finishm 0.0.1
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- data/lib/assembly/a_b_visualiser.rb +169 -0
- data/lib/assembly/acyclic_connection_finder.rb +81 -0
- data/lib/assembly/all_orfs.rb +615 -0
- data/lib/assembly/bad_format_writer.rb +46 -0
- data/lib/assembly/bam_probe_read_selector.rb +48 -0
- data/lib/assembly/bubbly_assembler.rb +842 -0
- data/lib/assembly/c_probe_node_finder.rb +38 -0
- data/lib/assembly/connection_interpreter.rb +350 -0
- data/lib/assembly/contig_printer.rb +400 -0
- data/lib/assembly/coverage_based_graph_filter.rb +68 -0
- data/lib/assembly/depth_first_search.rb +63 -0
- data/lib/assembly/dijkstra.rb +216 -0
- data/lib/assembly/fluffer.rb +253 -0
- data/lib/assembly/graph_explorer.rb +85 -0
- data/lib/assembly/graph_generator.rb +315 -0
- data/lib/assembly/height_finder.rb +355 -0
- data/lib/assembly/hybrid_velvet_graph.rb +70 -0
- data/lib/assembly/input_genome.rb +182 -0
- data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
- data/lib/assembly/node_finder.rb +171 -0
- data/lib/assembly/oriented_node_trail.rb +507 -0
- data/lib/assembly/paired_end_assembler.rb +53 -0
- data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
- data/lib/assembly/probed_graph.rb +105 -0
- data/lib/assembly/read_input.rb +79 -0
- data/lib/assembly/read_to_node.rb +37 -0
- data/lib/assembly/scaffold_breaker.rb +126 -0
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- data/lib/external/VERSION +1 -0
- data/lib/finishm/assemble.rb +224 -0
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- data/lib/finishm/finisher.rb +303 -0
- data/lib/finishm/fluff.rb +122 -0
- data/lib/finishm/gapfiller.rb +325 -0
- data/lib/finishm/orfs_finder.rb +88 -0
- data/lib/finishm/path_counter.rb +90 -0
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- data/lib/finishm/primers_check.rb +176 -0
- data/lib/finishm/roundup.rb +344 -0
- data/lib/finishm/sequence.rb +142 -0
- data/lib/finishm/visualise.rb +430 -0
- data/lib/finishm/wander.rb +270 -0
- data/lib/kmer_abundance_pattern.rb +79 -0
- data/lib/kmer_multi_abundance_file.rb +48 -0
- data/lib/oligo_designer.rb +88 -0
- data/lib/priner.rb +66 -0
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- data/spec/all_orfs_spec.rb +443 -0
- data/spec/assemble_spec.rb +186 -0
- data/spec/bubbly_assembler_spec.rb +707 -0
- data/spec/c_node_finder_spec.rb +58 -0
- data/spec/connection_interpreter_spec.rb +284 -0
- data/spec/contig_printer_spec.rb +291 -0
- data/spec/coverage_based_graph_filter_spec.rb +102 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
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- data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
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- data/spec/data/assembly_visualiser/Graph +46 -0
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- data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
- data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
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- data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
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- data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
- data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
- data/spec/data/kmers_count1.csv +2 -0
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- data/spec/data/out +3 -0
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- data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
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- data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
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- data/spec/fluffer_spec.rb +155 -0
- data/spec/gapfiller_spec.rb +107 -0
- data/spec/graph_explorer_spec.rb +475 -0
- data/spec/graph_generator_spec.rb +99 -0
- data/spec/height_finder_spec.rb +306 -0
- data/spec/kmer_abundance_pattern_spec.rb +56 -0
- data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
- data/spec/kmer_profile_finder_spec.rb +38 -0
- data/spec/kmers_count_tabulate_spec.rb +120 -0
- data/spec/oriented_node_trail_spec.rb +221 -0
- data/spec/paired_end_neighbours_spec.rb +126 -0
- data/spec/paths_between_nodes_spec.rb +349 -0
- data/spec/priner_spec.rb +7 -0
- data/spec/read_input_spec.rb +23 -0
- data/spec/read_selection_by_kmer_spec.rb +166 -0
- data/spec/read_to_node_spec.rb +35 -0
- data/spec/roundup_spec.rb +366 -0
- data/spec/scaffold_breaker_spec.rb +144 -0
- data/spec/sequence_spec.rb +43 -0
- data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
- data/spec/single_coherent_wanderer_spec.rb +120 -0
- data/spec/single_ended_assembler_spec.rb +398 -0
- data/spec/spec_helper.rb +310 -0
- data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
- data/spec/visualise_spec.rb +105 -0
- data/spec/wander_spec.rb +119 -0
