--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/FindFiles.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,113 @@
+package fileIO;
+
+import java.io.File;
+import java.util.ArrayList;
+
+
+public class FindFiles {
+	
+	
+	public static void main(String[] args){
+		
+		String root=args[0];
+//		if(root.equals(".")){root=null;}
+		String prefix=args[1];
+		String suffix=(args[2].equals("null") ? null : args[2]);
+		String middle=null;
+		
+		if(args.length>3){
+			middle=(args[3].equals("null") ? null : args[3]);
+		}
+
+		boolean NEWLINE=true;
+		boolean BOTH=true;
+
+		ArrayList<String> results=findFiles(root, prefix, suffix, middle);
+		for(String s : results){
+			if(NEWLINE){
+				System.out.println(s);
+			}else{
+				System.out.print(s+" ");
+			}
+		}
+
+
+		if(BOTH){
+			System.out.println();
+			NEWLINE=!NEWLINE;
+			for(String s : results){
+				if(NEWLINE){
+					System.out.println(s);
+				}else{
+					System.out.print(s+" ");
+				}
+			}
+		}
+	}
+	
+	
+	public FindFiles(String pre, String suf, String mid){
+		assert(!"*".equals(pre)) : "Use # instead of *, which has problems from the command line";
+		assert(!"*".equals(suf)) : "Use # instead of *, which has problems from the command line";
+		prefix=((pre==null || pre.equals("*") || pre.equals("#")) ? null : pre.toLowerCase());
+		suffix=((suf==null || suf.equals("*") || suf.equals("#")) ? null : suf.toLowerCase());
+		middle=((mid==null || mid.equals("*") || mid.equals("#")) ? null : mid.toLowerCase());
+	}
+	
+	public static ArrayList<String> findFiles(String root, String prefix, String suffix){
+		return findFiles(root, prefix, suffix, null);
+	}
+	
+	public static ArrayList<String> findFiles(String root, String prefix, String suffix, String mid){
+		FindFiles ff=new FindFiles(prefix, suffix, mid);
+		return ff.findFiles(root);
+	}
+	
+	public ArrayList<String> findFiles(String path){
+		findFiles(new File(path==null ? "." : path));
+		return results;
+	}
+	
+	public ArrayList<String> findFiles(File path){
+		
+		if(path.isDirectory()){
+			File[] array=path.listFiles();
+			if(array==null){System.err.println("null contents for "+path.getAbsolutePath());}
+			else{for(File f : array){findFiles(f);}}
+		}else{
+			consider(path);
+		}
+		return results;
+	}
+	
+	public void consider(File in){
+//		System.out.println("Considering "+in.getAbsolutePath()+" versus '"+prefix+"' '"+suffix+"'");
+		if(!in.exists()){return;}
+		assert(in.exists()) : in;
+		assert(in.isFile());
+		String abs=in.getAbsolutePath();
+//		System.out.println("Considering "+abs);
+		String abs2=abs.toLowerCase();
+		int slashLoc=abs2.lastIndexOf(slash);
+		if(slashLoc>-1){
+			abs2=abs2.substring(slashLoc+1);
+		}
+//		System.out.println("a");
+		if(prefix!=null && !abs2.startsWith(prefix)){return;}
+//		System.out.println("b");
+		if(suffix!=null && !abs2.endsWith(suffix)){return;}
+//		System.out.println("c");
+		
+		if(middle!=null && !abs2.contains(middle)){return;}
+		
+		results.add(abs);
+	}
+	
+	
+	public ArrayList<String> results=new ArrayList<String>();
+	public String prefix;
+	public String suffix;
+	public String middle;
+	public static final char slash=System.getProperty("file.separator").charAt(0);
+	
+}