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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:Graph::CyclesDetection.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-Graph::CyclesDetection-"></a> 1 <span class="k">package </span><span class="i">Graph::CyclesDetection</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: CyclesDetection.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:49:06 $</span> | |
| 18 5 <span class="c"># $Revision: 1.27 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Graph</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">Graph::Path</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Graph::PathGraph</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">BitVector</span><span class="sc">;</span> | |
| 49 36 | |
| 50 37 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
| 51 38 | |
| 52 39 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> | |
| 53 40 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 54 41 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 55 42 | |
| 56 43 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 57 44 | |
| 58 45 <span class="c"># Setup class variables...</span> | |
| 59 46 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 60 47 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 | |
| 62 49 <span class="c"># Overload Perl functions...</span> | |
| 63 50 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyCyclesDetection'</span><span class="sc">;</span> | |
| 64 51 | |
| 65 52 <span class="c"># Class constructor...</span> | |
| 66 <a name="new-"></a> 53 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 67 54 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">$Graph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 68 55 | |
| 69 56 <span class="c"># Initialize object...</span> | |
| 70 57 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
| 71 58 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> | |
| 72 59 <span class="i">$This</span><span class="i">->_InitializeCyclesDetection</span><span class="s">(</span><span class="i">$Graph</span><span class="s">)</span><span class="sc">;</span> | |
| 73 60 | |
| 74 61 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 75 62 <span class="s">}</span> | |
| 76 63 | |
| 77 64 <span class="c"># Initialize object data...</span> | |
| 78 <a name="_InitializeCyclesDetection-"></a> 65 <span class="k">sub </span><span class="m">_InitializeCyclesDetection</span> <span class="s">{</span> | |
| 79 66 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Graph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 80 67 | |
| 81 68 <span class="i">$This</span>->{<span class="w">Graph</span>} = <span class="i">$Graph</span><span class="sc">;</span> | |
| 82 69 | |
| 83 70 <span class="c"># Cycles list...</span> | |
| 84 71 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 85 72 | |
| 86 73 <span class="c"># Cyclic paths which are not part of any other cycle...</span> | |
| 87 74 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 88 75 | |
| 89 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 90 77 <span class="s">}</span> | |
| 91 78 | |
| 92 79 <span class="c"># Initialize class ...</span> | |
| 93 <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 94 81 <span class="c">#Class name...</span> | |
| 95 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 96 83 <span class="s">}</span> | |
| 97 84 | |
| 98 85 <span class="c"># Detect all cycles in graph...</span> | |
| 99 86 <span class="c">#</span> | |
| 100 <a name="DetectCycles-"></a> 87 <span class="k">sub </span><span class="m">DetectCycles</span> <span class="s">{</span> | |
| 101 88 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 102 89 | |
| 103 90 <span class="k">return</span> <span class="i">$This</span><span class="i">->DetectCyclesUsingCollapsingPathGraphMethodology</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 104 91 <span class="s">}</span> | |
| 105 92 | |
| 106 93 <span class="c"># Detect all cycles in the graph using collapsing path graph [Ref 31] methodology...</span> | |
| 107 94 <span class="c">#</span> | |
| 108 95 <span class="c"># Note:</span> | |
| 109 96 <span class="c"># . For topologically complex graphs containing large number of cycles,</span> | |
| 110 97 <span class="c"># CollapseVertexAndCollectCyclicPathsDetectCycles method implemented in</span> | |
| 111 98 <span class="c"># PathGraph can time out in which case no cycles are detected or</span> | |
