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
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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
- data/lib/finishm/primers.rb +425 -0
- 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
- data/spec/acyclic_connection_finder_spec.rb +551 -0
- 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
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- data/spec/contig_printer_spec.rb +291 -0
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- data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
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- data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
- 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
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
- data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Graph +46 -0
- data/spec/data/assembly_visualiser/start_kmers1 +2 -0
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- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
- data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
- data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
- data/spec/data/c_probe_node_finder/1/Log +756 -0
- data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
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- data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
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- data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
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- data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
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- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
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- data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
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- data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
- data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
- data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
- data/spec/data/explore/1/a.fa +2 -0
- data/spec/data/explore/1/seq1_and_a.fa +3 -0
- data/spec/data/explore/1/seq2.fa +2 -0
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- data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
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- data/spec/data/gapfilling/1/reads.fa +171 -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
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- data/spec/data/kmers_count1.csv +2 -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/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
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- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
- metadata +899 -0
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----------------------------------------------------------------
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-- ZLib for Ada thick binding. --
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-- --
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-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
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-- --
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-- Open source license information is in the zlib.ads file. --
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----------------------------------------------------------------
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-- $Id: zlib-streams.adb,v 1.10 2004/05/31 10:53:40 vagul Exp $
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with Ada.Unchecked_Deallocation;
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package body ZLib.Streams is
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-----------
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-- Close --
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-----------
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procedure Close (Stream : in out Stream_Type) is
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procedure Free is new Ada.Unchecked_Deallocation
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(Stream_Element_Array, Buffer_Access);
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begin
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if Stream.Mode = Out_Stream or Stream.Mode = Duplex then
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Flush (Stream, Finish);
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Close (Stream.Writer);
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end if;
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if Stream.Mode = In_Stream or Stream.Mode = Duplex then
