/**
* Check equality of the substring of given length of this object starting at zero with another
* {@code LiteralByteString} substring starting at offset.
*
* @param other what to compare a substring in
* @param offset offset into other
* @param length number of bytes to compare
* @return true for equality of substrings, else false.
*/
@Override
final boolean equalsRange(ByteString other, int offset, int length) {
if (length > other.size()) {
throw new IllegalArgumentException("Length too large: " + length + size());
}
if (offset + length > other.size()) {
throw new IllegalArgumentException(
"Ran off end of other: " + offset + ", " + length + ", " + other.size());
}
if (other instanceof LiteralByteString) {
LiteralByteString lbsOther = (LiteralByteString) other;
byte[] thisBytes = bytes;
byte[] otherBytes = lbsOther.bytes;
int thisLimit = getOffsetIntoBytes() + length;
for (int thisIndex = getOffsetIntoBytes(),
otherIndex = lbsOther.getOffsetIntoBytes() + offset;
(thisIndex < thisLimit);
++thisIndex, ++otherIndex) {
if (thisBytes[thisIndex] != otherBytes[otherIndex]) {
return false;
}
}
return true;
}
return other.substring(offset, offset + length).equals(substring(0, length));
}
/**
* Concatenate the given {@code ByteString} to this one. Short concatenations, of total size
* smaller than {@link ByteString#CONCATENATE_BY_COPY_SIZE}, are produced by copying the
* underlying bytes (as per Rope.java, <a
* href="http://www.cs.ubc.ca/local/reading/proceedings/spe91-95/spe/vol25/issue12/spe986.pdf">
* BAP95 </a>. In general, the concatenate involves no copying.
*
* @param other string to concatenate
* @return a new {@code ByteString} instance
*/
public final ByteString concat(ByteString other) {
if (Integer.MAX_VALUE - size() < other.size()) {
throw new IllegalArgumentException(
"ByteString would be too long: " + size() + "+" + other.size());
}
return RopeByteString.concatenate(this, other);
}
/**
* Concatenate the given {@code ByteString} to this one. Short concatenations, of total size
* smaller than {@link ByteString#CONCATENATE_BY_COPY_SIZE}, are produced by copying the
* underlying bytes (as per Rope.java, <a
* href="http://www.cs.ubc.ca/local/reading/proceedings/spe91-95/spe/vol25/issue12/spe986.pdf">
* BAP95 </a>. In general, the concatenate involves no copying.
*
* @param other string to concatenate
* @return a new {@code ByteString} instance
*/
public ByteString concat(ByteString other) {
int thisSize = size();
int otherSize = other.size();
if ((long) thisSize + otherSize >= Integer.MAX_VALUE) {
throw new IllegalArgumentException(
"ByteString would be too long: " + thisSize + "+" + otherSize);
}
return RopeByteString.concatenate(this, other);
}
public void testSerialization() throws Exception {
TestAllTypes message = TestUtil.getAllSet();
ByteString rawBytes = message.toByteString();
assertEquals(rawBytes.size(), message.getSerializedSize());
TestAllTypes message2 = TestAllTypes.parseFrom(rawBytes);
TestUtil.assertAllFieldsSet(message2);
}
public FollowerToSnapshot(ByteString snapshotBytes) {
this.snapshotBytes = snapshotBytes;
int size = snapshotBytes.size();
totalChunks =
(size / context.getConfigParams().getSnapshotChunkSize())
+ ((size % context.getConfigParams().getSnapshotChunkSize()) > 0 ? 1 : 0);
if (LOG.isDebugEnabled()) {
LOG.debug("{}: Snapshot {} bytes, total chunks to send:{}", logName(), size, totalChunks);
}
replyReceivedForOffset = -1;
chunkIndex = AbstractLeader.FIRST_CHUNK_INDEX;
}
public void testSerializeExtensions() throws Exception {
// TestAllTypes and TestAllExtensions should have compatible wire formats,
// so if we serealize a TestAllExtensions then parse it as TestAllTypes
// it should work.