| 112 99 <span class="c"># assigned.</span> | |
| 113 100 <span class="c">#</span> | |
| 114 <a name="DetectCyclesUsingCollapsingPathGraphMethodology-"></a> 101 <span class="k">sub </span><span class="m">DetectCyclesUsingCollapsingPathGraphMethodology</span> <span class="s">{</span> | |
| 115 102 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 116 103 <span class="k">my</span><span class="s">(</span><span class="i">$PathGraph</span><span class="s">)</span><span class="sc">;</span> | |
| 117 104 | |
| 118 105 <span class="c"># Create a path graph...</span> | |
| 119 106 <span class="i">$PathGraph</span> = <span class="i">new</span> <span class="i">Graph::PathGraph</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Graph</span>}<span class="s">)</span><span class="sc">;</span> | |
| 120 107 | |
| 121 108 <span class="c"># For a vertex to be in a cycle, its degree must be >=2. So delete vertices recursively</span> | |
| 122 109 <span class="c"># till all vertices with degree less than 2 have been deleted...</span> | |
| 123 110 <span class="i">$PathGraph</span><span class="i">->DeleteVerticesWithDegreeLessThan</span><span class="s">(</span><span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
| 124 111 | |
| 125 112 <span class="c"># Setup a VertexID and EdgeID to index map usage during retrieval of independent cycles to</span> | |
| 126 113 <span class="c"># avoid going over all vertices in all cylic paths later...</span> | |
| 127 114 <span class="c">#</span> | |
| 128 115 <span class="k">my</span><span class="s">(</span><span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 129 116 <span class="s">(</span><span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupVertexIDsToIndicesMap</span><span class="s">(</span><span class="i">$PathGraph</span><span class="s">)</span><span class="sc">;</span> | |
| 130 117 <span class="s">(</span><span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupEdgeIDsToIndicesMap</span><span class="s">(</span><span class="i">$PathGraph</span><span class="s">)</span><span class="sc">;</span> | |
| 131 118 | |
| 132 119 <span class="c"># Recursively collapse vertices with lowest degree...</span> | |
| 133 120 <span class="k">my</span><span class="s">(</span><span class="i">$VertexID</span><span class="cm">,</span> <span class="i">$CycleVertexID</span><span class="s">)</span><span class="sc">;</span> | |
| 134 121 <span class="k">while</span> <span class="s">(</span><span class="i">$VertexID</span> = <span class="i">$PathGraph</span><span class="i">->GetVertexWithSmallestDegree</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 135 122 <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathGraph</span><span class="i">->CollapseVertexAndCollectCyclicPaths</span><span class="s">(</span><span class="i">$VertexID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 136 123 <span class="c"># Cycles detection didn't finish...</span> | |
| 137 124 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 138 125 <span class="s">}</span> | |
| 139 126 <span class="s">}</span> | |
| 140 127 | |
| 141 128 <span class="c"># Get detected cycles and save 'em sorted by size...</span> | |
| 142 129 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="cm">,</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span> <=> <span class="i">$b</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">$PathGraph</span><span class="i">->GetCyclicPaths</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 143 130 | |
| 144 131 <span class="c"># Retrieve independent cyclic paths...</span> | |
| 145 132 <span class="k">return</span> <span class="i">$This</span><span class="i">->_RetrieveIndependentCycles</span><span class="s">(</span><span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 146 133 <span class="s">}</span> | |
| 147 134 | |
| 148 135 <span class="c"># Retrieve and save independent cyclic paths...</span> | |
| 149 136 <span class="c">#</span> | |
| 150 137 <span class="c"># Set of independent cycles identified using this method doesn't correspond to basis set of</span> | |
| 151 138 <span class="c"># rings or smallest set of smallest rings (SSSR) [ Refs 29-30 ]; instead, set of cycles identified</span> | |
| 152 139 <span class="c"># as independent cycles simply correspond to cycles which contain no other cycle as their</span> | |
| 153 140 <span class="c"># subcycles and can't be described as linear combination of smaller cycles. And it also happen</span> | |