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Free (Stream.Buffer);
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end if;
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end Close;
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------------
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-- Create --
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------------
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procedure Create
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Mode : in Stream_Mode;
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Back : in Stream_Access;
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Back_Compressed : in Boolean;
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Level : in Compression_Level := Default_Compression;
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Strategy : in Strategy_Type := Default_Strategy;
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Header : in Header_Type := Default;
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Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
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:= Default_Buffer_Size;
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Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
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:= Default_Buffer_Size)
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is
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subtype Buffer_Subtype is Stream_Element_Array (1 .. Read_Buffer_Size);
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procedure Init_Filter
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(Filter : in out Filter_Type;
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Compress : in Boolean);
|
60
|
+
|
61
|
+
-----------------
|
62
|
+
-- Init_Filter --
|
63
|
+
-----------------
|
64
|
+
|
65
|
+
procedure Init_Filter
|
66
|
+
(Filter : in out Filter_Type;
|
67
|
+
Compress : in Boolean) is
|
68
|
+
begin
|
69
|
+
if Compress then
|
70
|
+
Deflate_Init
|
71
|
+
(Filter, Level, Strategy, Header => Header);
|
72
|
+
else
|
73
|
+
Inflate_Init (Filter, Header => Header);
|
74
|
+
end if;
|
75
|
+
end Init_Filter;
|
76
|
+
|
77
|
+
begin
|
78
|
+
Stream.Back := Back;
|
79
|
+
Stream.Mode := Mode;
|
80
|
+
|
81
|
+
if Mode = Out_Stream or Mode = Duplex then
|
82
|
+
Init_Filter (Stream.Writer, Back_Compressed);
|
83
|
+
Stream.Buffer_Size := Write_Buffer_Size;
|
84
|
+
else
|
85
|
+
Stream.Buffer_Size := 0;
|
86
|
+
end if;
|
87
|
+
|
88
|
+
if Mode = In_Stream or Mode = Duplex then
|
89
|
+
Init_Filter (Stream.Reader, not Back_Compressed);
|
90
|
+
|
91
|
+
Stream.Buffer := new Buffer_Subtype;
|
92
|
+
Stream.Rest_First := Stream.Buffer'Last + 1;
|
93
|
+
Stream.Rest_Last := Stream.Buffer'Last;
|
94
|
+
end if;
|
95
|
+
end Create;
|
96
|
+
|
97
|
+
-----------
|
98
|
+
-- Flush --
|
99
|
+
-----------
|
100
|
+
|
101
|
+
procedure Flush
|
102
|
+
(Stream : in out Stream_Type;
|
103
|
+
Mode : in Flush_Mode := Sync_Flush)
|
104
|
+
is
|
105
|
+
Buffer : Stream_Element_Array (1 .. Stream.Buffer_Size);
|
106
|
+
Last : Stream_Element_Offset;
|
107
|
+
begin
|
108
|
+
loop
|
109
|
+
Flush (Stream.Writer, Buffer, Last, Mode);
|
110
|
+
|
111
|
+
Ada.Streams.Write (Stream.Back.all, Buffer (1 .. Last));
|
112
|
+
|
113
|
+
exit when Last < Buffer'Last;
|
114
|
+
end loop;
|
115
|
+
end Flush;
|
116
|
+
|
117
|
+
-------------
|
118
|
+
-- Is_Open --
|
119
|
+
-------------
|
120
|
+
|
121
|
+
function Is_Open (Stream : Stream_Type) return Boolean is
|
122
|
+
begin
|
123
|
+
return Is_Open (Stream.Reader) or else Is_Open (Stream.Writer);
|
124
|
+
end Is_Open;
|
125
|
+
|
126
|
+
----------
|
127
|
+
-- Read --
|
128
|
+
----------
|
129
|
+
|
130
|
+
procedure Read
|
131
|
+
(Stream : in out Stream_Type;
|
132
|
+
Item : out Stream_Element_Array;
|
133
|
+
Last : out Stream_Element_Offset)
|
134
|
+
is
|
135
|
+
|
136
|
+
procedure Read
|
137
|
+
(Item : out Stream_Element_Array;
|
138
|
+
Last : out Stream_Element_Offset);
|
139
|
+
|
140
|
+
----------
|
141
|
+
-- Read --
|
142
|
+
----------
|
143
|
+
|
144
|
+
procedure Read
|
145
|
+
(Item : out Stream_Element_Array;
|
146
|
+
Last : out Stream_Element_Offset) is
|
147
|
+
begin
|
148
|
+
Ada.Streams.Read (Stream.Back.all, Item, Last);
|
149
|
+
end Read;
|
150
|
+
|
151
|
+
procedure Read is new ZLib.Read
|
152
|
+
(Read => Read,
|
153
|
+
Buffer => Stream.Buffer.all,
|
154
|
+
Rest_First => Stream.Rest_First,
|
155
|
+
Rest_Last => Stream.Rest_Last);
|
156
|
+
|
157
|
+
begin
|
158
|
+
Read (Stream.Reader, Item, Last);
