License file and headers

marbl · Jul 18, 2014 · 12d2cd8 · 12d2cd8
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,44 @@
+PURPOSE
+
+Harvest is a file format conversion tool for use with the Harvest tool
+suite (github.com/marbl/harvest). Harvest is implemented in C++ and
+uses Google Protocol Buffers for serialization.
+
+COPYRIGHT LICENSE
+
+Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+Adam Phillippy
+
+This Software was prepared for the Department of Homeland Security
+(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as
+part of contract HSHQDC-07-C-00020 to manage and operate the National
+Biodefense Analysis and Countermeasures Center (NBACC), a Federally
+Funded Research and Development Center.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+1. Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+contributors may be used to endorse or promote products derived from
+this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/src/harvest/AnnotationList.cpp b/src/harvest/AnnotationList.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "AnnotationList.h"
 #include <fstream>

diff --git a/src/harvest/AnnotationList.h b/src/harvest/AnnotationList.h
@@ -1,3 +1,9 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 #ifndef AnnotationList_h
 #define AnnotationList_h
 

diff --git a/src/harvest/HarvestIO.cpp b/src/harvest/HarvestIO.cpp
@@ -1,4 +1,8 @@
-
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "HarvestIO.h"
 

diff --git a/src/harvest/HarvestIO.h b/src/harvest/HarvestIO.h
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #ifndef HarvestIO_h
 #define HarvestIO_h

diff --git a/src/harvest/LcbList.cpp b/src/harvest/LcbList.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "harvest/LcbList.h"
 #include <iostream>

diff --git a/src/harvest/LcbList.h b/src/harvest/LcbList.h
@@ -1,3 +1,9 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 #ifndef LcbList_h
 #define LcbList_h
 

diff --git a/src/harvest/PhylogenyTree.cpp b/src/harvest/PhylogenyTree.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "PhylogenyTree.h"
 #include <fstream>

diff --git a/src/harvest/PhylogenyTree.h b/src/harvest/PhylogenyTree.h
@@ -1,3 +1,9 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 #ifndef harvest_PhylogenyTree
 #define harvest_PhylogenyTree
 

diff --git a/src/harvest/PhylogenyTreeNode.cpp b/src/harvest/PhylogenyTreeNode.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "PhylogenyTreeNode.h"
 

diff --git a/src/harvest/PhylogenyTreeNode.h b/src/harvest/PhylogenyTreeNode.h
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #ifndef PhylogenyTreeNode_h
 #define PhylogenyTreeNode_h

diff --git a/src/harvest/ReferenceList.cpp b/src/harvest/ReferenceList.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include <fstream>
 #include "ReferenceList.h"
@@ -55,7 +60,10 @@ int ReferenceList::getReferenceSequenceFromGi(long int gi) const
 		}
 	}
 
-	throw GiNotFoundException(std::to_string(gi));
+	char giString[1024];
+	sprintf(giString, "%ld", gi);
+
+	throw GiNotFoundException(giString);
 
 	return undef;
 }

diff --git a/src/harvest/ReferenceList.h b/src/harvest/ReferenceList.h
@@ -1,9 +1,16 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 #ifndef ReferenceList_h
 #define ReferenceList_h
 
 #include <string>
 #include <vector>
 #include <iostream>
+#include <stdexcept>
 
 #include "harvest/pb/harvest.pb.h"
 

diff --git a/src/harvest/TrackList.cpp b/src/harvest/TrackList.cpp
@@ -1,3 +1,9 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 #include "harvest/TrackList.h"
 
 using namespace::std;

diff --git a/src/harvest/TrackList.h b/src/harvest/TrackList.h
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #ifndef TrackList_h
 #define TrackList_h

diff --git a/src/harvest/VariantList.cpp b/src/harvest/VariantList.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "harvest/VariantList.h"
 #include <fstream>

diff --git a/src/harvest/VariantList.h b/src/harvest/VariantList.h
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #ifndef VariantList_h
 #define VariantList_h

diff --git a/src/harvest/harvest.cpp b/src/harvest/harvest.cpp
@@ -1,10 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
 //
-//  main.cpp
-//  harvest
-//
-//  Created by Brian Ondov on 6/19/13.
-//
-//
+// See the LICENSE.txt file included with this software for license information.
 
 #include <iostream>
 #include <fstream>

diff --git a/src/harvest/parse.cpp b/src/harvest/parse.cpp
@@ -1,3 +1,8 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
 
 #include "parse.h"
 #include <string.h>

diff --git a/src/harvest/parse.h b/src/harvest/parse.h
@@ -1,3 +1,9 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 #ifndef parse_h
 #define parse_h
 

diff --git a/src/harvest/pb/harvest.proto b/src/harvest/pb/harvest.proto
@@ -1,3 +1,9 @@
+// Copyright © 2014, Battelle National Biodefense Institute (BNBI);
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
+// Adam Phillippy
+//
+// See the LICENSE.txt file included with this software for license information.
+
 message Harvest
 {
 	message Reference