From 6f454662bf3681b55242fa6faf88f92c1078b395 Mon Sep 17 00:00:00 2001
From: tfenne <tfenne@tfenne.com>
Date: Mon, 2 Jul 2018 16:55:27 -0400
Subject: [PATCH] Sketch of basic input io interface.

---
 .gitignore                                    |  25 +---
 build.sc                                      |   5 +
 .../samtools/htsjdk/core/io/ByteSource.java   | 107 ++++++++++++++++++
 3 files changed, 114 insertions(+), 23 deletions(-)
 create mode 100644 build.sc
 create mode 100644 core/src/org/samtools/htsjdk/core/io/ByteSource.java

diff --git a/.gitignore b/.gitignore
index a1c2a23..18fe4bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,23 +1,2 @@
-# Compiled class file
-*.class
-
-# Log file
-*.log
-
-# BlueJ files
-*.ctxt
-
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
-
-# Package Files #
-*.jar
-*.war
-*.nar
-*.ear
-*.zip
-*.tar.gz
-*.rar
-
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
+# Mill output directory
+out/
diff --git a/build.sc b/build.sc
new file mode 100644
index 0000000..d7e83c9
--- /dev/null
+++ b/build.sc
@@ -0,0 +1,5 @@
+import mill._, scalalib._
+
+object core extends JavaModule {
+  
+}
diff --git a/core/src/org/samtools/htsjdk/core/io/ByteSource.java b/core/src/org/samtools/htsjdk/core/io/ByteSource.java
new file mode 100644
index 0000000..9748097
--- /dev/null
+++ b/core/src/org/samtools/htsjdk/core/io/ByteSource.java
@@ -0,0 +1,107 @@
+package org.samtools.htsjdk.core.io;
+
+import java.nio.ByteBuffer;
+
+/**
+ * Interface for classes that produce binary data (i.e. bytes) that can be decoded
+ * into other datatypes.
+ *
+ * Methods should throw exceptions if:
+ * - The underlying data source/stream/channel is closed
+ * - There are insufficient bytes available (after blocking) to read a single item of the datatype requested
+ *
+ * NOTES:
+ *   - Almost all the methods here could have default implementations that read via one of the readBytes() methods.
+ *   - Should think through how to deal with unsigned types
+ *   - Need to think how this would work with BlockCompressed data
+ */
+public interface ByteSource extends AutoCloseable {
+    /** Returns a description of the underlying source of the bytes, e.g. a path, stdin, a URL etc. */
+    String getDescription();
+
+    // Methods related to buffering/repositioning/skipping etc.
+    /** Returns true if the source has a known finite length, false otherwise. */
+    boolean hasLength();
+
+    /** Returns the length if {@link #hasLength()} is true, otherwise throws an exception. */
+    default long length() { throw new UnsupportedOperationException(); }
+
+    /** Returns the offset of the next byte that will be read by any operation. */
+    long position();
+
+    /** Returns true if the source can skip bytes without reading them. */
+    boolean canNavigateForward();
+
+    /** Returns true if the source can always be repositioned behind the current position. Note that a buffered
+     * source may allow limited backwards navigation within the buffered data, while returning false here. */
+    boolean canNavigateBackwards();
+
+    /** Position the source at numBytes after the current position. May be implemented by skipping if the
+     * underlying source is capable of skipping, or by reading and discarding numBytes.
+     *
+     * @param numBytes the number of bytes desired to be skipped.
+     * @return either numBytes or a smaller number if EOF is hit before numBytes is read
+     */
+    int navigateForward(final long numBytes); // TODO: implement default method that reads
+
+    /** Position the source at numBytes before the current position.
+     *
+     * @param numBytes the number of bytes desired to be skipped.
+     * @return either numBytes or a smaller number if numBytes > position
+     */
+    default int navigateBackward(final long numBytes) {
+        throw new UnsupportedOperationException();
+    }
+
+    /** Positions the source such that the next byte read will be at offset `position`. */
+    default int navigateToPosition(final long position) {
+        throw new UnsupportedOperationException();
+    }
+
+    // Methods for actually reading stuff
+
+    /** Attempt to fill the array with bytes and returns the number of bytes read. */
+    int readBytes(final byte[] buffer);
+
+    /** Attempt to fill the regions of the array with bytes and returns the number of bytes read. */
+    int readBytes(final byte[] buffer, final int offset, final int length);
+
+    /** Attempt to read numBytes bytes into the buffer starting at the buffer's current position. */
+    int readBytes(final ByteBuffer buffer, final int numBytes);
+
+    /** Reads a single byte. */
+    byte readByte();
+
+    /** Reads a boolean. */
+    boolean readBoolean();
+
+    /** Reads a little endian signed short. */
+    short readShort();
+
+    /** Reads a little endian signed int. */
+    int readInt();
+
+    /** Reads a little endian signed long. */
+    long readLong();
+
+    /** Reads a little endian unsigned byte. */
+    short readUnsignedByte();
+
+    /** Reads a little endian unsigned short. */
+    int readUnsignedShort();
+
+    /** Reads a little endian unsigned int. */
+    long readUnsignedInt();
+
+    /** Reads a little endian float. */
+    float readFloat();
+
+    /** Reads a little endian double. */
+    double readDouble();
+
+    /** Reads an ascii string, with one-byte per character, of the given length. */
+    String readAsciiString(final int length);
+
+    /** Reads a null-terminated string, with one byte per character, of unknown length. */
+    String readNullTerminatedAsciiString();
+}