Added comments that fix line endings
Making it easier to compare files
This commit is contained in:
Pedro Fontanarrosa
parent
ab858c8f3c
commit
f349ecc3c3
1 changed files with 370 additions and 369 deletions
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@ -1,369 +1,370 @@
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/*******************************************************************************
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*
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* This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
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* for the latest version of iBioSim.
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*
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* Copyright (C) 2017 University of Utah
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*
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* This library is free software; you can redistribute it and/or modify it
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* under the terms of the Apache License. A copy of the license agreement is provided
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* in the file named "LICENSE.txt" included with this software distribution
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* and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
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*
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*******************************************************************************/
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package edu.utah.ece.async.ibiosim.dataModels.util;
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import java.io.File;
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import java.util.regex.Pattern;
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/**
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*
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*
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* @author
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* @author Chris Myers
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* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim Contributors </a>
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* @version %I%
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*/
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public class GlobalConstants {
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public static final String ACTIVATED_RNAP_BINDING_STRING = "Kao";
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public static final String FORWARD_ACTIVATED_RNAP_BINDING_STRING = "kao_f";
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public static final String REVERSE_ACTIVATED_RNAP_BINDING_STRING = "kao_r";
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public static final String RNAP_BINDING_STRING = "Ko";
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public static final String FORWARD_RNAP_BINDING_STRING = "ko_f";
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public static final String REVERSE_RNAP_BINDING_STRING = "ko_r";
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public static final String KREP_STRING = "Kr";
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public static final String FORWARD_KREP_STRING = "kr_f";
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public static final String REVERSE_KREP_STRING = "kr_r";
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public static final String KACT_STRING = "Ka";
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public static final String FORWARD_KACT_STRING = "ka_f";
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public static final String REVERSE_KACT_STRING = "ka_r";
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public static final String KCOMPLEX_STRING = "Kc";
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public static final String FORWARD_KCOMPLEX_STRING = "kc_f";
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public static final String REVERSE_KCOMPLEX_STRING = "kc_r";
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public static final String MEMDIFF_STRING = "kmdiff";
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public static final String FORWARD_MEMDIFF_STRING = "kmdiff_f";
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public static final String REVERSE_MEMDIFF_STRING = "kmdiff_r";
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// public static final String KBIO_STRING = "Kbio";
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public static final String OCR_STRING = "ko";
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public static final String KBASAL_STRING = "kb";
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public static final String ACTIVATED_STRING = "ka";
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public static final String KDECAY_STRING = "kd";
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public static final String KECDIFF_STRING = "kecdiff";
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public static final String KECDECAY_STRING = "kecd";
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public static final String PROMOTER_COUNT_STRING = "ng";
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public static final String RNAP_STRING = "nr";
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public static final String STOICHIOMETRY_STRING = "np";
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public static final String COOPERATIVITY_STRING = "nc";
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public static final String COMPLEX = "complex";
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public static final String DIFFUSIBLE = "diffusible";
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public static final String KASSOCIATION_STRING = "Kassociation"; // Dimerization value
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public static final String GENE_PRODUCT = "gene product";
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public static final String TRANSCRIPTION_FACTOR = "transcription factor";
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// public static final String KREP_VALUE = ".5";
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// public static final String KACT_VALUE = ".0033";
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// public static final String KBIO_VALUE = ".05";
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// public static final String PROMOTER_COUNT_VALUE = "2";
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// public static final String KASSOCIATION_VALUE = ".05";
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// public static final String KBASAL_VALUE = ".0001";
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// public static final String OCR_VALUE = ".05";
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// public static final String KDECAY_VALUE = ".0075";