TestAllExtensions message = TestUtil.getAllExtensionsSet();
ByteString rawBytes = message.toByteString();
assertEquals(rawBytes.size(), message.getSerializedSize());
TestAllTypes message2 = TestAllTypes.parseFrom(rawBytes);
TestUtil.assertAllFieldsSet(message2);
}
/**
* Acccepts snaphot as ByteString, enters into map for future chunks creates and return a
* ByteString chunk
*/
private ByteString getNextSnapshotChunk(String followerId, ByteString snapshotBytes)
throws IOException {
FollowerToSnapshot followerToSnapshot = mapFollowerToSnapshot.get(followerId);
if (followerToSnapshot == null) {
followerToSnapshot = new FollowerToSnapshot(snapshotBytes);
mapFollowerToSnapshot.put(followerId, followerToSnapshot);
}
ByteString nextChunk = followerToSnapshot.getNextChunk();
LOG.debug(
"{}: next snapshot chunk size for follower {}: {}",
logName(),
followerId,
nextChunk.size());
return nextChunk;
}
/**
* Tests if this bytestring ends with the specified suffix. Similar to {@link
* String#endsWith(String)}
*
* @param suffix the suffix.
* @return <code>true</code> if the byte sequence represented by the argument is a suffix of the
* byte sequence represented by this string; <code>false</code> otherwise.
*/
public final boolean endsWith(ByteString suffix) {
return size() >= suffix.size() && substring(size() - suffix.size()).equals(suffix);
}
/**
* Tests if this bytestring starts with the specified prefix. Similar to {@link
* String#startsWith(String)}
*
* @param prefix the prefix.
* @return <code>true</code> if the byte sequence represented by the argument is a prefix of the
* byte sequence represented by this string; <code>false</code> otherwise.
*/
public final boolean startsWith(ByteString prefix) {
return size() >= prefix.size() && substring(0, prefix.size()).equals(prefix);
}
@Override
public int write(ByteBuffer bb) {
ByteString b = reviveInDungeonResponseProto.toByteString();
b.copyTo(bb);
return b.size();
}
@Override
public int write(ByteBuffer bb) {
ByteString b = buildConsumableResponseProto.toByteString();
b.copyTo(bb);
return b.size();
}
@Override
public int write(ByteBuffer bb) {
ByteString b = retractRequestJoinClanResponseProto.toByteString();
b.copyTo(bb);
return b.size();
}
@Override
public int write(ByteBuffer bb) {
ByteString b = recordClanRaidStatsResponseProto.toByteString();
b.copyTo(bb);
return b.size();
}
@Override
public int write(ByteBuffer bb) {
ByteString b = forceLogoutResponseProto.toByteString();
b.copyTo(bb);
return b.size();
}
@GuardedBy("lock")
private void receiveVersionMessage(Protos.TwoWayChannelMessage msg) throws VerificationException {
checkState(step == InitStep.WAITING_ON_CLIENT_VERSION && msg.hasClientVersion());
final Protos.ClientVersion clientVersion = msg.getClientVersion();
final int major = clientVersion.getMajor();
if (major != SERVER_MAJOR_VERSION) {
error(
"This server needs protocol version "
+ SERVER_MAJOR_VERSION
+ " , client offered "
+ major,
Protos.Error.ErrorCode.NO_ACCEPTABLE_VERSION,
CloseReason.NO_ACCEPTABLE_VERSION);
return;
}
Protos.ServerVersion.Builder versionNegotiationBuilder =
Protos.ServerVersion.newBuilder()
.setMajor(SERVER_MAJOR_VERSION)
.setMinor(SERVER_MINOR_VERSION);
conn.sendToClient(
Protos.TwoWayChannelMessage.newBuilder()
.setType(Protos.TwoWayChannelMessage.MessageType.SERVER_VERSION)
.setServerVersion(versionNegotiationBuilder)
.build());
ByteString reopenChannelContractHash = clientVersion.getPreviousChannelContractHash();
if (reopenChannelContractHash != null && reopenChannelContractHash.size() == 32) {
Sha256Hash contractHash = new Sha256Hash(reopenChannelContractHash.toByteArray());
