Description: Reimplement BufferedRandomAccessFile
 Original implementation partially overriden RandomAccessFile methods.
 This patch provides a replacement implementation that aggregates
 RandomAccessFile and uses the same serialization logic.
 This resolves the dependency on RandomAccessFile implementation
 details.
 The write methods and logic were removed as they are not used in the
 main code.
Author: Vladimir Petko <vladimir.petko@canonical.com>
Bug: https://github.com/rdpstaff/ReadSeq/issues/4
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1128172
Last-Update: 2026-02-25

--- a/src/edu/msu/cme/rdp/readseq/utils/BufferedRandomAccessFile.java
+++ b/src/edu/msu/cme/rdp/readseq/utils/BufferedRandomAccessFile.java
@@ -16,177 +16,239 @@
  */
 package edu.msu.cme.rdp.readseq.utils;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.RandomAccessFile;
+import java.io.*;
+import java.lang.invoke.MethodHandles;
+import java.lang.invoke.VarHandle;
+import java.nio.ByteOrder;
 
 /**
- *
- * @author fishjord
+ * The buffered wrapper around RandomAccessFile.
+ * Original implementation inherited RandomAccessFile and relied on
+ * partially overriding its methods.
+ * This implementation aggregates RandomAccessFile and implements DataInput
+ * using the same serialization logic as RandomAccessFile.
  */
-public class BufferedRandomAccessFile extends RandomAccessFile {
+public class BufferedRandomAccessFile implements DataInput {
 
-    private byte[] buf;
-    private long realPos;
-    private int bufPos;
-    private int bufEnd;
-    private boolean sync = false;
+    private final RandomAccessFile raf;
+    private final byte[] buffer;
+    private long bufferStart;
+    private int bufferLimit;
+    private int bufferPos;
+    private final Converter converter = new Converter();
 
-    public BufferedRandomAccessFile(File f, String mode, int bufSize) throws IOException {
-        super(f, mode);
-        buf = new byte[bufSize];
-        fillBuffer();
-    }
+    // the code is copied from jdk.internal.util.ByteAray
+    private static class Converter {
+        private static final VarHandle INT = create(int[].class);
+        private static final VarHandle LONG = create(long[].class);
+        private final byte[] buffer = new byte[8];
 
-    @Override
-    public int skipBytes(int n) throws IOException{
-        return super.skipBytes(n);
+        private static VarHandle create(Class<?> viewArrayClass) {
+            return MethodHandles.byteArrayViewVarHandle(viewArrayClass, ByteOrder.BIG_ENDIAN);
+        }
+
+        public int getInt(BufferedRandomAccessFile f) throws IOException {
+            f.readFully(this.buffer, 0, 4);
+            return (int) INT.get(this.buffer, 0);
+        }
+
+        public long getLong(BufferedRandomAccessFile f) throws IOException {
+            f.readFully(this.buffer, 0, 8);
+            return (long) LONG.get(this.buffer, 0);
+        }
     }
 
-    @Override
-    public final int read() throws IOException {
-        if (bufPos >= bufEnd) {
-            if (fillBuffer() < 0) {
-                return -1;
-            }
+    public BufferedRandomAccessFile(File name, int bufferSize) throws IOException {
+        if (bufferSize <= 0) {
+            throw new IllegalArgumentException("bufferSize must be > 0, got: " + bufferSize);
         }
+        this.raf = new RandomAccessFile(name, "r");
+        this.buffer = new byte[bufferSize];
+        this.bufferStart = 0;
+        this.bufferLimit = 0;
+        this.bufferPos = 0;
+    }
 
-        if (bufEnd == 0) {
-            return -1;
+
+    public void seek(long pos) throws IOException {
+        if (pos >= bufferStart && pos < bufferStart + bufferLimit) {
+            bufferPos = (int) (pos - bufferStart);
         } else {
-            return buf[bufPos++] & 0xff;
+            raf.seek(pos);
+            bufferStart = pos;
+            bufferLimit = 0;
+            bufferPos = 0;
         }
     }
 
-    @Override
-    public int read(byte b[]) throws IOException {
-        return read(b, 0, b.length);
+    public long getFilePointer() throws IOException {
+        return bufferStart + bufferPos;
     }
 