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// public static final String RNAP_VALUE = "30";
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// public static final String RNAP_BINDING_VALUE = ".033";
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// public static final String STOICHIOMETRY_VALUE = "10";
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// public static final String COOPERATIVITY_VALUE = "2";
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// public static final String ACTIVED_VALUE = ".25";
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public static final String ID = "ID";
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public static final String COMPONENT = "Component";
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public static final String SPECIES = "Species";
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public static final String INFLUENCE = "Influence";
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public static final String COMPONENT_CONNECTION = "Component Connection";
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public static final String PRODUCTION = "Production";
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public static final String DEGRADATION = "Degradation";
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public static final String COMPLEXATION = "Complex";
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public static final String REACTION = "Reaction";
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public static final String MODIFIER = "Modifier";
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public static final String REACTION_EDGE = "Reaction_Edge";
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public static final String MODIFIER_REACTION_EDGE = "Modifier_Reaction_Edge";
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public static final String RULE_EDGE = "Rule_Edge";
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public static final String CONSTRAINT_EDGE = "Constraint_Edge";
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public static final String EVENT_EDGE = "Event_Edge";
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public static final String PETRI_NET_EDGE = "Petri_Net_Edge";
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public static final String GRID_RECTANGLE = "Grid Rectangle";
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public static final String PORTMAP = "Port Map";
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public static final String SBOTERM = "SBO Term:";
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public static final String PORT = "port";
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public static final String NAME = "Name";
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public static final String CONSTANT = "boundary";
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public static final String SPASTIC = "constitutive";
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public static final String DEGRADES = "degrades";
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public static final String NORMAL = "normal";
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public static final String INPUT = "input";
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public static final String OUTPUT = "output";
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public static final String INTERNAL = "internal";
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public static final String TYPE = "Type";
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public static final String PORTTYPE = "Port Type";
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public static final String MAX_DIMER_STRING = "N-mer as trascription factor";
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public static final String INITIAL_STRING = "ns";
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public static final String PROMOTER = "Promoter";
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public static final String VARIABLE = "Variable";
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public static final String PLACE = "Place";
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public static final String BOOLEAN = "Boolean";
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public static final String MRNA = "mRNA";
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public static final String EXPLICIT_PROMOTER = "ExplicitPromoter";
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public static final String SBMLFILE = "SBML file";
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public static final String BIOABS = "Biochemical abstraction";
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public static final String DIMABS = "Dimerization abstraction";
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public static final String COMPARTMENT = "compartment";
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public static final String PARAMETER = "parameter";
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public static final String LOCALPARAMETER = "localParameter";
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public static final String SBMLSPECIES = "species";
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public static final String SBMLREACTION = "reaction";
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public static final String EVENT = "event";
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public static final String TRANSITION = "transition";
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public static final String CONSTRAINT = "constraint";
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public static final String FUNCTION = "functionDefinition";
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public static final String UNIT = "unitDefinition";
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public static final String RULE = "rule";
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public static final String ASSIGNMENT_RULE = "assignmentRule";
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public static final String INITIAL_ASSIGNMENT = "initialAssignment";
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public static final String RATE_RULE = "rateRule";
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public static final String ALGEBRAIC_RULE = "algebraicRule";
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public static final String GLYPH = "Glyph";
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public static final String REFERENCE_GLYPH = "ReferenceGlyph";
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public static final String REACTANT_GLYPH = "ReactantGlyph";
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public static final String PRODUCT_GLYPH = "ProductGlyph";
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public static final String MODIFIER_GLYPH = "ModifierGlyph";