| 154 141 <span class="c"># to contain all the rings in basis set of rings and SSSR. In other words, it's a superset of basis set</span> | |
| 155 142 <span class="c"># of cycles and SSSR. For example, six four membered cycles are identified for cubane which is one</span> | |
| 156 143 <span class="c"># more than the basis set of cycles.</span> | |
| 157 144 <span class="c">#</span> | |
| 158 <a name="_RetrieveIndependentCycles-"></a> 145 <span class="k">sub </span><span class="m">_RetrieveIndependentCycles</span> <span class="s">{</span> | |
| 159 146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 160 147 | |
| 161 148 <span class="c"># Only 1 or 0 cyclic paths...</span> | |
| 162 149 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}} <= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 163 150 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="sc">;</span> | |
| 164 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 165 152 <span class="s">}</span> | |
| 166 153 | |
| 167 154 <span class="c"># Setup bit vectors for each cyclic path with size of each bit vector corresponding to</span> | |
| 168 155 <span class="c"># maximum vertex index plus one...</span> | |
| 169 156 <span class="k">my</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="cm">,</span> <span class="i">$BitVector</span><span class="cm">,</span> <span class="i">@BitNums</span><span class="cm">,</span> <span class="i">@CyclicPathBitVectors</span><span class="cm">,</span> <span class="i">@CyclicPathEdgeIDsBitVectors</span><span class="s">)</span><span class="sc">;</span> | |
| 170 157 | |
| 171 158 <span class="i">@CyclicPathBitVectors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@CyclicPathEdgeIDsBitVectors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 172 159 | |
| 173 160 <span class="c"># Set bits corresponding to VertexIDs EdgeIDs using their indices...</span> | |
| 174 161 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 175 162 <span class="i">$BitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 176 163 <span class="i">@BitNums</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$VertexIDsToIndicesRef</span>->{<span class="i">$_</span>} <span class="s">}</span> <span class="i">$CyclicPath</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 177 164 <span class="i">$BitVector</span><span class="i">->SetBits</span><span class="s">(</span><span class="i">@BitNums</span><span class="s">)</span><span class="sc">;</span> | |
| 178 165 <span class="k">push</span> <span class="i">@CyclicPathBitVectors</span><span class="cm">,</span> <span class="i">$BitVector</span><span class="sc">;</span> | |
| 179 166 | |
| 180 167 <span class="i">$BitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 181 168 <span class="i">@BitNums</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$EdgeIDsToIndicesRef</span>->{<span class="i">$_</span>} <span class="s">}</span> <span class="i">$This</span><span class="i">->_GetPathEdgeIDs</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span> | |
| 182 169 <span class="i">$BitVector</span><span class="i">->SetBits</span><span class="s">(</span><span class="i">@BitNums</span><span class="s">)</span><span class="sc">;</span> | |
| 183 170 <span class="k">push</span> <span class="i">@CyclicPathEdgeIDsBitVectors</span><span class="cm">,</span> <span class="i">$BitVector</span><span class="sc">;</span> | |
| 184 171 <span class="s">}</span> | |
| 185 172 | |
| 186 173 <span class="c"># First smallest cyclic path always ends up as an independent cyclic path...</span> | |
| 187 174 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}[<span class="n">0</span>]<span class="sc">;</span> | |
| 188 175 | |
| 189 176 <span class="c"># Retrieve other independent cyclic paths...</span> | |
| 190 177 <span class="k">my</span><span class="s">(</span><span class="i">$CurrentIndex</span><span class="cm">,</span> <span class="i">$PreviousIndex</span><span class="cm">,</span> <span class="i">$CurrentCyclicPath</span><span class="cm">,</span> <span class="i">$PreviousCyclicPath</span><span class="cm">,</span> <span class="i">$CurrentPathLength</span><span class="cm">,</span> <span class="i">$PreviousPathLength</span><span class="cm">,</span> <span class="i">$CurrentBitVector</span><span class="cm">,</span> <span class="i">$PreviousBitVector</span><span class="cm">,</span> <span class="i">$CurrentAndPreviousBitVectpor</span><span class="cm">,</span> <span class="i">$AllPreviousSmallerPathsBitVector</span><span class="cm">,</span> <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span><span class="cm">,</span> <span class="i">$CurrentEdgeIDsBitVector</span><span class="cm">,</span> <span class="i">$AndBitVector</span><span class="cm">,</span> <span class="i">%SmallerPathAlreadyAdded</span><span class="cm">,</span> <span class="i">%SkipPath</span><span class="s">)</span><span class="sc">;</span> | |
