new filter planar

README.md

@@ -49,7 +49,7 @@ In: Huber, K. and Gusfield, D. (eds.) Proceedings of WABI 2019. LIPIcs. 143, Sch
 
 ## Requirements
 
-For the main program, there are no strict dependencies other than C++ version 14.  
+For the main program, there are no strict dependencies other than C++ version 17.
 To read in **compressed** fasta/fastq files, it could be necessary to install zlib:
 ```
 sudo apt install libz-dev
@@ -129,6 +129,7 @@ Specify your input by `-i <list>` where `<list>` is either a file-of-files or in
 If you want a **tree**, use `-f strict`. In this case, `-N <newick-file>` can be used to write the resulting tree into a newick file; instead or additionally to `-o <split-file>`.
 If you want a **network**, use one of the following filters:
 * `weakly`: a split is kept if it is weakly compatible to all previously filtered splits (see publication for definition of "weak compatibility").
+* `planar`: a split is kept if the resulting set of splits can be displayed in the plain without any edges crossing (a.k.a. circular compatible, outer-labeled planar)
 * `2-tree`: two sets of compatible splits (=trees) are maintained. A split is added to the first if possible (compatible); if not to the second if possible.
   `3-tree`: three sets of compatible splits (=trees) are maintained. A split is added to the first if possible (compatible); if not to the second if possible; if not to the third if possible.
 
@@ -348,6 +349,7 @@ SANS is provided as a service of the [German Network for Bioinformatics Infrastr
 
 * The sparse-map library is licensed under the [MIT license](https://github.com/Tessil/sparse-map/blob/master/LICENSE).
 * The Bifrost library is licensed under the [BSD-2 license](https://github.com/pmelsted/bifrost/blob/master/LICENSE).
+* The [PC-tree library](https://github.com/N-Coder/pc-tree) is licensed under the [OGDF license](https://github.com/N-Coder/pc-tree/blob/main/LICENSE.txt).
 * SANS uses gzstream, licensed under the [LGPL license](/src/gz/COPYING.LIB).
 * SANS is licensed under the [GNU general public license](/LICENSE).
 

makefile

@@ -1,5 +1,5 @@
 # MAX. K-MER LENGTH, NUMBER OF FILES
-CC = g++ -O3 -march=native -DmaxK=64 -DmaxN=64 -std=c++14
+CC = g++ -O3 -march=native -DmaxK=64 -DmaxN=64 -std=c++17
 XX = -lpthread -lz
 
 ## IF DEBUG
@@ -16,6 +16,7 @@ CFLAGS = gcc -O3 -march=native
 SRCDIR		:= src
 BUILDDIR 	:= obj
 
+
 # Wrap Windows / Unix commands
 ifeq ($(OS), Windows_NT)
 	TD = $(BUILDDIR)
@@ -39,9 +40,9 @@ endif
 all: makefile start SANS done
 
 SANS: makefile $(BUILDDIR)/main.o