-    @Override
-    public int read(byte b[], int off, int len) throws IOException {
-        int readCount = 0;
-        for(int index = off;index < len;index++) {
-            int r = this.read();
-            if(r == -1) {
+    public long length() throws IOException {
+        return raf.length();
+    }
+
+    public void close() throws IOException {
+        raf.close();
+    }
+
+    private boolean ensureData() throws IOException {
+        if (bufferPos < bufferLimit) {
+            return true;
+        }
+        long nextFilePos = bufferStart + bufferLimit;
+        raf.seek(nextFilePos);
+        int n = raf.read(buffer);
+        if (n <= 0) {
+            return false;
+        }
+        bufferStart = nextFilePos;
+        bufferLimit = n;
+        bufferPos = 0;
+        return true;
+    }
+
+    private int readBytes(byte[] dest, int off, int len) throws IOException {
+        int remaining = len;
+        int destOff = off;
+        while (remaining > 0) {
+            if (!ensureData()) {
                 break;
             }
-
-            readCount++;
-            b[index] = (byte)r;
+            int available = bufferLimit - bufferPos;
+            int toCopy = Math.min(available, remaining);
+            System.arraycopy(buffer, bufferPos, dest, destOff, toCopy);
+            bufferPos += toCopy;
+            destOff += toCopy;
+            remaining -= toCopy;
         }
-        return readCount;
+        return len - remaining;
     }
 
     @Override
-    public final void write(int b) throws IOException {
-        if (bufPos >= buf.length) {
-            fillBuffer();
+    public void readFully(byte[] b) throws IOException {
+        if (readBytes(b, 0, b.length) != b.length) {
+            throw new EOFException("Could not read fully into buffer");
         }
+    }
 
-        buf[bufPos++] = (byte) b;
-        if (bufPos >= bufEnd) {
-            bufEnd = bufPos;
+    @Override
+    public void readFully(byte[] b, int off, int len) throws IOException {
+        if (off < 0 || len < 0 || off + len > b.length) {
+            throw new IndexOutOfBoundsException();
         }
+        if (readBytes(b, off, len) != len) {
+            throw new EOFException("Could not read fully into buffer");
+        }
+    }
 
-        sync = true;
+    @Override
+    public int skipBytes(int n) throws IOException {
+        if (n <= 0)
+            return 0;
+        long current = getFilePointer();
+        long fileLen = raf.length();
+        long skip = Math.min(n, fileLen - current);
+        if (skip > 0) {
+            seek(current + skip);
+        }
+        return (int) skip;
     }
 
     @Override
-    public long getFilePointer() throws IOException {
-        long l = realPos;
-        return (l - bufEnd + bufPos);
+    public boolean readBoolean() throws IOException {
+        return read() != 0;
     }
 
     @Override
-    public void seek(long pos) throws IOException {
-        int n = (int) (realPos - pos);
+    public byte readByte() throws IOException {
+        return (byte) read();
+    }
+
+    public int read() throws IOException {
+        if (!ensureData()) {
+            return -1;
+        }
+        return buffer[bufferPos++] & 0xFF;
+    }
+
+    public int read(byte[] buf) throws IOException {
+        return readBytes(buf, 0, buf.length);
+    }
 
-        if (n >= 0 && n <= bufEnd) {
-            bufPos = bufEnd - n;
+    @Override
+    public int readUnsignedByte() throws IOException {
+        int ch = this.read();
+        if (ch < 0) {
+            throw new EOFException();
         } else {
-            sync();
-            super.seek(pos);
-            invalidate();
+            return ch;
         }
     }
 
     @Override
-    public void write(byte[] b) throws IOException {
-        throw new UnsupportedOperationException();
+    public short readShort() throws IOException {
+        return (short)this.readUnsignedShort();
     }
 
     @Override
-    public void write(byte b[], int off, int len) throws IOException {
-        throw new UnsupportedOperationException();
+    public int readUnsignedShort() throws IOException {
+        this.readFully(this.buffer, 0, 2);
+        return (this.buffer[1] & 255) + ((this.buffer[0] & 255) << 8);
     }
 
     @Override
-    public void close() throws IOException {
-        sync();
-        super.close();
+    public char readChar() throws IOException {
+        return (char) readUnsignedShort();
     }
 
-    private void sync() throws IOException {
-        if (sync) {
-            super.seek(realPos - bufEnd);
-            super.write(buf, 0, bufEnd);
-            sync = false;
-            //invalidate();
-        }
+    @Override
+    public int readInt() throws IOException {
+        return converter.getInt(this);
     }
 
-    private int fillBuffer() throws IOException {
-        sync();
+    @Override
+    public long readLong() throws IOException {
+        return converter.getLong(this);
+    }
 
