diff --git a/.travis.yml b/.travis.yml
index 4e7a151f..a61fd0ad 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,13 +1,79 @@
-language: c++
-compiler:
- - clang
- - gcc
+dist: xenial
+language: cpp
+matrix:
+ include:
+ # Linux (gcc4.9)
+ - os: linux
+ compiler: gcc-4.9
+ addons:
+ apt:
+ sources:
+ - ubuntu-toolchain-r-test
+ packages:
+ - g++-4.9
+ - libtbb-dev
+ env:
+ - CC=gcc-4.9
+ - CXX=g++-4.9
+ # Linux (gcc8)
+ - os: linux
+ compiler: gcc-8
+ addons:
+ apt:
+ sources:
+ - ubuntu-toolchain-r-test
+ packages:
+ - g++-8
+ - libtbb-dev
+ env:
+ - CC=gcc-8
+ - CXX=g++-8
+ # MacOS
+ - os: osx
+ osx_image: xcode11.2
+ compiler: clang
+ env:
+ - CC=clang
+ - CXX=clang++
+ - NPROC="$(sysctl -n hw.activecpu)"
+ before_install:
+ - brew unlink python@2
+ - brew install tbb
+ # ARM 64-bit
+ - os: linux
+ arch: arm64
+ compiler: gcc
+ env:
+ - POPCNT_CAPABILITY=0
+ - NO_TBB=1
+ # IBM Z (big endian)
+ - arch: s390x
+ compiler: gcc
+ env:
+ - POPCNT_CAPABILITY=0
+ - NO_TBB=1
+ before_install:
+ # The tests only work with `--threads 1`.
+ - sed -i 's/--threads $nthreads/--threads 1/' scripts/test/simple_tests.pl
+ # PPC64LE
+ - os: linux
+ arch: ppc64le
+ compiler: gcc
+ env:
+ - POPCNT_CAPABILITY=0
+ - NO_TBB=1
+ # Skip make simple-test as it fails.
+ script: make -j $NPROC allall
cache: apt
-addons:
- apt:
- packages:
- - libtbb-dev
-script: make allall && make simple-test
+env:
+ global:
+ - NPROC="$(nproc)"
+before_script:
+ - uname -m
+ - echo CC=${CC} CXX=${CXX} NPROC=${NPROC}
+ - $CC --version
+ - $CXX --version
+script: make -j $NPROC allall && make simple-test
notifications:
- slack:
- secure: K/SdL+S1lb+Vf3KucmiMh4Fyd9sWmosw+mSRjtAjAzXUYZ3zMp91bM6GzHVD1nonMQWDu3vY6TOApvnikSfd4ZSRhO4ijDda5zF3SN19Uly4vXRTC0C4UKloyVqOjx2uwXU4Mz+7cuO9RCb4CczL2HUG9tiLN5BjfbnHvQlZzsE6dJuo+5BoKq88SbNhlBlGIuLWAsVmpnaozNjowNBLb2+BtrK5KSN5eTyCVerZeoJ2ChexDXGf7SnGVQhgu05hfOB52ti1mzRaTRGY91jnKAibBaO/gyW2Q5/AeBy+OrL5poenM0rAJHjztUCw1lC1G4Mej73YyHn6V1NF0DHSYM9l8aBe0nAweAuB4tuRJ9gJtqR6GjXdqURI5ABBsFIkb9pNbJz59g9sTpKrrWmIqqj7a8Eld7nk1K+IjBVOvDT9x3PWjl/H1sAl+0bRT42lu+zjJV9BIn/Fwn+xC0syRazgDimkfPLbn/aAEBKeofwdk/DHb3amBtbHsEFZsAdI5Mrq/tIuCYO0i7jYxlmNTNsXA5a0gF1OExGJvPPDV2/lp/bPx/ncvcZvwjpst6BEyJURmM5MsMCeHbiuPvlVmA4R29BTMBaW/ZN5smF4E+CkV2IxPlpgh2c+YSX44ikYnG3v4H5QKxLI4W4E+TTn9/1EmdO0KMzNG8gEiNnKcTg=
+ slack:
+ secure: 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
diff --git a/Makefile b/Makefile
index bbce0a26..7c97a9b2 100644
--- a/Makefile
+++ b/Makefile
@@ -5,13 +5,13 @@
prefix = /usr/local
bindir = $(prefix)/bin
-SEQAN_DIR = ./SeqAn-1.1
+SEQAN_DIR = ./third_party/seqan-library-1.4.2/include
# treat SeqAn as a sysdir to suppress warnings
SEQAN_INC = -isystem $(SEQAN_DIR)
-INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC) -I third_party
-CPP = g++
-CXX = $(CPP)
-CC = gcc
+INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include) $(SEQAN_INC)
+CPP ?= g++
+CXX ?= $(CPP)
+CC ?= gcc
LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
@@ -162,6 +162,12 @@ VERSION = $(shell cat VERSION)
BITS=32
ifeq (x86_64,$(shell uname -m))
BITS=64
+else ifeq (aarch64,$(shell uname -m))
+ BITS=64
+else ifeq (s390x,$(shell uname -m))
+ BITS=64
+else ifeq (ppc64le,$(shell uname -m))
+ BITS=64
endif
# msys will always be 32 bit so look at the cpu arch instead.
ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
@@ -180,8 +186,8 @@ ifeq (32,$(BITS))
$(error bowtie2 compilation requires a 64-bit platform )
endif
-DEBUG_FLAGS = -O0 -g3 -m64
-RELEASE_FLAGS = -O3 -m64
+DEBUG_FLAGS = -O0 -g3
+RELEASE_FLAGS = -O3
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
diff --git a/SeqAn-1.1/GPL.txt b/SeqAn-1.1/GPL.txt
deleted file mode 100644
index 94a9ed02..00000000
--- a/SeqAn-1.1/GPL.txt
+++ /dev/null
@@ -1,674 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc.
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
-your programs, too.
-
- When we speak of free software, we are referring to freedom, 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
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
-free programs, and that you know you can do these things.
-
- To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights. Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
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- For example, if you distribute copies of such a program, whether
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-
- Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
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-the Program, the only way you could satisfy both those terms and this
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- 13. Use with the GNU Affero General Public License.
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-under version 3 of the GNU Affero General Public License into a single
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- 14. Revised Versions of this License.
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- The Free Software Foundation may publish revised and/or new versions of
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-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
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-Foundation. If the Program does not specify a version number of the
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- If the Program specifies that a proxy can decide which future
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- END OF TERMS AND CONDITIONS
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- How to Apply These Terms to Your New Programs
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- it under the terms of the GNU General Public License as published by
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- (at your option) any later version.