|
159
|
+
end Read;
|
160
|
+
|
161
|
+
-------------------
|
162
|
+
-- Read_Total_In --
|
163
|
+
-------------------
|
164
|
+
|
165
|
+
function Read_Total_In (Stream : in Stream_Type) return Count is
|
166
|
+
begin
|
167
|
+
return Total_In (Stream.Reader);
|
168
|
+
end Read_Total_In;
|
169
|
+
|
170
|
+
--------------------
|
171
|
+
-- Read_Total_Out --
|
172
|
+
--------------------
|
173
|
+
|
174
|
+
function Read_Total_Out (Stream : in Stream_Type) return Count is
|
175
|
+
begin
|
176
|
+
return Total_Out (Stream.Reader);
|
177
|
+
end Read_Total_Out;
|
178
|
+
|
179
|
+
-----------
|
180
|
+
-- Write --
|
181
|
+
-----------
|
182
|
+
|
183
|
+
procedure Write
|
184
|
+
(Stream : in out Stream_Type;
|
185
|
+
Item : in Stream_Element_Array)
|
186
|
+
is
|
187
|
+
|
188
|
+
procedure Write (Item : in Stream_Element_Array);
|
189
|
+
|
190
|
+
-----------
|
191
|
+
-- Write --
|
192
|
+
-----------
|
193
|
+
|
194
|
+
procedure Write (Item : in Stream_Element_Array) is
|
195
|
+
begin
|
196
|
+
Ada.Streams.Write (Stream.Back.all, Item);
|
197
|
+
end Write;
|
198
|
+
|
199
|
+
procedure Write is new ZLib.Write
|
200
|
+
(Write => Write,
|
201
|
+
Buffer_Size => Stream.Buffer_Size);
|
202
|
+
|
203
|
+
begin
|
204
|
+
Write (Stream.Writer, Item, No_Flush);
|
205
|
+
end Write;
|
206
|
+
|
207
|
+
--------------------
|
208
|
+
-- Write_Total_In --
|
209
|
+
--------------------
|
210
|
+
|
211
|
+
function Write_Total_In (Stream : in Stream_Type) return Count is
|
212
|
+
begin
|
213
|
+
return Total_In (Stream.Writer);
|
214
|
+
end Write_Total_In;
|
215
|
+
|
216
|
+
---------------------
|
217
|
+
-- Write_Total_Out --
|
218
|
+
---------------------
|
219
|
+
|
220
|
+
function Write_Total_Out (Stream : in Stream_Type) return Count is
|
221
|
+
begin
|
222
|
+
return Total_Out (Stream.Writer);
|
223
|
+
end Write_Total_Out;
|
224
|
+
|
225
|
+
end ZLib.Streams;
|
@@ -0,0 +1,114 @@
|
|
1
|
+
----------------------------------------------------------------
|
2
|
+
-- ZLib for Ada thick binding. --
|
3
|
+
-- --
|
4
|
+
-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
|
5
|
+
-- --
|
6
|
+
-- Open source license information is in the zlib.ads file. --
|
7
|
+
----------------------------------------------------------------
|
8
|
+
|
9
|
+
-- $Id: zlib-streams.ads,v 1.12 2004/05/31 10:53:40 vagul Exp $
|
10
|
+
|
11
|
+
package ZLib.Streams is
|
12
|
+
|
13
|
+
type Stream_Mode is (In_Stream, Out_Stream, Duplex);
|
14
|
+
|
15
|
+
type Stream_Access is access all Ada.Streams.Root_Stream_Type'Class;
|
16
|
+
|
17
|
+
type Stream_Type is
|
18
|
+
new Ada.Streams.Root_Stream_Type with private;
|
19
|
+
|
20
|
+
procedure Read
|
21
|
+
(Stream : in out Stream_Type;
|
22
|
+
Item : out Ada.Streams.Stream_Element_Array;
|
23
|
+
Last : out Ada.Streams.Stream_Element_Offset);
|
24
|
+
|
25
|
+
procedure Write
|
26
|
+
(Stream : in out Stream_Type;
|
27
|
+
Item : in Ada.Streams.Stream_Element_Array);
|
28
|
+
|
29
|
+
procedure Flush
|
30
|
+
(Stream : in out Stream_Type;
|
31
|
+
Mode : in Flush_Mode := Sync_Flush);
|
32
|
+
-- Flush the written data to the back stream,
|
33
|
+
-- all data placed to the compressor is flushing to the Back stream.
|
34
|
+
-- Should not be used untill necessary, becouse it is decreasing
|
35
|
+
-- compression.
|
36
|
+
|
37
|
+
function Read_Total_In (Stream : in Stream_Type) return Count;
|
38
|
+
pragma Inline (Read_Total_In);
|
39
|
+
-- Return total number of bytes read from back stream so far.
|
40
|
+
|
41
|
+
function Read_Total_Out (Stream : in Stream_Type) return Count;
|
42
|
+
pragma Inline (Read_Total_Out);
|
43
|
+
-- Return total number of bytes read so far.
|
44
|
+
|
45
|
+
function Write_Total_In (Stream : in Stream_Type) return Count;
|
46
|
+
pragma Inline (Write_Total_In);
|
47
|
+
-- Return total number of bytes written so far.
|
48
|
+
|
49
|
+
function Write_Total_Out (Stream : in Stream_Type) return Count;
|
50
|
+
pragma Inline (Write_Total_Out);
|
51
|
+
-- Return total number of bytes written to the back stream.
|
52
|
+
|
53
|
+
procedure Create
|
54
|
+
(Stream : out Stream_Type;
|
55
|
+
Mode : in Stream_Mode;
|
56
|
+
Back : in Stream_Access;
|
57
|
+
Back_Compressed : in Boolean;
|
58
|
+
Level : in Compression_Level := Default_Compression;
|
59
|
+
Strategy : in Strategy_Type := Default_Strategy;
|
60
|
+
Header : in Header_Type := Default;
|
61
|
+
Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
|
62
|
+
:= Default_Buffer_Size;
|
63
|
+
Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
|
64
|
+
:= Default_Buffer_Size);
|
65
|
+
-- Create the Comression/Decompression stream.