- data/spec/watch_for_changes.sh +16 -0
- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
- metadata +899 -0
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// � Copyright Henrik Ravn 2004
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// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
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//
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using System;
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using System.Diagnostics;
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namespace DotZLib
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internal class CircularBuffer
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#region Private data
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public int Get(byte[] destination, int offset, int count)
|
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{
|
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int trueCount = Math.Min(count,Size);
|
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for (int i = 0; i < trueCount; ++i)
|
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destination[offset + i] = _buffer[(_head+i) % _capacity];
|
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_head += trueCount;
|
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_head %= _capacity;
|
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+
_size -= trueCount;
|
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return trueCount;
|
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+
}
|
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|
+
|
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|
+
public int Get()
|
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|
+
{
|
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|
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if (Size == 0)
|
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|
+
return -1;
|
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|
+
|
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|
+
int result = (int)_buffer[_head++ % _capacity];
|
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|
+
--_size;
|
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|
+
return result;
|
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|
+
}
|
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|
+
|
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|
+
}
|
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|
+
}
|
@@ -0,0 +1,198 @@
|
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//
|
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// � Copyright Henrik Ravn 2004
|
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//
|
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|
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// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
|
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|
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// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
|
6
|
+
//
|
7
|
+
|
8
|
+
using System;
|
9
|
+
using System.Runtime.InteropServices;
|
10
|
+
|
11
|
+
namespace DotZLib
|
12
|
+
{
|
13
|
+
/// <summary>
|
14
|
+
/// Implements the common functionality needed for all <see cref="Codec"/>s
|
15
|
+
/// </summary>
|
16
|
+
public abstract class CodecBase : Codec, IDisposable
|
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|
+
{
|
18
|
+
|
19
|
+
#region Data members
|
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|
+
|
21
|
+
/// <summary>
|
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|
+
/// Instance of the internal zlib buffer structure that is
|
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|
+
/// passed to all functions in the zlib dll
|
24
|
+
/// </summary>
|
25
|
+
internal ZStream _ztream = new ZStream();
|
26
|
+
|
27
|
+
/// <summary>
|
28
|
+
/// True if the object instance has been disposed, false otherwise
|
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|
+
/// </summary>
|
30
|
+
protected bool _isDisposed = false;
|
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|
+
|
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|
+
/// <summary>
|
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|
+
/// The size of the internal buffers
|
34
|
+
/// </summary>
|
35
|
+
protected const int kBufferSize = 16384;
|
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|
+
|
37
|
+
private byte[] _outBuffer = new byte[kBufferSize];
|
38
|
+
private byte[] _inBuffer = new byte[kBufferSize];
|
39
|
+
|
40
|
+
private GCHandle _hInput;
|
41
|
+
private GCHandle _hOutput;
|
42
|
+
|
43
|
+
private uint _checksum = 0;
|
44
|
+
|
45
|
+
#endregion
|
46
|
+
|
47
|
+
/// <summary>
|
48
|
+
/// Initializes a new instance of the <c>CodeBase</c> class.