| 191 178 | |
| 192 179 <span class="i">%SkipPath</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 193 180 <span class="i">%SmallerPathAlreadyAdded</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 194 181 <span class="i">$AllPreviousSmallerPathsBitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 195 182 <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 196 183 | |
| 197 184 <span class="j">CURRENT:</span> <span class="k">for</span> <span class="i">$CurrentIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 198 185 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SkipPath</span>{<span class="i">$CurrentIndex</span>}<span class="s">)</span> <span class="s">{</span> | |
| 199 186 <span class="k">next</span> <span class="j">CURRENT</span><span class="sc">;</span> | |
| 200 187 <span class="s">}</span> | |
| 201 188 <span class="i">$CurrentCyclicPath</span> = <span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}[<span class="i">$CurrentIndex</span>]<span class="sc">;</span> | |
| 202 189 <span class="i">$CurrentBitVector</span> = <span class="i">$CyclicPathBitVectors</span>[<span class="i">$CurrentIndex</span>]<span class="sc">;</span> | |
| 203 190 <span class="i">$CurrentPathLength</span> = <span class="i">$CurrentCyclicPath</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 204 191 | |
| 205 192 <span class="j">PREVIOUS:</span> <span class="k">for</span> <span class="i">$PreviousIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$CurrentIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 206 193 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SkipPath</span>{<span class="i">$PreviousIndex</span>}<span class="s">)</span> <span class="s">{</span> | |
| 207 194 <span class="k">next</span> <span class="j">PREVIOUS</span><span class="sc">;</span> | |
| 208 195 <span class="s">}</span> | |
| 209 196 <span class="i">$PreviousCyclicPath</span> = <span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}[<span class="i">$PreviousIndex</span>]<span class="sc">;</span> | |
| 210 197 <span class="i">$PreviousBitVector</span> = <span class="i">$CyclicPathBitVectors</span>[<span class="i">$PreviousIndex</span>]<span class="sc">;</span> | |
| 211 198 | |
| 212 199 <span class="c"># Is previous path a subset of current path?</span> | |
| 213 200 <span class="i">$CurrentAndPreviousBitVectpor</span> = <span class="i">$PreviousBitVector</span> & <span class="i">$CurrentBitVector</span><span class="sc">;</span> | |
| 214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$CurrentAndPreviousBitVectpor</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 215 202 <span class="c"># Current path doesn't qualify an independent path...</span> | |
| 216 203 <span class="i">$SkipPath</span>{<span class="i">$CurrentIndex</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 217 204 <span class="k">next</span> <span class="j">CURRENT</span><span class="sc">;</span> | |
| 218 205 <span class="s">}</span> | |
| 219 206 | |
| 220 207 <span class="i">$PreviousPathLength</span> = <span class="i">$PreviousCyclicPath</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 221 208 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousPathLength</span> < <span class="i">$CurrentPathLength</span><span class="s">)</span> <span class="s">{</span> | |
| 222 209 <span class="c"># Mark cycle vertices seen in cyclic paths with length smaller than current path...</span> | |
| 223 210 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$SmallerPathAlreadyAdded</span>{<span class="i">$PreviousIndex</span>}<span class="s">)</span> <span class="s">{</span> | |
| 224 211 <span class="i">$SmallerPathAlreadyAdded</span>{<span class="i">$PreviousIndex</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 225 212 <span class="i">$AllPreviousSmallerPathsBitVector</span> = <span class="i">$AllPreviousSmallerPathsBitVector</span> | <span class="i">$PreviousBitVector</span><span class="sc">;</span> | |
