--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/Query.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,186 @@
+package tax;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.Locale;
+
+import shared.Shared;
+import shared.Timer;
+
+public class Query {
+	
+	/** For testing throughput */
+	public static void main(String[] args){
+		
+//		sun.net.http.errorstream.enableBuffering=true;
+
+//		System.setProperty("sun.net.http.errorstream.enableBuffering", "true");
+//		System.setProperty("http.errorstream.enableBuffering", "true");
+//////		System.setProperty("", "");
+//		System.setProperty("http.keepAlive", "true");
+//		System.setProperty("http.maxConnections", "50");
+////		System.setProperty("", "");
+////		System.setProperty("", "");
+//
+//		System.out.println("sun.net.http.errorstream.enableBuffering="+System.getProperty("sun.net.http.errorstream.enableBuffering"));
+//		System.out.println("sun.net.http.errorstream.timeout="+System.getProperty("sun.net.http.errorstream.timeout"));
+//		System.out.println("sun.net.http.errorstream.bufferSize="+System.getProperty("sun.net.http.errorstream.bufferSize"));
+//		System.out.println("http.keepAlive="+System.getProperty("http.keepAlive"));
+//		System.out.println("http.maxConnections="+System.getProperty("http.maxConnections"));
+//		System.out.println(System.getProperties());
+//		System.out.println("="+System.getProperty(""));
+//		System.out.println("="+System.getProperty(""));
+//		System.out.println("="+System.getProperty(""));
+		
+		String x=args[0];
+		int requests=(args.length>1 ? Integer.parseInt(args[1]) : 1);
+
+		Timer t=new Timer();
+		Timer t2=new Timer();
+		Timer t3=new Timer();
+		
+//		URL url=toUrl(x);
+		for(int i=0; i<requests; i++){
+			String s=request(x);
+//			System.out.println(s);
+			if(i==0){t3.start();}
+			//t2.stop("");
+			//t2.start();
+		}
+		
+		t3.stop();
+		
+		t.stop("Time:  \t");
+		double qps=requests*1000000000.0/(t.elapsed);
+		System.err.println(String.format(Locale.ROOT, "Qps:   \t%.2f", qps));
+		
+		System.err.println("Time2: \t"+t3);
+		double qps2=(requests-1)*1000000000.0/(t3.elapsed);
+		System.err.println(String.format(Locale.ROOT, "Qps2:  \t%.2f", qps2));
+		
+//		System.out.println(s);
+		
+//		BufferedReader reader;
+//		try {
+//			reader = new BufferedReader(new InputStreamReader(url.openStream(), "UTF-8"));
+//
+//			for (String line; (line = reader.readLine()) != null;) {
+//				System.out.println(line);
+//			}
+//
+//		} catch (UnsupportedEncodingException e) {
+//			// TODO Auto-generated catch block
+//			e.printStackTrace();
+//		} catch (IOException e) {
+//			// TODO Auto-generated catch block
+//			e.printStackTrace();
+//		}
+	}
+	
+	public static int[] getGi(String...args){
+		return get("pt_gi", args);
+	}
+	
+	public static int[] getAccession(String...args){
+		return get("pt_accession", args);
+	}
+	
+	public static int[] get(String type, String...args){
+		String host=Shared.taxServer();
+		StringBuilder sb=new StringBuilder(host.length()+32);
+		sb.append(host);
+		sb.append(type);
+		sb.append('\t');
+		String comma="";
+		for(String arg : args){
+			sb.append(comma);
+			sb.append(arg);
+			comma=",";
+		}
+		String result=request(sb.toString());
+		String[] split=result.split(",");
+		int[] ret=new int[split.length];
+		for(int i=0; i<split.length; i++){
+			ret[i]=Integer.parseInt(split[i]);
+		}
+		return ret;
+	}
+	
+	public static String request(String x){
+		InputStream is=toStream(x);
+		if(is==null){return null;}
+		try {
+			byte[] buffer=new byte[256];
+			int count=is.read(buffer);
+			int next=0;
+			while(count>-1){
+				next+=count;
+				if(next>=buffer.length){
+					buffer=Arrays.copyOf(buffer, buffer.length*2);
+				}
+				count=is.read(buffer, next, buffer.length-next);
+			}
+			is.close(); //TODO: Why am I not closing this stream?
+			return new String(buffer, 0, next);
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		try {
+			is.close();
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return null;
+	}
+	
+	public static InputStream toStream(String x){
+		URL url=null;
+		
+		try {
+			url = new URL(x);
+		} catch (MalformedURLException e1) {
+			// TODO Auto-generated catch block
+			e1.printStackTrace();
+			return null;
+		}
+		
+		try {
+			InputStream is=url.openStream();
+			return is;
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		return null;
+	}
+	
+//	public static URL toUrl(String x){
+//		URL url=null;
+//		try {
+//			url = new URL(x);
+//		} catch (MalformedURLException e1) {
+//			// TODO Auto-generated catch block
+//			e1.printStackTrace();
+//		}
+//
+//		return url;
+//	}
+//
+//	public static URLConnection toUrlConnection(URL url, String x){
+//		URLConnection urlc=null;
+//
+//		try {
+//			urlc = url.openConnection();
+//		} catch (IOException e) {
+//			// TODO Auto-generated catch block
+//			e.printStackTrace();
+//		}
+//		return urlc;
+//	}
+	
+}