|
49
|
+
/// </summary>
|
50
|
+
public CodecBase()
|
51
|
+
{
|
52
|
+
try
|
53
|
+
{
|
54
|
+
_hInput = GCHandle.Alloc(_inBuffer, GCHandleType.Pinned);
|
55
|
+
_hOutput = GCHandle.Alloc(_outBuffer, GCHandleType.Pinned);
|
56
|
+
}
|
57
|
+
catch (Exception)
|
58
|
+
{
|
59
|
+
CleanUp(false);
|
60
|
+
throw;
|
61
|
+
}
|
62
|
+
}
|
63
|
+
|
64
|
+
|
65
|
+
#region Codec Members
|
66
|
+
|
67
|
+
/// <summary>
|
68
|
+
/// Occurs when more processed data are available.
|
69
|
+
/// </summary>
|
70
|
+
public event DataAvailableHandler DataAvailable;
|
71
|
+
|
72
|
+
/// <summary>
|
73
|
+
/// Fires the <see cref="DataAvailable"/> event
|
74
|
+
/// </summary>
|
75
|
+
protected void OnDataAvailable()
|
76
|
+
{
|
77
|
+
if (_ztream.total_out > 0)
|
78
|
+
{
|
79
|
+
if (DataAvailable != null)
|
80
|
+
DataAvailable( _outBuffer, 0, (int)_ztream.total_out);
|
81
|
+
resetOutput();
|
82
|
+
}
|
83
|
+
}
|
84
|
+
|
85
|
+
/// <summary>
|
86
|
+
/// Adds more data to the codec to be processed.
|
87
|
+
/// </summary>
|
88
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
89
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
90
|
+
public void Add(byte[] data)
|
91
|
+
{
|
92
|
+
Add(data,0,data.Length);
|
93
|
+
}
|
94
|
+
|
95
|
+
/// <summary>
|
96
|
+
/// Adds more data to the codec to be processed.
|
97
|
+
/// </summary>
|
98
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
99
|
+
/// <param name="offset">The index of the first byte to add from <c>data</c></param>
|
100
|
+
/// <param name="count">The number of bytes to add</param>
|
101
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
102
|
+
/// <remarks>This must be implemented by a derived class</remarks>
|
103
|
+
public abstract void Add(byte[] data, int offset, int count);
|
104
|
+
|
105
|
+
/// <summary>
|
106
|
+
/// Finishes up any pending data that needs to be processed and handled.
|
107
|
+
/// </summary>
|
108
|
+
/// <remarks>This must be implemented by a derived class</remarks>
|
109
|
+
public abstract void Finish();
|
110
|
+
|
111
|
+
/// <summary>
|
112
|
+
/// Gets the checksum of the data that has been added so far
|
113
|
+
/// </summary>
|
114
|
+
public uint Checksum { get { return _checksum; } }
|
115
|
+
|
116
|
+
#endregion
|
117
|
+
|
118
|
+
#region Destructor & IDisposable stuff
|
119
|
+
|
120
|
+
/// <summary>
|
121
|
+
/// Destroys this instance
|
122
|
+
/// </summary>
|
123
|
+
~CodecBase()
|
124
|
+
{
|
125
|
+
CleanUp(false);
|
126
|
+
}
|
127
|
+
|
128
|
+
/// <summary>
|
129
|
+
/// Releases any unmanaged resources and calls the <see cref="CleanUp()"/> method of the derived class
|
130
|
+
/// </summary>
|
131
|
+
public void Dispose()
|
132
|
+
{
|
133
|
+
CleanUp(true);
|
134
|
+
}
|
135
|
+
|
136
|
+
/// <summary>
|
137
|
+
/// Performs any codec specific cleanup
|
138
|
+
/// </summary>
|
139
|
+
/// <remarks>This must be implemented by a derived class</remarks>
|
140
|
+
protected abstract void CleanUp();
|
141
|
+
|
142
|
+
// performs the release of the handles and calls the dereived CleanUp()
|
143
|
+
private void CleanUp(bool isDisposing)
|
144
|
+
{
|
145
|
+
if (!_isDisposed)
|
146
|
+
{
|
147
|
+
CleanUp();
|
148
|
+
if (_hInput.IsAllocated)
|
149
|
+
_hInput.Free();
|
150
|
+
if (_hOutput.IsAllocated)
|
151
|
+
_hOutput.Free();
|
152
|
+
|
153
|
+