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public static final String TEXT_GLYPH = "TextGlyph";
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public static final String ENCLOSING_COMPARTMENT = "enclosingCompartment";
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public static final String DEFAULT_COMPARTMENT = "defaultCompartment";
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public static final String FAIL = "fail";
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public static final String FAIL_TRANSITION = "failTransition";
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public static final String RATE = "rate";
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public static final String TRIGGER = "trigger";
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public static final String SBOL_PROMOTER = "sbolPromoter";
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public static final String SBOL_TERMINATOR = "sbolTerminator";
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public static final String SBOL_RBS = "sbolRBS";
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public static final String SBOL_CDS = "sbolCDS";
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public static final String SO_PROMOTER = "SO_0000167";
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public static final String SO_TERMINATOR = "SO_0000141";
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public static final String SO_RBS = "SO_0000139";
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public static final String SO_CDS = "SO_0000316";
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public static final String SO_AUTHORITY = "purl.obolibrary.org";
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public static final String SO_AUTHORITY2 = "identifiers.org";
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public static final String SBOL_COMPONENTDEFINITION = "ComponentDefinition";
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public static final String SBOL_MODULEDEFINITION = "ModuleDefinition";
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public static final String GENETIC_CONSTRUCT_REGEX_DEFAULT =
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SO_PROMOTER + "(" + SO_RBS + "," + SO_CDS + ")+" + SO_TERMINATOR + "+";
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public static final String GENETIC_CONSTRUCT_REGEX_PREFERENCE = "biosim.assembly.regex";
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public static final String SBOL_AUTHORITY_DEFAULT = "http://dummy.org/";
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public static final String CONSTRUCT_ASSEMBLY_DEFAULT = "False";
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public static final String CONSTRUCT_ASSEMBLY_PREFERENCE = "biosim.assembly.validation";
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public static final String CONSTRUCT_VALIDATION_DEFAULT = "False";
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public static final String CONSTRUCT_VALIDATION_PREFERENCE = "biosim.assembly.validation";
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public static final String CONSTRUCT_VALIDATION_WARNING_DEFAULT = "False";
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public static final String CONSTRUCT_VALIDATION_WARNING_PREFERENCE = "biosim.assembly.warning";
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public static final String CONSTRUCT_VALIDATION_FAIL_STATE_ID = "Sf";
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public static final String SBOL_ASSEMBLY_PLUS_STRAND = "+";
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public static final String SBOL_ASSEMBLY_MINUS_STRAND = "-";
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public static final int MEAN_CDS_LENGTH = 695;
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public static final int SD_CDS_LENGTH = 268;
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public static final int MEAN_PROMOTER_LENGTH = 62;
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public static final int SD_PROMOTER_LENGTH = 23;
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public static final int RBS_LENGTH = 12;
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public static final int TERMINATOR_LENGTH = 12;
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public static final int MEAN_GENE_LENGTH = 781;
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public static final int SD_GENE_LENGTH = 269;
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public static final String SBOL_FILE_EXTENSION = ".sbol";
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public static final String RDF_FILE_EXTENSION = ".rdf";
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public static final String SBOL_SYNTH_PROPERTIES_EXTENSION = ".sbolsynth.properties";
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public static final String SBOL_SYNTH_SPEC_PROPERTY = "synthesis.spec";
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public static final String SBOL_SYNTH_LIBS_PROPERTY = "synthesis.libraries";
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public static final String SBOL_SYNTH_LIBS_PREFERENCE = "biosim." + SBOL_SYNTH_LIBS_PROPERTY;
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public static final String SBOL_SYNTH_LIBS_DEFAULT = "";
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public static final String SBOL_SYNTH_METHOD_PROPERTY = "synthesis.method";
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public static final String SBOL_SYNTH_METHOD_PREFERENCE = "biosim." + SBOL_SYNTH_METHOD_PROPERTY;
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public static final String SBOL_SYNTH_EXHAUST_BB = "Exact Branch and Bound";
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public static final String SBOL_SYNTH_METHOD_DEFAULT = SBOL_SYNTH_EXHAUST_BB;
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public static final String SBOL_SYNTH_GREEDY_BB = "Greedy Branch and Bound";
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public static final String SBOL_SYNTH_STRUCTURAL_METHODS = SBOL_SYNTH_EXHAUST_BB + "," + SBOL_SYNTH_GREEDY_BB;
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public static final String SBOL_SYNTH_NUM_SOLNS_PROPERTY = "synthesis.numsolutions";
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public static final String SBOL_SYNTH_NUM_SOLNS_PREFERENCE = "biosim." + SBOL_SYNTH_NUM_SOLNS_PROPERTY;
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public static final String SBOL_SYNTH_NUM_SOLNS_DEFAULT = "1";
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public static final String SBOL_SYNTH_COMMAND = "synthesis_project";
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public static final String BIO = "biochem";
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public static final String ACTIVATION = "activation";
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public static final String REPRESSION = "repression";