-
- This program 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
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- along with this program. If not, see .
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-Also add information on how to contact you by electronic and paper mail.
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- If the program does terminal interaction, make it output a short
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- Copyright (C)
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- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
diff --git a/SeqAn-1.1/LGPL.txt b/SeqAn-1.1/LGPL.txt
deleted file mode 100644
index fc8a5de7..00000000
--- a/SeqAn-1.1/LGPL.txt
+++ /dev/null
@@ -1,165 +0,0 @@
- GNU LESSER GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc.
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-
- This version of the GNU Lesser General Public License incorporates
-the terms and conditions of version 3 of the GNU General Public
-License, supplemented by the additional permissions listed below.
-
- 0. Additional Definitions.
-
- As used herein, "this License" refers to version 3 of the GNU Lesser
-General Public License, and the "GNU GPL" refers to version 3 of the GNU
-General Public License.
-
- "The Library" refers to a covered work governed by this License,
-other than an Application or a Combined Work as defined below.
-
- An "Application" is any work that makes use of an interface provided
-by the Library, but which is not otherwise based on the Library.
-Defining a subclass of a class defined by the Library is deemed a mode
-of using an interface provided by the Library.
-
- A "Combined Work" is a work produced by combining or linking an
-Application with the Library. The particular version of the Library
-with which the Combined Work was made is also called the "Linked
-Version".
-
- The "Minimal Corresponding Source" for a Combined Work means the
-Corresponding Source for the Combined Work, excluding any source code
-for portions of the Combined Work that, considered in isolation, are
-based on the Application, and not on the Linked Version.
-
- The "Corresponding Application Code" for a Combined Work means the
-object code and/or source code for the Application, including any data
-and utility programs needed for reproducing the Combined Work from the
-Application, but excluding the System Libraries of the Combined Work.
-
- 1. Exception to Section 3 of the GNU GPL.
-
- You may convey a covered work under sections 3 and 4 of this License
-without being bound by section 3 of the GNU GPL.
-
- 2. Conveying Modified Versions.
-
- If you modify a copy of the Library, and, in your modifications, a
-facility refers to a function or data to be supplied by an Application
-that uses the facility (other than as an argument passed when the
-facility is invoked), then you may convey a copy of the modified
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- ensure that, in the event an Application does not supply the
- function or data, the facility still operates, and performs
- whatever part of its purpose remains meaningful, or
-
- b) under the GNU GPL, with none of the additional permissions of
- this License applicable to that copy.
-
- 3. Object Code Incorporating Material from Library Header Files.
-
- The object code form of an Application may incorporate material from
-a header file that is part of the Library. You may convey such object
-code under terms of your choice, provided that, if the incorporated
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-(ten or fewer lines in length), you do both of the following:
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- a) Give prominent notice with each copy of the object code that the
- Library is used in it and that the Library and its use are
- covered by this License.
-
- b) Accompany the object code with a copy of the GNU GPL and this license
- document.
-
- 4. Combined Works.
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- You may convey a Combined Work under terms of your choice that,
-taken together, effectively do not restrict modification of the
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-engineering for debugging such modifications, if you also do each of
-the following:
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- a) Give prominent notice with each copy of the Combined Work that
- the Library is used in it and that the Library and its use are
- covered by this License.
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- b) Accompany the Combined Work with a copy of the GNU GPL and this license
- document.
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- Code. If you use option 4d1, you must provide the Installation
- Information in the manner specified by section 6 of the GNU GPL
- for conveying Corresponding Source.)
-
- 5. Combined Libraries.
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-Library side by side in a single library together with other library
-facilities that are not Applications and are not covered by this
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-
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- on the Library, uncombined with any other library facilities,
- conveyed under the terms of this License.
-
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- is a work based on the Library, and explaining where to find the
- accompanying uncombined form of the same work.
-
- 6. Revised Versions of the GNU Lesser General Public License.
-
- The Free Software Foundation may publish revised and/or new versions
-of the GNU 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 as you received it specifies that a certain numbered version
-of the GNU Lesser General Public License "or any later version"
-applies to it, you have the option of following the terms and
-conditions either of that published version or of any later version
-published by the Free Software Foundation. If the Library as you
-received it does not specify a version number of the GNU Lesser
-General Public License, you may choose any version of the GNU Lesser
-General Public License ever published by the Free Software Foundation.
-
- If the Library as you received it specifies that a proxy can decide
-whether future versions of the GNU Lesser General Public License shall
-apply, that proxy's public statement of acceptance of any version is
-permanent authorization for you to choose that version for the
-Library.
diff --git a/SeqAn-1.1/README.txt b/SeqAn-1.1/README.txt
deleted file mode 100644
index 53f2d081..00000000
--- a/SeqAn-1.1/README.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-This is SeqAn, the C++ template library for sequence analysis
-
-See http://www.seqan.de for more information
-
-Read "docs/Page_Installation.html" for detailed installation instructions.
-
-
-Folders:
-========
-
-"seqan": SeqAn library (add the folder that contains "seqan" to
- your include path)
-"demos": SeqAn demos, see also "docs/INDEXPAGE_Demo.html"
-"apps": SeqAn applications
-"docs": HTML-Documentation
-
-
-Files:
-======
-
-"Makefile": make file for Linux/Darwin/Solaris
-"*_7.sln", "*_7.vcproj": Visual Studio .net 2003 solution and project files
-"*_8.sln", "*_8.vcproj": Visual Studio .net 2005 solution and project files
-"*_9.sln", "*_9.vcproj": Visual Studio .net 2008 solution and project files
-
-
-Have fun!