_isDisposed = true;
|
154
|
+
}
|
155
|
+
}
|
156
|
+
|
157
|
+
|
158
|
+
#endregion
|
159
|
+
|
160
|
+
#region Helper methods
|
161
|
+
|
162
|
+
/// <summary>
|
163
|
+
/// Copies a number of bytes to the internal codec buffer - ready for proccesing
|
164
|
+
/// </summary>
|
165
|
+
/// <param name="data">The byte array that contains the data to copy</param>
|
166
|
+
/// <param name="startIndex">The index of the first byte to copy</param>
|
167
|
+
/// <param name="count">The number of bytes to copy from <c>data</c></param>
|
168
|
+
protected void copyInput(byte[] data, int startIndex, int count)
|
169
|
+
{
|
170
|
+
Array.Copy(data, startIndex, _inBuffer,0, count);
|
171
|
+
_ztream.next_in = _hInput.AddrOfPinnedObject();
|
172
|
+
_ztream.total_in = 0;
|
173
|
+
_ztream.avail_in = (uint)count;
|
174
|
+
|
175
|
+
}
|
176
|
+
|
177
|
+
/// <summary>
|
178
|
+
/// Resets the internal output buffers to a known state - ready for processing
|
179
|
+
/// </summary>
|
180
|
+
protected void resetOutput()
|
181
|
+
{
|
182
|
+
_ztream.total_out = 0;
|
183
|
+
_ztream.avail_out = kBufferSize;
|
184
|
+
_ztream.next_out = _hOutput.AddrOfPinnedObject();
|
185
|
+
}
|
186
|
+
|
187
|
+
/// <summary>
|
188
|
+
/// Updates the running checksum property
|
189
|
+
/// </summary>
|
190
|
+
/// <param name="newSum">The new checksum value</param>
|
191
|
+
protected void setChecksum(uint newSum)
|
192
|
+
{
|
193
|
+
_checksum = newSum;
|
194
|
+
}
|
195
|
+
#endregion
|
196
|
+
|
197
|
+
}
|
198
|
+
}
|
@@ -0,0 +1,106 @@
|
|
1
|
+
//
|
2
|
+
// � Copyright Henrik Ravn 2004
|
3
|
+
//
|
4
|
+
// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
|
5
|
+
// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
|
6
|
+
//
|
7
|
+
|
8
|
+
using System;
|
9
|
+
using System.Diagnostics;
|
10
|
+
using System.Runtime.InteropServices;
|
11
|
+
|
12
|
+
namespace DotZLib
|
13
|
+
{
|
14
|
+
|
15
|
+
/// <summary>
|
16
|
+
/// Implements a data compressor, using the deflate algorithm in the ZLib dll
|
17
|
+
/// </summary>
|
18
|
+
public sealed class Deflater : CodecBase
|
19
|
+
{
|
20
|
+
#region Dll imports
|
21
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl, CharSet=CharSet.Ansi)]
|
22
|
+
private static extern int deflateInit_(ref ZStream sz, int level, string vs, int size);
|
23
|
+
|
24
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
25
|
+
private static extern int deflate(ref ZStream sz, int flush);
|
26
|
+
|
27
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
28
|
+
private static extern int deflateReset(ref ZStream sz);
|
29
|
+
|
30
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
31
|
+
private static extern int deflateEnd(ref ZStream sz);
|
32
|
+
#endregion
|
33
|
+
|
34
|
+
/// <summary>
|
35
|
+
/// Constructs an new instance of the <c>Deflater</c>
|
36
|
+
/// </summary>
|
37
|
+
/// <param name="level">The compression level to use for this <c>Deflater</c></param>
|
38
|
+
public Deflater(CompressLevel level) : base()
|
39
|
+
{
|
40
|
+
int retval = deflateInit_(ref _ztream, (int)level, Info.Version, Marshal.SizeOf(_ztream));
|
41
|
+
if (retval != 0)
|
42
|
+
throw new ZLibException(retval, "Could not initialize deflater");
|
43
|
+
|
44
|
+
resetOutput();
|
45
|
+
}
|
46
|
+
|
47
|
+
/// <summary>
|
48
|
+
/// Adds more data to the codec to be processed.