log.info("New client that wants to resume {}", contractHash);
StoredPaymentChannelServerStates channels =
(StoredPaymentChannelServerStates)
wallet.getExtensions().get(StoredPaymentChannelServerStates.EXTENSION_ID);
if (channels != null) {
StoredServerChannel storedServerChannel = channels.getChannel(contractHash);
if (storedServerChannel != null) {
final PaymentChannelServer existingHandler =
storedServerChannel.setConnectedHandler(this, false);
if (existingHandler != this) {
log.warn(" ... and that channel is already in use, disconnecting other user.");
existingHandler.close();
storedServerChannel.setConnectedHandler(this, true);
}
log.info("Got resume version message, responding with VERSIONS and CHANNEL_OPEN");
state = storedServerChannel.getOrCreateState(wallet, broadcaster);
step = InitStep.CHANNEL_OPEN;
conn.sendToClient(
Protos.TwoWayChannelMessage.newBuilder()
.setType(Protos.TwoWayChannelMessage.MessageType.CHANNEL_OPEN)
.build());
conn.channelOpen(contractHash);
return;
} else {
log.error(" ... but we do not have any record of that contract! Resume failed.");
}
} else {
log.error(" ... but we do not have any stored channels! Resume failed.");
}
}
log.info(
"Got initial version message, responding with VERSIONS and INITIATE: min value={}",
minAcceptedChannelSize.value);
myKey = new ECKey();
wallet.freshReceiveKey();
expireTime = Utils.currentTimeSeconds() + truncateTimeWindow(clientVersion.getTimeWindowSecs());
step = InitStep.WAITING_ON_UNSIGNED_REFUND;
Protos.Initiate.Builder initiateBuilder =
Protos.Initiate.newBuilder()
.setMultisigKey(ByteString.copyFrom(myKey.getPubKey()))
.setExpireTimeSecs(expireTime)
.setMinAcceptedChannelSize(minAcceptedChannelSize.value)
.setMinPayment(Transaction.REFERENCE_DEFAULT_MIN_TX_FEE.value);
conn.sendToClient(
Protos.TwoWayChannelMessage.newBuilder()
.setInitiate(initiateBuilder)
.setType(Protos.TwoWayChannelMessage.MessageType.INITIATE)
.build());
}
/**
* Construct alignment blocks from the Goby alignment entry. This method uses the convention that
* '=' denotes a match to the reference.
*
* <p>Conventions for storing sequence variations in Goby alignments are described <a
* href="http://tinyurl.com/goby-sequence-variations">here</a>
*
* @param alignmentEntry The Goby alignment entry to use
*/
public void buildBlocks(Alignments.AlignmentEntry alignmentEntry) {
ObjectArrayList<AlignmentBlock> blocks = new ObjectArrayList<AlignmentBlock>();
ObjectArrayList<AlignmentBlock> insertionBlocks = new ObjectArrayList<AlignmentBlock>();
int start = alignmentEntry.getPosition();
ByteArrayList bases = new ByteArrayList();
ByteArrayList scores = new ByteArrayList();
int readLength = alignmentEntry.getQueryLength();
byte[] readBases = new byte[readLength];
byte[] readQual = new byte[readLength];
Arrays.fill(readBases, (byte) '=');
if (alignmentEntry.hasReadQualityScores()) {
readQual = alignmentEntry.getReadQualityScores().toByteArray();
} else {
Arrays.fill(readQual, (byte) 40);
}
int j = 0;
int insertedBases = 0;
int deletedBases = 0;
final int leftPadding = alignmentEntry.getQueryPosition();
boolean showSoftClipped =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SAM_SHOW_SOFT_CLIPPED);
if (showSoftClipped && entry.hasSoftClippedBasesLeft()) {
int clipLength = entry.getSoftClippedBasesLeft().length();
addSoftClipBlock(
blocks,
Math.max(0, entry.getPosition() - clipLength),
entry.getSoftClippedBasesLeft(),
readQual,
entry.hasSoftClippedQualityLeft(),
entry.getSoftClippedQualityLeft().toByteArray(),
0);
}
for (Alignments.SequenceVariation var : alignmentEntry.getSequenceVariationsList()) {
final String from = var.getFrom();
