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switched to gpl 3.

fixed sse header problem on clang 3.1.
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1 parent cf4acca commit 761f030c44e23ccbf04d8007727d7a5193fd3620 @sim82 committed May 29, 2012
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@@ -27,7 +27,7 @@ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -D_SCL_SECURE_NO_WARNINGS")
file(GLOB ALL_HEADERS *.h)
ELSE()
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -march=corei7")
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -march=native")
set( BOOST_LIBS boost_thread boost_program_options)
set(SYSDEP_LIBS pthread)
#LINK_DIRECTORIES( ${LINK_DIRECTORIES} /usr/lib64/atlas-sse2 )
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674 LICENSE

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@@ -1,3 +1,22 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
#ifndef __align_pvec_vec_h
#define __align_pvec_vec_h
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@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#ifndef __align_utils_h__
#define __align_utils_h__
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@@ -1,15 +1,20 @@
/*
- * Copyright (C) 2011 Simon A. Berger
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
*
- * This program is free software; you may redistribute it and/or modify its
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option)
- * any later version.
+ * papara 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 General Public License for more details.
*
- * 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 GNU General Public License
- * for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __align_vec_h
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@@ -1,16 +1,23 @@
/*
- * Copyright (C) 2011 Simon A. Berger
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
*
- * This program is free software; you may redistribute it and/or modify its
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option)
- * any later version.
+ * papara 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 General Public License for more details.
*
- * 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 GNU General Public License
- * for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
+
+
#ifndef __aligned_buffer_h
#define __aligned_buffer_h
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@@ -1,3 +1,21 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
//
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23 dtw.cpp
@@ -1,15 +1,20 @@
/*
- * Copyright (C) 2011 Simon A. Berger
+ * Copyright (C) 2009-2012 Simon A. Berger
*
- * This program is free software; you may redistribute it and/or modify its
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option)
- * any later version.
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
*
- * 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 GNU General Public License
- * for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iostream>
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23 dtw.h
@@ -1,15 +1,20 @@
/*
- * Copyright (C) 2011 Simon A. Berger
+ * Copyright (C) 2009-2012 Simon A. Berger
*
- * This program is free software; you may redistribute it and/or modify its
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option)
- * any later version.
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
*
- * 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 GNU General Public License
- * for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __dtw_h
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@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#include <iostream>
#include "ivymike/tree_traversal_utils.h"
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23 fasta.h
@@ -1,15 +1,20 @@
/*
- * Copyright (C) 2011 Simon A. Berger
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
*
- * This program is free software; you may redistribute it and/or modify its
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option)
- * any later version.
+ * papara 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 General Public License for more details.
*
- * 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 GNU General Public License
- * for more details.
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __fasta_h
View
@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
// just a test if i can write this faster in c++ than in ruby (I always forget half of the ruby syntax and hate to look up the details again and again...)
#include <iostream>
View
@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#include <iostream>
#include <algorithm>
#include <iterator>
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@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#include <iostream>
#include <iterator>
#include <iomanip>
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@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#include <stdint.h>
#include <iostream>
// #include "ivymike/sdf.h"
View
@@ -1,3 +1,23 @@
+/*
+ * Copyright (C) 2009-2012 Simon A. Berger
+ *
+ * This file is part of papara.
+ *
+ * papara is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * papara 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with papara. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+
#include "ivymike/multiple_alignment.h"
#include <stdexcept>
#include <iostream>
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