annotate BEDTools-Version-2.14.3/src/utils/gzstream/gzstream.C @ 0:dfcd8b6c1bda

Uploaded
author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
1 // ============================================================================
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
2 // gzstream, C++ iostream classes wrapping the zlib compression library.
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
3 // Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
4 //
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
5 // This library is free software; you can redistribute it and/or
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
6 // modify it under the terms of the GNU Lesser General Public
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
7 // License as published by the Free Software Foundation; either
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
8 // version 2.1 of the License, or (at your option) any later version.
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
9 //
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
10 // This library is distributed in the hope that it will be useful,
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
11 // but WITHOUT ANY WARRANTY; without even the implied warranty of
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
12 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
13 // Lesser General Public License for more details.
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
14 //
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
15 // You should have received a copy of the GNU Lesser General Public
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
16 // License along with this library; if not, write to the Free Software
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
17 // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
18 // ============================================================================
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
19 //
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
20 // File : gzstream.C
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
21 // Revision : $Revision: 1.7 $
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
22 // Revision_date : $Date: 2003/01/08 14:41:27 $
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
23 // Author(s) : Deepak Bandyopadhyay, Lutz Kettner
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
24 //
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
25 // Standard streambuf implementation following Nicolai Josuttis, "The
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
26 // Standard C++ Library".
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
27 // ============================================================================
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
28
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
29 #include <gzstream.h>
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
30 #include <iostream>
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
31 #include <string.h> // for memcpy
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
32
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
33 #ifdef GZSTREAM_NAMESPACE
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
34 namespace GZSTREAM_NAMESPACE {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
35 #endif
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
36
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
37 // ----------------------------------------------------------------------------
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
38 // Internal classes to implement gzstream. See header file for user classes.
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
39 // ----------------------------------------------------------------------------
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
40
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
41 // --------------------------------------
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
42 // class gzstreambuf:
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
43 // --------------------------------------
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
44
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
45 gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
46 if ( is_open())
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
47 return (gzstreambuf*)0;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
48 mode = open_mode;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
49 // no append nor read/write mode
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
50 if ((mode & std::ios::ate) || (mode & std::ios::app)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
51 || ((mode & std::ios::in) && (mode & std::ios::out)))
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
52 return (gzstreambuf*)0;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
53 char fmode[10];
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
54 char* fmodeptr = fmode;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
55 if ( mode & std::ios::in)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
56 *fmodeptr++ = 'r';
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
57 else if ( mode & std::ios::out)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
58 *fmodeptr++ = 'w';
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
59 *fmodeptr++ = 'b';
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
60 *fmodeptr = '\0';
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
61 file = gzopen( name, fmode);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
62 if (file == 0)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
63 return (gzstreambuf*)0;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
64 opened = 1;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
65 return this;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
66 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
67
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
68 gzstreambuf * gzstreambuf::close() {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
69 if ( is_open()) {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
70 sync();
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
71 opened = 0;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
72 if ( gzclose( file) == Z_OK)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
73 return this;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
74 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
75 return (gzstreambuf*)0;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
76 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
77
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
78 int gzstreambuf::underflow() { // used for input buffer only
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
79 if ( gptr() && ( gptr() < egptr()))
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
80 return * reinterpret_cast<unsigned char *>( gptr());
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
81
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
82 if ( ! (mode & std::ios::in) || ! opened)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
83 return EOF;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
84 // Josuttis' implementation of inbuf
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
85 int n_putback = gptr() - eback();
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
86 if ( n_putback > 4)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
87 n_putback = 4;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
88 memcpy( buffer + (4 - n_putback), gptr() - n_putback, n_putback);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
89
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
90 int num = gzread( file, buffer+4, bufferSize-4);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
91 if (num <= 0) // ERROR or EOF
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
92 return EOF;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
93
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
94 // reset buffer pointers
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
95 setg( buffer + (4 - n_putback), // beginning of putback area
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
96 buffer + 4, // read position
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
97 buffer + 4 + num); // end of buffer
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
98
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
99 // return next character
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
100 return * reinterpret_cast<unsigned char *>( gptr());
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
101 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
102
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
103 int gzstreambuf::flush_buffer() {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
104 // Separate the writing of the buffer from overflow() and
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
105 // sync() operation.
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
106 int w = pptr() - pbase();
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
107 if ( gzwrite( file, pbase(), w) != w)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
108 return EOF;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
109 pbump( -w);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
110 return w;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
111 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
112
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
113 int gzstreambuf::overflow( int c) { // used for output buffer only
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
114 if ( ! ( mode & std::ios::out) || ! opened)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
115 return EOF;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
116 if (c != EOF) {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
117 *pptr() = c;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
118 pbump(1);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
119 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
120 if ( flush_buffer() == EOF)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
121 return EOF;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
122 return c;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
123 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
124
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
125 int gzstreambuf::sync() {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
126 // Changed to use flush_buffer() instead of overflow( EOF)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
127 // which caused improper behavior with std::endl and flush(),
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
128 // bug reported by Vincent Ricard.
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
129 if ( pptr() && pptr() > pbase()) {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
130 if ( flush_buffer() == EOF)
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
131 return -1;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
132 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
133 return 0;
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
134 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
135
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
136 // --------------------------------------
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
137 // class gzstreambase:
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
138 // --------------------------------------
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
139
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
140 gzstreambase::gzstreambase( const char* name, int mode) {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
141 init( &buf);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
142 open( name, mode);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
143 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
144
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
145 gzstreambase::~gzstreambase() {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
146 buf.close();
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
147 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
148
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
149 void gzstreambase::open( const char* name, int open_mode) {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
150 if ( ! buf.open( name, open_mode))
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
151 clear( rdstate() | std::ios::badbit);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
152 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
153
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
154 void gzstreambase::close() {
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
155 if ( buf.is_open())
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
156 if ( ! buf.close())
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
157 clear( rdstate() | std::ios::badbit);
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
158 }
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
159
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
160 #ifdef GZSTREAM_NAMESPACE
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
161 } // namespace GZSTREAM_NAMESPACE
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
162 #endif
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
163
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
164 // ============================================================================
dfcd8b6c1bda Uploaded
aaronquinlan
parents:
diff changeset
165 // EOF //