|
49
|
+
/// </summary>
|
50
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
51
|
+
/// <param name="offset">The index of the first byte to add from <c>data</c></param>
|
52
|
+
/// <param name="count">The number of bytes to add</param>
|
53
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
54
|
+
public override void Add(byte[] data, int offset, int count)
|
55
|
+
{
|
56
|
+
if (data == null) throw new ArgumentNullException();
|
57
|
+
if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
|
58
|
+
if ((offset+count) > data.Length) throw new ArgumentException();
|
59
|
+
|
60
|
+
int total = count;
|
61
|
+
int inputIndex = offset;
|
62
|
+
int err = 0;
|
63
|
+
|
64
|
+
while (err >= 0 && inputIndex < total)
|
65
|
+
{
|
66
|
+
copyInput(data, inputIndex, Math.Min(total - inputIndex, kBufferSize));
|
67
|
+
while (err >= 0 && _ztream.avail_in > 0)
|
68
|
+
{
|
69
|
+
err = deflate(ref _ztream, (int)FlushTypes.None);
|
70
|
+
if (err == 0)
|
71
|
+
while (_ztream.avail_out == 0)
|
72
|
+
{
|
73
|
+
OnDataAvailable();
|
74
|
+
err = deflate(ref _ztream, (int)FlushTypes.None);
|
75
|
+
}
|
76
|
+
inputIndex += (int)_ztream.total_in;
|
77
|
+
}
|
78
|
+
}
|
79
|
+
setChecksum( _ztream.adler );
|
80
|
+
}
|
81
|
+
|
82
|
+
|
83
|
+
/// <summary>
|
84
|
+
/// Finishes up any pending data that needs to be processed and handled.
|
85
|
+
/// </summary>
|
86
|
+
public override void Finish()
|
87
|
+
{
|
88
|
+
int err;
|
89
|
+
do
|
90
|
+
{
|
91
|
+
err = deflate(ref _ztream, (int)FlushTypes.Finish);
|
92
|
+
OnDataAvailable();
|
93
|
+
}
|
94
|
+
while (err == 0);
|
95
|
+
setChecksum( _ztream.adler );
|
96
|
+
deflateReset(ref _ztream);
|
97
|
+
resetOutput();
|
98
|
+
}
|
99
|
+
|
100
|
+
/// <summary>
|
101
|
+
/// Closes the internal zlib deflate stream
|
102
|
+
/// </summary>
|
103
|
+
protected override void CleanUp() { deflateEnd(ref _ztream); }
|
104
|
+
|
105
|
+
}
|
106
|
+
}
|
@@ -0,0 +1,288 @@
|
|
1
|
+
//
|
2
|
+
// � Copyright Henrik Ravn 2004
|
3
|
+
//
|
4
|
+
// Use, modification and distribution are subject to the Boost Software License, Version 1.0.
