From 5ca056923b7d320fce80abd9044c895fa7e58dae Mon Sep 17 00:00:00 2001 From: Ruth Hoffmann Date: Tue, 24 Jul 2018 08:21:54 +0100 Subject: [PATCH] Update website for PatternClass 2.4.2 --- PackageInfo.g | 5 +- README.md | 19 ++++--- _data/package.yml | 6 +- doc/chap0.html | 4 +- doc/chap0.txt | 11 +++- doc/chap0_mj.html | 6 +- doc/chap1.html | 8 +-- doc/chap1.txt | 8 +-- doc/chap10_mj.html | 2 +- doc/chap1_mj.html | 10 ++-- doc/chap2.html | 2 +- doc/chap2.txt | 2 +- doc/chap2_mj.html | 4 +- doc/chap3.html | 2 +- doc/chap3.txt | 46 ++++++++-------- doc/chap3_mj.html | 4 +- doc/chap4.html | 2 +- doc/chap4.txt | 2 +- doc/chap4_mj.html | 4 +- doc/chap5.txt | 3 +- doc/chap5_mj.html | 2 +- doc/chap6.html | 2 +- doc/chap6.txt | 8 ++- doc/chap6_mj.html | 4 +- doc/chap7.txt | 3 +- doc/chap7_mj.html | 2 +- doc/chap8.html | 6 +- doc/chap8.txt | 30 +++++----- doc/chap8_mj.html | 8 +-- doc/chap9.html | 6 +- doc/chap9.txt | 29 ++++++---- doc/chap9_mj.html | 8 +-- doc/chapBib.html | 16 +++--- doc/chapBib.txt | 23 ++++---- doc/chapBib_mj.html | 18 +++--- doc/chapInd.html | 128 +++++++++++++++++++++---------------------- doc/chapInd.txt | 128 +++++++++++++++++++++---------------------- doc/chapInd_mj.html | 130 ++++++++++++++++++++++---------------------- 38 files changed, 365 insertions(+), 336 deletions(-) diff --git a/PackageInfo.g b/PackageInfo.g index 7906aff..5e468b2 100644 --- a/PackageInfo.g +++ b/PackageInfo.g @@ -10,8 +10,8 @@ SetPackageInfo( rec( PackageName := "PatternClass", Subtitle := "A permutation pattern class package", -Version := "2.4.1", -Date := "28/09/2017", # dd/mm/yyyy format +Version := "2.4.2", +Date := "24/07/2018", # dd/mm/yyyy format Persons := [ rec( @@ -75,7 +75,6 @@ SourceRepository := rec( URL := Concatenation( "https://github.com/gap-packages/", ~.PackageName ), ), IssueTrackerURL := Concatenation( ~.SourceRepository.URL, "/issues" ), -#SupportEmail := "TODO", PackageWWWHome := "https://gap-packages.github.io/PatternClass/", PackageInfoURL := Concatenation( ~.PackageWWWHome, "PackageInfo.g" ), README_URL := Concatenation( ~.PackageWWWHome, "README.md" ), diff --git a/README.md b/README.md index d88acc6..f9130ac 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ patched functions are located in lib/automata.* . Introduction ------------ -This is version 2.4 of the 'PatternClass' package. +This is version 2.4.2 of the 'PatternClass' package. The 'PatternClass' package allows you to explore the permutation pattern classes build by token passing networks. @@ -54,12 +54,12 @@ If you get 'PatternClass' as a compressed file unpack it in the pkg/ folder in the gap4r4 folder where GAP is installed on your computer. To uncompress the .tar.gz file on UNIX use the following command - tar xzf PatternClass2.4.tar.gz + tar xzf PatternClass2.4.2.tar.gz If your version of tar does not support the z option use - gunzip PatternClass2.4.tar.gz - tar xf PatternClass2.4.tar + gunzip PatternClass2.4.2.tar.gz + tar xf PatternClass2.4.2.tar This will create the folder PatternClass in pkg/ and within that you will find the directories and files mentioned above. @@ -72,11 +72,11 @@ Loading Automata 1.13 For help, type: ?Automata: ---------------------------------------------------------------- ───────────────────────────────────────────────────────────────────────────── -Loading PatternClass 2.4 (A permutation pattern class package) -by Ruth Hoffmann (TODO), +Loading PatternClass 2.4.2 (A permutation pattern class package) +by Ruth Hoffmann (https://rh347.host.cs.st-andrews.ac.uk/), Steve Linton (http://sal.host.cs.st-andrews.ac.uk/), and Michael Albert (http://www.cs.otago.ac.nz/staff/michael.html). -Homepage: https://RuthHoffmann.github.io/PatternClass/ +Homepage: https://gap-packages.github.io/PatternClass/ ───────────────────────────────────────────────────────────────────────────── true gap> @@ -89,6 +89,11 @@ online or within GAP help. Changes ------- +Changes from 2.4 to 2.4.2: +- Changed the name of HashSet due to clash with DataStructure Package +- Removed TODOs from code +<<<>>><<<>>><<<>>><<<>>> + Changes from 2.3 to 2.4: - Improved the runtime of InbetweenPermSet when the subpermutation is of length 1. - Added IsSumPerm function diff --git a/_data/package.yml b/_data/package.yml index cdb0620..0631081 100644 --- a/_data/package.yml +++ b/_data/package.yml @@ -1,6 +1,6 @@ name: PatternClass -version: 2.4.1 -date: 2017-09-28 +version: 2.4.2 +date: 2018-07-24 description: | A permutation pattern class package @@ -32,7 +32,7 @@ packageinfo: https://gap-packages.github.io/PatternClass/PackageInfo.g downloads: - name: .tar.gz - url: https://github.com/gap-packages/PatternClass/releases/download/v2.4.1/PatternClass-2.4.1.tar.gz + url: https://github.com/gap-packages/PatternClass/releases/download/v2.4.2/PatternClass-2.4.2.tar.gz abstract: | The PatternClass package is build on the idea of token passing networks building permutation pattern classes. Those classes are best determined by their basis. Both sets can be encoded by rank encoding their permutations. Each, the class and its basis, in their encoded form build a rational language. Rational languages can be easily computed by using automata, which also can be build directly from the token passing networks. Both ways will build the same language, i.e. the same automaton. diff --git a/doc/chap0.html b/doc/chap0.html index 8d9c21b..e2043ea 100644 --- a/doc/chap0.html +++ b/doc/chap0.html @@ -44,8 +44,8 @@

A permutation pattern class package


Email: rh347@icloud.com -
Homepage: TODO -
Address:
TODO
+
Homepage: https://rh347.host.cs.st-andrews.ac.uk/ +
Address:
Ruth Hoffmann
School of Computer Science,
University of St. Andrews,
North Haugh,
St. Andrews,
Fife,
KY16 9SS,
SCOTLAND

Steve Linton diff --git a/doc/chap0.txt b/doc/chap0.txt index b282f78..5c18aa2 100644 --- a/doc/chap0.txt +++ b/doc/chap0.txt @@ -22,8 +22,15 @@ Ruth Hoffmann Email: mailto:rh347@icloud.com - Homepage: TODO - Address: TODO + Homepage: https://rh347.host.cs.st-andrews.ac.uk/ + Address: Ruth Hoffmann + School of Computer Science, + University of St. Andrews, + North Haugh, + St. Andrews, + Fife, + KY16 9SS, + SCOTLAND Steve Linton diff --git a/doc/chap0_mj.html b/doc/chap0_mj.html index 1c6737c..0b7dabf 100644 --- a/doc/chap0_mj.html +++ b/doc/chap0_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Contents @@ -47,8 +47,8 @@

A permutation pattern class package


Email: rh347@icloud.com -
Homepage: TODO -
Address:
TODO
+
Homepage: https://rh347.host.cs.st-andrews.ac.uk/ +
Address:
Ruth Hoffmann
School of Computer Science,
University of St. Andrews,
North Haugh,
St. Andrews,
Fife,
KY16 9SS,
SCOTLAND

Steve Linton diff --git a/doc/chap1.html b/doc/chap1.html index 5cb686c..a14cee9 100644 --- a/doc/chap1.html +++ b/doc/chap1.html @@ -26,13 +26,13 @@

1 Introduction

-

Token passing networks (TPNs) are directed graphs with nodes that can hold at most one token. Also each graph has a designated input node, which generates an ordered sequence of numbered tokens and a designated output node that collects the tokens in the order they arrive at it. The input node has no incoming edges, whereas the output node has no outgoing edges. A token t travels through the graph, from node to node, if there is an edge connecting the nodes, if the node the token is moving from is either the input node and the tokens 1, ..., t-1 have been released or the node is not the output node, and lastly if the destination node contains no token or it is the output node. [3]

+

Token passing networks (TPNs) are directed graphs with nodes that can hold at most one token. Also each graph has a designated input node, which generates an ordered sequence of numbered tokens and a designated output node that collects the tokens in the order they arrive at it. The input node has no incoming edges, whereas the output node has no outgoing edges. A token t travels through the graph, from node to node, if there is an edge connecting the nodes, if the node the token is moving from is either the input node and the tokens 1, ..., t-1 have been released or the node is not the output node, and lastly if the destination node contains no token or it is the output node. [ALTd.]