-        int n = super.read(buf, 0, buf.length);
-        if (n >= 0) {
-            //System.out.println("Filling buffer...read in " + n + " bytes");
-            realPos += n;
-            bufEnd = n;
-            bufPos = 0;
-        }
-        return n;
+    @Override
+    public float readFloat() throws IOException {
+        return Float.intBitsToFloat(readInt());
     }
 
-    private void invalidate() throws IOException {
-        bufEnd = 0;
-        bufPos = 0;
-        realPos = super.getFilePointer();
+    @Override
+    public double readDouble() throws IOException {
+        return Double.longBitsToDouble(readLong());
     }
 
-    public static void main(String[] args) throws Exception {
+    @Override
+    public String readLine() throws IOException {
+        StringBuilder sb = new StringBuilder();
+        int c;
         try {
-            File file = new File("tmp.bin");
-            if (file.exists()) {
-                file.delete();
+            c = read();
+        } catch (EOFException e) {
+            return null;
+        }
+        while (c != '\n' && c != -1) {
+            if (c != '\r') {
+                sb.append((char) c);
+            }
+            try {
+                c = read();
+            } catch (EOFException e) {
+                break;
             }
-
-            BufferedRandomAccessFile f = new BufferedRandomAccessFile(file, "rw", 1);
-
-            f.writeInt(1);
-            f.writeInt(2);
-            f.writeInt(3);
-            f.writeInt(4);
-            f.writeInt(5);
-
-            f.seek(0);
-
-            System.out.println(f.readInt());
-            System.out.println(f.readInt());
-            f.writeInt(6);
-            System.out.println(f.readInt());
-            System.out.println(f.readInt());
-
-            f.seek(0);
-
-            System.out.println(f.readInt());
-            System.out.println(f.readInt());
-            System.out.println(f.readInt());
-            System.out.println(f.readInt());
-            System.out.println(f.readInt());
-            f.close();
-        } catch (Exception e) {
         }
+        if (sb.isEmpty() && c == -1)
+            return null;
+        return sb.toString();
+    }
+
+    @Override
+    public String readUTF() throws IOException {
+        return DataInputStream.readUTF(this);
     }
 }
--- a/src/edu/msu/cme/rdp/readseq/readers/core/SeqReaderCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/SeqReaderCore.java
@@ -56,11 +56,11 @@
         }
     }
     private boolean seekable;
-    private RandomAccessFile rawRAFile = null;
+    private BufferedRandomAccessFile rawRAFile = null;
     private DataInputStream is = null;
 
     public SeqReaderCore(File seqFile) throws IOException {
-        this.rawRAFile = new BufferedRandomAccessFile(seqFile, "r", 4096);
+        this.rawRAFile = new BufferedRandomAccessFile(seqFile, 4096);
         seekable = true;
     }
 
@@ -69,7 +69,7 @@
         seekable = false;
     }
 
-    protected final RandomAccessFile getRawFile() throws IOException {
+    protected final BufferedRandomAccessFile getRawFile() throws IOException {
         if (!seekable) {
             throw new IOException("Stream seq cores are not seekable");
         }
--- a/src/edu/msu/cme/rdp/readseq/readers/core/STKCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/STKCore.java
@@ -17,6 +17,8 @@
 package edu.msu.cme.rdp.readseq.readers.core;
 
 import edu.msu.cme.rdp.readseq.readers.Sequence;
+import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile;
+
 import java.io.File;
 import java.io.IOException;
 import java.io.RandomAccessFile;
@@ -37,7 +39,7 @@
 
     public STKCore(File f) throws IOException {
         super(f);
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         long firstSeqStart = -1;
 
@@ -103,7 +105,7 @@
 
                 seqid = sid.toString();
             }
-            
+
             if (firstSeqStart == -1) {
                 firstSeqStart = currSeqIndex;
             }
@@ -130,8 +132,8 @@
 
     @Override
     public Sequence readNextSeq() throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
-        
+        BufferedRandomAccessFile seqFile = super.getRawFile();
+
         long seqStart = seqFile.getFilePointer();
 
