//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"name != null", "! ( location == null && output == null )", "! ( enableOnTheFlyIndexing && location == null )"}) protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal IndexingVariantContextWriter(string name, File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing)
{
outputStream = output;
this.name = name;
this.refDict = refDict;
if (enableOnTheFlyIndexing)
{
try
{
idxStream = new LittleEndianOutputStream(new FileOutputStream(Tribble.indexFile(location)));
//System.out.println("Creating index on the fly for " + location);
indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
indexer.initialize(location, indexer.defaultBinSize());
positionalOutputStream = new PositionalOutputStream(output);
outputStream = positionalOutputStream;
}
catch (IOException ex)
{
// No matter what we keep going, since we don't care if we can't create the index file
idxStream = null;
indexer = null;
positionalOutputStream = null;
}
}
}
public void TestFormatRun()
{
UnicodeString.FormatRun fr = new UnicodeString.FormatRun((short)4, (short)0x15c);
Assert.AreEqual(4, fr.CharacterPos);
Assert.AreEqual(0x15c, fr.FontIndex);
MemoryStream baos = new MemoryStream();
LittleEndianOutputStream out1 = new LittleEndianOutputStream(baos);
fr.Serialize(out1);
byte[] b = baos.ToArray();
Assert.AreEqual(4, b.Length);
Assert.AreEqual(4, b[0]);
Assert.AreEqual(0, b[1]);
Assert.AreEqual(0x5c, b[2]);
Assert.AreEqual(0x01, b[3]);
LittleEndianInputStream inp = new LittleEndianInputStream(
new MemoryStream(b)
);
fr = new UnicodeString.FormatRun(inp);
Assert.AreEqual(4, fr.CharacterPos);
Assert.AreEqual(0x15c, fr.FontIndex);
}
public void ProcessPOIFSWriterEvent(POIFSWriterEvent event1)
{
try
{
LittleEndianOutputStream leos = new LittleEndianOutputStream(event1.Stream);
// StreamSize (8 bytes): An unsigned integer that specifies the number of bytes used by data
// encrypted within the EncryptedData field, not including the size of the StreamSize field.
// Note that the actual size of the \EncryptedPackage stream (1) can be larger than this
// value, depending on the block size of the chosen encryption algorithm
leos.WriteLong(countBytes);
long rawPos = rawStream.Position;
//FileStream fis = new FileStream(fileOut.FullName, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
IOUtils.Copy(rawStream, leos.out1);
//fis.Close();
rawStream.Position = rawPos;
//File.Delete(fileOut.FullName + ".copy");
fileOut.Delete();
leos.Close();
}
catch (IOException e)
{
throw new EncryptedDocumentException(e);
}
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"name != null", "! ( location == null && output == null )", "! ( enableOnTheFlyIndexing && location == null )"}) protected IndexingVariantContextWriter(final String name, final File location, final OutputStream output, final net.sf.samtools.SAMSequenceDictionary refDict, final boolean enableOnTheFlyIndexing)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal IndexingVariantContextWriter(string name, File location, OutputStream output, SAMSequenceDictionary refDict, bool enableOnTheFlyIndexing)
{
outputStream = output;
this.name = name;
this.refDict = refDict;
if (enableOnTheFlyIndexing)
{
try
{
idxStream = new LittleEndianOutputStream(new FileOutputStream(Tribble.indexFile(location)));
//System.out.println("Creating index on the fly for " + location);
indexer = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
indexer.initialize(location, indexer.defaultBinSize());
positionalOutputStream = new PositionalOutputStream(output);
outputStream = positionalOutputStream;
}
catch (IOException ex)
{
// No matter what we keep going, since we don't care if we can't create the index file
idxStream = null;
indexer = null;
positionalOutputStream = null;
}
}
}
private void TestReadWrite(byte[] data, string message)
{
RecordInputStream is1 = TestcaseRecordInputStream.Create(81, data);
DConRefRecord d = new DConRefRecord(is1);
MemoryStream bos = new MemoryStream(data.Length);
LittleEndianOutputStream o = new LittleEndianOutputStream(bos);
d.Serialize(o);
o.Flush();
Assert.IsTrue(Arrays.Equals(data, bos.ToArray()), message);
}
/**
* Have the contents printer out into an OutputStream, used when writing a
* file back out to disk (Normally, atom classes will keep their bytes
* around, but non atom classes will just request the bytes from their
* children, then chuck on their header and return)
*/
public void WriteOut(Stream out1)
{
byte[] intbuf = new byte[LittleEndianConsts.INT_SIZE];
byte[] shortbuf = new byte[LittleEndianConsts.SHORT_SIZE];
byte[] zerobuf = { 0, 0, 0, 0 };
LittleEndianOutputStream leosOut = new LittleEndianOutputStream(out1);
switch (mode)
{
case EncodingMode.parsed:
{
MemoryStream bos = new MemoryStream();
LittleEndianOutputStream leos = new LittleEndianOutputStream(bos);
// total size, will be determined later ..
leos.WriteShort(Flags1);
leos.Write(Encoding.GetEncoding(ISO1).GetBytes(Label));
leos.WriteByte(0);
leos.Write(Encoding.GetEncoding(ISO1).GetBytes(FileName));
leos.WriteByte(0);
leos.WriteShort(Flags2);
leos.WriteShort(Unknown1);
leos.WriteInt(Command.Length + 1);
leos.Write(Encoding.GetEncoding(ISO1).GetBytes(Command));
leos.WriteByte(0);
leos.WriteInt(DataSize);
leos.Write(DataBuffer);
leos.WriteShort(Flags3);
//leos.Close(); // satisfy compiler ...