-

The set of permutations resulting from a TPN is closed under the property of containment. A permutation a contains a permutation b of shorter length if in a there is a subsequence that is isomorphic to b. This class of permutations can be represented by its anti-chain, which in this context is called the basis. [2]

+

The set of permutations resulting from a TPN is closed under the property of containment. A permutation a contains a permutation b of shorter length if in a there is a subsequence that is isomorphic to b. This class of permutations can be represented by its anti-chain, which in this context is called the basis. [AAR03]

-

To enhance the computability of permutation pattern classes, each permutation can be encoded, using the so called rank encoding. For a permutation p_1 ... p_n, it is the sequence e_1... e_n where e_i is the rank of p_i among {p_i,p_i+1,...,p_n}. It can be shown that the sets of encoded permutations of the class and the basis, both are a rational languages. Rational languages can be represented by automata. [2]

+

To enhance the computability of permutation pattern classes, each permutation can be encoded, using the so called rank encoding. For a permutation p_1 ... p_n, it is the sequence e_1... e_n where e_i is the rank of p_i among {p_i,p_i+1,...,p_n}. It can be shown that the sets of encoded permutations of the class and the basis, both are a rational languages. Rational languages can be represented by automata. [AAR03]

-

There is another approach to get from TPNs to their corresponding automata. Namely building equivalence classes from TPNs using the different dispositions of tokens within them. These equivalence classes of dispositions and the rank encoding of the permutations allow to build the same rational language as from the process above. [3]

+

There is another approach to get from TPNs to their corresponding automata. Namely building equivalence classes from TPNs using the different dispositions of tokens within them. These equivalence classes of dispositions and the rank encoding of the permutations allow to build the same rational language as from the process above. [ALTd.]

 [Top of Book]  [Contents]   [Previous Chapter]   [Next Chapter] 
diff --git a/doc/chap1.txt b/doc/chap1.txt index a78c85f..640f591 100644 --- a/doc/chap1.txt +++ b/doc/chap1.txt @@ -10,24 +10,24 @@ connecting the nodes, if the node the token is moving from is either the input node and the tokens 1, ..., t-1 have been released or the node is not the output node, and lastly if the destination node contains no token or it - is the output node. [3] + is the output node. [ALTd.] The set of permutations resulting from a TPN is closed under the property of containment. A permutation a contains a permutation b of shorter length if in a there is a subsequence that is isomorphic to b. This class of permutations can be represented by its anti-chain, which in this context is - called the basis. [2] + called the basis. [AAR03] To enhance the computability of permutation pattern classes, each permutation can be encoded, using the so called rank encoding. For a permutation p_1 ... p_n, it is the sequence e_1... e_n where e_i is the rank of p_i among {p_i,p_i+1,...,p_n}. It can be shown that the sets of encoded permutations of the class and the basis, both are a rational languages. - Rational languages can be represented by automata. [2] + Rational languages can be represented by automata. [AAR03] There is another approach to get from TPNs to their corresponding automata. Namely building equivalence classes from TPNs using the different dispositions of tokens within them. These equivalence classes of dispositions and the rank encoding of the permutations allow to build the - same rational language as from the process above. [3] + same rational language as from the process above. [ALTd.] diff --git a/doc/chap10_mj.html b/doc/chap10_mj.html index e26d8c7..5697c5c 100644 --- a/doc/chap10_mj.html +++ b/doc/chap10_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 10: Miscellaneous functions diff --git a/doc/chap1_mj.html b/doc/chap1_mj.html index ed64dbd..fc9d3f7 100644 --- a/doc/chap1_mj.html +++ b/doc/chap1_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 1: Introduction @@ -29,13 +29,13 @@

1 Introduction

-

Token passing networks (TPNs) are directed graphs with nodes that can hold at most one token. Also each graph has a designated input node, which generates an ordered sequence of numbered tokens and a designated output node that collects the tokens in the order they arrive at it. The input node has no incoming edges, whereas the output node has no outgoing edges. A token \(t\) travels through the graph, from node to node, if there is an edge connecting the nodes, if the node the token is moving from is either the input node and the tokens \(1, \ldots, t-1\) have been released or the node is not the output node, and lastly if the destination node contains no token or it is the output node. [3]

+

Token passing networks (TPNs) are directed graphs with nodes that can hold at most one token. Also each graph has a designated input node, which generates an ordered sequence of numbered tokens and a designated output node that collects the tokens in the order they arrive at it. The input node has no incoming edges, whereas the output node has no outgoing edges. A token \(t\) travels through the graph, from node to node, if there is an edge connecting the nodes, if the node the token is moving from is either the input node and the tokens \(1, \ldots, t-1\) have been released or the node is not the output node, and lastly if the destination node contains no token or it is the output node. [ALTd.]

-

The set of permutations resulting from a TPN is closed under the property of containment. A permutation \(a\) contains a permutation \(b\) of shorter length if in \(a\) there is a subsequence that is isomorphic to \(b\). This class of permutations can be represented by its anti-chain, which in this context is called the basis. [2]

+

The set of permutations resulting from a TPN is closed under the property of containment. A permutation \(a\) contains a permutation \(b\) of shorter length if in \(a\) there is a subsequence that is isomorphic to \(b\). This class of permutations can be represented by its anti-chain, which in this context is called the basis. [AAR03]

-

To enhance the computability of permutation pattern classes, each permutation can be encoded, using the so called rank encoding. For a permutation \(p_{1} \ldots p_{n}\), it is the sequence \(e_{1}\ldots e_{n}\) where \(e_{i}\) is the rank of \(p_{i}\) among \(\{p_{i},p_{i+1},\ldots,p_{n}\}\). It can be shown that the sets of encoded permutations of the class and the basis, both are a rational languages. Rational languages can be represented by automata. [2]

+

To enhance the computability of permutation pattern classes, each permutation can be encoded, using the so called rank encoding. For a permutation \(p_{1} \ldots p_{n}\), it is the sequence \(e_{1}\ldots e_{n}\) where \(e_{i}\) is the rank of \(p_{i}\) among \(\{p_{i},p_{i+1},\ldots,p_{n}\}\). It can be shown that the sets of encoded permutations of the class and the basis, both are a rational languages. Rational languages can be represented by automata. [AAR03]

-

There is another approach to get from TPNs to their corresponding automata. Namely building equivalence classes from TPNs using the different dispositions of tokens within them. These equivalence classes of dispositions and the rank encoding of the permutations allow to build the same rational language as from the process above. [3]

+

There is another approach to get from TPNs to their corresponding automata. Namely building equivalence classes from TPNs using the different dispositions of tokens within them. These equivalence classes of dispositions and the rank encoding of the permutations allow to build the same rational language as from the process above. [ALTd.]

 [Top of Book]  [Contents]   [Previous Chapter]   [Next Chapter] 
diff --git a/doc/chap2.html b/doc/chap2.html index e79ae6c..2e2bf83 100644 --- a/doc/chap2.html +++ b/doc/chap2.html @@ -35,7 +35,7 @@

2 Token Passing Networks

A token passing network is a directed graph with a designated input node and a designated output node. The input node has no incoming edges whereas the output node has no outgoing edges. Also the input node generates a sequence of tokens, labelled 1, 2, 3, ... . These tokens are passed on to the nodes within the graph, where each node, apart from the input and output node, can hold at most one token at any time. The edges do not hold tokens but are there to pass them on. The following must hold if a token t moves from the node x to the node y.

-

There is an edge from x to y; x is the input node, and the tokens 1, 2, 3, ... , t-1 have been moved, or x is any other node but not the output node; lastly either y is the output node or y is not the input node and currently is not occupied by a token. [3]

+

There is an edge from x to y; x is the input node, and the tokens 1, 2, 3, ... , t-1 have been moved, or x is any other node but not the output node; lastly either y is the output node or y is not the input node and currently is not occupied by a token. [ALTd.]

Token passing networks, or TPNs, are represented in GAP as a list. Each entry of the list is the index of the node within the TPN and contains a list of the "destinations", i.e. the end of the edge or arrow where it is directed to.

diff --git a/doc/chap2.txt b/doc/chap2.txt index 3c26a91..23d1d0e 100644 --- a/doc/chap2.txt +++ b/doc/chap2.txt @@ -13,7 +13,7 @@ There is an edge from x to y; x is the input node, and the tokens 1, 2, 3, ... , t-1 have been moved, or x is any other node but not the output node; lastly either y is the output node or y is not the input node and currently - is not occupied by a token. [3] + is not occupied by a token. [ALTd.] Token passing networks, or TPNs, are represented in GAP as a list. Each entry of the list is the index of the node within the TPN and contains a diff --git a/doc/chap2_mj.html b/doc/chap2_mj.html index 8659cc5..4b66d85 100644 --- a/doc/chap2_mj.html +++ b/doc/chap2_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 2: Token Passing Networks @@ -38,7 +38,7 @@

2 Token Passing Networks

A token passing network is a directed graph with a designated input node and a designated output node. The input node has no incoming edges whereas the output node has no outgoing edges. Also the input node generates a sequence of tokens, labelled 1, 2, 3, ... . These tokens are passed on to the nodes within the graph, where each node, apart from the input and output node, can hold at most one token at any time. The edges do not hold tokens but are there to pass them on. The following must hold if a token \(t\) moves from the node \(x\) to the node \(y\).