-	$(CC) -o SANS $(BUILDDIR)/nexus_color.o $(BUILDDIR)/main.o $(BUILDDIR)/graph.o $(BUILDDIR)/kmer.o $(BUILDDIR)/kmerAmino.o $(BUILDDIR)/color.o $(BUILDDIR)/util.o $(BUILDDIR)/translator.o $(BUILDDIR)/cleanliness.o $(BUILDDIR)/gzstream.o $(XX)
+	$(CC) -o SANS $(BUILDDIR)/nexus_color.o $(BUILDDIR)/main.o $(BUILDDIR)/graph.o $(BUILDDIR)/kmer.o $(BUILDDIR)/kmerAmino.o $(BUILDDIR)/color.o $(BUILDDIR)/util.o $(BUILDDIR)/translator.o $(BUILDDIR)/cleanliness.o $(BUILDDIR)/gzstream.o  $(BUILDDIR)/PCTree_basic.o $(BUILDDIR)/PCTree_construction.o $(BUILDDIR)/PCTreeForest.o $(BUILDDIR)/PCTree_restriction.o $(BUILDDIR)/PCTree_intersect.o $(BUILDDIR)/PCNode.o $(XX)
 
-$(BUILDDIR)/main.o: makefile $(SRCDIR)/main.cpp $(SRCDIR)/main.h $(BUILDDIR)/color.o $(BUILDDIR)/translator.o $(BUILDDIR)/graph.o $(BUILDDIR)/util.o $(BUILDDIR)/cleanliness.o $(BUILDDIR)/gzstream.o $(BUILDDIR)/nexus_color.o
+$(BUILDDIR)/main.o: makefile $(SRCDIR)/main.cpp $(SRCDIR)/main.h $(BUILDDIR)/color.o $(BUILDDIR)/translator.o $(BUILDDIR)/graph.o $(BUILDDIR)/util.o $(BUILDDIR)/cleanliness.o $(BUILDDIR)/gzstream.o $(BUILDDIR)/nexus_color.o $(BUILDDIR)/PCTree_construction.o $(BUILDDIR)/PCTree_basic.o $(BUILDDIR)/PCTreeForest.o $(BUILDDIR)/PCTree_restriction.o $(BUILDDIR)/PCTree_intersect.o $(BUILDDIR)/PCNode.o
 	$(CC) -c $(SRCDIR)/main.cpp -o $(BUILDDIR)/main.o
 
 $(BUILDDIR)/graph.o: makefile $(SRCDIR)/graph.cpp $(SRCDIR)/graph.h $(BUILDDIR)/kmer.o $(BUILDDIR)/kmerAmino.o $(BUILDDIR)/color.o
@@ -56,7 +57,7 @@ $(BUILDDIR)/kmerAmino.o: makefile $(SRCDIR)/kmerAmino.cpp $(SRCDIR)/kmerAmino.h
 $(BUILDDIR)/color.o: makefile $(SRCDIR)/color.cpp $(SRCDIR)/color.h
 	$(CC) -c $(SRCDIR)/color.cpp -o $(BUILDDIR)/color.o
 
-$(BUILDDIR)/nexus_color.o: makefile $(SRCDIR)/nexus_color.cpp $(SRCDIR)/nexus_color.h
+$(BUILDDIR)/nexus_color.o: $(SRCDIR)/nexus_color.cpp $(SRCDIR)/nexus_color.h
 	$(CC) -c $(SRCDIR)/nexus_color.cpp -o $(BUILDDIR)/nexus_color.o
 
 $(BUILDDIR)/util.o: $(SRCDIR)/util.cpp $(SRCDIR)/util.h
@@ -72,6 +73,29 @@ $(BUILDDIR)/gzstream.o: $(SRCDIR)/gz/gzstream.C $(SRCDIR)/gz/gzstream.h
 	$(CFLAGS) -c $(SRCDIR)/gz/gzstream.C  -o $(BUILDDIR)/gzstream.o
 
 
+# PC-Tree
+
+
+$(BUILDDIR)/PCNode.o: $(SRCDIR)/pctree/PCNode.cpp $(SRCDIR)/pctree/PCNode.h $(BUILDDIR)/PCTreeForest.o
+	$(CC) -c $(SRCDIR)/pctree/PCNode.cpp -o $(BUILDDIR)/PCNode.o
+
+$(BUILDDIR)/PCTree_basic.o: $(SRCDIR)/pctree/PCTree_basic.cpp $(BUILDDIR)/PCNode.o 
+	$(CC) -c $(SRCDIR)/pctree/PCTree_basic.cpp -o $(BUILDDIR)/PCTree_basic.o
+
+$(BUILDDIR)/PCTree_construction.o: $(SRCDIR)/pctree/PCTree_construction.cpp $(BUILDDIR)/PCNode.o 
+	$(CC) -c $(SRCDIR)/pctree/PCTree_construction.cpp -o $(BUILDDIR)/PCTree_construction.o
+
+$(BUILDDIR)/PCTreeForest.o: $(SRCDIR)/pctree/PCTreeForest.cpp $(SRCDIR)/pctree/PCTreeForest.h
