diff --git a/CMakeLists.txt b/CMakeLists.txt index c0d920427..26e0f3fd5 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -214,7 +214,6 @@ include_directories(lib/simde) include_directories(lib) include_directories(lib/simd) -include_directories(lib/gzstream) include_directories(lib/alp) include_directories(lib/cacode) include_directories(lib/ksw2) diff --git a/lib/gzstream/LICENSE b/lib/gzstream/LICENSE deleted file mode 100644 index b1e3f5a26..000000000 --- a/lib/gzstream/LICENSE +++ /dev/null @@ -1,504 +0,0 @@ - GNU LESSER GENERAL PUBLIC LICENSE - Version 2.1, February 1999 - - Copyright (C) 1991, 1999 Free Software Foundation, Inc. - 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - -[This is the first released version of the Lesser GPL. It also counts - as the successor of the GNU Library Public License, version 2, hence - the version number 2.1.] - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. By contrast, the GNU General Public -Licenses are intended to guarantee your freedom to share and change -free software--to make sure the software is free for all its users. - - This license, the Lesser General Public License, applies to some -specially designated software packages--typically libraries--of the -Free Software Foundation and other authors who decide to use it. You -can use it too, but we suggest you first think carefully about whether -this license or the ordinary General Public License is the better -strategy to use in any particular case, based on the explanations below. - - When we speak of free software, we are referring to freedom of use, -not price. Our General Public Licenses are designed to make sure that -you have the freedom to distribute copies of free software (and charge -for this service if you wish); that you receive source code or can get -it if you want it; that you can change the software and use pieces of -it in new free programs; and that you are informed that you can do -these things. - - To protect your rights, we need to make restrictions that forbid -distributors to deny you these rights or to ask you to surrender these -rights. These restrictions translate to certain responsibilities for -you if you distribute copies of the library or if you modify it. - - For example, if you distribute copies of the library, whether gratis -or for a fee, you must give the recipients all the rights that we gave -you. You must make sure that they, too, receive or can get the source -code. If you link other code with the library, you must provide -complete object files to the recipients, so that they can relink them -with the library after making changes to the library and recompiling -it. And you must show them these terms so they know their rights. - - We protect your rights with a two-step method: (1) we copyright the -library, and (2) we offer you this license, which gives you legal -permission to copy, distribute and/or modify the library. - - To protect each distributor, we want to make it very clear that -there is no warranty for the free library. Also, if the library is -modified by someone else and passed on, the recipients should know -that what they have is not the original version, so that the original -author's reputation will not be affected by problems that might be -introduced by others. - - Finally, software patents pose a constant threat to the existence of -any free program. We wish to make sure that a company cannot -effectively restrict the users of a free program by obtaining a -restrictive license from a patent holder. Therefore, we insist that -any patent license obtained for a version of the library must be -consistent with the full freedom of use specified in this license. - - Most GNU software, including some libraries, is covered by the -ordinary GNU General Public License. This license, the GNU Lesser -General Public License, applies to certain designated libraries, and -is quite different from the ordinary General Public License. We use -this license for certain libraries in order to permit linking those -libraries into non-free programs. - - When a program is linked with a library, whether statically or using -a shared library, the combination of the two is legally speaking a -combined work, a derivative of the original library. The ordinary -General Public License therefore permits such linking only if the -entire combination fits its criteria of freedom. The Lesser General -Public License permits more lax criteria for linking other code with -the library. - - We call this license the "Lesser" General Public License because it -does Less to protect the user's freedom than the ordinary General -Public License. It also provides other free software developers Less -of an advantage over competing non-free programs. These disadvantages -are the reason we use the ordinary General