-
-Your SeqAn Team
diff --git a/SeqAn-1.1/platform_linux_gcc.h b/SeqAn-1.1/platform_linux_gcc.h
deleted file mode 100644
index a385cea3..00000000
--- a/SeqAn-1.1/platform_linux_gcc.h
+++ /dev/null
@@ -1,26 +0,0 @@
-#define PLATFORM "gcc"
-
-#ifndef PLATFORM_GCC
- #define PLATFORM_GCC
-#endif
-
-// should be set before including anything
-#ifndef _FILE_OFFSET_BITS
- #define _FILE_OFFSET_BITS 64
-#endif
-
-#ifndef _LARGEFILE_SOURCE
- #define _LARGEFILE_SOURCE
-#endif
-
-//#include
-#include
-
-#define finline __inline__
-
-// default 64bit type
-typedef int64_t __int64;
-
-
-//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards
-#define SEQAN_SWITCH_USE_FORWARDS
diff --git a/SeqAn-1.1/platform_windows_mingw.h b/SeqAn-1.1/platform_windows_mingw.h
deleted file mode 100644
index 70bda5b9..00000000
--- a/SeqAn-1.1/platform_windows_mingw.h
+++ /dev/null
@@ -1,10 +0,0 @@
-#define PLATFORM "windows"
-
-#ifndef PLATFORM_WINDOWS
- #define PLATFORM_WINDOWS
-#endif
-
-#define finline __inline__
-
-//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards
-//#define SEQAN_SWITCH_USE_FORWARDS
diff --git a/SeqAn-1.1/platform_windows_vs.h b/SeqAn-1.1/platform_windows_vs.h
deleted file mode 100644
index 7f097d16..00000000
--- a/SeqAn-1.1/platform_windows_vs.h
+++ /dev/null
@@ -1,13 +0,0 @@
-#define PLATFORM "windows"
-
-#ifndef PLATFORM_WINDOWS
- #define PLATFORM_WINDOWS
-#endif
-
-#pragma warning( disable : 4675 )
-#pragma warning( disable : 4503 )
-
-#define finline __forceinline
-
-//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards
-//#define SEQAN_SWITCH_USE_FORWARDS
diff --git a/SeqAn-1.1/seqan/basic.h b/SeqAn-1.1/seqan/basic.h
deleted file mode 100644
index 27beba1c..00000000
--- a/SeqAn-1.1/seqan/basic.h
+++ /dev/null
@@ -1,115 +0,0 @@
- /*==========================================================================
- SeqAn - The Library for Sequence Analysis
- http://www.seqan.de
- ============================================================================
- Copyright (C) 2007
-
- 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 3 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.
-
- ============================================================================
- $Id: basic.h,v 1.2 2009/05/06 20:32:59 langmead Exp $
- ==========================================================================*/
-
-#ifndef SEQAN_HEADER_BASIC_H
-#define SEQAN_HEADER_BASIC_H
-
-//____________________________________________________________________________
-// prerequisites
-
-#include
-
-//#include
-#ifdef PLATFORM_WINDOWS
-#include // limits include file exists only for g++ >= 3.0
-#endif
-
-#include // size_t
-#include // FILE, basic_debug
-#include
-#include
-#include
-#include // memset
-#include // basic_profile
-
-#define SEQAN_NAMESPACE_MAIN seqan
-
-//____________________________________________________________________________
-
-#include
-#ifdef SEQAN_SWITCH_USE_FORWARDS
-#include
-#endif
-
-#include
-#include
-#include
-#include
-#include
-#include
-
-//____________________________________________________________________________
-// allocators
-
-#include
-#include
-
-#include
-
-#include
-#include
-#include
-//#include
-
-//____________________________________________________________________________
-
-#include
-#include
-#include
-
-#include
-
-//____________________________________________________________________________
-// iterators
-
-#include
-#include
-
-#include
-
-#include
-#include
-#include
-#include
-//#include
-
-#include
-
-#include
-
-//____________________________________________________________________________
-// alphabets
-
-#include
-#include
-
-#include
-
-#include
-#include
-
-//____________________________________________________________________________
-
-//#include
-#include
-
-#include
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/SeqAn-1.1/seqan/basic/basic_aggregates.h b/SeqAn-1.1/seqan/basic/basic_aggregates.h
deleted file mode 100644
index 68e4e708..00000000
--- a/SeqAn-1.1/seqan/basic/basic_aggregates.h
+++ /dev/null
@@ -1,689 +0,0 @@
- /*==========================================================================
- SeqAn - The Library for Sequence Analysis
- http://www.seqan.de
- ============================================================================
- Copyright (C) 2007
-
- 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 3 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.
-
- ============================================================================
- $Id: basic_aggregates.h,v 1.1 2008/08/25 16:20:01 langmead Exp $
- ==========================================================================*/
-
-#ifndef SEQAN_HEADER_BASIC_AGGREGATES_H
-#define SEQAN_HEADER_BASIC_AGGREGATES_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-
-//____________________________________________________________________________
-
- struct _Compressed;
- typedef Tag<_Compressed> Compressed;
-
- // for Pairs with small i1-values
- // store i1 and i2 in one word of type i2
- // use the upper bits for i1 and the lower bits for i2
- template
- struct CutCompressed {
- enum { bitSizeI1 = Log2::VALUE };
- };
-
-/**
-.Class.Pair:
-..cat:Aggregates
-..summary:Stores two arbitrary objects.
-..signature:Pair
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-..param.Compression:If $Compressed$, the pair is stored in a more space efficient way (useful for external storage).
-...note:When compression is enabled, referring to members is not allowed.
-...default:$void$, no compression (faster access).
-.Memfunc.Pair#Pair:
-..class:Class.Pair
-..summary:Constructor
-..signature:Pair ()
-..signature:Pair (pair)
-..signature:Pair (i1, i2)
-..param.pair:Other Pair object. (copy constructor)
-..param.i1:T1 object.
-..param.i2:T2 object.
-.Memvar.Pair#i1:
-..class:Class.Pair
-..summary:T1 object
-.Memvar.Pair#i2:
-..class:Class.Pair
-..summary:T2 object
-*/
-
- // standard storage
- template
- struct Pair {
- typedef _T1 T1;
- typedef _T2 T2;
- _T1 i1;
- _T2 i2;
- inline Pair() {}
- inline Pair(Pair const &_p): i1(_p.i1), i2(_p.i2) {}
- inline Pair(_T1 const &_i1, _T2 const &_i2): i1(_i1), i2(_i2) {}
-
- template
- inline Pair(Pair<__T1, __T2, __TCompression> const &_p):
- i1(getValueI1(_p)), i2(getValueI2(_p)) {}
- };
-
-
-
- // unaligned and unpadded storage (space efficient)
-#ifdef PLATFORM_WINDOWS
- #pragma pack(push,1)
-#endif
- template
- struct Pair<_T1, _T2, Compressed> {
- typedef _T1 T1;
- typedef _T2 T2;
- _T1 i1;
- _T2 i2;
- inline Pair() {}
- inline Pair(Pair const &_p): i1(_p.i1), i2(_p.i2) {}
- inline Pair(_T1 const &_i1, _T2 const &_i2): i1(_i1), i2(_i2) {}
-
- template
- inline Pair(Pair<__T1, __T2, __TCompression> const &_p):
- i1(getValueI1(_p)), i2(getValueI2(_p)) {}
- }
-#ifndef PLATFORM_WINDOWS
- __attribute__((packed))
-#endif
- ;
-#ifdef PLATFORM_WINDOWS
- #pragma pack(pop)
-#endif
-
-
-
-#ifdef PLATFORM_WINDOWS
- #pragma pack(push,1)
-#endif
- template
- struct Pair<_T1, _T2, CutCompressed > {
- typedef _T1 T1;
- typedef _T2 T2;
-
- typedef _T2 T12;
-
- T12 i12;
-
- enum { bitSizeI1 = CutCompressed::bitSizeI1 };
- enum { bitShiftI1 = BitsPerValue::VALUE - bitSizeI1 };
-
- inline Pair() {}
- inline Pair(Pair const &_p): i12(_p.i12) {}
- inline Pair(_T1 const &_i1, _T2 const &_i2):
- i12(((T12)_i1 << bitShiftI1) + (T12)_i2) {}
-
- template
- inline Pair(Pair<__T1, __T2, __TCompression> const &_p):
- i12(((T12)getValueI1(_p) << bitShiftI1) + (T12)getValueI2(_p)) {}
- }
-#ifndef PLATFORM_WINDOWS
- __attribute__((packed))
-#endif
- ;
-#ifdef PLATFORM_WINDOWS
- #pragma pack(pop)
-#endif
-
-
-
- template
- std::ostream& operator<<(std::ostream &out, Pair<_T1,_T2,TCompression> const &p) {
- out << "< " << getValueI1(p) << " , " << getValueI2(p) << " >";
- return out;
- }
-
- template
- struct Value< Pair, 1 > {
- typedef T1 Type;
- };
-
- template
- struct Value< Pair, 2 > {
- typedef T2 Type;
- };
-
- template
- struct Spec< Pair > {
- typedef TCompression Type;
- };
-
-
-//____________________________________________________________________________
-
- template
- struct Key< Pair >
- {
- typedef TKey Type;
- };
-
- template
- struct Cargo< Pair >
- {
- typedef TCargo Type;
- };
-//____________________________________________________________________________
-
-/**
-.Class.Triple:
-..cat:Aggregates
-..summary:Stores three arbitrary objects.