| 226 213 <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> = <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> | <span class="i">$CyclicPathEdgeIDsBitVectors</span>[<span class="i">$PreviousIndex</span>]<span class="sc">;</span> | |
| 227 214 <span class="s">}</span> | |
| 228 215 <span class="s">}</span> | |
| 229 216 <span class="s">}</span> | |
| 230 217 <span class="k">if</span> <span class="s">(</span><span class="i">$AllPreviousSmallerPathsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 231 218 <span class="c"># Is current path a linear combination of smaller paths?</span> | |
| 232 219 <span class="i">$AndBitVector</span> = <span class="i">$AllPreviousSmallerPathsBitVector</span> & <span class="i">$CurrentBitVector</span><span class="sc">;</span> | |
| 233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 234 221 <span class="c"># Are all edges in the current path already present in smaller paths?</span> | |
| 235 222 <span class="i">$CurrentEdgeIDsBitVector</span> = <span class="i">$CyclicPathEdgeIDsBitVectors</span>[<span class="i">$CurrentIndex</span>]<span class="sc">;</span> | |
| 236 223 <span class="i">$AndBitVector</span> = <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> & <span class="i">$CurrentEdgeIDsBitVector</span><span class="sc">;</span> | |
| 237 224 | |
| 238 225 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentEdgeIDsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 239 226 <span class="c"># Current path doesn't qualify an independent path...</span> | |
| 240 227 <span class="i">$SkipPath</span>{<span class="i">$CurrentIndex</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 241 228 <span class="k">next</span> <span class="j">CURRENT</span><span class="sc">;</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 <span class="s">}</span> | |
| 244 231 <span class="s">}</span> | |
| 245 232 <span class="c"># It's an independent cyclic path...</span> | |
| 246 233 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="cm">,</span> <span class="i">$CurrentCyclicPath</span><span class="sc">;</span> | |
| 247 234 <span class="s">}</span> | |
| 248 235 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 249 236 <span class="s">}</span> | |
| 250 237 | |
| 251 238 <span class="c"># Setup a VertexID to index map...</span> | |
| 252 239 <span class="c">#</span> | |
| 253 <a name="_SetupVertexIDsToIndicesMap-"></a> 240 <span class="k">sub </span><span class="m">_SetupVertexIDsToIndicesMap</span> <span class="s">{</span> | |
| 254 241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathGraph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 255 242 <span class="k">my</span><span class="s">(</span><span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">@VertexIDs</span><span class="cm">,</span> <span class="i">%VertexIDsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 256 243 | |
| 257 244 <span class="i">%VertexIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@VertexIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$LargestVertexIndex</span> = <span class="n">0</span><span class="sc">;</span> | |
| 258 245 | |
| 259 246 <span class="i">@VertexIDs</span> = <span class="i">$PathGraph</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 260 247 <span class="k">if</span> <span class="s">(</span>! <span class="i">@VertexIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 261 248 <span class="k">return</span> <span class="s">(</span>\<span class="i">%VertexIDsMap</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 262 249 <span class="s">}</span> | |
| 263 250 <span class="i">@VertexIDsMap</span>{ <span class="i">@VertexIDs</span> } = <span class="s">(</span><span class="n">0</span> .. <span class="i">$#VertexIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 264 251 <span class="i">$LargestVertexIndex</span> = <span class="k">scalar</span> <span class="i">@VertexIDs</span><span class="sc">;</span> | |
| 265 252 | |
| 266 253 <span class="k">return</span> <span class="s">(</span>\<span class="i">%VertexIDsMap</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 267 254 <span class="s">}</span> | |
| 268 255 | |
| 269 256 <span class="c"># Setup a Edge to index map using paths associated to egdes in an intial</span> | |
| 270 257 <span class="c"># path graph...</span> | |
| 271 258 <span class="c">#</span> | |
| 272 <a name="_SetupEdgeIDsToIndicesMap-"></a> 259 <span class="k">sub </span><span class="m">_SetupEdgeIDsToIndicesMap</span> <span class="s">{</span> | |