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public static final String REGULATION = "regulation";
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public static final String NOINFLUENCE = "no_influence";
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public static final String SBO_FRAMEWORK = "SBO:0000004";
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public static final String SBO_MATERIAL_ENTITY = "SBO:0000240";
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public static final String SBO_INTERACTION = "SBO:0000231";
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public static final String SBO_PARTICIPANT_ROLE = "SBO:0000003";
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public static final String SBO_MATHEMATICAL_EXPRESSION = "SBO:0000064";
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public static final String SBO_PARAMETER = "SBO:0000545";
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// Material entities
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public static final String SBO_DNA = "SBO:0000251";
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public static final String SBO_DNA_SEGMENT = "SBO:0000634";
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public static final String SBO_RNA = "SBO:0000250";
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public static final String SBO_RNA_SEGMENT = "SBO:0000635";
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public static final String SBO_PROTEIN = "SBO:0000252";
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public static final String SBO_NONCOVALENT_COMPLEX = "SBO:0000253";
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public static final String SBO_SIMPLE_CHEMICAL = "SBO:0000247";
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public static final int SBO_ACTIVATION = 459;
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public static final int SBO_REPRESSION = 20;
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public static final int SBO_DUAL_ACTIVITY = 595;
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public static final int SBO_NEUTRAL = 594;
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public static final int SBO_PROMOTER_MODIFIER = 598;
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public static final int SBO_PROMOTER_BINDING_REGION = 590;
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public static final int SBO_MRNA = 250;
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public static final int SBO_PETRI_NET_PLACE = 593;
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public static final int SBO_LOGICAL = 602;
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public static final int SBO_PETRI_NET_TRANSITION = 591;
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public static final int SBO_INPUT_PORT = 600;
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public static final int SBO_OUTPUT_PORT = 601;
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public static final int SBO_DEGRADATION = 179;
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public static final int SBO_DIFFUSION = 185;
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public static final int SBO_GENETIC_PRODUCTION = 589;
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public static final int SBO_ASSOCIATION = 177;
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public static final int SBO_CONSTITUTIVE = 396;
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public static final int SBO_TRANSCRIPTION = 183;
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public static final int SBO_TRANSLATION = 184;
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// obsolete
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public static final int SBO_REGULATION = 19;
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public static final int SBO_OLD_PROMOTER_SPECIES = 369;
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public static final int SBO_PROMOTER = 535;
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public static final int SBO_PROMOTER_SPECIES = 354;
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public static final int SBO_MRNA_OLD = 278;
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public static final int SBO_BOOLEAN = 547;
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public static final int SBO_PLACE = 546;
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public static final int SBO_TRANSITION = 464;
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public static final int SBO_PRODUCTION = 183;
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public static final int SBO_COMPLEX = 526;
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// Model frameworks
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public static final int SBO_NONSPATIAL_CONTINUOUS = 293;
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public static final int SBO_SPATIAL_CONTINUOUS = 292;
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public static final int SBO_NONSPATIAL_DISCRETE = 295;
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public static final int SBO_SPATIAL_DISCRETE = 294;
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public static final int SBO_BOOLEAN_LOGICAL = 547;
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public static final int SBO_FLUX_BALANCE = 624;
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public static final String KISAO_GENERIC = "KISAO:0000000";
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public static final String KISAO_MONTE_CARLO = "KISAO:0000319";
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public static final String KISAO_GILLESPIE = "KISAO:0000241";
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public static final String KISAO_GILLESPIE_DIRECT = "KISAO:0000029";
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public static final String KISAO_SSA_CR = "KISAO:0000329";
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public static final String KISAO_EULER = "KISAO:0000030";
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public static final String KISAO_RUNGE_KUTTA_FEHLBERG = "KISAO:0000086";
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public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000087";
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public static final String KISAO_LSODA = "KISAO:0000088";
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public static final String KISAO_FBA = "KISAO:0000437";
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public static final String KISAO_MINIMUM_STEP_SIZE = "KISAO:0000485";
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public static final String KISAO_MAXIMUM_STEP_SIZE = "KISAO:0000467";
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public static final String KISAO_ABSOLUTE_TOLERANCE = "KISAO:0000211";
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public static final String KISAO_RELATIVE_TOLERANCE = "KISAO:0000209";
