--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/GiToTaxid.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,463 @@
+package tax;
+
+import java.io.File;
+import java.util.ArrayList;
+
+import fileIO.ByteFile;
+import fileIO.ReadWrite;
+import shared.Parse;
+import shared.Shared;
+import shared.Tools;
+import structures.IntList;
+
+/**
+ * @author Brian Bushnell
+ * @date Mar 10, 2015
+ *
+ */
+public class GiToTaxid {
+	
+	public static void main(String[] args){
+		ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.USE_PIGZ=true;
+		ReadWrite.ZIPLEVEL=9;
+		ReadWrite.PIGZ_BLOCKSIZE=256;
+//		ReadWrite.PIGZ_ITERATIONS=30;
+		
+		for(String arg : args){
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			shared.Parser.parseZip(arg, a, b);
+		}
+//		if(args.length>2 && false){//Run a test
+//			test(args);
+//		}else 
+		if(args.length>=2){//Write array
+			initialize(args[0]);
+			ReadWrite.write(array, args[1], true);
+		}
+	}
+	
+	public static void test(String[] args){
+		System.err.println(getID(1000));
+		System.err.println(getID(10000));
+		System.err.println(getID(10001));
+		System.err.println(getID(10002));
+		System.err.println(getID(10003));
+		System.err.println(getID(10004));
+		System.err.println(getID(10005));
+		System.err.println(getID(100000));
+		System.err.println(getID(1000000));
+		System.err.println(getID(10000000));
+		
+		TaxTree tree=null;
+		if(args.length>1){
+			tree=TaxTree.loadTaxTree(args[0], System.err, true, true);
+		}
+		
+		System.err.println("Strings:");
+		int x;
+		x=getID("gi|18104025|emb|AJ427095.1| Ceratitis capitata centromeric or pericentromeric satellite DNA, clone 44");
+		System.err.println(x);
+		if(tree!=null){
+			System.err.println(tree.getNode(x));
+			tree.incrementRaw(x, 30);
+		}
+		x=getID("gi|15982920|gb|AY057568.1| Arabidopsis thaliana AT5g43500/MWF20_22 mRNA, complete cds");
+		System.err.println(x);
+		if(tree!=null){
+			System.err.println(tree.getNode(x));
+			tree.incrementRaw(x, 40);
+		}
+		x=getID("gi|481043749|gb|KC494054.1| Plesiochorus cymbiformis isolate ST05-58 internal transcribed spacer 2, partial sequence");
+		System.err.println(x);
+		if(tree!=null){
+			System.err.println(tree.getNode(x));
+			tree.incrementRaw(x, 20);
+		}
+		
+		if(tree!=null){
+			tree.percolateUp();
+			ArrayList<TaxNode> nodes=tree.gatherNodesAtLeastLimit(35);
+			for(TaxNode n : nodes){
+				System.err.println(n);
+			}
+		}
+	}
+	
+	public static int parseGiToTaxid(String s){return parseGiToTaxid(s, '|');}
+	public static int parseGiToTaxid(String s, char delimiter){
+		long x=parseGiNumber(s, delimiter);
+		assert(x>=0) : x+", "+s;
+		return getID(x);
+	}
+	
+
+	public static int parseGiToTaxid(byte[] s){return parseGiToTaxid(s, '|');}
+	public static int parseGiToTaxid(byte[] s, char delimiter){
+		long x=parseGiNumber(s, delimiter);
+		return x<0 ? -1 : getID(x);
+	}
+	
+	/** Parse a gi number, or return -1 if formatted incorrectly. */
+	static long parseGiNumber(String s, char delimiter){
+		if(s==null || s.length()<4){return -1;}
+		if(s.charAt(0)=='>'){return getID(s.substring(1), delimiter);}
+		if(!s.startsWith("gi")){return -1;}
+		int initial=s.indexOf(delimiter);
+		if(initial<0){
+			if(delimiter!='~'){
+				delimiter='~';
+				initial=s.indexOf(delimiter);
+			}
+			if(initial<0){
+				delimiter='_';
+				initial=s.indexOf(delimiter);
+			}
+			if(initial<0){return -1;}
+		}
+		if(!Tools.isDigit(s.charAt(initial+1))){return -1;}
+		
+		long number=0;
+		for(int i=initial+1; i<s.length(); i++){
+			char c=s.charAt(i);
+			if(c==delimiter){break;}
+			assert(Tools.isDigit(c));
+			number=(number*10)+(c-'0');
+		}
+		return number;
+	}