-

There is an edge from \(x\) to \(y\); \(x\) is the input node, and the tokens 1, 2, 3, ... , \(t-1\) have been moved, or \(x\) is any other node but not the output node; lastly either \(y\) is the output node or \(y\) is not the input node and currently is not occupied by a token. [3]

+

There is an edge from \(x\) to \(y\); \(x\) is the input node, and the tokens 1, 2, 3, ... , \(t-1\) have been moved, or \(x\) is any other node but not the output node; lastly either \(y\) is the output node or \(y\) is not the input node and currently is not occupied by a token. [ALTd.]

Token passing networks, or TPNs, are represented in GAP as a list. Each entry of the list is the index of the node within the TPN and contains a list of the "destinations", i.e. the end of the edge or arrow where it is directed to.

diff --git a/doc/chap3.html b/doc/chap3.html index cddfe65..d12331b 100644 --- a/doc/chap3.html +++ b/doc/chap3.html @@ -33,7 +33,7 @@

3 Permutation Encoding

-

A permutation π=π_1 ... π_n has rank encoding p_1 ... p_n where p_i= |{j : j ≥ i, π_j ≤ π_i } |. In other words the rank encoded permutation is a sequence of p_i with 1≤ i≤ n, where p_i is the rank of π_i in {π_i,π_i+1,... ,π_n}. [2]

+

A permutation π=π_1 ... π_n has rank encoding p_1 ... p_n where p_i= |{j : j ≥ i, π_j ≤ π_i } |. In other words the rank encoded permutation is a sequence of p_i with 1≤ i≤ n, where p_i is the rank of π_i in {π_i,π_i+1,... ,π_n}. [AAR03]

The encoding of the permutation 3 2 5 1 6 7 4 8 9 is done as follows:

diff --git a/doc/chap3.txt b/doc/chap3.txt index 65d169f..c689a8d 100644 --- a/doc/chap3.txt +++ b/doc/chap3.txt @@ -4,21 +4,21 @@ A permutation π=π_1 ... π_n has rank encoding p_1 ... p_n where p_i= |{j : j ≥ i, π_j ≤ π_i } |. In other words the rank encoded permutation is a sequence of p_i with 1≤ i≤ n, where p_i is the rank of π_i in {π_i,π_i+1,... - ,π_n}. [2] + ,π_n}. [AAR03] The encoding of the permutation 3 2 5 1 6 7 4 8 9 is done as follows: - Permutation │ Encoding │ Assisting list - 325167489 │ ∅ │ 123456789 - 25167489 │ 3 │ 12456789 - 5167489 │ 32 │ 1456789 - 167489 │ 323 │ 146789 - 67489 │ 3231 │ 46789 - 7489 │ 32312 │ 4789 - 489 │ 323122 │ 489 - 89 │ 3231221 │ 89 - 9 │ 32312211 │ 9 - ∅ │ 323122111 │ ∅ + Permutation │ Encoding │ Assisting list + 325167489 │ ∅ │ 123456789 + 25167489 │ 3 │ 12456789 + 5167489 │ 32 │ 1456789 + 167489 │ 323 │ 146789 + 67489 │ 3231 │ 46789 + 7489 │ 32312 │ 4789 + 489 │ 323122 │ 489 + 89 │ 3231221 │ 89 + 9 │ 32312211 │ 9 + ∅ │ 323122111 │ ∅ Decoding a permutation is done in a similar fashion, taking the sequence p_1 ... p_n and using the reverse process will lead to the permutation π=π_1 ... @@ -27,17 +27,17 @@ The sequence 3 2 3 1 2 2 1 1 1 is decoded as: - Encoding │ Permutation │ Assisting list - 323122111 │ ∅ │ 123456789 - 23122111 │ 3 │ 12456789 - 3122111 │ 32 │ 1456789 - 122111 │ 325 │ 146789 - 22111 │ 3251 │ 46789 - 2111 │ 32516 │ 4789 - 111 │ 325167 │ 489 - 11 │ 3251674 │ 89 - 1 │ 32516748 │ 9 - ∅ │ 325167489 │ ∅ + Encoding │ Permutation │ Assisting list + 323122111 │ ∅ │ 123456789 + 23122111 │ 3 │ 12456789 + 3122111 │ 32 │ 1456789 + 122111 │ 325 │ 146789 + 22111 │ 3251 │ 46789 + 2111 │ 32516 │ 4789 + 111 │ 325167 │ 489 + 11 │ 3251674 │ 89 + 1 │ 32516748 │ 9 + ∅ │ 325167489 │ ∅ 3.1 Encoding and Decoding diff --git a/doc/chap3_mj.html b/doc/chap3_mj.html index d659d3d..44eaa0c 100644 --- a/doc/chap3_mj.html +++ b/doc/chap3_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 3: Permutation Encoding @@ -36,7 +36,7 @@

3 Permutation Encoding

-

A permutation \(\pi=\pi_{1} \ldots \pi_{n}\) has rank encoding \(p_{1} \ldots p_{n}\) where \( p_{i}= |\{j : j \geq i, \pi_{j} \leq \pi_{i} \} | \). In other words the rank encoded permutation is a sequence of \(p_{i}\) with \(1\leq i\leq n\), where \(p_{i}\) is the rank of \(\pi_{i}\) in \(\{\pi_{i},\pi_{i+1},\ldots ,\pi_{n}\}\). [2]

+

A permutation \(\pi=\pi_{1} \ldots \pi_{n}\) has rank encoding \(p_{1} \ldots p_{n}\) where \( p_{i}= |\{j : j \geq i, \pi_{j} \leq \pi_{i} \} | \). In other words the rank encoded permutation is a sequence of \(p_{i}\) with \(1\leq i\leq n\), where \(p_{i}\) is the rank of \(\pi_{i}\) in \(\{\pi_{i},\pi_{i+1},\ldots ,\pi_{n}\}\). [AAR03]

The encoding of the permutation 3 2 5 1 6 7 4 8 9 is done as follows:

diff --git a/doc/chap4.html b/doc/chap4.html index f9305c6..4ced4db 100644 --- a/doc/chap4.html +++ b/doc/chap4.html @@ -32,7 +32,7 @@

4 From Networks to Automata

-

It is known that the language of all encoded permutations of a TPN is rational, and thus is it indeed possible to turn a TPN into an automaton. The idea is to inspect all dispositions of tokens within the TPN and find equivalence classes of these dispositions, for more details consult [3]. Adding a constraint, which limits the number of tokens at any time within the TPN, is also considered in this chapter.

+

It is known that the language of all encoded permutations of a TPN is rational, and thus is it indeed possible to turn a TPN into an automaton. The idea is to inspect all dispositions of tokens within the TPN and find equivalence classes of these dispositions, for more details consult [ALTd.]. Adding a constraint, which limits the number of tokens at any time within the TPN, is also considered in this chapter.

The algorithms featured in this chapter do not return the minimal automata representing the input TPN as they are exactly visualising the equivalence classes of the dispositions of the tokens in the TPN. The automaton can be minimalised by choice, as it simplifies future computations involving the automaton also is makes the automata more legible.

diff --git a/doc/chap4.txt b/doc/chap4.txt index 3b9eb16..d3c29d5 100644 --- a/doc/chap4.txt +++ b/doc/chap4.txt @@ -4,7 +4,7 @@ It is known that the language of all encoded permutations of a TPN is rational, and thus is it indeed possible to turn a TPN into an automaton. The idea is to inspect all dispositions of tokens within the TPN and find - equivalence classes of these dispositions, for more details consult [3]. + equivalence classes of these dispositions, for more details consult [ALTd.]. Adding a constraint, which limits the number of tokens at any time within the TPN, is also considered in this chapter. diff --git a/doc/chap4_mj.html b/doc/chap4_mj.html index c000afc..d5700ab 100644 --- a/doc/chap4_mj.html +++ b/doc/chap4_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 4: From Networks to Automata @@ -35,7 +35,7 @@

4 From Networks to Automata

-

It is known that the language of all encoded permutations of a TPN is rational, and thus is it indeed possible to turn a TPN into an automaton. The idea is to inspect all dispositions of tokens within the TPN and find equivalence classes of these dispositions, for more details consult [3]. Adding a constraint, which limits the number of tokens at any time within the TPN, is also considered in this chapter.

+

It is known that the language of all encoded permutations of a TPN is rational, and thus is it indeed possible to turn a TPN into an automaton. The idea is to inspect all dispositions of tokens within the TPN and find equivalence classes of these dispositions, for more details consult [ALTd.]. Adding a constraint, which limits the number of tokens at any time within the TPN, is also considered in this chapter.

