Description: using GeneratedMessageV3 from protobuf to replace GeneratedMessage
 The protobuf package has changed quite a bit since the version goby 3.3.1
 relies on was edited.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2021-08-04

--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java
@@ -20,7 +20,7 @@
 
 import com.google.protobuf.ByteString;
 import com.google.protobuf.CodedInputStream;
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import com.google.protobuf.Message;
 import org.campagnelab.goby.compression.*;
 import org.campagnelab.goby.compression.FastArithmeticCoder;
@@ -177,7 +177,7 @@
     }
 
     @Override
-    public GeneratedMessage parse(final InputStream uncompressedStream) throws IOException {
+    public GeneratedMessageV3 parse(final InputStream uncompressedStream) throws IOException {
         final byte[] bytes = IOUtils.toByteArray(uncompressedStream);
         final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);
         codedInput.setSizeLimit(Integer.MAX_VALUE);
--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java
@@ -20,7 +20,7 @@
 
 package org.campagnelab.goby.compression;
 
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import org.campagnelab.goby.exception.GobyRuntimeException;
 import it.unimi.dsi.fastutil.bytes.ByteSet;
 import it.unimi.dsi.fastutil.io.FastBufferedInputStream;
@@ -215,7 +215,7 @@
      * @return True if the input has more entries, False otherwise.
      */
     @Override
-    public boolean hasNext(final GeneratedMessage collection, final int collectionSize) {
+    public boolean hasNext(final GeneratedMessageV3 collection, final int collectionSize) {
         if (collection == null || entryIndex >= collectionSize) {
             if (input != null) {
                 try {
--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java
@@ -20,7 +20,7 @@
 
 package org.campagnelab.goby.compression;
 
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import org.campagnelab.goby.exception.GobyRuntimeException;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
@@ -85,7 +85,7 @@
      * @param collectionSize The size of the current collection (can be zero).
      * @return True if the input has more entries, False otherwise.
      */
-    public boolean hasNext(final GeneratedMessage collection, final int collectionSize) {
+    public boolean hasNext(final GeneratedMessageV3 collection, final int collectionSize) {
         if (collection == null || entryIndex >= collectionSize) {
             if (in == null) {
                 compressedBytes = null;
--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java
@@ -124,7 +124,7 @@
      * @param collectionBuilder The builder prepared with the growing collection of entries.
      * @throws IOException if there was an error writing the entries
      */
-    public void writeAsNeeded(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder) {
+    public void writeAsNeeded(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder) {
 
         writeAsNeeded(collectionBuilder, 1);
     }
@@ -139,7 +139,7 @@
      *                          was just appended.
      * @throws IOException if there was an error writing the entries
      */
-    public synchronized  long writeAsNeeded(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder,
+    public synchronized  long writeAsNeeded(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder,
                               final int multiplicity) {
         totalEntriesWritten += Math.max(1, multiplicity);
         if (++numAppended >= numEntriesPerChunk) {
@@ -162,7 +162,7 @@
      *
      * @param collectionBuilder The builder prepared with the growing collection of entries.
      */
-    public synchronized void flush(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder) {
+    public synchronized void flush(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder) {
         // Write the separation between two chunks: eight bytes with value 0xFF.
 
         // If we are flushing a completely empty file, that's OK, the flush() should occur.
@@ -221,7 +221,7 @@
      * @param collectionBuilder The builder prepared with the growing collection of entries.
      * @throws IOException if there is a problem closing the stream unerlying stream
      */
-    public void close(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder)
+    public void close(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder)
             throws IOException {
         flush(collectionBuilder);
         out.writeByte(0xFF);  // termination codec is always GZIP
--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/ProtobuffCollectionHandler.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/ProtobuffCollectionHandler.java
@@ -18,7 +18,7 @@
 
 package org.campagnelab.goby.compression;
 
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import com.google.protobuf.Message;
 
 import java.io.ByteArrayOutputStream;
@@ -46,7 +46,7 @@
      */
     public int getType();
 
-    public GeneratedMessage parse(InputStream uncompressedStream) throws IOException;
+    public GeneratedMessageV3 parse(InputStream uncompressedStream) throws IOException;
 
     /**
      * Transform a collection to a stream of compressed bits, and return the left-over collection.
--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.java
@@ -1,7 +1,7 @@
 package org.campagnelab.goby.compression;
 
 import com.google.protobuf.CodedInputStream;
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import com.google.protobuf.Message;
 import org.apache.commons.io.IOUtils;
 
@@ -21,7 +21,7 @@
     }
 
     @Override
-    public GeneratedMessage parse(final InputStream compressedBytes) throws IOException {
+    public GeneratedMessageV3 parse(final InputStream compressedBytes) throws IOException {
         final byte[] bytes = IOUtils.toByteArray(compressedBytes);
         final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);
         codedInput.setSizeLimit(Integer.MAX_VALUE);
--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.java
@@ -1,7 +1,7 @@
 package org.campagnelab.goby.compression;
 
 import com.google.protobuf.CodedInputStream;
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import com.google.protobuf.Message;
 import org.apache.commons.io.IOUtils;
 import org.campagnelab.dl.varanalysis.protobuf.BaseInformationRecords;
@@ -27,7 +27,7 @@
     }
 
     @Override
-    public GeneratedMessage parse(InputStream uncompressedStream) throws IOException {
+    public GeneratedMessageV3 parse(InputStream uncompressedStream) throws IOException {
         final byte[] bytes = IOUtils.toByteArray(uncompressedStream);
         final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);
         codedInput.setSizeLimit(Integer.MAX_VALUE);
--- a/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.java
@@ -19,7 +19,7 @@
 package org.campagnelab.goby.reads;
 
 import com.google.protobuf.CodedInputStream;
-import com.google.protobuf.GeneratedMessage;
+import com.google.protobuf.GeneratedMessageV3;
 import com.google.protobuf.Message;
 import org.campagnelab.goby.compression.ProtobuffCollectionHandler;
 import org.apache.commons.io.IOUtils;
@@ -42,7 +42,7 @@
     }
 
     @Override
-    public GeneratedMessage parse(final InputStream compressedBytes) throws IOException {
+    public GeneratedMessageV3 parse(final InputStream compressedBytes) throws IOException {
         final byte[] bytes = IOUtils.toByteArray(compressedBytes);
         final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);
         codedInput.setSizeLimit(Integer.MAX_VALUE);