Public License for many -libraries. However, the Lesser license provides advantages in certain -special circumstances. - - For example, on rare occasions, there may be a special need to -encourage the widest possible use of a certain library, so that it becomes -a de-facto standard. To achieve this, non-free programs must be -allowed to use the library. A more frequent case is that a free -library does the same job as widely used non-free libraries. In this -case, there is little to gain by limiting the free library to free -software only, so we use the Lesser General Public License. - - In other cases, permission to use a particular library in non-free -programs enables a greater number of people to use a large body of -free software. For example, permission to use the GNU C Library in -non-free programs enables many more people to use the whole GNU -operating system, as well as its variant, the GNU/Linux operating -system. - - Although the Lesser General Public License is Less protective of the -users' freedom, it does ensure that the user of a program that is -linked with the Library has the freedom and the wherewithal to run -that program using a modified version of the Library. - - The precise terms and conditions for copying, distribution and -modification follow. Pay close attention to the difference between a -"work based on the library" and a "work that uses the library". The -former contains code derived from the library, whereas the latter must -be combined with the library in order to run. - - GNU LESSER GENERAL PUBLIC LICENSE - TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION - - 0. This License Agreement applies to any software library or other -program which contains a notice placed by the copyright holder or -other authorized party saying it may be distributed under the terms of -this Lesser General Public License (also called "this License"). -Each licensee is addressed as "you". - - A "library" means a collection of software functions and/or data -prepared so as to be conveniently linked with application programs -(which use some of those functions and data) to form executables. - - The "Library", below, refers to any such software library or work -which has been distributed under these terms. A "work based on the -Library" means either the Library or any derivative work under -copyright law: that is to say, a work containing the Library or a -portion of it, either verbatim or with modifications and/or translated -straightforwardly into another language. (Hereinafter, translation is -included without limitation in the term "modification".) - - "Source code" for a work means the preferred form of the work for -making modifications to it. For a library, complete source code means -all the source code for all modules it contains, plus any associated -interface definition files, plus the scripts used to control compilation -and installation of the library. - - Activities other than copying, distribution and modification are not -covered by this License; they are outside its scope. The act of -running a program using the Library is not restricted, and output from -such a program is covered only if its contents constitute a work based -on the Library (independent of the use of the Library in a tool for -writing it). Whether that is true depends on what the Library does -and what the program that uses the Library does. - - 1. You may copy and distribute verbatim copies of the Library's -complete source code as you receive it, in any medium, provided that -you conspicuously and appropriately publish on each copy an -appropriate copyright notice and disclaimer of warranty; keep intact -all the notices that refer to this License and to the absence of any -warranty; and distribute a copy of this License along with the -Library. - - You may charge a fee for the physical act of transferring a copy, -and you may at your option offer warranty protection in exchange for a -fee. - - 2. You may modify your copy or copies of the Library or any portion -of it, thus forming a work based on the Library, and copy and -distribute such modifications or work under the terms of Section 1 -above, provided that you also meet all of these conditions: - - a) The modified work must itself be a software library. - - b) You must cause the files modified to carry prominent notices - stating that you changed the files and the date of any change. - - c) You must cause the whole of the work to be licensed at no - charge to all third parties under the terms of this License. - - d) If a facility in the modified Library refers to a function or a - table of data to be supplied by an application program that uses - the facility, other than as an argument passed when the facility - is invoked, then you must make a good faith effort to ensure that, - in