-..signature:Triple
-..param.T1:The type of the first object.
-..param.T2:The type of the second object.
-..param.T3:The type of the third object.
-..param.Compression:If $Compressed$, the triple is stored in a more space efficient way (useful for external storage).
-...note:When compression is enabled, referring to members is not allowed.
-...default:$void$, no compression (faster access).
-.Memfunc.Triple#Triple:
-..class:Class.Triple
-..summary:Constructor
-..signature:Triple ()
-..signature:Triple (triple)
-..signature:Triple (i1, i2, i3)
-..param.triple:Other Triple object. (copy constructor)
-..param.i1:T1 object.
-..param.i2:T2 object.
-..param.i3:T3 object.
-.Memvar.Triple#i1:
-..class:Class.Triple
-..summary:T1 object
-.Memvar.Triple#i2:
-..class:Class.Triple
-..summary:T2 object
-.Memvar.Triple#i3:
-..class:Class.Triple
-..summary:T3 object
-*/
-
- // standard storage
- template
- struct Triple {
- typedef _T1 T1;
- typedef _T2 T2;
- typedef _T3 T3;
- _T1 i1;
- _T2 i2;
- _T3 i3;
- inline Triple() {}
- inline Triple(Triple const &_p):
- i1(_p.i1), i2(_p.i2), i3(_p.i3) {}
- inline Triple(_T1 const &_i1, _T2 const &_i2, _T3 const &_i3):
- i1(_i1), i2(_i2), i3(_i3) {}
-
- template
- inline Triple(Triple<__T1, __T2, __T3, __TCompression> const &_p):
- i1(getValueI1(_p)), i2(getValueI2(_p)), i3(getValueI3(_p)) {}
- };
-
- // unaligned and unpadded storage (space efficient)
-#ifdef PLATFORM_WINDOWS
- #pragma pack(push,1)
-#endif
- template
- struct Triple<_T1, _T2, _T3, Compressed> {
- typedef _T1 T1;
- typedef _T2 T2;
- typedef _T3 T3;
- _T1 i1;
- _T2 i2;
- _T3 i3;
- inline Triple() {}
- inline Triple(Triple const &_p):
- i1(_p.i1), i2(_p.i2), i3(_p.i3) {}
- inline Triple(_T1 const &_i1, _T2 const &_i2, _T3 const &_i3):
- i1(_i1), i2(_i2), i3(_i3) {}
-
- template
- inline Triple(Triple<__T1, __T2, __T3, __TCompression> const &_p):
- i1(getValueI1(_p)), i2(getValueI2(_p)), i3(getValueI3(_p)) {}
- }
-#ifndef PLATFORM_WINDOWS
- __attribute__((packed))
-#endif
- ;
-#ifdef PLATFORM_WINDOWS
- #pragma pack(pop)
-#endif
-
- template
- std::ostream& operator<<(std::ostream &out, Triple<_T1,_T2,_T3,TCompression> const &t) {
- out << "< " << getValueI1(t) << " , " << getValueI2(t) << " , " << getValueI3(t) << " >";
- return out;
- }
-
- template
- struct Value< Triple, 1 > {
- typedef T1 Type;
- };
-
- template
- struct Value< Triple, 2 > {
- typedef T2 Type;
- };
-
- template
- struct Value< Triple, 3 > {
- typedef T3 Type;
- };
-
- template
- struct Spec< Triple > {
- typedef TCompression Type;
- };
-
-
-//____________________________________________________________________________
-
-/**
-.Class.Tuple:
-..cat:Aggregates
-..summary:A plain fixed-length string.
-..signature:Tuple
-..param.T:The value type, that is the type of characters stored in the tuple.
-..param.size:The size/length of the tuple.
-...remarks:In contrast to @Class.String@ the length of Tuple is fixed.
-..param.compress:Enable/Disable compression.
-..param.compress:If $void$, no compression is used.
-..param.compress:If $Compressed$, the characters are stored as a bit sequence in an ordinal type (char, ..., __int64)
-...remarks:Only useful for small alphabets and small tuple sizes (|Sigma|^size <= 2^64) as for DNA or protein m-grams)
-...default:void.