leosOut.WriteInt((int)bos.Length); // total size
bos.WriteTo(out1);
break;
}
case EncodingMode.compact:
leosOut.WriteInt(DataSize + LittleEndianConsts.SHORT_SIZE);
leosOut.WriteShort(Flags1);
out1.Write(DataBuffer, 0, DataBuffer.Length);
break;
default:
case EncodingMode.unparsed:
leosOut.WriteInt(DataSize);
out1.Write(DataBuffer, 0, DataBuffer.Length);
break;
}
}
public void TestStore()
{
CellRangeAddress cref = new CellRangeAddress(0, 0, 0, 0);
byte[] recordBytes;
//ByteArrayOutputStream baos = new ByteArrayOutputStream();
MemoryStream baos = new MemoryStream();
LittleEndianOutputStream output = new LittleEndianOutputStream(baos);
try
{
// With nothing set
cref.Serialize(output);
recordBytes = baos.ToArray();
Assert.AreEqual(recordBytes.Length, data.Length);
for (int i = 0; i < data.Length; i++)
{
Assert.AreEqual(0, recordBytes[i], "At offset " + i);
}
// Now set the flags
cref.FirstRow = ((short)2);
cref.LastRow = ((short)4);
cref.FirstColumn = ((short)0);
cref.LastColumn = ((short)3);
// Re-test
//baos.reset();
baos.Seek(0, SeekOrigin.Begin);
cref.Serialize(output);
recordBytes = baos.ToArray();
Assert.AreEqual(recordBytes.Length, data.Length);
for (int i = 0; i < data.Length; i++)
{
Assert.AreEqual(data[i], recordBytes[i], "At offset " + i);
}
}
finally
{
//output.Close();
}
}
public void TestRead()
{
MemoryStream baos = new MemoryStream();
ILittleEndianOutput leo = new LittleEndianOutputStream(baos);
leo.WriteInt(12345678);
leo.WriteShort(12345);
leo.WriteByte(123);
leo.WriteShort(40000);
leo.WriteByte(200);
leo.WriteLong(1234567890123456789L);
leo.WriteDouble(123.456);
ILittleEndianInput lei = new LittleEndianInputStream(new MemoryStream(baos.ToArray()));
Assert.AreEqual(12345678, lei.ReadInt());
Assert.AreEqual(12345, lei.ReadShort());
Assert.AreEqual(123, lei.ReadByte());
Assert.AreEqual(40000, lei.ReadUShort());
Assert.AreEqual(200, lei.ReadUByte());
Assert.AreEqual(1234567890123456789L, lei.ReadLong());
Assert.AreEqual(123.456, lei.ReadDouble(), 0.0);
}
public void TestExtRstFromEmpty()
{
UnicodeString.ExtRst ext = new UnicodeString.ExtRst();
Assert.AreEqual(0, ext.NumberOfRuns);
Assert.AreEqual(0, ext.FormattingFontIndex);
Assert.AreEqual(0, ext.FormattingOptions);
Assert.AreEqual("", ext.PhoneticText);
Assert.AreEqual(0, ext.PhRuns.Length);
Assert.AreEqual(10, ext.DataSize); // Excludes 4 byte header
MemoryStream baos = new MemoryStream();
LittleEndianOutputStream out1 = new LittleEndianOutputStream(baos);
ContinuableRecordOutput cout = new ContinuableRecordOutput(out1, 0xffff);
ext.Serialize(cout);
cout.WriteContinue();
byte[] b = baos.ToArray();
Assert.AreEqual(20, b.Length);
// First 4 bytes from the outputstream
Assert.AreEqual(-1, (sbyte)b[0]);
Assert.AreEqual(-1, (sbyte)b[1]);
Assert.AreEqual(14, b[2]);
Assert.AreEqual(00, b[3]);
// Reserved
Assert.AreEqual(1, b[4]);
Assert.AreEqual(0, b[5]);
// Data size
Assert.AreEqual(10, b[6]);
Assert.AreEqual(00, b[7]);
// Font*2
Assert.AreEqual(0, b[8]);
Assert.AreEqual(0, b[9]);
Assert.AreEqual(0, b[10]);
Assert.AreEqual(0, b[11]);
// 0 Runs
Assert.AreEqual(0, b[12]);
Assert.AreEqual(0, b[13]);
// Size=0, *2
Assert.AreEqual(0, b[14]);
Assert.AreEqual(0, b[15]);
Assert.AreEqual(0, b[16]);
Assert.AreEqual(0, b[17]);
// Last 2 bytes from the outputstream
Assert.AreEqual(ContinueRecord.sid, b[18]);
Assert.AreEqual(0, b[19]);
// Load in again and re-test
byte[] data = new byte[14];
Array.Copy(b, 4, data, 0, data.Length);
LittleEndianInputStream inp = new LittleEndianInputStream(
new MemoryStream(data)
);
ext = new UnicodeString.ExtRst(inp, data.Length);
Assert.AreEqual(0, ext.NumberOfRuns);
Assert.AreEqual(0, ext.FormattingFontIndex);
Assert.AreEqual(0, ext.FormattingOptions);
Assert.AreEqual("", ext.PhoneticText);
Assert.AreEqual(0, ext.PhRuns.Length);
}