+	
+	/** Parse a ncbi number, or return -1 if formatted incorrectly. */
+	public static int parseTaxidNumber(String s, char delimiter){
+		if(s==null || s.length()<5){return -1;}
+		if(s.charAt(0)=='>'){return parseTaxidNumber(s.substring(1), delimiter);}
+		if(!s.startsWith("ncbi") && !s.startsWith("tid")){return -1;}
+		int initial=s.indexOf(delimiter);
+		if(initial<0){
+			delimiter='_';
+			initial=s.indexOf(delimiter);
+			if(initial<0){return -1;}
+		}
+		if(!Tools.isDigit(s.charAt(initial+1))){return -1;}
+		
+		int number=0;
+		for(int i=initial+1; i<s.length(); i++){
+			char c=s.charAt(i);
+			if(c==delimiter || c==' '){break;}
+			assert(Tools.isDigit(c)) : c+"\n"+s;
+			number=(number*10)+(c-'0');
+		}
+		return number;
+	}
+	
+
+	public static int getID(String s){return getID(s, '|');}
+	/** Get the taxID from a header starting with a taxID or gi number */
+	public static int getID(String s, char delimiter){
+		long x=parseTaxidNumber(s, delimiter);
+		if(x>=0){return (int)x;}
+		x=parseGiNumber(s, delimiter);
+		return x<0 ? -1 : getID(x);
+	}
+	
+	/** Parse a gi number, or return -1 if formatted incorrectly. */
+	static long parseGiNumber(byte[] s, char delimiter){
+		if(s==null || s.length<4){return -1;}
+		if(!Tools.startsWith(s, "gi") && !Tools.startsWith(s, ">gi")){return -1;}
+		int initial=Tools.indexOf(s, (byte)delimiter);
+		if(initial<0){
+			delimiter='_';
+			initial=Tools.indexOf(s, (byte)delimiter);
+			if(initial<0){return -1;}
+		}
+		if(!Tools.isDigit(s[initial+1])){return -1;}
+		
+		long number=0;
+		for(int i=initial+1; i<s.length; i++){
+			byte c=s[i];
+			if(c==delimiter){break;}
+			assert(Tools.isDigit(c));
+			number=(number*10)+(c-'0');
+		}
+		return number;
+	}
+	
+	/** Parse a gi number, or return -1 if formatted incorrectly. */
+	static int parseNcbiNumber(byte[] s, char delimiter){
+		if(s==null || s.length<3){return -1;}
+		if(!Tools.startsWith(s, "ncbi") && !Tools.startsWith(s, ">ncbi") && !Tools.startsWith(s, "tid") && !Tools.startsWith(s, ">tid")){return -1;}
+		int initial=Tools.indexOf(s, (byte)delimiter);
+		if(initial<0){
+			delimiter='_';
+			initial=Tools.indexOf(s, (byte)delimiter);
+			if(initial<0){return -1;}
+		}
+		if(!Tools.isDigit(s[initial+1])){return -1;}
+		
+		int number=0;
+		for(int i=initial+1; i<s.length; i++){
+			byte c=s[i];
+			if(c==delimiter){break;}
+			assert(Tools.isDigit(c));
+			number=(number*10)+(c-'0');
+		}
+		return number;
+	}
+
+	public static int getID(byte[] s){return getID(s, '|');}
+	/** Get the taxID from a header starting with a taxID or gi number */
+	public static int getID(byte[] s, char delimiter){
+		long x=parseGiNumber(s, delimiter);
+		if(x>=0){return getID(x, true);}
+		return parseNcbiNumber(s, delimiter);
+	}
+	
+	/** Get the taxID from a gi number;
+	 * -1 if not present or invalid (negative input),
+	 * -2 if out of range (too high) */
+	public static int getID(long gi){
+		return getID(gi, true);
+	}
+	
+	/** Get the taxID from a gi number;
+	 * 0 if not present,
+	 * -1 if invalid (negative input),
+	 * -2 if out of range (too high) */
+	public static int getID(long gi, boolean assertInRange){
+		assert(initialized) : "To use gi numbers, you must load a gi table.";
+		if(gi<0 || gi>maxGiLoaded){
+			assert(!assertInRange) : gi<0 ? "gi number "+gi+" is invalid." : 
+				"The gi number "+gi+" is too big: Max loaded gi number is "+maxGiLoaded+".\n"
+				+ "Please update the gi table with the latest version from NCBI"
+				+ " as per the instructions in gitable.sh.\n"
+				+ "To ignore this problem, please run with the -da flag.\n";
+			return gi<0 ? -1 : -2;
+		}
+		final long upper=gi>>>SHIFT;
