--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/IDTree.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,216 @@
+package tax;
+
+import java.io.PrintStream;
+import java.util.ArrayList;
+
+import fileIO.FileFormat;
+import fileIO.ReadWrite;
+import fileIO.TextFile;
+import shared.Parse;
+import shared.Parser;
+import shared.PreParser;
+import shared.Shared;
+import shared.Timer;
+import shared.Tools;
+import stream.Read;
+
+/**
+ * Creates a taxonomic tree from an identity matrix.
+ * @author Brian Bushnell
+ * @date July 1, 2016
+ *
+ */
+public class IDTree {
+
+	/*--------------------------------------------------------------*/
+	/*----------------        Initialization        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Code entrance from the command line.
+	 * @param args Command line arguments
+	 */
+	public static void main(String[] args){
+		Timer t=new Timer();
+		IDTree x=new IDTree(args);
+		x.process(t);
+		
+		//Close the print stream if it was redirected
+		Shared.closeStream(x.outstream);
+	}
+	
+	/**
+	 * Constructor.
+	 * @param args Command line arguments
+	 */
+	public IDTree(String[] args){
+		
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, getClass(), false);
+			args=pp.args;
+			outstream=pp.outstream;
+		}
+		
+		//Set shared static variables
+		Shared.capBuffers(4);
+		ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
+		ReadWrite.MAX_ZIP_THREADS=Shared.threads();
+		
+		//Create a parser object
+		Parser parser=new Parser();
+		
+		//Parse each argument
+		for(int i=0; i<args.length; i++){
+			String arg=args[i];
+			
+			//Break arguments into their constituent parts, in the form of "a=b"
+			String[] split=arg.split("=");
+			String a=split[0].toLowerCase();
+			String b=split.length>1 ? split[1] : null;
+			
+			if(parser.parse(arg, a, b)){//Parse standard flags in the parser
+				//do nothing
+			}else if(a.equals("verbose")){
+				verbose=Parse.parseBoolean(b);
+			}else if(a.equals("parse_flag_goes_here")){
+				//Set a variable here
+			}else{
+				outstream.println("Unknown parameter "+args[i]);
+				assert(false) : "Unknown parameter "+args[i];
+				//				throw new RuntimeException("Unknown parameter "+args[i]);
+			}
+		}
+		
+		{//Process parser fields
+			
+			overwrite=parser.overwrite;
+			append=parser.append;
+			
+			in1=parser.in1;
+
+			out1=parser.out1;
+			
+			maxLines=parser.maxReads;
+		}
+		
+		//Ensure there is an input file
+		if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
+		
+		//Ensure output files can be written
+		if(!Tools.testOutputFiles(overwrite, append, false, out1)){
+			outstream.println((out1==null)+", "+out1);
+			throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output file "+out1+"\n");
+		}
+		
+		//Ensure input files can be read
+		if(!Tools.testInputFiles(false, true, in1)){
+			throw new RuntimeException("\nCan't read some input files.\n");  
+		}
+		
+		//Ensure that no file was specified multiple times
+		if(!Tools.testForDuplicateFiles(true, in1, out1)){
+			throw new RuntimeException("\nSome file names were specified multiple times.\n");
+		}
+		
+		//Create output FileFormat objects
+		ffout1=FileFormat.testOutput(out1, FileFormat.TEXT, null, true, overwrite, append, false);
+
+		//Create input FileFormat objects
+		ffin1=FileFormat.testInput(in1, FileFormat.TEXT, null, true, true);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Outer Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Create read streams and process all data */
+	void process(Timer t){
+		
+		ArrayList<IDNode> list=new ArrayList<IDNode>();
+		TextFile tf=new TextFile(in1);
+		for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
+			if(maxLines>=0 && list.size()>=maxLines){break;}
+			if(!line.startsWith("#")){
+				String[] split=line.split("\t");
+				double[] array=new double[list.size()];
+				for(int i=0; i<array.length; i++){
+					array[i]=Double.parseDouble(split[i+1]);
+				}
+				IDNode n=new IDNode(array, list.size(), split[0]);
+				list.add(n);
+			}
+		}
+		tf.close();
+		
+		IDNode[] nodes=list.toArray(new IDNode[0]);
+		IDNode head=IDNode.makeTree(nodes);
+		
+		StringBuilder sb=head.toNewick();
+		sb.append(';');
+		
+		if(out1!=null){
+			ReadWrite.writeString(sb, out1);
+			outstream.println("Wrote tree to "+out1);
+		}
+		
+		t.stop();
+		outstream.println("Time: \t"+t);
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Inner Methods        ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/**
+	 * Process a single read pair.
+	 * @param r1 Read 1
+	 * @param r2 Read 2 (may be null)
+	 * @return True if the reads should be kept, false if they should be discarded.
+	 */
+	boolean processReadPair(final Read r1, final Read r2){
+		throw new RuntimeException("TODO");
+	}
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            Fields            ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file path */
+	private String in1=null;
+
+	/** Primary output file path */
+	private String out1=null;
+	
+	/*--------------------------------------------------------------*/
+
+	/** Number of lines processed */
+	protected long linesProcessed=0;
+	
+	protected long maxLines=-1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Final Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+
+	/** Primary input file */
+	private final FileFormat ffin1;
+	
+	/** Primary output file */
+	private final FileFormat ffout1;
+	
+	/*--------------------------------------------------------------*/
+	/*----------------        Common Fields         ----------------*/
+	/*--------------------------------------------------------------*/
+	
+	/** Print status messages to this output stream */
+	private PrintStream outstream=System.err;
+	/** Print verbose messages */
+	public static boolean verbose=false;
+	/** True if an error was encountered */
+	public boolean errorState=false;
+	/** Overwrite existing output files */
+	private boolean overwrite=false;
+	/** Append to existing output files */
+	private boolean append=false;
+	
+}