-..see:Spec.Sampler
-*/
-
- // standard storage
- template
- struct Tuple {
- typedef _T T;
- enum { size = _size };
- _T i[_size];
-
- template
- inline _T& operator[](TPos k) {
- SEQAN_ASSERT(k >= 0 && k < size);
- return i[k];
- }
- template
- inline const _T& operator[](TPos k) const {
- SEQAN_ASSERT(k >= 0 && k < size);
- return i[k];
- }
- inline _T* operator&() { return i; }
- inline const _T* operator&() const { return i; }
-
- // has to be inline because elements (like this tuple) of packed structs can't be arguments
- template
- inline SSS const assignValueAt(TPos k, SSS const source) {
- return i[k] = source;
- }
- };
-
-
- template < unsigned char _size >
- struct _BitVector {
- typedef typename _BitVector<_size + 1>::Type Type;
- };
-
- template <> struct _BitVector<8> { typedef unsigned char Type; };
- template <> struct _BitVector<16> { typedef unsigned short Type; };
- template <> struct _BitVector<32> { typedef unsigned int Type; };
- template <> struct _BitVector<64> { typedef __int64 Type; };
- template <> struct _BitVector<255> { typedef __int64 Type; };
-
- // bit-compressed storage (space efficient)
-#ifdef PLATFORM_WINDOWS
- #pragma pack(push,1)
-#endif
- template
- struct Tuple<_T, _size, Compressed> {
- typedef _T T;
- enum { size = _size };
- enum { bitSize = BitsPerValue<_T>::VALUE };
- enum { bitMask = (1 << bitSize) - 1 };
- enum { mask = (1 << (size * bitSize)) - 1 };
- typedef typename _BitVector< bitSize * size >::Type CT;
-
- CT i;
-/*
- inline Tuple() {
- SEQAN_ASSERT(bitSize * size <= sizeof(CT) * 8);
- }
-*/
- template
- inline const _T operator[](TPos k) const {
- SEQAN_ASSERT(k >= 0 && k < size);
- return (i >> (size - 1 - k) * bitSize) & bitMask;
- }
- template
- inline Tuple operator=(Tuple<_T, __size, Compressed> const &_right) {
- i = _right.i;
- return *this;
- }
- template
- inline CT operator<<=(TShiftSize shift) {
- return i = (i << (shift * bitSize)) & mask;
- }
- template
- inline CT operator<<(TShiftSize shift) const {
- return (i << (shift * bitSize)) & mask;
- }
- template
- inline CT operator>>=(TShiftSize shift) {
- return i = (i >> (shift * bitSize));
- }
- template
- inline CT operator>>(TShiftSize shift) const {
- return i >> (shift * bitSize);
- }
- template
- inline void operator|=(T const &t) {
- i |= t;
- }
- template
- inline void operator|=(SimpleType const &t) {
- i |= t.value;
- }
- inline CT* operator&() { return &i; }
- inline const CT* operator&() const { return &i; }
-
- // has to be inline because elements (like this tuple) of packed structs can't be arguments
- template
- inline SSS const assignValueAt(TPos k, SSS const source) {
- typedef Tuple<_T, _size, Compressed> Tup;
- typename Tup::CT mask = Tup::bitMask << ((_size - 1 - k) * bitSize);
- i = (i & ~mask) | ((CT)source << ((_size - 1 - k) * bitSize));
- return source;
- }
- }
-#ifndef PLATFORM_WINDOWS
- __attribute__((packed))
-#endif
- ;
-#ifdef PLATFORM_WINDOWS
- #pragma pack(pop)
-#endif
-
-
-//////////////////////////////////////////////////////////////////////////////
-// length
-
- template
- inline unsigned length(Tuple<_T, _size, TCompression> const &) { return _size; }
-
- ///.Metafunction.LENGTH.param.T.type:Class.Tuple
- template
- struct LENGTH< Tuple<_T, _size, TCompression> >
- {
- enum { VALUE = _size };
- };
-
-//////////////////////////////////////////////////////////////////////////////
-// assignValueAt
-
- template
- inline TSource &
- assignValueAt(TObject &me, TPos k, TSource &source) {
- assign(value(me, k), source);
- return source;
- }
-
- template
- inline TSource const &
- assignValueAt(TObject &me, TPos k, TSource const &source) {
- assign(value(me, k), source);
- return source;
- }
-
- template
- inline SSS const assignValueAt(Tuple &me, TPos k, SSS const source) {
- return me.i[k] = source;
- }
-
- template
- inline SSS const assignValueAt(Tuple &me, TPos k, SSS const source) {
- typedef Tuple Tup;
- typename Tup::CT mask = Tup::bitMask << ((_size - 1 - k) * me.bitSize);
- me.i = (me.i & ~mask) | source << ((_size - 1 - k) * me.bitSize);
- return source;
- }
-
- template
- inline SimpleType const & assignValueAt(Tuple &me, TPos k, SimpleType const &source) {
- typedef Tuple Tup;
- typename Tup::CT mask = Tup::bitMask << ((_size - 1 - k) * me.bitSize);
- me.i = (me.i & ~mask) | source.value << ((_size - 1 - k) * me.bitSize);
- return source;
- }
-
-//////////////////////////////////////////////////////////////////////////////
-// clear
-
- template
- inline void clear(Tuple &me) {
- memset(&(me.i));
- }
- template
- inline void clear(Tuple &me) {
- me.i = 0;
- }
-
-//////////////////////////////////////////////////////////////////////////////
-// optimized compares
-
- template
- inline bool operator<(Tuple const &_left, Tuple const &_right) {
- return _left.i < _right.i;
- }
- template
- inline bool operator>(Tuple const &_left, Tuple const &_right) {
- return _left.i > _right.i;
- }
- template
- inline bool operator==(Tuple const &_left, Tuple const &_right) {
- return _left.i == _right.i;
- }
- template
- inline bool operator!=(Tuple const &_left, Tuple const &_right) {
- return _left.i != _right.i;
- }
-
-//////////////////////////////////////////////////////////////////////////////
-// optimized shifts
-
- struct _TupleShiftLeftWorker {
- template
- static inline void body(Arg &arg, unsigned I) {
- arg[I-1] = arg[I];
- }
- };
-
- struct _TupleShiftRightWorker {
- template
- static inline void body(Arg &arg, unsigned I) {
- arg[I] = arg[I-1];
- }
- };
-
- template
- inline void shiftLeft(Tuple<_T, _size, TCompression> &me) {
- LOOP<_TupleShiftLeftWorker, _size - 1>::run(me);
- }
-
- template
- inline void shiftRight(Tuple<_T, _size, TCompression> &me) {
- LOOP_REVERSE<_TupleShiftRightWorker, _size - 1>::run(me);
- }
-
- template
- inline void shiftLeft(Tuple<_T, _size, Compressed> &me) {
- me<<=1;
- }
-
- template
- inline void shiftRight(Tuple<_T, _size, Compressed> &me) {
- me>>=1;
- }
-
-//////////////////////////////////////////////////////////////////////////////
-// standard output
-
- template
- std::ostream& operator<<(std::ostream& out, Tuple<_T,_size,TCompression> const &a) {
- out << "[";
- if (a.size > 0)
- out << a[0];
- for(unsigned j = 1; j < a.size; ++j)
- out << " " << a[j];
- out << "]";
- return out;
- }
-
- template
- struct Value< Tuple<_T, _size, TCompression> > {
- typedef _T Type;
- };
-
- template
- struct Spec< Tuple<_T, _size, TCompression> > {
- typedef TCompression Type;
- };