The algorithms featured in this chapter do not return the minimal automata representing the input TPN as they are exactly visualising the equivalence classes of the dispositions of the tokens in the TPN. The automaton can be minimalised by choice, as it simplifies future computations involving the automaton also is makes the automata more legible.

diff --git a/doc/chap5.txt b/doc/chap5.txt index 3fc78b9..711c940 100644 --- a/doc/chap5.txt +++ b/doc/chap5.txt @@ -73,7 +73,8 @@ If i,j ∈ Q ∖ { n+1 },with i < j, and i',j' ∈ S, i=i', j=j' then - f(i,i')=i, f(i,j')=j, f(j,j')=j, f(j,i')=j-1 or n+1. + f(i,i')=i, f(i,j')=j, f(j,j')=j, f(j,i')=j-1 or n+1. +  Example  gap> x:=Automaton("det",4,2,[[1,3,1,4],[2,2,4,4]],[1],[2]); diff --git a/doc/chap5_mj.html b/doc/chap5_mj.html index 7c6f31f..70f5ce1 100644 --- a/doc/chap5_mj.html +++ b/doc/chap5_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 5: From Automata to Networks diff --git a/doc/chap6.html b/doc/chap6.html index efc0de0..685d55f 100644 --- a/doc/chap6.html +++ b/doc/chap6.html @@ -61,7 +61,7 @@

6 Pattern Classes

Permutation pattern classes can be determined using their corresponding basis. The basis of a pattern class is the anti-chain of the class, under the order of containment. A permutation π contains another permutation σ (of shorter length) if there is a subsequence in π, which is isomorphic to σ.

-

With the rational language of the rank encoded class, it is also possible to find the rational language of the basis and vice versa. Several specific kinds of transducers are used in this process. [2]

+

With the rational language of the rank encoded class, it is also possible to find the rational language of the basis and vice versa. Several specific kinds of transducers are used in this process. [AAR03]

diff --git a/doc/chap6.txt b/doc/chap6.txt index ce7e6eb..e7d5c8b 100644 --- a/doc/chap6.txt +++ b/doc/chap6.txt @@ -8,7 +8,7 @@ With the rational language of the rank encoded class, it is also possible to find the rational language of the basis and vice versa. Several specific - kinds of transducers are used in this process. [2] + kinds of transducers are used in this process. [AAR03] 6.1 Transducers @@ -158,7 +158,8 @@ permutations which do not belong to the class. Using - B(L)=(L^r D^t)^r ∩ L^c + B(L)=(L^r D^t)^r ∩ L^c + it is possible using the deletion transducer D and the language of rank encoded permutations L to find the language of the rank encoded permutations @@ -213,7 +214,8 @@ encoded basis of a permutation class, and using the formula - L=B_k ∩ ((B(L)^r I^t)^c )^r + L=B_k ∩ ((B(L)^r I^t)^c )^r + returns the automaton that accepts the rank encoded permutations of the class. In the formula, B_k is the automaton that accepts all permutations of diff --git a/doc/chap6_mj.html b/doc/chap6_mj.html index f424c83..2d0b482 100644 --- a/doc/chap6_mj.html +++ b/doc/chap6_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 6: Pattern Classes @@ -64,7 +64,7 @@

6 Pattern Classes

Permutation pattern classes can be determined using their corresponding basis. The basis of a pattern class is the anti-chain of the class, under the order of containment. A permutation \(\pi\) contains another permutation \(\sigma\) (of shorter length) if there is a subsequence in \(\pi\), which is isomorphic to \(\sigma\).

-

With the rational language of the rank encoded class, it is also possible to find the rational language of the basis and vice versa. Several specific kinds of transducers are used in this process. [2]

+

With the rational language of the rank encoded class, it is also possible to find the rational language of the basis and vice versa. Several specific kinds of transducers are used in this process. [AAR03]

diff --git a/doc/chap7.txt b/doc/chap7.txt index 70b31d1..8188dde 100644 --- a/doc/chap7.txt +++ b/doc/chap7.txt @@ -15,7 +15,8 @@ The complement of a permutation τ=τ_1...τ_n is the permutation - τ^C=(n+1)-τ_1 (n+1)-τ_2... (n+1)-τ_n + τ^C=(n+1)-τ_1 (n+1)-τ_2... (n+1)-τ_n + . diff --git a/doc/chap7_mj.html b/doc/chap7_mj.html index ca34401..caadcb8 100644 --- a/doc/chap7_mj.html +++ b/doc/chap7_mj.html @@ -6,7 +6,7 @@ GAP (PatternClass) - Chapter 7: Some Permutation Essentials diff --git a/doc/chap8.html b/doc/chap8.html index 87c5818..efab993 100644 --- a/doc/chap8.html +++ b/doc/chap8.html @@ -107,7 +107,7 @@
8.2-1 IsSimplePerm
‣ IsSimplePerm( perm )( function )

Returns: true if perm is simple.

-

To check whether perm (length of perm = n) is a simple permutation IsSimplePerm uses the basic algorithm proposed by Uno and Yagiura in [8] to compare the perm against the identity permutation of the same length.

+

To check whether perm (length of perm = n) is a simple permutation IsSimplePerm uses the basic algorithm proposed by Uno and Yagiura in [UY00] to compare the perm against the identity permutation of the same length.

 
@@ -123,7 +123,7 @@ 
8.2-1 IsSimplePerm

 
 
8.3  Point Deletion in Simple Permutations 

 
-
In [7] it is shown how one can get chains of permutations by starting with a simple permutation and then removing either a single point or two points and the resulting permutation would still be simple. We have applied this theory to create functions such that the set of simple permutations of shorter length, by one deletion, can be found.

+
In [PR12] it is shown how one can get chains of permutations by starting with a simple permutation and then removing either a single point or two points and the resulting permutation would still be simple. We have applied this theory to create functions such that the set of simple permutations of shorter length, by one deletion, can be found.

 
 

 
@@ -184,7 +184,7 @@ 
8.3-3 PointDeletion

 
 
8.4  Block-Decomposition 

 
-
Given a permutation π of length m and nonempty permutations α_1,...,α_m the inflation of π by α_1,...,α_m, written as π[α_1,...,α_m], is the permutation obtained by replacing each entry π(i) by an interval that is order isomorphic to α_i [4]. Conversely a block-decomposition of σ is any expression of σ as an inflation σ=π[α_1,...,α_m]. The block decomposition of a permutation is unique if and only if σ,π,α_1,...,α_n all are in the same pattern class and π is simple and π≠ 1 2, 2 1 [1].

+
Given a permutation π of length m and nonempty permutations α_1,...,α_m the inflation of π by α_1,...,α_m, written as π[α_1,...,α_m], is the permutation obtained by replacing each entry π(i) by an interval that is order isomorphic to α_i [Bri08]. Conversely a block-decomposition of σ is any expression of σ as an inflation σ=π[α_1,...,α_m]. The block decomposition of a permutation is unique if and only if σ,π,α_1,...,α_n all are in the same pattern class and π is simple and π≠ 1 2, 2 1 [AA05].

 
 
For example the inflation of 25413[21,1,1,1,2413]=3 2 8 9 1 5 7 4 6, written in GAP this is [[2,5,4,1,3],[2,1],[1],[1],[1],[2,4,1,3]]. This decomposition of 3 2 8 9 1 5 7 4 6 is not unique. The unique block-decomposition, as described above, for 3 2 8 9 1 5 7 4 6=2413[21,12,1,2413] or in GAP notation [3,2,8,9,1,5,7,4,6]=[[2,4,1,3],[2,1],[1,2],[1],[2,4,1,3]].

 
diff --git a/doc/chap8.txt b/doc/chap8.txt
index 9eb98e1..c5ef7e3 100644
--- a/doc/chap8.txt
+++ b/doc/chap8.txt
@@ -49,8 +49,8 @@
   Returns:  true if perm is simple.
   
   To  check  whether  perm  (length  of  perm  =  n)  is  a simple permutation
-  IsSimplePerm  uses the basic algorithm proposed by Uno and Yagiura in [8] to
-  compare the perm against the identity permutation of the same length.
+  IsSimplePerm  uses the basic algorithm proposed by Uno and Yagiura in [UY00]
+  to compare the perm against the identity permutation of the same length.
   
     Example  
     gap> IsSimplePerm([2,3,4,5,1,1,1,1]);
@@ -65,11 +65,11 @@
   
   8.3 Point Deletion in Simple Permutations
   
-  In [7] it is shown how one can get chains of permutations by starting with a
-  simple permutation and then removing either a single point or two points and
-  the resulting permutation would still be simple. We have applied this theory
-  to  create  functions  such  that  the set of simple permutations of shorter
-  length, by one deletion, can be found.
+  In  [PR12]  it  is  shown how one can get chains of permutations by starting
+  with  a  simple  permutation  and then removing either a single point or two
+  points  and the resulting permutation would still be simple. We have applied
+  this  theory to create functions such that the set of simple permutations of
+  shorter length, by one deletion, can be found.
   
   8.3-1 OnePointDelete
   
@@ -129,10 +129,10 @@
   Given  a permutation π of length m and nonempty permutations α_1,...,α_m the
   inflation of π by α_1,...,α_m, written as π[α_1,...,α_m], is the permutation
   obtained  by  replacing  each  entry  π(i)  by  an  interval  that  is order
-  isomorphic  to  α_i  [4].  Conversely  a  block-decomposition  of  σ  is any
+  isomorphic  to  α_i  [Bri08].  Conversely  a block-decomposition of σ is any
   expression of σ as an inflation σ=π[α_1,...,α_m]. The block decomposition of
   a  permutation  is unique if and only if σ,π,α_1,...,α_n all are in the same
-  pattern class and π is simple and π≠ 1 2, 2 1 [1].
+  pattern class and π is simple and π≠ 1 2, 2 1 [AA05].
   
