1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
|
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);
|