+	$(CC) -c $(SRCDIR)/pctree/PCTreeForest.cpp -o $(BUILDDIR)/PCTreeForest.o
+
+$(BUILDDIR)/PCTree_intersect.o: $(SRCDIR)/pctree/PCTree_intersect.cpp
+	$(CC) -c $(SRCDIR)/pctree/PCTree_intersect.cpp -o $(BUILDDIR)/PCTree_intersect.o
+
+$(BUILDDIR)/PCTree_restriction.o: $(SRCDIR)/pctree/PCTree_restriction.cpp $(BUILDDIR)/PCNode.o
+	$(CC) -c $(SRCDIR)/pctree/PCTree_restriction.cpp -o $(BUILDDIR)/PCTree_restriction.o
+
+
+
 # [Internal rules]
 
 # Print info at compile start

src/graph.cpp

@@ -1,5 +1,6 @@
 #include "graph.h"
 #include "util.h"
+#include "pctree/PCTree.h"
 #include <mutex>
 #include <thread>
 #include <algorithm>
@@ -1727,6 +1728,58 @@ void graph::filter_weakly(multimap_<double, color_t>& split_list, bool& verbose)
     }
 }
 
+/**
+ * This function filters a planar graph compatible subset.
+ *
+ * @param split_list list of splits to be filtered
+ * @param verbose print progress
+ */
+void graph::filter_planar(multimap_<double, color_t>& split_list, bool& verbose) {
+
+    auto it = split_list.begin();
+    color_t split_copy;
+
+    // single bit of split
+    int state = 0;
+
+    // construct PC-Tree with maxN nodes
+    vector<pc_tree::PCNode*> leaves; 
+	pc_tree::PCTree tree(maxN, &leaves);
+
+
+loop:
+    while(it != split_list.end()) {
+
+        vector<pc_tree::PCNode*> consecutiveLeaves = {}; 
+
+        // current split
+        split_copy = it->second;
+
+        // read all bits of the current split
+        for(int j=0;j<maxN;j++) {
+            state = (split_copy & 0b1u);
+            split_copy >>= 01u;
+
+            //collect all leaves which should be consecutive
+            if (state == 1) {
+                consecutiveLeaves.push_back(leaves.at(j));
+            }
+        }
+
+        // if possible, insert the new split in pc-tree
+        if (tree.makeConsecutive(consecutiveLeaves)) { 
+            ++it; goto loop;
+        }
+
+        // delete the split, if it is not compatible to the pc-tree
+        it = split_list.erase(it); 
+
+
+    }
+
+}
+
+
 /**
  * This function filters a greedy maximum weight n-tree compatible subset and returns a string with all trees in newick format.
  *

src/graph.h

@@ -455,6 +455,14 @@ class graph {
      */
     static void filter_weakly(multimap_<double, color_t>& split_list, bool& verbose);
 
+    /**
+     * This function filters a planar graph compatible subset.
+     * @param split_list list of splits to be filtered
+     * @param verbose print progress
+     */
+    static void filter_planar(multimap_<double, color_t>& split_list, bool& verbose);
+
+
     /**
      * This function filters a greedy maximum weight n-tree compatible subset.
