svf-tools 1.0.285 → 1.0.286

package/SVF-doxygen/html/html/globals_func_h.html

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package/SVF-doxygen/html/html/globals_h.html

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package/SVF-doxygen/html/html/globals_r.html

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package/SVF-doxygen/html/html/globals_s.html

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+Copyright:
+  * fastcluster_dm.cpp & fastcluster_R_dm.cpp:
+     © 2011 Daniel Müllner <http://danifold.net>
+  * fastcluster.(h|cpp) & demo.cpp & plotresult.r:
+     © 2018 Christoph Dalitz <http://www.hsnr.de/ipattern/>
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+  * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+  * 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.
+
+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.

package/include/FastCluster/fastcluster.h

@@ -0,0 +1,79 @@
+//
+// C++ standalone verion of fastcluster by Daniel Muellner
+//
+// Copyright: Daniel Muellner, 2011
+//            Christoph Dalitz, 2020
+// License:   BSD style license
+//            (see the file LICENSE for details)
+//
+
+#ifndef fastclustercpp_H
+#define fastclustercpp_H
+
+//
+// Assigns cluster labels (0, ..., nclust-1) to the n points such
+// that the cluster result is split into nclust clusters.
+//
+// Input arguments:
+//   n      = number of observables
+//   merge  = clustering result in R format
+//   nclust = number of clusters
+// Output arguments:
+//   labels = allocated integer array of size n for result
+//
+void cutree_k(int n, const int* merge, int nclust, int* labels);
+
+//
+// Assigns cluster labels (0, ..., nclust-1) to the n points such
+// that the hierarchical clsutering is stopped at cluster distance cdist
+//
+// Input arguments:
+//   n      = number of observables
+//   merge  = clustering result in R format
+//   height = cluster distance at each merge step
+//   cdist  = cutoff cluster distance
+// Output arguments:
+//   labels = allocated integer array of size n for result
+//
+void cutree_cdist(int n, const int* merge, double* height, double cdist, int* labels);
+
+//
+// Hierarchical clustering with one of Daniel Muellner's fast algorithms
+//
+// Input arguments:
+//   n       = number of observables
+//   distmat = condensed distance matrix, i.e. an n*(n-1)/2 array representing
+//             the upper triangle (without diagonal elements) of the distance
+//             matrix, e.g. for n=4:
+//               d00 d01 d02 d03
+//               d10 d11 d12 d13   ->  d01 d02 d03 d12 d13 d23
+//               d20 d21 d22 d23
+//               d30 d31 d32 d33
+//   method  = cluster metric (see enum hclust_fast_methods)
+// Output arguments:
+//   merge   = allocated (n-1)x2 matrix (2*(n-1) array) for storing result.
+//             Result follows R hclust convention:
+//              - observabe indices start with one
+//              - merge[i][] contains the merged nodes in step i
+//              - merge[i][j] is negative when the node is an atom
+//   height  = allocated (n-1) array with distances at each merge step
+// Return code:
+//   0 = ok
+//   1 = invalid method
+//
+int hclust_fast(int n, double* distmat, int method, int* merge, double* height);
+enum hclust_fast_methods {
+  // single link with the minimum spanning tree algorithm (Rohlf, 1973)
+  HCLUST_METHOD_SINGLE = 0,
+  // complete link with the nearest-neighbor-chain algorithm (Murtagh, 1984)
+  HCLUST_METHOD_COMPLETE = 1,
+  // omplete link with the nearest-neighbor-chain algorithm (Murtagh, 1984)
+  HCLUST_METHOD_AVERAGE = 2,
+  // median link with the generic algorithm (Müllner, 2011)
+  HCLUST_METHOD_MEDIAN = 3,
+  // To indicate to try all methods and pick the best.
+  HCLUST_METHOD_SVF_BEST = 4
+};
+  
+
+#endif

package/lib/CMakeLists.txt

@@ -19,7 +19,10 @@ file (GLOB SOURCES
         WPA/*.cpp
         MTA/*.cpp
         SABER/*.cpp
-        DDA/*.cpp)
+        DDA/*.cpp
+        FastCluster/*.cpp
+)
+
 add_llvm_library(Svf STATIC ${SOURCES} LINK_LIBS Cudd ${Z3_LIBRARIES})
 
 link_directories(${CMAKE_BINARY_DIR}/lib/Cudd)

package/lib/FastCluster/LICENSE.TXT

@@ -0,0 +1,13 @@
+Copyright:
+  * fastcluster_dm.cpp & fastcluster_R_dm.cpp:
+     © 2011 Daniel Müllner <http://danifold.net>
+  * fastcluster.(h|cpp) & demo.cpp & plotresult.r:
+     © 2018 Christoph Dalitz <http://www.hsnr.de/ipattern/>
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+  * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+  * 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.
+
+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.