Biologie et InformatiqueAMAPmod Reference manual crochet AML functions by module
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PART I  AMAPmod

1 Introduction
2 Installation
2.1 Mininum system requirements
2.2 Getting the software
2.3 Test the executable
2.4 File access convention
3 AMAPmod: an overview
3.1 Introduction
3.2 AMAPmod system overview
3.2.1 Plant architecture databases
3.2.2 Coding individuals
3.2.3 Exploration: a simple example
3.2.4 The AMAPmod querying language: AML
3.2.5 Types of extracted data
3.2.6 Statsitical exploration and model building
3.3 Illustration
3.3.1 Biological context and data collection
3.3.2 3D visualisation of real plants
3.3.3 Extraction of data samples
3.3.4 Extraction and analysis of biological sequences
4 The AML language
4.1 Starting an AMAPmod session
4.2 AML
4.3 Data structures
4.3.1 Simple types
4.3.2 Array
4.3.3 Sets
4.3.4 Lists
4.4 Iterators
4.5 Functions
4.6 Comments
4.7 Access to shell commands
4.8 Input and Output
5 The MTG module
5.1 AML primitives related to MTGs
6 The STAT module
6.1 L'organisaion du module STAT
6.1.1 Application lois et combinaisons de lois
6.1.2 Application processus de renouvellement
6.1.3 Application modèle Markoviens
6.1.4 Application analyse des cimes
6.2 Les fonctions AML du module STAT
6.2.1 Les fonctions d'entrées/sorties
6.2.2 Les fonctiions de manipulation des données
6.2.3 Les fonctions algorithmiques

PART II  REFERENCE MANUAL

1 The Kernel module of AML
1.1 Alphabetic list
1.2 Sort by type
2The MTG module of AML
2.1 Alphabetic list
2.2 Sort by type
3 The STAT module of AML
3.1 Alphabetic list
3.2 Sort by categorie
3.4 Sort by type
4 File syntax
4.1 General conventions
4.2 MTGs
4.2.1 Coding files
4.2.2 Les fichiers de codages
4.2.3 Example of coding strategies in different classical situations
4.2 Dressing Files (.drf)
4.2.1 Definition of basis geometric models associated with plant components
4.2.2 Definition of virtual elements
4.2.3 Definition of defaults parameters
4.2.4 Example of dressing file
4.3 Curve Files (.crv)
4.5 Geom Files
4.5.1 Overview
4.5.1 File format syntax
4.5.1 Geoms format reference
4.6 Glance configuration file(.cfg)
4.7 STAT
4.7.1 type COMPOUND
4.7.2 type COMVOLUTION
4.7.3 type DISTRIBUTION, type RENEWAL
4.7.4 type HIDDEN_MARKOV
4.7.5 type HIDDEN_SEMI_MARKOV
4.7.6 type HISTOGRAM
4.7.7 type MARKOV
4.7.8 type MIXTURE
4.7.9 type SEMI_MARKOV
4.7.10 type SEQUENCES
4.7.11 type TIME_EVENTS
4.7.12 type TOPS
4.7.13 type TOPS_PARAMETERS
4.7.14 type VECTOR_DISTANCE
4.7.15 type VECTORS
Appendice A File example
Appendice B Bibliography
Appendice C Copyright
Index