   For example the inflation of 25413[21,1,1,1,2413]=3 2 8 9 1 5 7 4 6, written
   in GAP this is [[2,5,4,1,3],[2,1],[1],[1],[1],[2,4,1,3]]. This decomposition
@@ -193,7 +193,8 @@
   uniquely in the following form,
   
   
-  σ = 12 [α_1,α_2]
+        σ = 12 [α_1,α_2]
+  
   
   where α_1 is not plus-decomposable.
   
@@ -228,7 +229,8 @@
   written uniquely in the following form,
   
   
-  σ = 21 [α_1,α_2]
+        σ = 21 [α_1,α_2]
+  
   
   where α_1 is not minus-decomposable.
   
@@ -263,12 +265,14 @@
   as,
   
   
-  σ ⊕ τ = σ_1 σ_2...σ_k τ_1+k τ_2+k...τ_l+k .
+        σ ⊕ τ = σ_1 σ_2...σ_k τ_1+k τ_2+k...τ_l+k .
+  
   
   In a similar fashion the skew sum of σ, τ is
   
   
-  σ ⊖ τ = σ_1+l σ_2+l...σ_k+l τ_1 τ_2...τ_l .
+        σ ⊖ τ = σ_1+l σ_2+l...σ_k+l τ_1 τ_2...τ_l .
+  
   
   The  calculation  of the direct and skew sums of permutations using the rank
   encoding  is  also  straight  forward and is used in the functions described
diff --git a/doc/chap8_mj.html b/doc/chap8_mj.html
index f14f980..05086ef 100644
--- a/doc/chap8_mj.html
+++ b/doc/chap8_mj.html
@@ -6,7 +6,7 @@
 
 
 
 GAP (PatternClass) - Chapter 8: Properties of Permutations 
 
@@ -110,7 +110,7 @@ 
8.2-1 IsSimplePerm

 
‣ IsSimplePerm( perm )( function )

 
Returns: true if perm is simple.

 
-
To check whether perm (length of perm = \(n\)) is a simple permutation IsSimplePerm uses the basic algorithm proposed by Uno and Yagiura in [8] to compare the perm against the identity permutation of the same length.

+
To check whether perm (length of perm = \(n\)) is a simple permutation IsSimplePerm uses the basic algorithm proposed by Uno and Yagiura in [UY00] to compare the perm against the identity permutation of the same length.

 
 
 
 
@@ -126,7 +126,7 @@ 
8.2-1 IsSimplePerm

 
 
8.3  Point Deletion in Simple Permutations 

 
-
In [7] it is shown how one can get chains of permutations by starting with a simple permutation and then removing either a single point or two points and the resulting permutation would still be simple. We have applied this theory to create functions such that the set of simple permutations of shorter length, by one deletion, can be found.

+
In [PR12] it is shown how one can get chains of permutations by starting with a simple permutation and then removing either a single point or two points and the resulting permutation would still be simple. We have applied this theory to create functions such that the set of simple permutations of shorter length, by one deletion, can be found.

 
 

 
@@ -187,7 +187,7 @@ 
8.3-3 PointDeletion

 
 
8.4  Block-Decomposition 

 
-
Given a permutation \(\pi\) of length \(m\) and nonempty permutations \(\alpha_{1},\ldots,\alpha_{m}\) the inflation of \(\pi\) by \(\alpha_{1},\ldots,\alpha_{m}\), written as \(\pi[\alpha_{1},\ldots,\alpha_{m}]\), is the permutation obtained by replacing each entry \(\pi(i)\) by an interval that is order isomorphic to \(\alpha_{i}\) [4]. Conversely a block-decomposition of \(\sigma\) is any expression of \(\sigma\) as an inflation \(\sigma=\pi[\alpha_{1},\ldots,\alpha_{m}]\). The block decomposition of a permutation is unique if and only if \(\sigma,\pi,\alpha_{1},\ldots,\alpha_{n}\) all are in the same pattern class and \(\pi\) is simple and \(\pi\neq 1 2,\ 2 1\) [1].

+
Given a permutation \(\pi\) of length \(m\) and nonempty permutations \(\alpha_{1},\ldots,\alpha_{m}\) the inflation of \(\pi\) by \(\alpha_{1},\ldots,\alpha_{m}\), written as \(\pi[\alpha_{1},\ldots,\alpha_{m}]\), is the permutation obtained by replacing each entry \(\pi(i)\) by an interval that is order isomorphic to \(\alpha_{i}\) [Bri08]. Conversely a block-decomposition of \(\sigma\) is any expression of \(\sigma\) as an inflation \(\sigma=\pi[\alpha_{1},\ldots,\alpha_{m}]\). The block decomposition of a permutation is unique if and only if \(\sigma,\pi,\alpha_{1},\ldots,\alpha_{n}\) all are in the same pattern class and \(\pi\) is simple and \(\pi\neq 1 2,\ 2 1\) [AA05].

 
 
For example the inflation of \(25413[21,1,1,1,2413]=3 2 8 9 1 5 7 4 6\), written in GAP this is [[2,5,4,1,3],[2,1],[1],[1],[1],[2,4,1,3]]. This decomposition of \(3 2 8 9 1 5 7 4 6\) is not unique. The unique block-decomposition, as described above, for \(3 2 8 9 1 5 7 4 6=2413[21,12,1,2413]\) or in GAP notation [3,2,8,9,1,5,7,4,6]=[[2,4,1,3],[2,1],[1,2],[1],[2,4,1,3]].

 
diff --git a/doc/chap9.html b/doc/chap9.html
index de7d5cf..e3ed0b6 100644
--- a/doc/chap9.html
+++ b/doc/chap9.html
@@ -68,7 +68,7 @@ 
9  Regular Languages of Sets of Permutations 9.1  Inversions in Permutations 

 
-
An inversion in a permutation τ=τ_1...τ_n is a pair (i,j) such that 1≤ i<j≤ n and τ_i>τ_j [5].

+
An inversion in a permutation τ=τ_1...τ_n is a pair (i,j) such that 1≤ i<j≤ n and τ_i>τ_j [CJS11].

 
 

 
@@ -236,7 +236,7 @@ 
9.3  Language of all non-simple permutations E(hatΩ_k) is the sublanguage of E(Ω_k) excluding the words of length ≤ 1.

 
-
E(mathcalD_P(Ω_k)) is the language of all plus-decomposable permutations as described in [6].

+
E(mathcalD_P(Ω_k)) is the language of all plus-decomposable permutations as described in [HL13].

 
 

 
@@ -452,7 +452,7 @@ 
9.5 Exceptionality

 
 
m (2m) (m-1) (2m-1) ... 1 (m+1)

 
-
where m ≥ 2 [7].

+
where m ≥ 2 [PR12].

 
 

 
diff --git a/doc/chap9.txt b/doc/chap9.txt
index eafadb3..3ce8929 100644
--- a/doc/chap9.txt
+++ b/doc/chap9.txt
@@ -8,7 +8,7 @@
   9.1 Inversions in Permutations
   
   An  inversion in a permutation τ=τ_1...τ_n is a pair (i,j) such that 1≤ iτ_j [5].
+  n and τ_i>τ_j [CJS11].
   
   9.1-1 InversionAut
   
@@ -166,10 +166,14 @@
   highest rank k is described by the following equation,
   
   
-  E(NS_k) = E(Ω_k) ∩ ( ⋃_l=1^k-1 P_l ⋃_m=l^k-1 E(hatΩ_k-m)^+m ∪ ⋃_j=1^k-1 E(hatΩ_k-j)^+j ∪
+        E(NS_k) = E(Ω_k) ∩ ( ⋃_l=1^k-1 P_l ⋃_m=l^k-1 E(hatΩ_k-m)^+m ∪
+        ⋃_j=1^k-1 E(hatΩ_k-j)^+j ∪
   
   
-  ∪ ⋃_a=2^k-1 ⋃_b=0^k-1-a Q_a,b ⋃_i=0^a-2 (E(hatΩ_k-(b+i))^+b+i)^(a-i) ) Σ^* ∪ E(mathcalD_P(Ω_k))
+  
+        ∪ ⋃_a=2^k-1 ⋃_b=0^k-1-a Q_a,b ⋃_i=0^a-2 (E(hatΩ_k-(b+i))^+b+i)^(a-i) )
+        Σ^* ∪ E(mathcalD_P(Ω_k))
+  
   
   where Σ is the alphabet {1,...,k}, k∈N, k ≥ 3.
   
@@ -189,7 +193,7 @@
   E(hatΩ_k) is the sublanguage of E(Ω_k) excluding the words of length ≤ 1.
   
   E(mathcalD_P(Ω_k))  is the language of all plus-decomposable permutations as
-  described in [6].
+  described in [HL13].
   