the event an application does not supply such function or - table, the facility still operates, and performs whatever part of - its purpose remains meaningful. - - (For example, a function in a library to compute square roots has - a purpose that is entirely well-defined independent of the - application. Therefore, Subsection 2d requires that any - application-supplied function or table used by this function must - be optional: if the application does not supply it, the square - root function must still compute square roots.) - -These requirements apply to the modified work as a whole. If -identifiable sections of that work are not derived from the Library, -and can be reasonably considered independent and separate works in -themselves, then this License, and its terms, do not apply to those -sections when you distribute them as separate works. But when you -distribute the same sections as part of a whole which is a work based -on the Library, the distribution of the whole must be on the terms of -this License, whose permissions for other licensees extend to the -entire whole, and thus to each and every part regardless of who wrote -it. - -Thus, it is not the intent of this section to claim rights or contest -your rights to work written entirely by you; rather, the intent is to -exercise the right to control the distribution of derivative or -collective works based on the Library. - -In addition, mere aggregation of another work not based on the Library -with the Library (or with a work based on the Library) on a volume of -a storage or distribution medium does not bring the other work under -the scope of this License. - - 3. You may opt to apply the terms of the ordinary GNU General Public -License instead of this License to a given copy of the Library. To do -this, you must alter all the notices that refer to this License, so -that they refer to the ordinary GNU General Public License, version 2, -instead of to this License. (If a newer version than version 2 of the -ordinary GNU General Public License has appeared, then you can specify -that version instead if you wish.) Do not make any other change in -these notices. - - Once this change is made in a given copy, it is irreversible for -that copy, so the ordinary GNU General Public License applies to all -subsequent copies and derivative works made from that copy. - - This option is useful when you wish to copy part of the code of -the Library into a program that is not a library. - - 4. You may copy and distribute the Library (or a portion or -derivative of it, under Section 2) in object code or executable form -under the terms of Sections 1 and 2 above provided that you accompany -it with the complete corresponding machine-readable source code, which -must be distributed under the terms of Sections 1 and 2 above on a -medium customarily used for software interchange. - - If distribution of object code is made by offering access to copy -from a designated place, then offering equivalent access to copy the -source code from the same place satisfies the requirement to -distribute the source code, even though third parties are not -compelled to copy the source along with the object code. - - 5. A program that contains no derivative of any portion of the -Library, but is designed to work with the Library by being compiled or -linked with it, is called a "work that uses the Library". Such a -work, in isolation, is not a derivative work of the Library, and -therefore falls outside the scope of this License. - - However, linking a "work that uses the Library" with the Library -creates an executable that is a derivative of the Library (because it -contains portions of the Library), rather than a "work that uses the -library". The executable is therefore covered by this License. -Section 6 states terms for distribution of such executables. - - When a "work that uses the Library" uses material from a header file -that is part of the Library, the object code for the work may be a -derivative work of the Library even though the source code is not. -Whether this is true is especially significant if the work can be -linked without the Library, or if the work is itself a library. The -threshold for this to be true is not precisely defined by law. - - If such an object file uses only numerical parameters, data -structure layouts and accessors, and small macros and small inline -functions (ten lines or less in length), then the use of the object -file is unrestricted, regardless of whether it is legally a derivative -work. (Executables containing this object code plus portions of the -Library will still fall under Section 6.) - - Otherwise, if the work is a derivative of the Library, you may -distribute the object code for the work under the terms of Section 6. -Any executables containing that work