|
5
|
+
// (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
|
6
|
+
//
|
7
|
+
|
8
|
+
using System;
|
9
|
+
using System.IO;
|
10
|
+
using System.Runtime.InteropServices;
|
11
|
+
using System.Text;
|
12
|
+
|
13
|
+
|
14
|
+
namespace DotZLib
|
15
|
+
{
|
16
|
+
|
17
|
+
#region Internal types
|
18
|
+
|
19
|
+
/// <summary>
|
20
|
+
/// Defines constants for the various flush types used with zlib
|
21
|
+
/// </summary>
|
22
|
+
internal enum FlushTypes
|
23
|
+
{
|
24
|
+
None, Partial, Sync, Full, Finish, Block
|
25
|
+
}
|
26
|
+
|
27
|
+
#region ZStream structure
|
28
|
+
// internal mapping of the zlib zstream structure for marshalling
|
29
|
+
[StructLayoutAttribute(LayoutKind.Sequential, Pack=4, Size=0, CharSet=CharSet.Ansi)]
|
30
|
+
internal struct ZStream
|
31
|
+
{
|
32
|
+
public IntPtr next_in;
|
33
|
+
public uint avail_in;
|
34
|
+
public uint total_in;
|
35
|
+
|
36
|
+
public IntPtr next_out;
|
37
|
+
public uint avail_out;
|
38
|
+
public uint total_out;
|
39
|
+
|
40
|
+
[MarshalAs(UnmanagedType.LPStr)]
|
41
|
+
string msg;
|
42
|
+
uint state;
|
43
|
+
|
44
|
+
uint zalloc;
|
45
|
+
uint zfree;
|
46
|
+
uint opaque;
|
47
|
+
|
48
|
+
int data_type;
|
49
|
+
public uint adler;
|
50
|
+
uint reserved;
|
51
|
+
}
|
52
|
+
|
53
|
+
#endregion
|
54
|
+
|
55
|
+
#endregion
|
56
|
+
|
57
|
+
#region Public enums
|
58
|
+
/// <summary>
|
59
|
+
/// Defines constants for the available compression levels in zlib
|
60
|
+
/// </summary>
|
61
|
+
public enum CompressLevel : int
|
62
|
+
{
|
63
|
+
/// <summary>
|
64
|
+
/// The default compression level with a reasonable compromise between compression and speed
|
65
|
+
/// </summary>
|
66
|
+
Default = -1,
|
67
|
+
/// <summary>
|
68
|
+
/// No compression at all. The data are passed straight through.
|
69
|
+
/// </summary>
|
70
|
+
None = 0,
|
71
|
+
/// <summary>
|
72
|
+
/// The maximum compression rate available.
|
73
|
+
/// </summary>
|
74
|
+
Best = 9,
|
75
|
+
/// <summary>
|
76
|
+
/// The fastest available compression level.
|
77
|
+
/// </summary>
|
78
|
+
Fastest = 1
|
79
|
+
}
|
80
|
+
#endregion
|
81
|
+
|
82
|
+
#region Exception classes
|
83
|
+
/// <summary>
|
84
|
+
/// The exception that is thrown when an error occurs on the zlib dll
|
85
|
+
/// </summary>
|
86
|
+
public class ZLibException : ApplicationException
|
87
|
+
{
|
88
|
+
/// <summary>
|
89
|
+
/// Initializes a new instance of the <see cref="ZLibException"/> class with a specified
|
90
|
+
/// error message and error code
|
91
|
+
/// </summary>
|
92
|
+
/// <param name="errorCode">The zlib error code that caused the exception</param>
|
93
|
+
/// <param name="msg">A message that (hopefully) describes the error</param>
|
94
|
+
public ZLibException(int errorCode, string msg) : base(String.Format("ZLib error {0} {1}", errorCode, msg))
|
95
|
+
{
|
96
|
+
}
|
97
|
+
|
98
|
+
/// <summary>
|
99
|
+
/// Initializes a new instance of the <see cref="ZLibException"/> class with a specified
|
100
|
+
/// error code
|
101
|
+
/// </summary>
|
102
|
+
/// <param name="errorCode">The zlib error code that caused the exception</param>
|
103
|
+
public ZLibException(int errorCode) : base(String.Format("ZLib error {0}", errorCode))
|
104
|
+
{
|
105
|
+
}
|
106
|
+
}
|
107
|
+
#endregion
|
108
|
+
|
109
|
+
#region Interfaces
|
110
|
+
|
111
|
+
/// <summary>
|
112
|
+
/// Declares methods and properties that enables a running checksum to be calculated
|
113
|
+
/// </summary>
|
114
|
+
public interface ChecksumGenerator
|
115
|
+
{
|
116
|
+
/// <summary>
|
117
|
+
/// Gets the current value of the checksum
|
118
|
+
/// </summary>
|
119
|
+
uint Value { get; }
|
120
|
+
|
121
|
+
/// <summary>
|
122
|
+