   9.3-1 LengthBoundAut
   
@@ -373,7 +377,8 @@
   Ω_k
   
   
-  E(S_k) = E(Ω_k∖ NS_k) = E(Ω_k) ∖ E(NS_k) = E(Ω_k) ∩ E(NS_k)^C
+        E(S_k) = E(Ω_k∖ NS_k) = E(Ω_k) ∖ E(NS_k) = E(Ω_k) ∩ E(NS_k)^C
+  
   
   9.4-1 SimplePermAut
   
@@ -405,18 +410,22 @@
   forms,
   
   
-  2 4 6 ... (2m) 1 3 5 ... (2m-1)
+        2 4 6 ... (2m) 1 3 5 ... (2m-1)
+  
+  
+  
+        (2m-1) (2m-3) ... 1 (2m) (2m-2) ... 2
+  
   
   
-  (2m-1) (2m-3) ... 1 (2m) (2m-2) ... 2
+        (m+1) 1 (m+2) 2 (m+3) 3 ... (2m) m
   
   
-  (m+1) 1 (m+2) 2 (m+3) 3 ... (2m) m
   
+        m (2m) (m-1) (2m-1) ... 1 (m+1)
   
-  m (2m) (m-1) (2m-1) ... 1 (m+1)
   
-  where m ≥ 2 [7].
+  where m ≥ 2 [PR12].
   
   9.5-1 IsExceptionalPerm
   
diff --git a/doc/chap9_mj.html b/doc/chap9_mj.html
index 4f8bdcf..8985a7d 100644
--- a/doc/chap9_mj.html
+++ b/doc/chap9_mj.html
@@ -6,7 +6,7 @@
 
 
 
 GAP (PatternClass) - Chapter 9:  Regular Languages of Sets of Permutations 
 
@@ -71,7 +71,7 @@ 
9  Regular Languages of Sets of Permutations 9.1  Inversions in Permutations 

 
-
An inversion in a permutation \(\tau=\tau_{1}\ldots\tau_{n}\) is a pair \((i,j)\) such that \(1\leq i<j\leq n\) and \(\tau_{i}>\tau_{j}\) [5].

+
An inversion in a permutation \(\tau=\tau_{1}\ldots\tau_{n}\) is a pair \((i,j)\) such that \(1\leq i<j\leq n\) and \(\tau_{i}>\tau_{j}\) [CJS11].

 
 

 
@@ -250,7 +250,7 @@ 
9.3  Language of all non-simple permutations \(E(\hat{\Omega}_{k})\) is the sublanguage of \(E(\Omega_{k})\) excluding the words of length \(\leq 1\).

 
-
\(E(\mathcal{D}_{P}(\Omega_{k}))\) is the language of all plus-decomposable permutations as described in [6].

+
\(E(\mathcal{D}_{P}(\Omega_{k}))\) is the language of all plus-decomposable permutations as described in [HL13].

 
 

 
@@ -476,7 +476,7 @@ 
9.5 Exceptionality

 m (2m) (m-1) (2m-1) \ldots 1 (m+1)
 \]

 
-
where \(m \geq 2\) [7].

+
where \(m \geq 2\) [PR12].

 
 

 
diff --git a/doc/chapBib.html b/doc/chapBib.html
index 3868f4a..351e38e 100644
--- a/doc/chapBib.html
+++ b/doc/chapBib.html
@@ -27,7 +27,7 @@ 
References

 
 

 

-[1]   Albert, M. H. and Atkinson, M. D.,
+[AA05]   Albert, M. H. and Atkinson, M. D.,
  Simple permutations and pattern restricted permutations,
  Discrete Mathematics,
  300 (1--3)
@@ -39,7 +39,7 @@ 
References

 
 

 

-[2]   Albert, M. H., Atkinson, M. D. and Ru\v{s}kuc, N.,
+[AAR03]   Albert, M. H., Atkinson, M. D. and Ru\v{s}kuc, N.,
  Regular closed sets of permutations,
  Theoretical Computer Science,
  306
@@ -50,7 +50,7 @@ 
References

 
 

 

-[3]   Atkinson, M. D., Livesey, M. J. and Tulley, D.,
+[ALTd.]   Atkinson, M. D., Livesey, M. J. and Tulley, D.,
  Permutations generated by token passing in graphs,
  Theoretical Computer Science,
  178
@@ -61,7 +61,7 @@ 
References

 
 

 

-[4]   Brignall, R.,
+[Bri08]   Brignall, R.,
  A Survey of Simple Permutations,
  ArXiv e-prints
  (2008).
@@ -70,7 +70,7 @@ 
References

 
 

 

-[5]   Claesson, A., Jel{\'{i}}nek, V. and Steingr{\'{i}}msson, E.,
+[CJS11]   Claesson, A., Jel{\'{i}}nek, V. and Steingr{\'{i}}msson, E.,
  Upper bounds for the Stanley-Wilf limit of 1324 and other layered
       patterns,
  ArXiv e-prints
@@ -80,7 +80,7 @@ 
References

 
 

 

-[6]   Hoffmann, R. and Linton, S.,
+[HL13]   Hoffmann, R. and Linton, S.,
  Regular Languages of Plus- and Minus- (In)Decomposable
       Permutations,
  Pure Mathematics and Applications (to appear)
@@ -90,7 +90,7 @@ 
References

 
 

 

-[7]   Pierrot, A. and Rossin, D.,
+[PR12]   Pierrot, A. and Rossin, D.,
  Simple permutations poset,
  ArXiv e-prints
  (2012),
@@ -100,7 +100,7 @@ 
References

 
 

 

-[8]   Uno, T. and Yagiura, M.,
+[UY00]   Uno, T. and Yagiura, M.,
  Fast Algorithms to Enumerate All Common Intervals of Two
       Permutations,
  Algorithmica,
diff --git a/doc/chapBib.txt b/doc/chapBib.txt
index 64d735d..4b75514 100644
--- a/doc/chapBib.txt
+++ b/doc/chapBib.txt
@@ -2,31 +2,32 @@
   
   References
   
-  [1]  Albert,  M.  H.  and  Atkinson,  M. D., Simple permutations and pattern
+  [AA05]  Albert,  M.  H. and Atkinson, M. D., Simple permutations and pattern
   restricted  permutations,  Discrete  Mathematics, 300, 1--3 (2005), 1 -- 15,
   (()).
   
-  [2]  Albert,  M. H., Atkinson, M. D. and Ru\v{s}kuc, N., Regular closed sets
-  of permutations, Theoretical Computer Science, 306 (2003), 85 - 100.
+  [AAR03]  Albert,  M.  H., Atkinson, M. D. and Ru\v{s}kuc, N., Regular closed
+  sets of permutations, Theoretical Computer Science, 306 (2003), 85 - 100.
   
-  [3]  Atkinson,  M. D., Livesey, M. J. and Tulley, D., Permutations generated
-  by  token passing in graphs, Theoretical Computer Science, 178 (n.d.), 103 -
-  118.
+  [ALTd.]  Atkinson,  M.  D.,  Livesey,  M.  J.  and  Tulley, D., Permutations
+  generated  by  token  passing  in  graphs, Theoretical Computer Science, 178
+  (n.d.), 103 - 118.
   
-  [4] Brignall, R., A Survey of Simple Permutations, ArXiv e-prints (2008).
+  [Bri08]  Brignall,  R.,  A  Survey  of  Simple  Permutations, ArXiv e-prints
+  (2008).
   
-  [5]  Claesson,  A.,  Jel{\'{i}}nek,  V.  and  Steingr{\'{i}}msson, E., Upper
+  [CJS11]  Claesson,  A., Jel{\'{i}}nek, V. and Steingr{\'{i}}msson, E., Upper
   bounds  for the Stanley-Wilf limit of 1324 and other layered patterns, ArXiv
   e-prints (2011).
   
-  [6]  Hoffmann,  R.  and  Linton,  S.,  Regular Languages of Plus- and Minus-
+  [HL13]  Hoffmann,  R.  and Linton, S., Regular Languages of Plus- and Minus-
   (In)Decomposable Permutations, Pure Mathematics and Applications (to appear)
   (2013).
   
-  [7]  Pierrot,  A.  and Rossin, D., Simple permutations poset, ArXiv e-prints
+  [PR12] Pierrot, A. and Rossin, D., Simple permutations poset, ArXiv e-prints
   (2012), 1--15.
   
-  [8]  Uno,  T.  and  Yagiura,  M.,  Fast  Algorithms  to Enumerate All Common
+  [UY00]  Uno,  T.  and  Yagiura,  M., Fast Algorithms to Enumerate All Common
   Intervals of Two Permutations, Algorithmica, 26 (2000), 2000.
   
   
diff --git a/doc/chapBib_mj.html b/doc/chapBib_mj.html
index 48bc75d..d881206 100644
--- a/doc/chapBib_mj.html
+++ b/doc/chapBib_mj.html
@@ -6,7 +6,7 @@
 
 
 
 GAP (PatternClass) - References
 
@@ -30,7 +30,7 @@ 
References

 
 

 

-[1]   Albert, M. H. and Atkinson, M. D.,
+[AA05]   Albert, M. H. and Atkinson, M. D.,
  Simple permutations and pattern restricted permutations,
  Discrete Mathematics,
  300 (1--3)
@@ -42,7 +42,7 @@ 
References

 
 

 

-[2]   Albert, M. H., Atkinson, M. D. and Ru\v{s}kuc, N.,
+[AAR03]   Albert, M. H., Atkinson, M. D. and Ru\v{s}kuc, N.,
  Regular closed sets of permutations,
  Theoretical Computer Science,
  306
@@ -53,7 +53,7 @@ 
References

 
 

 

-[3]   Atkinson, M. D., Livesey, M. J. and Tulley, D.,
+[ALTd.]   Atkinson, M. D., Livesey, M. J. and Tulley, D.,
  Permutations generated by token passing in graphs,
  Theoretical Computer Science,
  178
@@ -64,7 +64,7 @@ 
References