also fall under Section 6, -whether or not they are linked directly with the Library itself. - - 6. As an exception to the Sections above, you may also combine or -link a "work that uses the Library" with the Library to produce a -work containing portions of the Library, and distribute that work -under terms of your choice, provided that the terms permit -modification of the work for the customer's own use and reverse -engineering for debugging such modifications. - - You must give prominent notice with each copy of the work that the -Library is used in it and that the Library and its use are covered by -this License. You must supply a copy of this License. If the work -during execution displays copyright notices, you must include the -copyright notice for the Library among them, as well as a reference -directing the user to the copy of this License. Also, you must do one -of these things: - - a) Accompany the work with the complete corresponding - machine-readable source code for the Library including whatever - changes were used in the work (which must be distributed under - Sections 1 and 2 above); and, if the work is an executable linked - with the Library, with the complete machine-readable "work that - uses the Library", as object code and/or source code, so that the - user can modify the Library and then relink to produce a modified - executable containing the modified Library. (It is understood - that the user who changes the contents of definitions files in the - Library will not necessarily be able to recompile the application - to use the modified definitions.) - - b) Use a suitable shared library mechanism for linking with the - Library. A suitable mechanism is one that (1) uses at run time a - copy of the library already present on the user's computer system, - rather than copying library functions into the executable, and (2) - will operate properly with a modified version of the library, if - the user installs one, as long as the modified version is - interface-compatible with the version that the work was made with. - - c) Accompany the work with a written offer, valid for at - least three years, to give the same user the materials - specified in Subsection 6a, above, for a charge no more - than the cost of performing this distribution. - - d) If distribution of the work is made by offering access to copy - from a designated place, offer equivalent access to copy the above - specified materials from the same place. - - e) Verify that the user has already received a copy of these - materials or that you have already sent this user a copy. - - For an executable, the required form of the "work that uses the -Library" must include any data and utility programs needed for -reproducing the executable from it. However, as a special exception, -the materials to be distributed need not include anything that is -normally distributed (in either source or binary form) with the major -components (compiler, kernel, and so on) of the operating system on -which the executable runs, unless that component itself accompanies -the executable. - - It may happen that this requirement contradicts the license -restrictions of other proprietary libraries that do not normally -accompany the operating system. Such a contradiction means you cannot -use both them and the Library together in an executable that you -distribute. - - 7. You may place library facilities that are a work based on the -Library side-by-side in a single library together with other library -facilities not covered by this License, and distribute such a combined -library, provided that the separate distribution of the work based on -the Library and of the other library facilities is otherwise -permitted, and provided that you do these two things: - - a) Accompany the combined library with a copy of the same work - based on the Library, uncombined with any other library - facilities. This must be distributed under the terms of the - Sections above. - - b) Give prominent notice with the combined library of the fact - that part of it is a work based on the Library, and explaining - where to find the accompanying uncombined form of the same work. - - 8. You may not copy, modify, sublicense, link with, or distribute -the Library except as expressly provided under this License. Any -attempt otherwise to copy, modify, sublicense, link with, or -distribute the Library is void, and will automatically terminate your -rights under this License. However, parties who have received copies, -or rights, from you under this License will not have their licenses -terminated so long as such parties remain in full compliance. - - 9. You are not required to accept this License, since you have not -signed it. However, nothing else grants you permission to modify or -distribute the Library or its