      *

src/main.cpp

@@ -88,6 +88,8 @@ int main(int argc, char* argv[]) {
         // cout << "                  \t filtered splits w.r.t. original splits" << endl;
         cout << "                  \t options: strict: compatible to a tree" << endl;
         cout << "                  \t          weakly: weakly compatible network" << endl;
+        cout << "                  \t          planar: compatible to a planar graph" << endl;
+        cout << "                  \t                  (a.k.a. circular compatible, outer labeled planar)" << endl;
         cout << "                  \t          n-tree: compatible to a union of n trees" << endl;
         cout << "                  \t                  (where n is an arbitrary number, e.g. 2-tree)" << endl;
         cout << endl;
@@ -382,7 +384,7 @@ int main(int argc, char* argv[]) {
         else if (strcmp(argv[i], "-f") == 0 || strcmp(argv[i], "--filter") == 0) {
             catch_missing_dependent_args(argv[i + 1], argv[i]);
             filter = argv[++i];    // Filter a greedy maximum weight subset
-            if (filter == "strict" || filter == "tree") {
+            if (filter == "strict" || filter == "tree" | filter == "planar") {
                 // compatible to a tree
             }
             else if (filter == "weakly") {
@@ -1737,6 +1739,9 @@ void apply_filter(string filter, string newick, std::function<string(const uint6
 			else if (filter == "weakly") {
 				graph::filter_weakly(split_list, verbose);
 			}
+            else if (filter == "planar") {
+                graph::filter_planar(split_list, verbose);
+            }
 			else if (filter.find("tree") != -1 && filter.substr(filter.find("tree")) == "tree") {
 				if (!newick.empty()) {
 					ofstream file(newick);    // output file stream

src/main.h

@@ -27,7 +27,7 @@ using namespace std;
 // SANS ambages
 // Symmetric Alignment-free phylogeNomic Splits
 // phylogenomics with Abundance-filter, Multi-threading and Bootstrapping on Amino-acid or GEnomic Sequences
-#define SANS_VERSION "2.5_1A"    // SANS ambages
+#define SANS_VERSION "2.5_1B"    // SANS ambages
 
 /**
  * This is the entry point of the program.

src/pctree/PCEnum.h

@@ -0,0 +1,71 @@
+/** \file
+ * \brief Predeclaration of various PC-tree related classes and enums.
+ *
+ * \author Simon D. Fink <ogdf@niko.fink.bayern>
+ *
+ * \par License:
+ * This file is part of the Open Graph Drawing Framework (OGDF).
+ *
+ * \par
+ * Copyright (C)<br>
+ * See README.md in the OGDF root directory for details.
+ *
+ * \par
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * Version 2 or 3 as published by the Free Software Foundation;
+ * see the file LICENSE.txt included in the packaging of this file
+ * for details.
+ *
+ * \par
+ * 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.
+ *
+ * \par
+ * You should have received a copy of the GNU General Public
+ * License along with this program; if not, see
+ * http://www.gnu.org/copyleft/gpl.html
+ */
+
+#pragma once
+
+#include "util/RegisteredArray.h"
+#include "util/RegisteredSet.h"
+#include "util/defines.h"
+
+#include <ostream>
+
+namespace pc_tree {
+enum class OGDF_EXPORT NodeLabel { Unknown, Partial, Full, Empty = Unknown };
+
+enum class OGDF_EXPORT PCNodeType { PNode, CNode, Leaf };
+
+class OGDF_EXPORT PCTree;
+
+class OGDF_EXPORT PCTreeForest;
+
+class OGDF_EXPORT PCTreeRegistry;
+
+class OGDF_EXPORT PCNode;
+
+#define OGDF_DECL_REG_ARRAY_TYPE(v, c) pc_tree::RegisteredArray<PCTreeRegistry, v, c>
+OGDF_DECL_REG_ARRAY(PCTreeNodeArray)
+#undef PCTREE_DECL_REG_ARRAY_TYPE
+
+template<bool SupportFastSizeQuery = true>
+using PCTreeNodeSet = pc_tree::RegisteredSet<PCTreeRegistry, SupportFastSizeQuery>;
+
+OGDF_EXPORT std::ostream& operator<<(std::ostream&, pc_tree::NodeLabel);
+
+OGDF_EXPORT std::ostream& operator<<(std::ostream&, pc_tree::PCNodeType);
+
+OGDF_EXPORT std::ostream& operator<<(std::ostream&, const pc_tree::PCTree*);
+
+OGDF_EXPORT std::ostream& operator<<(std::ostream&, const pc_tree::PCNode*);
+
+OGDF_EXPORT std::ostream& operator<<(std::ostream&, const pc_tree::PCTree&);
+
+OGDF_EXPORT std::ostream& operator<<(std::ostream&, const pc_tree::PCNode&);
+}