|
66
|
+
-- If mode is In_Stream then Write operation is disabled.
|
67
|
+
-- If mode is Out_Stream then Read operation is disabled.
|
68
|
+
|
69
|
+
-- If Back_Compressed is true then
|
70
|
+
-- Data written to the Stream is compressing to the Back stream
|
71
|
+
-- and data read from the Stream is decompressed data from the Back stream.
|
72
|
+
|
73
|
+
-- If Back_Compressed is false then
|
74
|
+
-- Data written to the Stream is decompressing to the Back stream
|
75
|
+
-- and data read from the Stream is compressed data from the Back stream.
|
76
|
+
|
77
|
+
-- !!! When the Need_Header is False ZLib-Ada is using undocumented
|
78
|
+
-- ZLib 1.1.4 functionality to do not create/wait for ZLib headers.
|
79
|
+
|
80
|
+
function Is_Open (Stream : Stream_Type) return Boolean;
|
81
|
+
|
82
|
+
procedure Close (Stream : in out Stream_Type);
|
83
|
+
|
84
|
+
private
|
85
|
+
|
86
|
+
use Ada.Streams;
|
87
|
+
|
88
|
+
type Buffer_Access is access all Stream_Element_Array;
|
89
|
+
|
90
|
+
type Stream_Type
|
91
|
+
is new Root_Stream_Type with
|
92
|
+
record
|
93
|
+
Mode : Stream_Mode;
|
94
|
+
|
95
|
+
Buffer : Buffer_Access;
|
96
|
+
Rest_First : Stream_Element_Offset;
|
97
|
+
Rest_Last : Stream_Element_Offset;
|
98
|
+
-- Buffer for Read operation.
|
99
|
+
-- We need to have this buffer in the record
|
100
|
+
-- becouse not all read data from back stream
|
101
|
+
-- could be processed during the read operation.
|
102
|
+
|
103
|
+
Buffer_Size : Stream_Element_Offset;
|
104
|
+
-- Buffer size for write operation.
|
105
|
+
-- We do not need to have this buffer
|
106
|
+
-- in the record becouse all data could be
|
107
|
+
-- processed in the write operation.
|
108
|
+
|
109
|
+
Back : Stream_Access;
|
110
|
+
Reader : Filter_Type;
|
111
|
+
Writer : Filter_Type;
|
112
|
+
end record;
|
113
|
+
|
114
|
+
end ZLib.Streams;
|
@@ -0,0 +1,141 @@
|
|
1
|
+
----------------------------------------------------------------
|
2
|
+
-- ZLib for Ada thick binding. --
|
3
|
+
-- --
|
4
|
+
-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
|
5
|
+
-- --
|
6
|
+
-- Open source license information is in the zlib.ads file. --
|
7
|
+
----------------------------------------------------------------
|
8
|
+
|
9
|
+
-- $Id: zlib-thin.adb,v 1.8 2003/12/14 18:27:31 vagul Exp $
|
10
|
+
|
11
|
+
package body ZLib.Thin is
|
12
|
+
|
13
|
+
ZLIB_VERSION : constant Chars_Ptr := zlibVersion;
|
14
|
+
|
15
|
+
Z_Stream_Size : constant Int := Z_Stream'Size / System.Storage_Unit;
|
16
|
+
|
17
|
+
--------------
|
18
|
+
-- Avail_In --
|
19
|
+
--------------
|
20
|
+
|
21
|
+
function Avail_In (Strm : in Z_Stream) return UInt is
|
22
|
+
begin
|
23
|
+
return Strm.Avail_In;
|
24
|
+
end Avail_In;
|
25
|
+
|
26
|
+
---------------
|
27
|
+
-- Avail_Out --
|
28
|
+
---------------
|
29
|
+
|
30
|
+
function Avail_Out (Strm : in Z_Stream) return UInt is