/// Clears the current checksum to 0
|
123
|
+
/// </summary>
|
124
|
+
void Reset();
|
125
|
+
|
126
|
+
/// <summary>
|
127
|
+
/// Updates the current checksum with an array of bytes
|
128
|
+
/// </summary>
|
129
|
+
/// <param name="data">The data to update the checksum with</param>
|
130
|
+
void Update(byte[] data);
|
131
|
+
|
132
|
+
/// <summary>
|
133
|
+
/// Updates the current checksum with part of an array of bytes
|
134
|
+
/// </summary>
|
135
|
+
/// <param name="data">The data to update the checksum with</param>
|
136
|
+
/// <param name="offset">Where in <c>data</c> to start updating</param>
|
137
|
+
/// <param name="count">The number of bytes from <c>data</c> to use</param>
|
138
|
+
/// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
|
139
|
+
/// <exception cref="ArgumentNullException"><c>data</c> is a null reference</exception>
|
140
|
+
/// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
|
141
|
+
void Update(byte[] data, int offset, int count);
|
142
|
+
|
143
|
+
/// <summary>
|
144
|
+
/// Updates the current checksum with the data from a string
|
145
|
+
/// </summary>
|
146
|
+
/// <param name="data">The string to update the checksum with</param>
|
147
|
+
/// <remarks>The characters in the string are converted by the UTF-8 encoding</remarks>
|
148
|
+
void Update(string data);
|
149
|
+
|
150
|
+
/// <summary>
|
151
|
+
/// Updates the current checksum with the data from a string, using a specific encoding
|
152
|
+
/// </summary>
|
153
|
+
/// <param name="data">The string to update the checksum with</param>
|
154
|
+
/// <param name="encoding">The encoding to use</param>
|
155
|
+
void Update(string data, Encoding encoding);
|
156
|
+
}
|
157
|
+
|
158
|
+
|
159
|
+
/// <summary>
|
160
|
+
/// Represents the method that will be called from a codec when new data
|
161
|
+
/// are available.
|
162
|
+
/// </summary>
|
163
|
+
/// <paramref name="data">The byte array containing the processed data</paramref>
|
164
|
+
/// <paramref name="startIndex">The index of the first processed byte in <c>data</c></paramref>
|
165
|
+
/// <paramref name="count">The number of processed bytes available</paramref>
|
166
|
+
/// <remarks>On return from this method, the data may be overwritten, so grab it while you can.
|
167
|
+
/// You cannot assume that startIndex will be zero.
|
168
|
+
/// </remarks>
|
169
|
+
public delegate void DataAvailableHandler(byte[] data, int startIndex, int count);
|
170
|
+
|
171
|
+
/// <summary>
|
172
|
+
/// Declares methods and events for implementing compressors/decompressors
|
173
|
+
/// </summary>
|
174
|
+
public interface Codec
|
175
|
+
{
|
176
|
+
/// <summary>
|
177
|
+
/// Occurs when more processed data are available.
|
178
|
+
/// </summary>
|
179
|
+
event DataAvailableHandler DataAvailable;
|
180
|
+
|
181
|
+
/// <summary>
|
182
|
+
/// Adds more data to the codec to be processed.
|
183
|
+
/// </summary>
|
184
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
185
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
186
|
+
void Add(byte[] data);
|
187
|
+
|
188
|
+
/// <summary>
|
189
|
+
/// Adds more data to the codec to be processed.
|
190
|
+
/// </summary>
|
191
|
+
/// <param name="data">Byte array containing the data to be added to the codec</param>
|
192
|
+
/// <param name="offset">The index of the first byte to add from <c>data</c></param>
|
193
|
+
/// <param name="count">The number of bytes to add</param>
|
194
|
+
/// <remarks>Adding data may, or may not, raise the <c>DataAvailable</c> event</remarks>
|
195
|
+
void Add(byte[] data, int offset, int count);
|
196
|
+
|
197
|
+
/// <summary>
|
198
|
+
/// Finishes up any pending data that needs to be processed and handled.