         String line = seqFile.readLine().trim();
--- a/src/edu/msu/cme/rdp/readseq/readers/core/EMBLCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/EMBLCore.java
@@ -19,6 +19,8 @@
 import edu.msu.cme.rdp.readseq.readers.Sequence;
 import edu.msu.cme.rdp.readseq.SequenceFormat;
 import edu.msu.cme.rdp.readseq.sequences.GenbankSequence;
+import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile;
+
 import java.io.DataOutputStream;
 import java.io.File;
 import java.io.IOException;
@@ -45,7 +47,7 @@
     }
 
     public Map<String, Long> scanInternal() throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         long firstHeader = seqFile.getFilePointer();
@@ -68,7 +70,7 @@
     }
 
     public int scanToStream(DataOutputStream out) throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         long firstHeader = seqFile.getFilePointer();
--- a/src/edu/msu/cme/rdp/readseq/readers/core/SFFCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/SFFCore.java
@@ -17,6 +17,7 @@
 package edu.msu.cme.rdp.readseq.readers.core;
 
 import edu.msu.cme.rdp.readseq.QSequence;
+import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile;
 import edu.msu.cme.rdp.readseq.utils.SeqUtils;
 import java.io.ByteArrayInputStream;
 import java.io.DataInput;
@@ -238,7 +239,7 @@
             return readIndex();
         }
 
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(commonHeader.headerLength);
         LinkedHashMap<String, Long> seqIndex = new LinkedHashMap(commonHeader.numReads);
@@ -270,9 +271,9 @@
             clipRight = readBlock.clipQualRight;
         }
         if (clipLeft  > clipRight )
-           return readNextSeq(); 
+           return readNextSeq();
         String seq = readBlock.seq.substring(clipLeft - 1, clipRight);
-        
+
 
         return new QSequence(readBlock.name, "", seq, Arrays.copyOfRange(readBlock.qual, clipLeft - 1, clipRight));
     }
@@ -354,7 +355,7 @@
             throw new IOException("Index offset is not set correctly");
         }
 
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         long seekBackTo = seqFile.getFilePointer();
         seqFile.seek(commonHeader.indexOffset);
--- a/src/edu/msu/cme/rdp/readseq/readers/core/FastaCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/FastaCore.java
@@ -17,6 +17,7 @@
 package edu.msu.cme.rdp.readseq.readers.core;
 
 import edu.msu.cme.rdp.readseq.readers.Sequence;
+import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile;
 import edu.msu.cme.rdp.readseq.SequenceFormat;
 import java.io.DataOutputStream;
 import java.io.File;
@@ -43,7 +44,7 @@
     }
 
     public Map<String, Long> scanInternal() throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         readUntilNext('>');
@@ -67,7 +68,7 @@
     }
 
     public int scanToStream(DataOutputStream out) throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         readUntilNext('>');
--- a/src/edu/msu/cme/rdp/readseq/readers/core/FastqCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/FastqCore.java
@@ -18,6 +18,7 @@
 
 import edu.msu.cme.rdp.readseq.QSequence;
 import edu.msu.cme.rdp.readseq.readers.Sequence;
+import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile;
 import edu.msu.cme.rdp.readseq.SequenceFormat;
 import java.io.DataOutputStream;
 import java.io.File;
@@ -65,7 +66,7 @@
     }
 
     public Map<String, Long> scanInternal() throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         readUntilNext('@');
@@ -76,10 +77,10 @@
 
         while (seqFile.getFilePointer() != seqFile.length()) {
             String sid = parseSid();
-            seqIndex.put(sid, lastHeader);    
+            seqIndex.put(sid, lastHeader);
             String temp = readUntilNext("\n@");
-            // when @ is the first char of the quality line    
-            String[] lines = temp.split("\n");            
+            // when @ is the first char of the quality line
+            String[] lines = temp.split("\n");
             if ( lines.length == 2){
                 readUntilNext("\n@");
             }
@@ -93,7 +94,7 @@
     }
 
     public int scanToStream(DataOutputStream out) throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         readUntilNext('@');
--- a/src/edu/msu/cme/rdp/readseq/readers/core/GenbankCore.java
+++ b/src/edu/msu/cme/rdp/readseq/readers/core/GenbankCore.java
@@ -17,6 +17,7 @@
 package edu.msu.cme.rdp.readseq.readers.core;
 
 import edu.msu.cme.rdp.readseq.readers.Sequence;
+import edu.msu.cme.rdp.readseq.utils.BufferedRandomAccessFile;
 import edu.msu.cme.rdp.readseq.SequenceFormat;
 import java.io.DataOutputStream;
 import java.io.File;
@@ -43,7 +44,7 @@
     }
 
     public Map<String, Long> scanInternal() throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         long firstHeader = seqFile.getFilePointer();
@@ -66,7 +67,7 @@
     }
 
     public int scanToStream(DataOutputStream out) throws IOException {
-        RandomAccessFile seqFile = super.getRawFile();
+        BufferedRandomAccessFile seqFile = super.getRawFile();
 
         seqFile.seek(0);
         long firstHeader = seqFile.getFilePointer();