| 273 260 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathGraph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 274 261 <span class="k">my</span><span class="s">(</span><span class="i">$Path</span><span class="cm">,</span> <span class="i">$LargestEdgeIndex</span><span class="cm">,</span> <span class="i">@EdgeIDs</span><span class="cm">,</span> <span class="i">%EdgeIDsMap</span><span class="s">)</span><span class="sc">;</span> | |
| 275 262 | |
| 276 263 <span class="i">%EdgeIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgeIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$LargestEdgeIndex</span> = <span class="n">0</span><span class="sc">;</span> | |
| 277 264 | |
| 278 265 <span class="i">@EdgeIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 279 266 <span class="k">for</span> <span class="i">$Path</span> <span class="s">(</span><span class="i">$PathGraph</span><span class="i">->GetPaths</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 280 267 <span class="k">push</span> <span class="i">@EdgeIDs</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->_GetPathEdgeIDs</span><span class="s">(</span><span class="i">$Path</span><span class="s">)</span><span class="sc">;</span> | |
| 281 268 <span class="s">}</span> | |
| 282 269 | |
| 283 270 <span class="k">if</span> <span class="s">(</span>! <span class="i">@EdgeIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 284 271 <span class="k">return</span> <span class="s">(</span>\<span class="i">%EdgeIDsMap</span><span class="cm">,</span> <span class="i">$LargestEdgeIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 285 272 <span class="s">}</span> | |
| 286 273 | |
| 287 274 <span class="i">@EdgeIDsMap</span>{ <span class="i">@EdgeIDs</span> } = <span class="s">(</span><span class="n">0</span> .. <span class="i">$#EdgeIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 288 275 <span class="i">$LargestEdgeIndex</span> = <span class="k">scalar</span> <span class="i">@EdgeIDs</span><span class="sc">;</span> | |
| 289 276 | |
| 290 277 <span class="k">return</span> <span class="s">(</span>\<span class="i">%EdgeIDsMap</span><span class="cm">,</span> <span class="i">$LargestEdgeIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 291 278 <span class="s">}</span> | |
| 292 279 | |
| 293 280 <span class="c"># Get path edge IDs or number of edges. The edge IDs are generated from</span> | |
| 294 281 <span class="c"># edge vertices and correpond to VertexID1-VertexID2 where VertexID1 <=</span> | |
| 295 282 <span class="c"># VertexID2.</span> | |
| 296 283 <span class="c">#</span> | |
| 297 <a name="_GetPathEdgeIDs-"></a> 284 <span class="k">sub </span><span class="m">_GetPathEdgeIDs</span> <span class="s">{</span> | |
| 298 285 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 299 286 <span class="k">my</span><span class="s">(</span><span class="i">@EdgesVertexIDs</span><span class="cm">,</span> <span class="i">@EdgeIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 300 287 | |
| 301 288 <span class="i">@EdgesVertexIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgeIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 302 289 <span class="i">@EdgesVertexIDs</span> = <span class="i">$Path</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 303 290 <span class="k">if</span> <span class="s">(</span>!<span class="i">@EdgesVertexIDs</span><span class="s">)</span> <span class="s">{</span> | |
| 304 291 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@EdgeIDs</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@EdgeIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 305 292 <span class="s">}</span> | |
| 306 293 | |
| 307 294 <span class="c"># Set up edge IDs...</span> | |
| 308 295 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$VertexID1</span><span class="cm">,</span> <span class="i">$VertexID2</span><span class="cm">,</span> <span class="i">$EdgeID</span><span class="s">)</span><span class="sc">;</span> | |
| 309 296 | |
| 310 297 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$#EdgesVertexIDs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span> | |
| 311 298 <span class="i">$VertexID1</span> = <span class="i">$EdgesVertexIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$VertexID2</span> = <span class="i">$EdgesVertexIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span> | |