derivative works. These actions are -prohibited by law if you do not accept this License. Therefore, by -modifying or distributing the Library (or any work based on the -Library), you indicate your acceptance of this License to do so, and -all its terms and conditions for copying, distributing or modifying -the Library or works based on it. - - 10. Each time you redistribute the Library (or any work based on the -Library), the recipient automatically receives a license from the -original licensor to copy, distribute, link with or modify the Library -subject to these terms and conditions. You may not impose any further -restrictions on the recipients' exercise of the rights granted herein. -You are not responsible for enforcing compliance by third parties with -this License. - - 11. If, as a consequence of a court judgment or allegation of patent -infringement or for any other reason (not limited to patent issues), -conditions are imposed on you (whether by court order, agreement or -otherwise) that contradict the conditions of this License, they do not -excuse you from the conditions of this License. If you cannot -distribute so as to satisfy simultaneously your obligations under this -License and any other pertinent obligations, then as a consequence you -may not distribute the Library at all. For example, if a patent -license would not permit royalty-free redistribution of the Library by -all those who receive copies directly or indirectly through you, then -the only way you could satisfy both it and this License would be to -refrain entirely from distribution of the Library. - -If any portion of this section is held invalid or unenforceable under any -particular circumstance, the balance of the section is intended to apply, -and the section as a whole is intended to apply in other circumstances. - -It is not the purpose of this section to induce you to infringe any -patents or other property right claims or to contest validity of any -such claims; this section has the sole purpose of protecting the -integrity of the free software distribution system which is -implemented by public license practices. Many people have made -generous contributions to the wide range of software distributed -through that system in reliance on consistent application of that -system; it is up to the author/donor to decide if he or she is willing -to distribute software through any other system and a licensee cannot -impose that choice. - -This section is intended to make thoroughly clear what is believed to -be a consequence of the rest of this License. - - 12. If the distribution and/or use of the Library is restricted in -certain countries either by patents or by copyrighted interfaces, the -original copyright holder who places the Library under this License may add -an explicit geographical distribution limitation excluding those countries, -so that distribution is permitted only in or among countries not thus -excluded. In such case, this License incorporates the limitation as if -written in the body of this License. - - 13. The Free Software Foundation may publish revised and/or new -versions of the Lesser General Public License from time to time. -Such new versions will be similar in spirit to the present version, -but may differ in detail to address new problems or concerns. - -Each version is given a distinguishing version number. If the Library -specifies a version number of this License which applies to it and -"any later version", you have the option of following the terms and -conditions either of that version or of any later version published by -the Free Software Foundation. If the Library does not specify a -license version number, you may choose any version ever published by -the Free Software Foundation. - - 14. If you wish to incorporate parts of the Library into other free -programs whose distribution conditions are incompatible with these, -write to the author to ask for permission. For software which is -copyrighted by the Free Software Foundation, write to the Free -Software Foundation; we sometimes make exceptions for this. Our -decision will be guided by the two goals of preserving the free status -of all derivatives of our free software and of promoting the sharing -and reuse of software generally. - - NO WARRANTY - - 15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO -WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. -EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR -OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY -KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE -LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME -THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - - 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN -WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY -AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU -FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR -CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE -LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING -RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A -FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF -SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH -DAMAGES. - - END OF TERMS AND CONDITIONS - - How to Apply These Terms to Your New Libraries - - If you develop a new library, and you want it to be of the greatest -possible use to the public, we recommend making it free software that -everyone can redistribute and change. You can do so by permitting -redistribution under these terms (or, alternatively, under the terms of the -ordinary General Public License). - - To apply these terms, attach the following notices to the library. It is -safest to attach them to the start of each source file to most effectively -convey the exclusion of warranty; and each file should have at least the -"copyright" line and a pointer to where the full notice is found. - - - Copyright (C) - - This library is free software; you can redistribute it and/or - modify it under the terms of the GNU Lesser General Public - License as published by the Free Software Foundation; either - version 2.1 of the License, or (at your option) any later version. - - This library is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - Lesser General Public License for more details. - - You should have received a copy of the GNU Lesser General Public - License along with this library; if not, write to the Free Software - Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - -Also add information on how to contact you by electronic and paper mail. - -You should also get your employer (if you work as a programmer) or your -school, if any, to sign a "copyright disclaimer" for the library, if -necessary. Here is a sample; alter the names: - - Yoyodyne, Inc., hereby disclaims all copyright interest in the - library `Frob' (a library for tweaking knobs) written by James Random Hacker. - - , 1 April 1990 - Ty Coon, President of Vice - -That's all there is to it! - - diff --git a/lib/gzstream/README b/lib/gzstream/README deleted file mode 100644 index 61d806044..000000000 --- a/lib/gzstream/README +++ /dev/null @@ -1,7 +0,0 @@ - - gzstream - C++ iostream classes wrapping the zlib compression library. -=========================================================================== - - Header Only version of this library from: - https://gist.github.com/piti118/1508048 diff --git a/lib/gzstream/gzstream.h b/lib/gzstream/gzstream.h deleted file mode 100644 index a3809a781..000000000 --- a/lib/gzstream/gzstream.h +++ /dev/null @@ -1,209 +0,0 @@ -// gzstream, C++ iostream classes wrapping the zlib compression library. -// Copyright (C) 2001 Deepak Bandyopadhyay, Lutz Kettner -// -// This library is free software; you can redistribute it and/or -// modify it under the terms of the GNU Lesser General Public -// License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// -// This library is distributed in the hope that it will be useful, -// but WITHOUT ANY WARRANTY; without even the implied warranty of -// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -// Lesser General Public License for more details. -// -// You should have received a copy of the GNU Lesser General Public -// License along with this library; if not, write to the Free Software -// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -// -// File : gzstream.h -// Revision : $Revision: 1.5 $ -// Revision_date : $Date: 2002/04/26 23:30:15 $ -// Author(s) : Deepak Bandyopadhyay, Lutz Kettner -// -// Standard streambuf implementation following Nicolai Josuttis, "The -// Standard C++ Library". - -#ifndef GZSTREAM_H -#define GZSTREAM_H - -#include -#include -#include -#include // for memcpy - -// Internal classes to implement gzstream. See below for user classes. -class gzstreambuf : public std::streambuf { -private: - static const int bufferSize = 47 + 256; // size of data buff - // totals 512 bytes under g++ for igzstream at the end. - - gzFile file; // file handle for compressed file - char buffer[bufferSize]; // data buffer - char opened; // open/close state of stream - int mode; // I/O mode - - int flush_buffer() { - // Separate the writing of the buffer from overflow() and - // sync() operation. - int w = pptr() - pbase(); - if (gzwrite(file, pbase(), w) != w) - return EOF; - pbump(-w); - return w; - } - -public: - gzstreambuf() : opened(0) { - setp(buffer, buffer + (bufferSize - 1)); - setg(buffer + 4, // beginning of putback area - buffer + 4, // read position - buffer + 4); // end position - // ASSERT: both input & output capabilities will not be used together - } - - int is_open() { return