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public static final String KISAO_SEED = "KISAO:0000488";
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public static final String KISAO_SAMPLES = "KISAO:0000326";
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public static final String KISAO_NUMBER_OF_RUNS = "KISAO:0000498";
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public static final String KISAO_DFBA = "KISAO_0000499";
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public static final String KISAO_DFBA_SOA = "KISAO:0000500";
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public static final String KISAO_DFBA_DOA = "KISAO:0000501 ";
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public static final String KISAO_DFBA_DA = "KISAO:0000501 ";
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public static final String TRUE = "true";
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public static final String FALSE = "false";
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public static final String NONE = "none";
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public static final String OK = "Ok";
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public static final String CANCEL = "Cancel";
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// public static final String MAX_DIMER_VALUE = "1";
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// public static final String INITIAL_VALUE = "0";
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// public static final String DIMER_COUNT_STRING = "label";
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// public static final String TYPE_STRING = "label";
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public static final int DEFAULT_SPECIES_WIDTH = 100;
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public static final int DEFAULT_SPECIES_HEIGHT = 30;
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public static final int DEFAULT_DNA_WIDTH = 100;
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public static final int DEFAULT_DNA_HEIGHT = 30;
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public static final int DEFAULT_RNA_WIDTH = 50;
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public static final int DEFAULT_RNA_HEIGHT = 20;
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public static final int DEFAULT_PROTEIN_WIDTH = 40;
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public static final int DEFAULT_PROTEIN_HEIGHT = 40;
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public static final int DEFAULT_SMALL_MOLECULE_WIDTH = 20;
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public static final int DEFAULT_SMALL_MOLECULE_HEIGHT = 20;
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public static final int DEFAULT_COMPLEX_WIDTH = 100;
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public static final int DEFAULT_COMPLEX_HEIGHT = 30;
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public static final int DEFAULT_REACTION_WIDTH = 20;
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public static final int DEFAULT_REACTION_HEIGHT = 20;
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public static final int DEFAULT_VARIABLE_WIDTH = 30;
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public static final int DEFAULT_VARIABLE_HEIGHT = 30;
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public static final int DEFAULT_RULE_WIDTH = 50;
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public static final int DEFAULT_RULE_HEIGHT = 50;
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public static final int DEFAULT_CONSTRAINT_WIDTH = 50;
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public static final int DEFAULT_CONSTRAINT_HEIGHT = 40;
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public static final int DEFAULT_EVENT_WIDTH = 75;
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public static final int DEFAULT_EVENT_HEIGHT = 25;
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public static final int DEFAULT_TRANSITION_WIDTH = 50;
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public static final int DEFAULT_TRANSITION_HEIGHT = 20;
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public static final int DEFAULT_COMPONENT_WIDTH = 80;
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public static final int DEFAULT_COMPONENT_HEIGHT = 40;
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public static final int DEFAULT_COMPARTMENT_WIDTH = 250;
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public static final int DEFAULT_COMPARTMENT_HEIGHT = 250;
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public static final int DEFAULT_TEXT_WIDTH = 40;
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public static final int DEFAULT_TEXT_HEIGHT = 10;
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//public static final String separator = (File.separator.equals("\\")) ? "\\\\" : File.separator;
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//public static final String separator = File.separator;
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public static final int SBML_LEVEL = 3;
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public static final int SBML_VERSION = 2;
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public static String[] splitPath(String path) {
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String[] subDirs = path.split(Pattern.quote(File.separator));
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return subDirs;
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}
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public static String getFilename(String path) {
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String[] subDirs = splitPath(path);
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return subDirs[subDirs.length-1];
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}
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public static String getPath(String path) {
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return path.substring(0, path.lastIndexOf(File.separator));
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}
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||||
|
||||
//Cello Parameters
|
||||
public static final double k_SD_DIM_S = 1.0/300;
|
||||
public static final double k_TF_DIM_S = 1.0/3600;
|
||||
public static final double CELLO_PARAMETER_K = 0.1295;
|
||||
public static final double CELLO_PARAMETER_N = 2.65;
|
||||
public static final double CELLO_PARAMETER_YMAX = 2.829583333;
|
||||
public static final double CELLO_PARAMETER_YMIN = 0.0464125;
|
||||
public static final double CELLO_PARAMETER_ALPHA = 0.408417245;
|
||||
public static final double CELLO_PARAMETER_BETA = 0.432373669;
|
||||
}
|
||||
/*******************************************************************************
|
||||
*
|
||||
* This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
|
||||
* for the latest version of iBioSim.