| 312 299 <span class="i">$EdgeID</span> = <span class="s">(</span><span class="i">$VertexID1</span> <= <span class="i">$VertexID2</span><span class="s">)</span> ? <span class="q">"$VertexID1-$VertexID2"</span> <span class="co">:</span> <span class="q">"$VertexID2-$VertexID1"</span><span class="sc">;</span> | |
| 313 300 <span class="k">push</span> <span class="i">@EdgeIDs</span><span class="cm">,</span> <span class="i">$EdgeID</span><span class="sc">;</span> | |
| 314 301 <span class="s">}</span> | |
| 315 302 | |
| 316 303 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@EdgeIDs</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@EdgeIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 317 304 <span class="s">}</span> | |
| 318 305 | |
| 319 306 <span class="c"># Return an array containing references to cyclic paths or number of cylic paths...</span> | |
| 320 307 <span class="c">#</span> | |
| 321 <a name="GetAllCyclicPaths-"></a> 308 <span class="k">sub </span><span class="m">GetAllCyclicPaths</span> <span class="s">{</span> | |
| 322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 323 310 | |
| 324 311 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="sc">;</span> | |
| 325 312 <span class="s">}</span> | |
| 326 313 | |
| 327 314 <span class="c"># Get cyclic paths which are independent. In otherwords, cycles which don't contain any other</span> | |
| 328 315 <span class="c"># cycle as their subset...</span> | |
| 329 316 <span class="c">#</span> | |
| 330 <a name="GetIndependentCyclicPaths-"></a> 317 <span class="k">sub </span><span class="m">GetIndependentCyclicPaths</span> <span class="s">{</span> | |
| 331 318 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 332 319 | |
| 333 320 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="sc">;</span> | |
| 334 321 <span class="s">}</span> | |
| 335 322 | |
| 336 323 <span class="c"># Return a string containg data for CyclesDetection object...</span> | |
| 337 <a name="StringifyCyclesDetection-"></a> 324 <span class="k">sub </span><span class="m">StringifyCyclesDetection</span> <span class="s">{</span> | |
| 338 325 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 339 326 <span class="k">my</span><span class="s">(</span><span class="i">$CyclesDetectionString</span><span class="cm">,</span> <span class="i">$CyclesCount</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span> | |
| 340 327 | |
| 341 328 <span class="i">$CyclesCount</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="sc">;</span> | |
| 342 329 <span class="i">$CyclesDetectionString</span> = <span class="q">"AllCycles: Count - $CyclesCount"</span><span class="sc">;</span> | |
| 343 330 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 344 331 <span class="i">$CyclesDetectionString</span> .= <span class="q">"; Cycle: "</span> . <span class="k">join</span><span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 345 332 <span class="s">}</span> | |
| 346 333 | |
| 347 334 <span class="i">$CyclesCount</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="sc">;</span> | |
| 348 335 <span class="i">$CyclesDetectionString</span> .= <span class="q">"\nIndependentCycles: Count - $CyclesCount"</span><span class="sc">;</span> | |
| 349 336 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 350 337 <span class="i">$CyclesDetectionString</span> .= <span class="q">"; Cycle: "</span> . <span class="k">join</span><span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span> | |
| 351 338 <span class="s">}</span> | |
| 352 339 | |
| 353 340 <span class="k">return</span> <span class="i">$CyclesDetectionString</span><span class="sc">;</span> | |
| 354 341 <span class="s">}</span> | |
| 355 342 | |
| 356 343 <span class="c"># Return a reference to new cycle detection object...</span> | |
| 357 <a name="Copy-"></a> 344 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span> | |
| 358 345 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 359 346 <span class="k">my</span><span class="s">(</span><span class="i">$NewCyclesDetection</span><span class="s">)</span><span class="sc">;</span> | |
| 360 347 | |
| 361 348 <span class="i">$NewCyclesDetection</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span> | |
| 362 349 | |
| 363 350 <span class="k">return</span> <span class="i">$NewCyclesDetection</span><span class="sc">;</span> | |
| 364 351 <span class="s">}</span> | |
| 365 352 | |
| 366 <a name="EOF-"></a></pre> | |
| 367 <p> </p> | |
| 368 <br /> | |
| 369 <center> | |
| 370 <img src="../../../images/h2o2.png"> | |
| 371 </center> | |
| 372 </body> | |
| 373 </html> |