+		final int lower=(int)(gi&LOWERMASK);
+		assert(upper<Shared.MAX_ARRAY_LEN && upper<array.length) : gi+", "+upper+", "+array.length;
+		final int[] slice=array[(int)upper];
+		return slice==null || slice.length<=lower ? 0 : slice[lower];
+	}
+	
+	public static void initialize(String fname){
+		assert(fname!=null);
+		if(fileString==null || !fileString.equals(fname)){
+			synchronized(GiToTaxid.class){
+				if(!initialized || fileString==null || !fileString.equals(fname)){
+					fileString=fname;
+					if(fname.contains(".int2d")){
+						array=ReadWrite.read(int[][].class, fname, true);
+						maxGiLoaded=-1;
+						if(array!=null && array.length>0){
+							int upper=array.length-1;
+							int[] section=array[upper];
+							int lower=section.length-1;
+							maxGiLoaded=(((long)upper)<<SHIFT)|lower;
+						}
+					}else if(fname.contains(".int1d")){
+						throw new RuntimeException("Old gi table format filename "+fname+".\n"
+								+ "Current files should end in .int2d.");
+						
+					}else{
+						array=makeArray(fname);
+					}
+				}
+				initialized=true;
+			}
+		}
+	}
+	
+	public static boolean isInitialized(){return initialized;}
+	
+	public static synchronized void unload(){
+		maxGiLoaded=-1;
+		array=null;
+		fileString=null;
+		initialized=false;
+	}
+	
+	private static int[][] makeArray(String fnames){
+		String[] split;
+		if(new File(fnames).exists()){split=new String[] {fnames};}
+		else if(fnames.indexOf(',')>=0){split=fnames.split(",");}
+		else if(fnames.indexOf('#')>=0){
+			assert(fnames.indexOf("/")<0) : "Note: Wildcard # only works for "
+					+ "relative paths in present working directory.";
+			File dir=new File(System.getProperty("user.dir"));
+			String prefix=fnames.substring(0, fnames.indexOf('#'));
+			String suffix=fnames.substring(fnames.indexOf('#')+1);
+			
+			File[] array=dir.listFiles();
+			StringBuilder sb=new StringBuilder();
+			String comma="";
+			for(File f : array){
+				String s=f.getName();
+				if(s.startsWith(prefix) && s.startsWith(suffix)){
+					sb.append(comma);
+					sb.append(s);
+					comma=",";
+				}
+			}
+			split=sb.toString().split(",");
+		}else{
+			throw new RuntimeException("Invalid file: "+fnames);
+		}
+		
+		int numLists=32;
+		IntList[] lists=new IntList[numLists];
+		
+		long total=0;
+		for(String s : split){
+			long count=addToList(s, lists);
+			total+=count;
+		}
+		for(int i=0; i<lists.length; i++){
+			if(lists[i]!=null && lists[i].size>0){
+				lists[i].shrink();
+				numLists=i+1;
+			}
+		}
+		int[][] table=new int[numLists][];
+		for(int i=0; i<numLists; i++){
+			table[i]=lists[i].array;
+		}
+		return table;
+	}
+	
+	private static long addToList(String fname, IntList[] lists){
+		boolean warned=false;
+		ByteFile bf=ByteFile.makeByteFile(fname, true);
+		long count=0, invalid=0;
+		byte[] line=bf.nextLine();
+		while(line!=null){
+			if(line.length>0 && Tools.isDigit(line[line.length-1])){//Invalid lines will end with tab or na
+				count++;
+				int tab2=Tools.indexOfNth(line, '\t', 2);
+				int tab3=Tools.indexOfNth(line, '\t', 1, tab2+1);
+				assert(tab2>0 && (tab2<tab3) && tab3<line.length) : tab2+", "+tab3+", "+line.length;
+				assert(tab2<line.length && line[tab2]=='\t') : tab2+", "+tab3+", '"+new String(line)+"'";
+				assert(tab3<line.length && line[tab3]=='\t') : tab2+", "+tab3+", '"+new String(line)+"'";
+				//assert(false) : tab2+", "+tab3+", '"+new String(line)+"'";
+				int tid=Parse.parseInt(line, tab2+1, tab3);
+				int gi=Parse.parseInt(line, tab3+1, line.length);
+				if(gi<0){
+					invalid++;
+				}else{
+					assert(gi>=0) : "tid="+tid+", gi="+gi+", line=\n'"+new String(line)+"'";
+					int old=setID(gi, tid, lists);