|
199
|
+
/// </summary>
|
200
|
+
void Finish();
|
201
|
+
|
202
|
+
/// <summary>
|
203
|
+
/// Gets the checksum of the data that has been added so far
|
204
|
+
/// </summary>
|
205
|
+
uint Checksum { get; }
|
206
|
+
|
207
|
+
|
208
|
+
}
|
209
|
+
|
210
|
+
#endregion
|
211
|
+
|
212
|
+
#region Classes
|
213
|
+
/// <summary>
|
214
|
+
/// Encapsulates general information about the ZLib library
|
215
|
+
/// </summary>
|
216
|
+
public class Info
|
217
|
+
{
|
218
|
+
#region DLL imports
|
219
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
220
|
+
private static extern uint zlibCompileFlags();
|
221
|
+
|
222
|
+
[DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
|
223
|
+
private static extern string zlibVersion();
|
224
|
+
#endregion
|
225
|
+
|
226
|
+
#region Private stuff
|
227
|
+
private uint _flags;
|
228
|
+
|
229
|
+
// helper function that unpacks a bitsize mask
|
230
|
+
private static int bitSize(uint bits)
|
231
|
+
{
|
232
|
+
switch (bits)
|
233
|
+
{
|
234
|
+
case 0: return 16;
|
235
|
+
case 1: return 32;
|
236
|
+
case 2: return 64;
|
237
|
+
}
|
238
|
+
return -1;
|
239
|
+
}
|
240
|
+
#endregion
|
241
|
+
|
242
|
+
/// <summary>
|
243
|
+
/// Constructs an instance of the <c>Info</c> class.
|
244
|
+
/// </summary>
|
245
|
+
public Info()
|
246
|
+
{
|
247
|
+
_flags = zlibCompileFlags();
|
248
|
+
}
|
249
|
+
|
250
|
+
/// <summary>
|
251
|
+
/// True if the library is compiled with debug info
|
252
|
+
/// </summary>
|
253
|
+
public bool HasDebugInfo { get { return 0 != (_flags & 0x100); } }
|
254
|
+
|
255
|
+
/// <summary>
|
256
|
+
/// True if the library is compiled with assembly optimizations
|
257
|
+
/// </summary>
|
258
|
+
public bool UsesAssemblyCode { get { return 0 != (_flags & 0x200); } }
|
259
|
+
|
260
|
+
/// <summary>
|
261
|
+
/// Gets the size of the unsigned int that was compiled into Zlib
|
262
|
+
/// </summary>
|
263
|
+
public int SizeOfUInt { get { return bitSize(_flags & 3); } }
|
264
|
+
|
265
|
+
/// <summary>
|
266
|
+
/// Gets the size of the unsigned long that was compiled into Zlib
|
267
|
+
/// </summary>
|
268
|
+
public int SizeOfULong { get { return bitSize((_flags >> 2) & 3); } }
|
269
|
+
|
270
|
+
/// <summary>
|
271
|
+
/// Gets the size of the pointers that were compiled into Zlib
|
272
|
+
/// </summary>
|
273
|
+
public int SizeOfPointer { get { return bitSize((_flags >> 4) & 3); } }
|
274
|
+
|
275
|
+
/// <summary>
|
276
|
+
/// Gets the size of the z_off_t type that was compiled into Zlib
|
277
|
+
/// </summary>
|
278
|
+
public int SizeOfOffset { get { return bitSize((_flags >> 6) & 3); } }
|
279
|
+
|
280
|
+
/// <summary>
|
281
|
+
/// Gets the version of ZLib as a string, e.g. "1.2.1"
|
282
|
+
/// </summary>
|
283
|
+
public static string Version { get { return zlibVersion(); } }
|
284
|
+
}
|
285
|
+
|
286
|
+
#endregion
|
287
|
+
|
288
|
+
}
|