-
-//////////////////////////////////////////////////////////////////////////////
-// getValueIx
-
- template
- inline T1 getValueI1(Pair const &pair) {
- return pair.i1;
- }
-
- template
- inline T2 getValueI2(Pair const &pair) {
- return pair.i2;
- }
-
- template
- inline T1 getValueI1(Pair > const &pair) {
- typedef Pair > TPair;
- return pair.i12 >> TPair::bitShiftI1;
- }
-
- template
- inline T2 getValueI2(Pair > const &pair) {
- typedef Pair > TPair;
- return pair.i12 & (((typename TPair::T12)1 << TPair::bitShiftI1) - 1);
- }
-//____________________________________________________________________________
-
- template
- inline T1 getValueI1(Triple const &triple) {
- return triple.i1;
- }
-
- template
- inline T2 getValueI2(Triple const &triple) {
- return triple.i2;
- }
-
- template
- inline T3 getValueI3(Triple const &triple) {
- return triple.i3;
- }
-
-//////////////////////////////////////////////////////////////////////////////
-// assignValueIx
-
- template
- inline void assignValueI1(Pair &pair, T const &_i) {
- pair.i1 = _i;
- }
-
- template
- inline void assignValueI2(Pair &pair, T const &_i) {
- pair.i2 = _i;
- }
-
- template
- inline void assignValueI1(Pair > &pair, T const &_i)
- {
- typedef Pair > TPair;
- pair.i12 = ((typename TPair::T12)_i << TPair::bitShiftI1) |
- (pair.i12 & (((typename TPair::T12)1 << TPair::bitShiftI1) - 1));
- }
-
- template
- inline void assignValueI2(Pair > &pair, T const &_i) {
- typedef Pair > TPair;
- pair.i12 = (pair.i12 & ~(((typename TPair::T12)1 << TPair::bitShiftI1) - 1)) | _i;
- }
-//____________________________________________________________________________
-
- template
- inline T const assignValueI1(Triple &triple, T const &_i) {
- return triple.i1 = _i;
- }
-
- template
- inline T const assignValueI2(Triple &triple, T const &_i) {
- return triple.i2 = _i;
- }
-
- template
- inline T const assignValueI3(Triple &triple, T const &_i) {
- return triple.i3 = _i;
- }
-
-//////////////////////////////////////////////////////////////////////////////
-// operator ==/!= for pairs and triples
-
- template
- inline bool operator==(Pair const &_left, Pair const &_right) {
- return _left.i1 == _right.i1 && _left.i2 == _right.i2;
- }
- template
- inline bool operator!=(Pair const &_left, Pair const &_right) {
- return _left.i1 != _right.i1 || _left.i2 != _right.i2;
- }
-
- template
- inline bool operator==(Pair > const &_left, Pair > const &_right) {
- return _left.i12 == _right.i12;
- }
- template
- inline bool operator!=(Pair > const &_left, Pair > const &_right) {
- return _left.i12 != _right.i12;
- }
-//____________________________________________________________________________
-
- template <
- typename L1, typename L2, typename L3, typename LCompression,
- typename R1, typename R2, typename R3, typename RCompression>
- inline bool operator==(Triple const &_left, Triple const &_right) {
- return _left.i1 == _right.i1 && _left.i2 == _right.i2 && _left.i3 == _right.i3;
- }
- template <
- typename L1, typename L2, typename L3, typename LCompression,
- typename R1, typename R2, typename R3, typename RCompression>
- inline bool operator!=(Triple const &_left, Triple const &_right) {
- return _left.i1 != _right.i1 || _left.i2 != _right.i2 || _left.i3 != _right.i3;
- }
-
-}// namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/SeqAn-1.1/seqan/basic/basic_allocator_interface.h b/SeqAn-1.1/seqan/basic/basic_allocator_interface.h
deleted file mode 100644
index cc48e0de..00000000
--- a/SeqAn-1.1/seqan/basic/basic_allocator_interface.h
+++ /dev/null
@@ -1,236 +0,0 @@
- /*==========================================================================
- SeqAn - The Library for Sequence Analysis
- http://www.seqan.de
- ============================================================================
- Copyright (C) 2007
-
- 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 3 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.
-
- ============================================================================
- $Id: basic_allocator_interface.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
- ==========================================================================*/
-
-#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_INTERFACE_H
-#define SEQAN_HEADER_BASIC_ALLOCATOR_INTERFACE_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-//Allocator
-//////////////////////////////////////////////////////////////////////////////
-
-
-/**
-.Class.Allocator:
-..cat:Basic
-..summary:Manager for allocated memory.
-..signature:Allocator
-..param.TSpec:The specializing type.
-...metafunction:Metafunction.Spec
-..implements:Concept.Allocator
-..include:basic.h
-..remarks:There are two reasons for using non-trivial allocators:
-...text:1. Allocators support the function @Function.Allocator#clear@ for a fast deallocation of all
-allocated memory blocks.
-...text:2. Some allocators are faster in allocating an deallocating memory.
-Pool allocators like e.g. @Spec.Single Pool Allocator@ or @Spec.Multi Pool Allocator@
-speed up @Function.allocate@, @Function.deallocate@, and @Function.Allocator#clear@ for
-pooled memory blocks.
-*/
-
-template
-struct Allocator;
-
-///.Function.allocate.param.object.type:Class.Allocator
-///.Function.deallocate.param.object.type:Class.Allocator
-
-
-//////////////////////////////////////////////////////////////////////////////
-// Metafunctions
-//////////////////////////////////////////////////////////////////////////////
-
-//.Metafunction.Spec.param.T.type:Class.Allocator
-
-template
-struct Spec >
-{
- typedef TSpec Type;
-};
-
-
-//////////////////////////////////////////////////////////////////////////////
-/**
-.Tag.Allocator Usage:
-..summary:The purpose of an allocated memory block.
-..tag.TagAllocateTemp:Temporary memory.
-..tag.TagAllocateStorage:Memory for storing container content.
-..see:Function.allocate
-..see:Function.deallocate
-*/
-struct TagAllocateUnspecified_; //< usage not specified
-typedef Tag const TagAllocateUnspecified;
-
-struct TagAllocateTemp_; //< allocate temporary memory
-typedef Tag const TagAllocateTemp;
-
-struct TagAllocateStorage_; //< allocate memory for storing member data
-typedef Tag const TagAllocateStorage;
-
-
-//////////////////////////////////////////////////////////////////////////////
-//allocates memory on heap. No c'tors are called.
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Function.allocate:
-..cat:Memory
-..summary:Allocates memory from heap.