 
 

 

-[4]   Brignall, R.,
+[Bri08]   Brignall, R.,
  A Survey of Simple Permutations,
  ArXiv e-prints
  (2008).
@@ -73,7 +73,7 @@ 
References

 
 

 

-[5]   Claesson, A., Jel{\'{i}}nek, V. and Steingr{\'{i}}msson, E.,
+[CJS11]   Claesson, A., Jel{\'{i}}nek, V. and Steingr{\'{i}}msson, E.,
  Upper bounds for the Stanley-Wilf limit of 1324 and other layered
       patterns,
  ArXiv e-prints
@@ -83,7 +83,7 @@ 
References

 
 

 

-[6]   Hoffmann, R. and Linton, S.,
+[HL13]   Hoffmann, R. and Linton, S.,
  Regular Languages of Plus- and Minus- (In)Decomposable
       Permutations,
  Pure Mathematics and Applications (to appear)
@@ -93,7 +93,7 @@ 
References

 
 

 

-[7]   Pierrot, A. and Rossin, D.,
+[PR12]   Pierrot, A. and Rossin, D.,
  Simple permutations poset,
  ArXiv e-prints
  (2012),
@@ -103,7 +103,7 @@ 
References

 
 

 

-[8]   Uno, T. and Yagiura, M.,
+[UY00]   Uno, T. and Yagiura, M.,
  Fast Algorithms to Enumerate All Common Intervals of Two
       Permutations,
  Algorithmica,
diff --git a/doc/chapInd.html b/doc/chapInd.html
index abd449f..05b48e0 100644
--- a/doc/chapInd.html
+++ b/doc/chapInd.html
@@ -25,70 +25,70 @@
 

 
Index

 
-AcceptedWords  6.4-4  

-AcceptedWordsR  6.4-5  

-AcceptedWordsReversed  6.4-5  

-AutStateTransitionMatrix  6.4-3  

-BasisAutomaton  6.2-1  

-BlockDecomposition  8.4-2  

-BoundedClassAutomaton  6.2-3  

-BufferAndStack  2.1-3  

-ClassAutFromBase  6.2-5  

-ClassAutFromBaseEncoding  6.2-4  

-ClassAutomaton  6.2-2  

-ClassDirectSum  6.3-1  

-CombineAutTransducer  6.1-5  

-ConstrainedGraphToAut  4.1-2  

-DeletionTransducer  6.1-2  

-ExceptionalBoundedAutomaton  9.5-2  

-ExpandAlphabet  6.2-6  

-GapAut  9.3-4  

-GapSumAut  9.3-6  

-GraphToAut  4.1-1  

-InbetweenPermAutomaton  10.1-1  

-InbetweenPermSet  10.1-2  

-Inflation  8.4-1  

-InversionAut  9.1-1  

-InversionAutOfClass  9.1-2  

-InvolvementTransducer  6.1-4  

-Is2StarReplaceable  5.1-2  

-IsExceptionalPerm  9.5-1  

-IsInterval  8.1-1  

-IsMinusDecomposable  8.6-1  

-IsPlusDecomposable  8.5-1  

-IsPossibleGraphAut  5.1-4  

-IsRankEncoding  7.2-1  

-IsSimplePerm  8.2-1  

-IsStarClosed  5.1-1  

-IsStratified  5.1-3  

-IsSubPerm  10.1-3  

-LengthBoundAut  9.3-1  

-LoopFreeAut  10.2-1  

-LoopVertexFreeAut  10.2-2  

-MinusDecomposableAut  9.2-3  

-MinusIndecomposableAut  9.2-4  

-NextGap  9.3-3  

-NonSimpleAut  9.3-7  

-NumberAcceptedWords  6.4-2  

-OnePointDelete  8.3-1  

-Parstacks  2.1-1  

-PermComplement  7.1-1  

-PermDirectSum  8.7-1  

-PermSkewSum  8.7-2  

-PlusDecomposableAut  9.2-1  

-PlusIndecomposableAut  9.2-2  

-PointDeletion  8.3-3  

-RankDecoding  3.1-2  

-RankEncoding  3.1-1  

-Seqstacks  2.1-2  

-SequencesToRatExp  3.1-3  

-ShiftAut  9.3-2  

-SimplePermAut  9.4-1  

-Spectrum  6.4-1  

-SumAut  9.3-5  

-Transducer  6.1-1  

-TransposedTransducer  6.1-3  

-TwoPointDelete  8.3-2  

+AcceptedWords  6.4-4

+AcceptedWordsR  6.4-5

+AcceptedWordsReversed  6.4-5

+AutStateTransitionMatrix  6.4-3

+BasisAutomaton  6.2-1

+BlockDecomposition  8.4-2

+BoundedClassAutomaton  6.2-3

+BufferAndStack  2.1-3

+ClassAutFromBase  6.2-5

+ClassAutFromBaseEncoding  6.2-4

+ClassAutomaton  6.2-2

+ClassDirectSum  6.3-1

+CombineAutTransducer  6.1-5

+ConstrainedGraphToAut  4.1-2

+DeletionTransducer  6.1-2

+ExceptionalBoundedAutomaton  9.5-2

+ExpandAlphabet  6.2-6

+GapAut  9.3-4

+GapSumAut  9.3-6

+GraphToAut  4.1-1

+InbetweenPermAutomaton  10.1-1

+InbetweenPermSet  10.1-2

+Inflation  8.4-1

+InversionAut  9.1-1

+InversionAutOfClass  9.1-2

+InvolvementTransducer  6.1-4

+Is2StarReplaceable  5.1-2

+IsExceptionalPerm  9.5-1

+IsInterval  8.1-1

+IsMinusDecomposable  8.6-1

+IsPlusDecomposable  8.5-1

+IsPossibleGraphAut  5.1-4

+IsRankEncoding  7.2-1

+IsSimplePerm  8.2-1

+IsStarClosed  5.1-1

+IsStratified  5.1-3

+IsSubPerm  10.1-3

+LengthBoundAut  9.3-1

+LoopFreeAut  10.2-1

+LoopVertexFreeAut  10.2-2

+MinusDecomposableAut  9.2-3

+MinusIndecomposableAut  9.2-4

+NextGap  9.3-3

+NonSimpleAut  9.3-7

+NumberAcceptedWords  6.4-2

+OnePointDelete  8.3-1

+Parstacks  2.1-1

+PermComplement  7.1-1

+PermDirectSum  8.7-1

+PermSkewSum  8.7-2

+PlusDecomposableAut  9.2-1

+PlusIndecomposableAut  9.2-2

+PointDeletion  8.3-3

+RankDecoding  3.1-2

+RankEncoding  3.1-1

+Seqstacks  2.1-2

+SequencesToRatExp  3.1-3

+ShiftAut  9.3-2

+SimplePermAut  9.4-1

+Spectrum  6.4-1

+SumAut  9.3-5

+Transducer  6.1-1

+TransposedTransducer  6.1-3

+TwoPointDelete  8.3-2

 
 

 

 
diff --git a/doc/chapInd.txt b/doc/chapInd.txt
index 35d6425..4755cfd 100644
--- a/doc/chapInd.txt
+++ b/doc/chapInd.txt
@@ -2,70 +2,70 @@
   