|
31
|
+
begin
|
32
|
+
return Strm.Avail_Out;
|
33
|
+
end Avail_Out;
|
34
|
+
|
35
|
+
------------------
|
36
|
+
-- Deflate_Init --
|
37
|
+
------------------
|
38
|
+
|
39
|
+
function Deflate_Init
|
40
|
+
(strm : Z_Streamp;
|
41
|
+
level : Int;
|
42
|
+
method : Int;
|
43
|
+
windowBits : Int;
|
44
|
+
memLevel : Int;
|
45
|
+
strategy : Int)
|
46
|
+
return Int is
|
47
|
+
begin
|
48
|
+
return deflateInit2
|
49
|
+
(strm,
|
50
|
+
level,
|
51
|
+
method,
|
52
|
+
windowBits,
|
53
|
+
memLevel,
|
54
|
+
strategy,
|
55
|
+
ZLIB_VERSION,
|
56
|
+
Z_Stream_Size);
|
57
|
+
end Deflate_Init;
|
58
|
+
|
59
|
+
------------------
|
60
|
+
-- Inflate_Init --
|
61
|
+
------------------
|
62
|
+
|
63
|
+
function Inflate_Init (strm : Z_Streamp; windowBits : Int) return Int is
|
64
|
+
begin
|
65
|
+
return inflateInit2 (strm, windowBits, ZLIB_VERSION, Z_Stream_Size);
|
66
|
+
end Inflate_Init;
|
67
|
+
|
68
|
+
------------------------
|
69
|
+
-- Last_Error_Message --
|
70
|
+
------------------------
|
71
|
+
|
72
|
+
function Last_Error_Message (Strm : in Z_Stream) return String is
|
73
|
+
use Interfaces.C.Strings;
|
74
|
+
begin
|
75
|
+
if Strm.msg = Null_Ptr then
|
76
|
+
return "";
|
77
|
+
else
|
78
|
+
return Value (Strm.msg);
|
79
|
+
end if;
|
80
|
+
end Last_Error_Message;
|
81
|
+
|
82
|
+
------------
|
83
|
+
-- Set_In --
|
84
|
+
------------
|
85
|
+
|
86
|
+
procedure Set_In
|
87
|
+
(Strm : in out Z_Stream;
|
88
|
+
Buffer : in Voidp;
|
89
|
+
Size : in UInt) is
|
90
|
+
begin
|
91
|
+
Strm.Next_In := Buffer;
|
92
|
+
Strm.Avail_In := Size;
|
93
|
+
end Set_In;
|
94
|
+
|
95
|
+
------------------
|
96
|
+
-- Set_Mem_Func --
|
97
|
+
------------------
|
98
|
+
|
99
|
+
procedure Set_Mem_Func
|
100
|
+
(Strm : in out Z_Stream;
|
101
|
+
Opaque : in Voidp;
|
102
|
+
Alloc : in alloc_func;
|
103
|
+
Free : in free_func) is
|
104
|
+
begin
|
105
|
+
Strm.opaque := Opaque;
|
106
|
+
Strm.zalloc := Alloc;
|
107
|
+
Strm.zfree := Free;
|
108
|
+
end Set_Mem_Func;
|
109
|
+
|
110
|
+
-------------
|
111
|
+
-- Set_Out --
|
112
|
+
-------------
|
113
|
+
|
114
|
+
procedure Set_Out
|
115
|
+
(Strm : in out Z_Stream;
|
116
|
+
Buffer : in Voidp;
|
117
|
+
Size : in UInt) is
|
118
|
+
begin
|
119
|
+
Strm.Next_Out := Buffer;
|
120
|
+
Strm.Avail_Out := Size;
|
121
|
+
end Set_Out;
|
122
|
+
|
123
|
+
--------------
|
124
|
+
-- Total_In --
|
125
|
+
--------------
|
126
|
+
|
127
|
+
function Total_In (Strm : in Z_Stream) return ULong is
|
128
|
+
begin
|
129
|
+
return Strm.Total_In;
|
130
|
+
end Total_In;
|
131
|
+
|
132
|
+
---------------
|
133
|
+
-- Total_Out --
|
134
|
+
---------------
|
135
|
+
|
136
|
+
function Total_Out (Strm : in Z_Stream) return ULong is
|
137
|
+
begin
|
138
|
+
return Strm.Total_Out;
|
139
|
+
end Total_Out;
|
140
|
+
|
141
|
+
end ZLib.Thin;
|