68: 				System.err.println("Can't find "+fname);
jpayne@68: 				return null;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		Read[] array=loadConsensusSequence(fname);
jpayne@68: 		if(removeMito){array=stripOrganelle(array, "mito");}
jpayne@68: 		if(removeChloro){array=stripOrganelle(array, "plastid");}
jpayne@68: 		return array;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static Read[] loadConsensusSequence(String fname){
jpayne@68: 		FileFormat ff=FileFormat.testInput(fname, FileFormat.FA, null, false, false);
jpayne@68: 		Read[] array=ReadInputStream.toReadArray(ff, -1);
jpayne@68: 		return array;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static Read[] stripOrganelle(Read[] array, String key){
jpayne@68: 		int removed=0;
jpayne@68: 		for(int j=0; j<array.length; j++){
jpayne@68: 			if(array[j].id.toLowerCase().startsWith(key)) {
jpayne@68: 				array[j]=null;
jpayne@68: 				removed++;
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		if(removed>0){array=Tools.condenseStrict(array);}
jpayne@68: 		return array;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/*--------------------------------------------------------------*/
jpayne@68: 	
jpayne@68: 	public static final int CDS=0, tRNA=1, r16S=2, r23S=3, r5S=4, r18S=5, r28S=6, RNA=7;
jpayne@68: 	public static String[] typeStrings=new String[] {"CDS", "tRNA", "16S", "23S", "5S", "18S", "28S", "RNA"};
jpayne@68: 	public static String[] typeStrings2=new String[] {"CDS", "tRNA", "rRNA", "rRNA", "rRNA", "rRNA", "rRNA", "RNA"};
jpayne@68: 	public static String[] specialTypeStrings=new String[] {null, "tRNA", "16S", "23S", "5S", "18S", "28S", null};
jpayne@68: 	public static boolean isSpecialType(String type){
jpayne@68: 		if(type==null){return false;}
jpayne@68: 		for(String s : specialTypeStrings){
jpayne@68: 			if(type.equalsIgnoreCase(s)){return true;}
jpayne@68: 		}
jpayne@68: 		return false;
jpayne@68: 	}
jpayne@68: 
jpayne@68: 	public static int kInnerRNA=6;
jpayne@68: 	public static int kStartRNA=3;
jpayne@68: 	public static int kStopRNA=3;
jpayne@68: 
jpayne@68: 	public static int kLongSSU=15;
jpayne@68: 	public static int kLongLSU=15;
jpayne@68: 	public static int kLong5S=15;
jpayne@68: 	public static int kLongTRna=15;
jpayne@68: 	
jpayne@68: 	public static float min16SIdentity=0.62f;
jpayne@68: 	public static float min23SIdentity=0.60f;
jpayne@68: 	public static float min5SIdentity=0.60f;
jpayne@68: 	public static float min18SIdentity=0.60f;
jpayne@68: 	
jpayne@68: 	static int ssuStartSlop=200;
jpayne@68: 	static int ssuStopSlop=0;
jpayne@68: 	static int lsuStartSlop=220;
jpayne@68: 	static int lsuStopSlop=0;
jpayne@68: 	static int r5SStartSlop=50;
jpayne@68: 	static int r5SStopSlop=50;
jpayne@68: 
jpayne@68: 	public static boolean callCDS=true;
jpayne@68: 	public static boolean calltRNA=true;
jpayne@68: 	public static boolean call16S=true;
jpayne@68: 	public static boolean call23S=true;
jpayne@68: 	public static boolean call5S=true;
jpayne@68: 	public static boolean call18S=false;
jpayne@68: 
jpayne@68: 	public static LongHashSet ssuKmers=null;
jpayne@68: 	public static LongHashSet lsuKmers=null;
jpayne@68: 	public static LongHashSet r5SKmers=null;
jpayne@68: 	public static LongHashSet trnaKmers=null;
jpayne@68: 
jpayne@68: 	public static Read[] trnaSequence=null;
jpayne@68: 	public static Read[] r16SSequence=null;
jpayne@68: 	public static Read[] r23SSequence=null;
jpayne@68: 	public static Read[] r5SSequence=null;
jpayne@68: 	public static Read[] r18SSequence=null;
jpayne@68: 
jpayne@68: 	public static boolean PROCESS_PLUS_STRAND=true;
jpayne@68: 	public static boolean PROCESS_MINUS_STRAND=true;
jpayne@68: 
jpayne@68: 	public static boolean loadSSUkmers=true;
jpayne@68: 	public static boolean loadLSUkmers=true;
jpayne@68: 	public static boolean load5Skmers=true;
jpayne@68: 	public static boolean loadtRNAkmers=true;
jpayne@68: 	private static boolean loadedLongKmers=false;
jpayne@68: 
jpayne@68: 	public static boolean loadtRNASequence=false;
jpayne@68: 	public static boolean load16SSequence=true;
jpayne@68: 	public static boolean load23SSequence=true;
jpayne@68: 	public static boolean load5SSequence=true;
jpayne@68: 	public static boolean load18SSequence=true;
jpayne@68: 	private static boolean loadedConsensusSequence=false;
jpayne@68: 	
jpayne@68: }