opened; } - - gzstreambuf *open(const char *name, int open_mode) { - if (is_open()) - return (gzstreambuf *) 0; - mode = open_mode; - // no append nor read/write mode - if ((mode & std::ios::ate) || (mode & std::ios::app) - || ((mode & std::ios::in) && (mode & std::ios::out))) - return (gzstreambuf *) 0; - char fmode[10]; - char *fmodeptr = fmode; - if (mode & std::ios::in) - *fmodeptr++ = 'r'; - else if (mode & std::ios::out) - *fmodeptr++ = 'w'; - *fmodeptr++ = 'b'; - *fmodeptr = '\0'; - file = gzopen(name, fmode); - if (file == 0) - return (gzstreambuf *) 0; - opened = 1; - return this; - } - - gzstreambuf *close() { - if (is_open()) { - sync(); - opened = 0; - if (gzclose(file) == Z_OK) - return this; - } - return (gzstreambuf *) 0; - } - - ~gzstreambuf() { close(); } - - virtual int overflow(int c = EOF) { // used for output buffer only - if (!(mode & std::ios::out) || !opened) - return EOF; - if (c != EOF) { - *pptr() = c; - pbump(1); - } - if (flush_buffer() == EOF) - return EOF; - return c; - } - - virtual int underflow() { // used for input buffer only - if (gptr() && (gptr() < egptr())) - return *reinterpret_cast( gptr()); - - if (!(mode & std::ios::in) || !opened) - return EOF; - // Josuttis' implementation of inbuf - int n_putback = gptr() - eback(); - if (n_putback > 4) - n_putback = 4; - memcpy(buffer + (4 - n_putback), gptr() - n_putback, n_putback); - - int num = gzread(file, buffer + 4, bufferSize - 4); - if (num <= 0) // ERROR or EOF - return EOF; - - // reset buffer pointers - setg(buffer + (4 - n_putback), // beginning of putback area - buffer + 4, // read position - buffer + 4 + num); // end of buffer - - // return next character - return *reinterpret_cast( gptr()); - } - - virtual int sync() { - // Changed to use flush_buffer() instead of overflow( EOF) - // which caused improper behavior with std::endl and flush(), - // bug reported by Vincent Ricard. - if (pptr() && pptr() > pbase()) { - if (flush_buffer() == EOF) - return -1; - } - return 0; - } -}; - -class gzstreambase : virtual public std::ios { -protected: - gzstreambuf buf; -public: - gzstreambase() { init(&buf); } - - gzstreambase(const char *name, int open_mode) { - init(&buf); - open(name, open_mode); - } - - ~gzstreambase() { - buf.close(); - } - - void open(const char *name, int open_mode) { - if (!buf.open(name, open_mode)) - clear(rdstate() | std::ios::badbit); - } - - void close() { - if (buf.is_open()) if (!buf.close()) - clear(rdstate() | std::ios::badbit); - } - - gzstreambuf *rdbuf() { return &buf; } -}; - -// User classes. Use igzstream and ogzstream analogously to ifstream and -// ofstream respectively. They read and write files based on the gz* -// function interface of the zlib. Files are compatible with gzip compression. -class igzstream : public gzstreambase, public std::istream { -public: - igzstream() : std::istream(&buf) { } - - igzstream(const char *name, int open_mode = std::ios::in) - : gzstreambase(name, open_mode), std::istream(&buf) { } - - gzstreambuf *rdbuf() { return gzstreambase::rdbuf(); } - - void open(const char *name, int open_mode = std::ios::in) { - gzstreambase::open(name, open_mode); - } -}; - -class ogzstream : public gzstreambase, public std::ostream { -public: - ogzstream() : std::ostream(&buf) { } - - ogzstream(const char *name, int mode = std::ios::out) - : gzstreambase(name, mode), std::ostream(&buf) { } - - gzstreambuf *rdbuf() { return gzstreambase::rdbuf(); } - - void open(const char *name, int open_mode = std::ios::out) { - gzstreambase::open(name, open_mode); - } -}; - -#endif diff --git a/src/commons/GzReader.h b/src/commons/GzReader.h new file mode 100644 index 000000000..85aa55a81 --- /dev/null +++ b/src/commons/GzReader.h @@ -0,0 +1,93 @@ +#include "Debug.h" + +#include +#include +#include + +#ifdef HAVE_ZLIB +#include +#endif + +class GzReader { +public: + enum Mode { + FILE_MODE, +#ifdef HAVE_ZLIB + GZ_MODE +#endif + }; + + GzReader(const std::string &filename) { + if (filename.size() >= 3 && filename.substr(filename.size() - 3) == ".gz") { +#ifdef HAVE_ZLIB + mode = GZ_MODE; + gzHandle = gzopen(filename.c_str(), "r"); + openFailed = !gzHandle; + return; +#else + Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Cannot read compressed input\n"; + EXIT(EXIT_FAILURE); +#endif + } + mode = FILE_MODE; + file = fopen(filename.c_str(), "r"); + openFailed = !file; + } + + ~GzReader() { + if (mode == FILE_MODE && file) fclose(file); +#ifdef HAVE_ZLIB + else if (mode == GZ_MODE && gzHandle) gzclose(gzHandle); +#endif + } + + bool fail() const { + return openFailed; + } + + bool getline(std::string &line) { + line.clear(); + if (openFailed) return false; + + char buffer[4096]; + bool complete = false; + while (!complete) { + if (mode == FILE_MODE) { + if (fgets(buffer, sizeof(buffer), file) != NULL) { + if (char *newline = strchr(buffer, '\n')) { + line.append(buffer, newline - buffer); + complete = true; + } else { + line.append(buffer); + } + } else { + return !line.empty(); + } + } + #ifdef HAVE_ZLIB + else if (mode == GZ_MODE) { + if (gzgets(gzHandle, buffer, sizeof(buffer)) != NULL) { + if (char *newline = strchr(buffer, '\n')) { + line.append(buffer, newline - buffer); + complete = true; + } else { + line.append(buffer); + } + } else { + return !line.empty(); + } + } + #endif + } + + return true; + } + +private: + Mode mode; + bool openFailed = false; + FILE *file = NULL; +#ifdef HAVE_ZLIB + gzFile gzHandle = NULL; +#endif +}; diff --git a/src/util/convertkb.cpp b/src/util/convertkb.cpp index 22a8dbadb..8221e28ac 100644 --- a/src/util/convertkb.cpp +++ b/src/util/convertkb.cpp @@ -4,10 +4,7 @@ #include "FileUtil.h" #include "Debug.h" #include "UniprotKB.h" - -#ifdef HAVE_ZLIB -#include "gzstream.h" -#endif +#include "GzReader.h" #include #include @@ -102,19 +99,8 @@ int convertkb(int argc, const char **argv, const Command &command) { Debug::Progress progress; for (std::vector::const_iterator it = par.filenames.begin(); it != par.filenames.end(); ++it) { - std::istream *kbIn; - if (Util::endsWith(".gz", *it)) { -#ifdef HAVE_ZLIB - kbIn = new igzstream((*it).c_str()); -#else - Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Can not read compressed input\n"; - EXIT(EXIT_FAILURE); -#endif - } else { - kbIn = new std::ifstream(*it); - } - - if (kbIn->fail()) { + GzReader kbIn(*it); + if (kbIn.fail()) { Debug(Debug::ERROR) << "File " << (*it) << " not found\n"; EXIT(EXIT_FAILURE); } @@ -122,7 +108,7 @@ int convertkb(int argc, const char **argv, const Command &command) { Debug(Debug::INFO) << "Extracting data from " << (*it) << "\n"; std::string line; unsigned int i = 0; - while (std::getline(*kbIn, line)) { + while (kbIn.getline(line)) { if (line.length() < 2) { Debug(Debug::WARNING) << "Invalid entry\n"; continue; @@ -156,7 +142,6 @@ int convertkb(int argc, const char **argv, const Command &command) { i++; } } - delete kbIn; } for (std::vector::const_iterator it = enabledColumns.begin(); it != enabledColumns.end(); ++it) { diff --git a/src/util/convertmsa.cpp b/src/util/convertmsa.cpp index 765664c78..9e8723ae3 100644 --- a/src/util/convertmsa.cpp +++ b/src/util/convertmsa.cpp @@ -2,33 +2,18 @@ #include "DBWriter.h" #include "Debug.h" #include "Util.h" +#include "GzReader.h" -#include #include #include -#ifdef HAVE_ZLIB -#include "gzstream.h" -#endif int convertmsa(int argc, const char **argv, const Command &command) { Parameters &par = Parameters::getInstance(); par.parseParameters(argc, argv, command, true, 0, 0); - std::istream *in; - if (Util::endsWith(".gz", par.db1)) { -#ifdef HAVE_ZLIB - in = new igzstream(par.db1.c_str()); -#else - Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Can not read compressed input!\n"; - return EXIT_FAILURE; -#endif - } else { - in = new std::ifstream(par.db1); - } - - - if (in->fail()) { + GzReader in(par.db1); + if (in.fail()) { Debug(Debug::ERROR) << "File " << par.db1 << " not found!\n"; return EXIT_FAILURE; } @@ -47,7 +32,7 @@ int convertmsa(int argc, const char **argv, const Command &command) { result.reserve(10 * 1024 * 1024); Debug::Progress progress; - while (std::getline(*in, line)) { + while (in.getline(line)) { size_t lineLength = line.length(); if (lineLength < 1) { continue; @@ -135,6 +120,5 @@ int convertmsa(int argc, const char **argv, const Command &command) { } writer.close(); - delete in; return EXIT_SUCCESS; } diff --git a/src/util/nrtotaxmapping.cpp b/src/util/nrtotaxmapping.cpp index 0dee3d3fb..4033da702 100644 --- a/src/util/nrtotaxmapping.cpp +++ b/src/util/nrtotaxmapping.cpp @@ -6,11 +6,7 @@ #include "NcbiTaxonomy.h" #include "FastSort.h" #include "MemoryMapped.h" - -#ifdef HAVE_ZLIB -#include "gzstream.h" -#endif -#include +#include "GzReader.h" #ifdef OPENMP #include @@ -65,26 +61,15 @@ int nrtotaxmapping(int argc, const char **argv, const Command& command) { std::vector> accessionMapping; for (size_t i = 0; i < par.filenames.size(); i++) { - std::istream *kbIn; - if (Util::endsWith(".gz", par.filenames[i])) { -#ifdef HAVE_ZLIB - kbIn = new igzstream(par.filenames[i].c_str()); -#else - Debug(Debug::ERROR) << "MMseqs2 was not compiled with zlib support. Cannot read compressed input\n"; - EXIT(EXIT_FAILURE); -#endif - } else { - kbIn = new std::ifstream(par.filenames[i]); - } - - if (kbIn->fail()) { + GzReader kbIn(par.filenames[i]); + if (kbIn.fail()) { Debug(Debug::ERROR) << "File " << par.filenames[i] << " not found\n"; EXIT(EXIT_FAILURE); } std::string line; const char *entry[255]; - while (std::getline(*kbIn, line)) { + while (kbIn.getline(line)) { progress.updateProgress(); const size_t columns = Util::getWordsOfLine(line.c_str(), entry, 255); if (columns < 4) {