final int fromLength = from.length();
final String to = var.getTo();
final int toLength = from.length();
final int sequenceVariationLength = Math.max(fromLength, toLength);
final ByteString toQuality = var.getToQuality();
if (hasReadInsertion(from)) {
bases.clear();
scores.clear();
for (int i = 0; i < sequenceVariationLength; i++) {
final char toChar = i >= toLength ? '-' : to.charAt(i);
int size = toQuality.size();
final byte qual = size > 0 && i < size ? toQuality.byteAt(i) : 40;
bases.add((byte) toChar);
scores.add(qual);
deletedBases++;
}
addBlock(insertionBlocks, alignmentEntry.getPosition() + var.getPosition(), bases, scores);
bases.clear();
scores.clear();
} else if (!to.contains("-")) {
for (int i = 0; i < toLength; i++) {
final int offset = j + var.getPosition() + i - 1 + leftPadding - insertedBases;
if (offset > 0 && offset < readBases.length) {
readBases[offset] = (byte) to.charAt(i);
if (i < toQuality.size()) {
readQual[offset] = toQuality.byteAt(i);
}
}
}
} else {
// has read deletion:
insertedBases++;
}
}
int pos = start;
int matchLength = alignmentEntry.getQueryAlignedLength() - deletedBases;
int endAlignmentRefPosition = matchLength + start;
bases.clear();
scores.clear();
int maxIndex = Math.min(readBases.length, readQual.length);
while (pos < endAlignmentRefPosition) {
final int index = pos - start + leftPadding;
if (index < maxIndex) {
bases.add(readBases[index]);
scores.add(readQual[index]);
} else {
break;
}
++pos;
}
addBlock(blocks, start, bases, scores);
blocks = introduceDeletions(blocks, entry);
if (showSoftClipped && entry.hasSoftClippedBasesRight()) {
int targetAlignedLength = entry.getTargetAlignedLength();
addSoftClipBlock(
blocks,
entry.getPosition() + targetAlignedLength,
entry.getSoftClippedBasesRight(),
readQual,
entry.hasSoftClippedQualityRight(),
entry.getSoftClippedQualityRight().toByteArray(),
entry.getQueryAlignedLength() + entry.getSoftClippedBasesLeft().length());
}
block = blocks.toArray(new AlignmentBlock[blocks.size()]);
Arrays.sort(block, blockComparator);
insertionBlock = insertionBlocks.toArray(new AlignmentBlock[insertionBlocks.size()]);
Arrays.sort(insertionBlock, blockComparator);
ObjectArrayList<GobyAlignment> list = null;
if (alignmentEntry.hasSplicedForwardAlignmentLink()
|| alignmentEntry.hasSplicedBackwardAlignmentLink()) {
// if has a forward link, store a reference to this alignment in the reader (which represents
// the window scope)
list = iterator.cacheSpliceComponent(this);
if (list.size() > 1 && spliceListIsValid(list)) {
final GobyAlignment spliceHeadAlignment = list.get(0);
ObjectArrayList<AlignmentBlock> splicedBlocks = new ObjectArrayList<AlignmentBlock>();
splicedBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.block));
splicedBlocks.addAll(blocks);
spliceHeadAlignment.block = splicedBlocks.toArray(new AlignmentBlock[splicedBlocks.size()]);
ObjectArrayList<AlignmentBlock> splicedInsertionBlocks =
new ObjectArrayList<AlignmentBlock>();
splicedInsertionBlocks.addAll(ObjectArrayList.wrap(spliceHeadAlignment.insertionBlock));
splicedInsertionBlocks.addAll(insertionBlocks);
spliceHeadAlignment.insertionBlock =
splicedInsertionBlocks.toArray(new AlignmentBlock[splicedInsertionBlocks.size()]);
if (spliceHeadAlignment.gapTypes == null) {
spliceHeadAlignment.gapTypes = new CharArrayList(10);
}
spliceHeadAlignment.gapTypes.add(SamAlignment.SKIPPED_REGION);
// Since the previous alignment carries this information, we clear up block and
// insertionBlock
// in this alignment, but keep any softClips:
this.block = keepSoftClips(block);
this.insertionBlock = new AlignmentBlock[0];
}
}
}