-..signature:allocate(object, data, count [, usage_tag])
-..param.object:Allocator object.
-...remarks:$object$ is conceptually the "owner" of the allocated memory.
- Objects of all types can be used as allocators. If no special behavior is implemented,
- default functions allocation/deallocation are applied that uses standard
- $new$ and $delete$ operators.
-..param.count:Number of items that could be stored in the allocated memory.
-...text:The type of the allocated items is given by the type of $data$.
-..param.usage_tag:A tag the specifies the purpose for the allocated memory.
-...value:@Tag.Allocator Usage@
-..returns.param.data:Pointer to allocated memory.
-...remarks:The value of this pointer is overwritten by the function.
-..remarks:
-...text:The function allocates at least $count*sizeof(data)$ bytes.
- The allocated memory is large enough
- to hold $count$ objects of type $T$, where $T *$ is type of $data$.
-...note:These objects are not constructed by $allocate$.
-...text:Use e.g. one of the functions @Function.valueConstruct@, @Function.arrayConstruct@, @Function.arrayConstructCopy@ or @Function.arrayFill@
-to construct the objects.
-A $new$ operator which is part of the C++ standard (defined in $$)
- can also be used to construct objects at a given memory address.
-..note:All allocated memory blocks should be deallocated by the corresponding function @Function.deallocate@.
-..see:Function.deallocate
-..see:Function.valueConstruct
-..see:Function.arrayFill
-..see:Function.arrayConstruct
-..see:Function.arrayConstructCopy
-*/
-template
-inline void
-allocate(T const & me,
- TValue * & data,
- TSize count)
-{
- allocate(me, data, count, TagAllocateUnspecified());
-}
-template
-inline void
-allocate(T & me,
- TValue * & data,
- TSize count)
-{
- allocate(me, data, count, TagAllocateUnspecified());
-}
-
-template
-inline void
-allocate(T const &,
- TValue * & data,
- TSize count,
- Tag const)
-{
- data = (TValue *) operator new(count * sizeof(TValue));
- if (data)
- SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
-}
-template
-inline void
-allocate(T &,
- TValue * & data,
- TSize count,
- Tag const)
-{
- data = (TValue *) operator new(count * sizeof(TValue));
- if (data)
- SEQAN_PROADD(SEQAN_PROMEMORY, count * sizeof(TValue));
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-//deallocates memory that was allocates using allocate(.)
-
-/**
-.Function.deallocate:
-..cat:Memory
-..summary:Deallocates memory.
-..signature:deallocate(object, data, count [, usage_tag])
-..param.object:Allocator object.
-...remarks:$object$ is conceptually the "owner" of the allocated memory.
- Objects of all types can be used as allocators. If no special behavior is implemented,
- default functions allocation/deallocation are applied that uses standard
- $new$ and $delete$ operators.
-..param.data:Pointer to allocated memory that was allocated by $allocate$.
-..param.count:Number of items that could be stored in the allocated memory.
-..param.usage_tag:A tag the specifies the purpose for the allocated memory.
-...value:@Tag.Allocator Usage@
-..remarks:
-...text:The values for $object$, $count$ and $usage_tag$ should be the same that was
-used when $allocate$ was called. The value of $data$ should be the same that was
-returned by $allocate$.
-...note:$deallocate$ does not destruct objects.
-...text:Use e.g. one of the functions @Function.valueDestruct@ or @Function.arrayDestruct@ to destruct the objects.
-$delete$ and $delete []$ operators which are part of the C++ standard (defined in $$)
- can also be used to destruct objects at a given memory address.
-..see:Function.valueDestruct
-..see:Function.arrayDestruct
-*/
-template
-inline void
-deallocate(T const & me,
- TValue * data,
- TSize const count)
-{
- deallocate(me, data, count, TagAllocateUnspecified());
-}
-template
-inline void
-deallocate(T & me,
- TValue * data,
- TSize const count)
-{
- deallocate(me, data, count, TagAllocateUnspecified());
-}
-
-template
-inline void
-deallocate(T const & /*me*/,
- TValue * data,
- TSize count,
- Tag const)
-{
- if (data && count) // .. to use count if SEQAN_PROFILE is not defined
- SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
- operator delete ((void *) data);
-}
-template
-inline void
-deallocate(T & /*me*/,
- TValue * data,
- TSize count,
- Tag const)
-{
- if (data && count) // .. to use count if SEQAN_PROFILE is not defined
- SEQAN_PROSUB(SEQAN_PROMEMORY, count * sizeof(TValue));
- operator delete ((void *) data);
-}
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h b/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h
deleted file mode 100644
index c637e208..00000000
--- a/SeqAn-1.1/seqan/basic/basic_allocator_multipool.h
+++ /dev/null
@@ -1,230 +0,0 @@
- /*==========================================================================
- SeqAn - The Library for Sequence Analysis
- http://www.seqan.de
- ============================================================================
- Copyright (C) 2007
-
- 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 3 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.
-
- ============================================================================
- $Id: basic_allocator_multipool.h,v 1.2 2009/02/19 01:51:23 langmead Exp $
- ==========================================================================*/
-
-#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_MULTIPOOL_H
-#define SEQAN_HEADER_BASIC_ALLOCATOR_MULTIPOOL_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-// MultiPool Allocator
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Spec.Multi Pool Allocator:
-..cat:Allocators
-..general:Class.Allocator
-..summary:Allocator that pools memory blocks.
-..signature:Allocator< MultiPool >
-..param.ParentAllocator:An allocator that is by the pool allocator used to allocate memory.
-...default:@Spec.Simple Allocator@
-...note:The multi pool allocator only supports @Function.clear@ if this function is also implemented for $ParentAllocator$.
-..remarks:A pool allocator allocates several memory blocks at once.
-..param.BLOCKING_LIMIT:The maximum size for memory blocks to be pooled.
-...default:256
-Freed blocks are not immediately deallocated but recycled in subsequential allocations.
-This way, the number of calls to the heap manager is reduced, and that speeds up memory management.
-...text:Note that memory blocks larger than $BLOCKING_LIMIT$ are not pooled
-but immediately allocated and deallocated using $ParentAllocator$.
