--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/MatrixFile.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,88 @@
+package fileIO;
+import dna.Matrix;
+
+
+
+public class MatrixFile extends TextFile{
+	
+	public static void main(String[] args){
+		
+		try {
+			//Name of mat file
+			String name=args[0];
+			
+			MatrixFile mat=new MatrixFile(name);
+			
+			String s=null;
+			
+			for(s=mat.readLine(); s!=null; s=mat.readLine()){
+				System.out.println(s);
+			}
+		} catch (Exception e) {
+			throw new RuntimeException(e);
+		}
+		
+	}
+	
+	
+	public MatrixFile(String name){super(name, false);}
+	
+	@Override
+	public String nextLine(){
+		String line=readLine();
+		
+		while(line!=null && line.charAt(0)!='{' && line.charAt(0)!='/'){
+			line=readLine();
+		}
+		return line;
+	}
+	
+	public Matrix nextMatrix(){
+		String line;
+		String[] split;
+		
+		line=nextLine();
+		if(line==null || line.startsWith("//end")){return null;}
+		
+		assert(line.startsWith("//name: ")) : line;
+		String name=line.replace("//name: ","").trim();
+		
+		line=nextLine();
+		assert(line.startsWith("//size: ")) : line;
+		line=line.replace("//size: ","");
+		split=line.split("x");
+		int length=Integer.parseInt(split[0]);
+		int width=Integer.parseInt(split[1]);
+		
+		line=nextLine();
+		assert(line.startsWith("//prefix: ")) : line;
+		line=line.replace("//prefix: ","");
+		int prefix=Integer.parseInt(line);
+		
+		line=nextLine();
+		assert(line.startsWith("//count: ")) : line;
+		line=line.replace("//count: ","");
+		int count=Integer.parseInt(line);
+		
+		
+		float[][] grid=new float[length][width];
+		for(int i=0; i<length; i++){
+			line=nextLine();
+			
+			while(line.startsWith("//")){line=nextLine();}
+			
+			assert(line.startsWith("{"));
+			if(line.endsWith(",")){line=line.substring(0, line.length()-1);}
+			assert(line.endsWith("}"));
+			line=line.replace("{", "").replace("}", "").replace(" ", "");
+			split=line.split(",");
+			assert(split.length==width);
+			for(int j=0; j<split.length; j++){
+				grid[i][j]=Float.parseFloat(split[j]);
+			}
+		}
+		
+		return new Matrix(grid, prefix, name);
+	}
+	
+}