   Index
   
-  AcceptedWords 6.4-4 
-  AcceptedWordsR 6.4-5 
-  AcceptedWordsReversed 6.4-5 
-  AutStateTransitionMatrix 6.4-3 
-  BasisAutomaton 6.2-1 
-  BlockDecomposition 8.4-2 
-  BoundedClassAutomaton 6.2-3 
-  BufferAndStack 2.1-3 
-  ClassAutFromBase 6.2-5 
-  ClassAutFromBaseEncoding 6.2-4 
-  ClassAutomaton 6.2-2 
-  ClassDirectSum 6.3-1 
-  CombineAutTransducer 6.1-5 
-  ConstrainedGraphToAut 4.1-2 
-  DeletionTransducer 6.1-2 
-  ExceptionalBoundedAutomaton 9.5-2 
-  ExpandAlphabet 6.2-6 
-  GapAut 9.3-4 
-  GapSumAut 9.3-6 
-  GraphToAut 4.1-1 
-  InbetweenPermAutomaton 10.1-1 
-  InbetweenPermSet 10.1-2 
-  Inflation 8.4-1 
-  InversionAut 9.1-1 
-  InversionAutOfClass 9.1-2 
-  InvolvementTransducer 6.1-4 
-  Is2StarReplaceable 5.1-2 
-  IsExceptionalPerm 9.5-1 
-  IsInterval 8.1-1 
-  IsMinusDecomposable 8.6-1 
-  IsPlusDecomposable 8.5-1 
-  IsPossibleGraphAut 5.1-4 
-  IsRankEncoding 7.2-1 
-  IsSimplePerm 8.2-1 
-  IsStarClosed 5.1-1 
-  IsStratified 5.1-3 
-  IsSubPerm 10.1-3 
-  LengthBoundAut 9.3-1 
-  LoopFreeAut 10.2-1 
-  LoopVertexFreeAut 10.2-2 
-  MinusDecomposableAut 9.2-3 
-  MinusIndecomposableAut 9.2-4 
-  NextGap 9.3-3 
-  NonSimpleAut 9.3-7 
-  NumberAcceptedWords 6.4-2 
-  OnePointDelete 8.3-1 
-  Parstacks 2.1-1 
-  PermComplement 7.1-1 
-  PermDirectSum 8.7-1 
-  PermSkewSum 8.7-2 
-  PlusDecomposableAut 9.2-1 
-  PlusIndecomposableAut 9.2-2 
-  PointDeletion 8.3-3 
-  RankDecoding 3.1-2 
-  RankEncoding 3.1-1 
-  Seqstacks 2.1-2 
-  SequencesToRatExp 3.1-3 
-  ShiftAut 9.3-2 
-  SimplePermAut 9.4-1 
-  Spectrum 6.4-1 
-  SumAut 9.3-5 
-  Transducer 6.1-1 
-  TransposedTransducer 6.1-3 
-  TwoPointDelete 8.3-2 
+  AcceptedWords  6.4-4
+  AcceptedWordsR  6.4-5
+  AcceptedWordsReversed  6.4-5
+  AutStateTransitionMatrix  6.4-3
+  BasisAutomaton  6.2-1
+  BlockDecomposition  8.4-2
+  BoundedClassAutomaton  6.2-3
+  BufferAndStack  2.1-3
+  ClassAutFromBase  6.2-5
+  ClassAutFromBaseEncoding  6.2-4
+  ClassAutomaton  6.2-2
+  ClassDirectSum  6.3-1
+  CombineAutTransducer  6.1-5
+  ConstrainedGraphToAut  4.1-2
+  DeletionTransducer  6.1-2
+  ExceptionalBoundedAutomaton  9.5-2
+  ExpandAlphabet  6.2-6
+  GapAut  9.3-4
+  GapSumAut  9.3-6
+  GraphToAut  4.1-1
+  InbetweenPermAutomaton  10.1-1
+  InbetweenPermSet  10.1-2
+  Inflation  8.4-1
+  InversionAut  9.1-1
+  InversionAutOfClass  9.1-2
+  InvolvementTransducer  6.1-4
+  Is2StarReplaceable  5.1-2
+  IsExceptionalPerm  9.5-1
+  IsInterval  8.1-1
+  IsMinusDecomposable  8.6-1
+  IsPlusDecomposable  8.5-1
+  IsPossibleGraphAut  5.1-4
+  IsRankEncoding  7.2-1
+  IsSimplePerm  8.2-1
+  IsStarClosed  5.1-1
+  IsStratified  5.1-3
+  IsSubPerm  10.1-3
+  LengthBoundAut  9.3-1
+  LoopFreeAut  10.2-1
+  LoopVertexFreeAut  10.2-2
+  MinusDecomposableAut  9.2-3
+  MinusIndecomposableAut  9.2-4
+  NextGap  9.3-3
+  NonSimpleAut  9.3-7
+  NumberAcceptedWords  6.4-2
+  OnePointDelete  8.3-1
+  Parstacks  2.1-1
+  PermComplement  7.1-1
+  PermDirectSum  8.7-1
+  PermSkewSum  8.7-2
+  PlusDecomposableAut  9.2-1
+  PlusIndecomposableAut  9.2-2
+  PointDeletion  8.3-3
+  RankDecoding  3.1-2
+  RankEncoding  3.1-1
+  Seqstacks  2.1-2
+  SequencesToRatExp  3.1-3
+  ShiftAut  9.3-2
+  SimplePermAut  9.4-1
+  Spectrum  6.4-1
+  SumAut  9.3-5
+  Transducer  6.1-1
+  TransposedTransducer  6.1-3
+  TwoPointDelete  8.3-2
   
   
   -------------------------------------------------------
diff --git a/doc/chapInd_mj.html b/doc/chapInd_mj.html
index 7d75a27..c232ad4 100644
--- a/doc/chapInd_mj.html
+++ b/doc/chapInd_mj.html
@@ -6,7 +6,7 @@
 
 
 
 GAP (PatternClass) - Index
 
@@ -28,70 +28,70 @@
 

 
Index

 
-AcceptedWords  6.4-4  

-AcceptedWordsR  6.4-5  

-AcceptedWordsReversed  6.4-5  

-AutStateTransitionMatrix  6.4-3  

-BasisAutomaton  6.2-1  

-BlockDecomposition  8.4-2  

-BoundedClassAutomaton  6.2-3  

-BufferAndStack  2.1-3  

-ClassAutFromBase  6.2-5  

-ClassAutFromBaseEncoding  6.2-4  

-ClassAutomaton  6.2-2  

-ClassDirectSum  6.3-1  

-CombineAutTransducer  6.1-5  

-ConstrainedGraphToAut  4.1-2  

-DeletionTransducer  6.1-2  

-ExceptionalBoundedAutomaton  9.5-2  

-ExpandAlphabet  6.2-6  

-GapAut  9.3-4  

-GapSumAut  9.3-6  

-GraphToAut  4.1-1  

-InbetweenPermAutomaton  10.1-1  

-InbetweenPermSet  10.1-2  

-Inflation  8.4-1  

-InversionAut  9.1-1  

-InversionAutOfClass  9.1-2  

-InvolvementTransducer  6.1-4  

-Is2StarReplaceable  5.1-2  

-IsExceptionalPerm  9.5-1  

-IsInterval  8.1-1  

-IsMinusDecomposable  8.6-1  

-IsPlusDecomposable  8.5-1  

-IsPossibleGraphAut  5.1-4  

-IsRankEncoding  7.2-1  

-IsSimplePerm  8.2-1  

-IsStarClosed  5.1-1  

-IsStratified  5.1-3  

-IsSubPerm  10.1-3  

-LengthBoundAut  9.3-1  

-LoopFreeAut  10.2-1  

-LoopVertexFreeAut  10.2-2  

-MinusDecomposableAut  9.2-3  

-MinusIndecomposableAut  9.2-4  

-NextGap  9.3-3  

-NonSimpleAut  9.3-7  

-NumberAcceptedWords  6.4-2  

-OnePointDelete  8.3-1  

-Parstacks  2.1-1  

-PermComplement  7.1-1  

-PermDirectSum  8.7-1  

-PermSkewSum  8.7-2  

-PlusDecomposableAut  9.2-1  

-PlusIndecomposableAut  9.2-2  

-PointDeletion  8.3-3  

-RankDecoding  3.1-2  

-RankEncoding  3.1-1  

-Seqstacks  2.1-2  

-SequencesToRatExp  3.1-3  

-ShiftAut  9.3-2  

-SimplePermAut  9.4-1  

-Spectrum  6.4-1  

-SumAut  9.3-5  

-Transducer  6.1-1  

-TransposedTransducer  6.1-3  

-TwoPointDelete  8.3-2  

+AcceptedWords  6.4-4

+AcceptedWordsR  6.4-5

+AcceptedWordsReversed  6.4-5

+AutStateTransitionMatrix  6.4-3

+BasisAutomaton  6.2-1

+BlockDecomposition  8.4-2

+BoundedClassAutomaton  6.2-3

+BufferAndStack  2.1-3

+ClassAutFromBase  6.2-5

+ClassAutFromBaseEncoding  6.2-4

+ClassAutomaton  6.2-2

+ClassDirectSum  6.3-1

+CombineAutTransducer  6.1-5

+ConstrainedGraphToAut  4.1-2

+DeletionTransducer  6.1-2

+ExceptionalBoundedAutomaton  9.5-2

+ExpandAlphabet  6.2-6

+GapAut  9.3-4

+GapSumAut  9.3-6

+GraphToAut  4.1-1

+InbetweenPermAutomaton  10.1-1

+InbetweenPermSet  10.1-2

+Inflation  8.4-1

+InversionAut  9.1-1

+InversionAutOfClass  9.1-2

+InvolvementTransducer  6.1-4

+Is2StarReplaceable  5.1-2

+IsExceptionalPerm  9.5-1

+IsInterval  8.1-1

+IsMinusDecomposable  8.6-1

+IsPlusDecomposable  8.5-1

+IsPossibleGraphAut  5.1-4

+IsRankEncoding  7.2-1

+IsSimplePerm  8.2-1

+IsStarClosed  5.1-1

+IsStratified  5.1-3

+IsSubPerm  10.1-3

+LengthBoundAut  9.3-1

+LoopFreeAut  10.2-1

+LoopVertexFreeAut  10.2-2

+MinusDecomposableAut  9.2-3

+MinusIndecomposableAut  9.2-4

+NextGap  9.3-3

+NonSimpleAut  9.3-7

+NumberAcceptedWords  6.4-2

+OnePointDelete  8.3-1

+Parstacks  2.1-1

+PermComplement  7.1-1

+PermDirectSum  8.7-1

+PermSkewSum  8.7-2

+PlusDecomposableAut  9.2-1

+PlusIndecomposableAut  9.2-2

+PointDeletion  8.3-3

+RankDecoding  3.1-2

+RankEncoding  3.1-1

+Seqstacks  2.1-2

+SequencesToRatExp  3.1-3

+ShiftAut  9.3-2

+SimplePermAut  9.4-1

+Spectrum  6.4-1

+SumAut  9.3-5

+Transducer  6.1-1

+TransposedTransducer  6.1-3

+TwoPointDelete  8.3-2