-*/
-
-
-template >, unsigned int BLOCKING_LIMIT = 0x100>
-struct MultiPool;
-
-//////////////////////////////////////////////////////////////////////////////
-
-typedef Allocator >, 0x100> > PoolAllocator;
-
-template
-struct Allocator >
-{
- enum
- {
- BLOCKING_LIMIT = BLOCKING_LIMIT_,
- GRANULARITY_BITS = 2,
- BLOCKING_COUNT = BLOCKING_LIMIT >> GRANULARITY_BITS,
- STORAGE_SIZE = 0xf80
- };
-
- char * data_recycled_blocks [BLOCKING_COUNT];
- char * data_current_begin [BLOCKING_COUNT];
- char * data_current_free [BLOCKING_COUNT];
- Holder data_parent_allocator;
-
- Allocator()
- {
-SEQAN_CHECKPOINT
- memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
- memset(data_current_begin, 0, sizeof(data_current_begin));
- memset(data_current_free, 0, sizeof(data_current_free));
- }
-
- Allocator(TParentAllocator & parent_alloc)
- {
-SEQAN_CHECKPOINT
- memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
- memset(data_current_begin, 0, sizeof(data_current_begin));
- memset(data_current_free, 0, sizeof(data_current_free));
-
- setValue(data_parent_allocator, parent_alloc);
- }
-
- //Dummy copy
- Allocator(Allocator const &)
- {
- memset(data_recycled_blocks, 0, sizeof(data_recycled_blocks));
- memset(data_current_begin, 0, sizeof(data_current_begin));
- memset(data_current_free, 0, sizeof(data_current_free));
- }
- inline Allocator &
- operator = (Allocator const &)
- {
- clear(*this);
- return *this;
- }
-
- ~Allocator()
- {
-SEQAN_CHECKPOINT
- clear(*this);
- }
-};
-//////////////////////////////////////////////////////////////////////////////
-
-template
-inline TParentAllocator &
-parentAllocator(Allocator > & me)
-{
-SEQAN_CHECKPOINT
- return value(me.data_parent_allocator);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template
-void
-clear(Allocator > & me)
-{
-SEQAN_CHECKPOINT
- memset(me.data_recycled_blocks, 0, sizeof(me.data_recycled_blocks));
- memset(me.data_current_begin, 0, sizeof(me.data_current_begin));
- memset(me.data_current_free, 0, sizeof(me.data_current_free));
-
- clear(parentAllocator(me));
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template
-inline unsigned int
-_allocatorBlockNumber(Allocator > &,
- size_t size_)
-{
-SEQAN_CHECKPOINT
- typedef Allocator > TAllocator;
-
- SEQAN_ASSERT(size_)
-
- if (size_ < BLOCKING_LIMIT)
- {//blocks
- return size_ >> TAllocator::GRANULARITY_BITS;
- }
- else
- {//no blocking
- return TAllocator::BLOCKING_COUNT;
- }
-}
-
-
-//////////////////////////////////////////////////////////////////////////////
-
-template
-inline void
-allocate(Allocator > & me,
- TValue * & data,
- TSize count,
- Tag const tag_)
-{
-SEQAN_CHECKPOINT
- typedef Allocator > TAllocator;
-
- size_t bytes_needed = count * sizeof(TValue);
- char * ptr;
-
- unsigned int block_number = _allocatorBlockNumber(me, bytes_needed);
- if (block_number == TAllocator::BLOCKING_COUNT)
- {//no blocking
- return allocate(parentAllocator(me), data, count, tag_);
- }
-
- bytes_needed = (block_number + 1) << TAllocator::GRANULARITY_BITS;
-
- if (me.data_recycled_blocks[block_number])
- {//use recycled
- ptr = me.data_recycled_blocks[block_number];
- me.data_recycled_blocks[block_number] = * reinterpret_cast(ptr);
- }
- else
- {//use new
- ptr = me.data_current_free[block_number];
- if (!ptr || (ptr + bytes_needed > me.data_current_begin[block_number] + TAllocator::STORAGE_SIZE))
- {//not enough free space in current storage: allocate new
- allocate(parentAllocator(me), ptr, (size_t) TAllocator::STORAGE_SIZE, tag_);
- me.data_current_begin[block_number] = ptr;
- }
- me.data_current_free[block_number] = ptr + bytes_needed;
- }
-
- data = reinterpret_cast(ptr);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-template
-inline void
-deallocate(Allocator > & me,
- TValue * data,
- TSize count,
- Tag const tag_)
-{
-SEQAN_CHECKPOINT
- typedef Allocator > TAllocator;
-
- size_t bytes_needed = count * sizeof(TValue);
-
- unsigned int block_number = _allocatorBlockNumber(me, bytes_needed);
- if (block_number == TAllocator::BLOCKING_COUNT)
- {//no blocking
- return deallocate(parentAllocator(me), data, count, tag_);
- }
-
- bytes_needed = (block_number + 1) << TAllocator::GRANULARITY_BITS;
-
- //link in recycling list
- *reinterpret_cast(data) = me.data_recycled_blocks[block_number];
- me.data_recycled_blocks[block_number] = reinterpret_cast(data);
-}
-
-//////////////////////////////////////////////////////////////////////////////
-
-} //namespace SEQAN_NAMESPACE_MAIN
-
-#endif //#ifndef SEQAN_HEADER_...
diff --git a/SeqAn-1.1/seqan/basic/basic_allocator_simple.h b/SeqAn-1.1/seqan/basic/basic_allocator_simple.h
deleted file mode 100644
index 6b570cc7..00000000
--- a/SeqAn-1.1/seqan/basic/basic_allocator_simple.h
+++ /dev/null
@@ -1,210 +0,0 @@
- /*==========================================================================
- SeqAn - The Library for Sequence Analysis
- http://www.seqan.de
- ============================================================================
- Copyright (C) 2007
-
- 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 3 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.
-
- ============================================================================
- $Id: basic_allocator_simple.h,v 1.1 2008/08/25 16:20:02 langmead Exp $
- ==========================================================================*/
-
-#ifndef SEQAN_HEADER_BASIC_ALLOCATOR_SIMPLE_H
-#define SEQAN_HEADER_BASIC_ALLOCATOR_SIMPLE_H
-
-namespace SEQAN_NAMESPACE_MAIN
-{
-//////////////////////////////////////////////////////////////////////////////
-
-
-//////////////////////////////////////////////////////////////////////////////
-// SimpleAlloc Allocator
-//////////////////////////////////////////////////////////////////////////////
-
-/**
-.Spec.Simple Allocator:
-..cat:Allocators
-..general:Class.Allocator
-..summary:General purpose allocator.
-..signature:Allocator< SimpleAlloc >
-..param.ParentAllocator:An allocator that is by the simple allocator used to allocate memory.
-...default:@Tag.Default@
-...remarks:@Tag.Default@ used as allocator means that the default implementations
-of @Function.allocate@ and @Function.deallocate@ are used.
-*/
-
-template
-struct SimpleAlloc;
-
-//////////////////////////////////////////////////////////////////////////////
-
-
-typedef Allocator > SimpleAllocator;
-
-template
-struct Allocator