+					assert(old<1 || old==tid) : "Contradictory entries for gi "+gi+": "+old+" -> "+tid+"\n'"+new String(line)+"'\ntab2="+tab2+", tab3="+tab3;
+				}
+			}else{
+				//if(line.length==0){System.err.println(fname+", "+count);}//debug
+				invalid++;
+			}
+			line=bf.nextLine();
+		}
+		if(verbose){System.err.println("Count: "+count+"; \tInvalid: "+invalid);}
+		bf.close();
+		return count;
+	}
+	
+	private static int getID(long gi, IntList[] lists){
+		assert(gi>=0) : "gi number "+gi+" is invalid.";
+		final long upper=gi>>>SHIFT;
+		final int lower=(int)(gi&LOWERMASK);
+		assert(upper<Shared.MAX_ARRAY_LEN) : gi+", "+upper;
+		IntList list=lists[(int)upper];
+		return lower<0 ? -1 : lower>=list.size ? -2 : list.get(lower);
+	}
+	
+	private static int setID(long gi, int tid, IntList[] lists){
+		assert(gi>=0) : "gi number "+gi+" is invalid.";
+		final long upper=gi>>>SHIFT;
+		final int lower=(int)(gi&LOWERMASK);
+		assert(upper<Shared.MAX_ARRAY_LEN) : gi+", "+upper;
+		IntList list=lists[(int)upper];
+		if(list==null){list=lists[(int)upper]=new IntList();}
+		int old=lower<0 ? -1 : lower>=list.size ? -2 : list.get(lower);
+		list.set(lower, tid);
+		maxGiLoaded=Tools.max(gi, maxGiLoaded);
+		return old;
+	}
+	
+//	private static int[] makeArrayOld(String fnames){
+//		String[] split;
+//		if(new File(fnames).exists()){split=new String[] {fnames};}
+//		else{split=fnames.split(",");}
+//		
+//		long max=0;
+//		for(String s : split){
+//			max=Tools.max(max, findMaxID(s));
+//		}
+//		
+//		assert(max<Integer.MAX_VALUE) : "Overflow.";
+//		int[] x=new int[(int)max+1];
+//		Arrays.fill(x, -1);
+//		
+//		long total=0;
+//		for(String s : split){
+//			long count=fillArray(s, x);
+//			total+=count;
+//		}
+//		return x;
+//	}
+//	
+//	private static long findMaxID(String fname){
+//		ByteFile bf=ByteFile.makeByteFile(fname, true);
+//		long count=0, max=0;
+//		byte[] line=bf.nextLine();
+//		while(line!=null){
+//			count++;
+//			int tab=Tools.indexOf(line, (byte)'\t');
+//			long gi=Parse.parseLong(line, 0, tab);
+//			max=Tools.max(max, gi);
+//			line=bf.nextLine();
+//		}
+//		bf.close();
+//		return max;
+//	}
+//	
+//	private static long fillArray(String fname, int[] x){
+//		boolean warned=false;
+//		ByteFile bf=ByteFile.makeByteFile(fname, true);
+//		long count=0;
+//		byte[] line=bf.nextLine();
+//		while(line!=null){
+//			count++;
+//			int tab=Tools.indexOf(line, (byte)'\t');
+//			int gi=Parse.parseInt(line, 0, tab);
+//			int ncbi=Parse.parseInt(line, tab+1, line.length);
+//			//assert(x[gi]==-1 || x[gi]==ncbi) : "Contradictory entries for gi "+gi+": "+x[gi]+" -> "+ncbi;
+//			if(x[gi]!=-1 && x[gi]!=ncbi){
+//				if(!warned){
+//					System.err.println("***WARNING*** For file "+fname+":\n"+
+//							("Contradictory entries for gi "+gi+": mapped to both taxID "+x[gi]+" and taxID "+ncbi)+
+//							"\nThis may be an error from NCBI and you may wish to report it, but it is\n"
+//							+ "being suppressed because NCBI data is known to contain multi-mapped gi numbers,\n"
+//							+ "at least between nucleotide and protein, and gi numbers are deprecated anyway.");
+//					warned=true;
+//				}
+//			}else{
+//				x[gi]=ncbi;
+//			}
+//			line=bf.nextLine();
+//		}
+//		if(verbose){System.err.println("Count: "+count);}
+//		bf.close();
+//		return count;
+//	}
+	
+	private static long maxGiLoaded=-1;
+	private static int[][] array;
+	private static final int SHIFT=30;
+	private static final long UPPERMASK=(-1L)<<SHIFT;
+	private static final long LOWERMASK=~UPPERMASK;
+	
+	private static String fileString;
+	
+	public static boolean verbose=false;
+	private static boolean initialized=false;
+}