|
||||
*
|
||||
* Copyright (C) 2017 University of Utah
|
||||
*
|
||||
* This library is free software; you can redistribute it and/or modify it
|
||||
* under the terms of the Apache License. A copy of the license agreement is provided
|
||||
* in the file named "LICENSE.txt" included with this software distribution
|
||||
* and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
|
||||
*
|
||||
*******************************************************************************/
|
||||
package edu.utah.ece.async.ibiosim.dataModels.util;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.regex.Pattern;
|
||||
|
||||
/**
|
||||
*
|
||||
*
|
||||
* @author
|
||||
* @author Chris Myers
|
||||
* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim Contributors </a>
|
||||
* @version %I%
|
||||
*/
|
||||
public class GlobalConstants {
|
||||
|
||||
public static final String ACTIVATED_RNAP_BINDING_STRING = "Kao";
|
||||
public static final String FORWARD_ACTIVATED_RNAP_BINDING_STRING = "kao_f";
|
||||
public static final String REVERSE_ACTIVATED_RNAP_BINDING_STRING = "kao_r";
|
||||
|
||||
public static final String RNAP_BINDING_STRING = "Ko";
|
||||
public static final String FORWARD_RNAP_BINDING_STRING = "ko_f";
|
||||
public static final String REVERSE_RNAP_BINDING_STRING = "ko_r";
|
||||
|
||||
public static final String KREP_STRING = "Kr";
|
||||
public static final String FORWARD_KREP_STRING = "kr_f";
|
||||
public static final String REVERSE_KREP_STRING = "kr_r";
|
||||
|
||||
public static final String KACT_STRING = "Ka";
|
||||
public static final String FORWARD_KACT_STRING = "ka_f";
|
||||
public static final String REVERSE_KACT_STRING = "ka_r";
|
||||
|
||||
public static final String KCOMPLEX_STRING = "Kc";
|
||||
public static final String FORWARD_KCOMPLEX_STRING = "kc_f";
|
||||
public static final String REVERSE_KCOMPLEX_STRING = "kc_r";
|
||||
|
||||
public static final String MEMDIFF_STRING = "kmdiff";
|
||||
public static final String FORWARD_MEMDIFF_STRING = "kmdiff_f";
|
||||
public static final String REVERSE_MEMDIFF_STRING = "kmdiff_r";
|
||||
|
||||
// public static final String KBIO_STRING = "Kbio";
|
||||
|
||||
public static final String OCR_STRING = "ko";
|
||||
public static final String KBASAL_STRING = "kb";
|
||||
public static final String ACTIVATED_STRING = "ka";
|
||||
public static final String KDECAY_STRING = "kd";
|
||||
|
||||
public static final String KECDIFF_STRING = "kecdiff";
|
||||
public static final String KECDECAY_STRING = "kecd";
|
||||
|
||||
public static final String PROMOTER_COUNT_STRING = "ng";
|
||||
public static final String RNAP_STRING = "nr";
|
||||
public static final String STOICHIOMETRY_STRING = "np";
|
||||
public static final String COOPERATIVITY_STRING = "nc";
|
||||
|
||||
public static final String COMPLEX = "complex";
|
||||
public static final String DIFFUSIBLE = "diffusible";
|
||||
public static final String KASSOCIATION_STRING = "Kassociation"; // Dimerization value
|
||||
public static final String GENE_PRODUCT = "gene product";
|
||||
public static final String TRANSCRIPTION_FACTOR = "transcription factor";
|
||||
|
||||
|
||||
// public static final String KREP_VALUE = ".5";
|
||||
// public static final String KACT_VALUE = ".0033";
|
||||
// public static final String KBIO_VALUE = ".05";
|
||||
// public static final String PROMOTER_COUNT_VALUE = "2";
|
||||
// public static final String KASSOCIATION_VALUE = ".05";
|
||||
// public static final String KBASAL_VALUE = ".0001";
|
||||
// public static final String OCR_VALUE = ".05";
|
||||
// public static final String KDECAY_VALUE = ".0075";
|
||||
// public static final String RNAP_VALUE = "30";
|
||||
// public static final String RNAP_BINDING_VALUE = ".033";
|
||||
// public static final String STOICHIOMETRY_VALUE = "10";
|
||||
// public static final String COOPERATIVITY_VALUE = "2";
|
||||
// public static final String ACTIVED_VALUE = ".25";
|
||||
|
||||
public static final String ID = "ID";
|
||||
public static final String COMPONENT = "Component";
|
||||
public static final String SPECIES = "Species";
|
||||
public static final String INFLUENCE = "Influence";
|
||||
public static final String COMPONENT_CONNECTION = "Component Connection";
|
||||
public static final String PRODUCTION = "Production";
|
||||
public static final String DEGRADATION = "Degradation";
|
||||
public static final String COMPLEXATION = "Complex";
|
||||
public static final String REACTION = "Reaction";
|
||||
public static final String MODIFIER = "Modifier";
|
||||
public static final String REACTION_EDGE = "Reaction_Edge";
|
||||
public static final String MODIFIER_REACTION_EDGE = "Modifier_Reaction_Edge";
|
||||
public static final String RULE_EDGE = "Rule_Edge";
|
||||
public static final String CONSTRAINT_EDGE = "Constraint_Edge";
|
||||
public static final String EVENT_EDGE = "Event_Edge";
|
||||
public static final String PETRI_NET_EDGE = "Petri_Net_Edge";
|
||||
public static final String GRID_RECTANGLE = "Grid Rectangle";
|
||||
public static final String PORTMAP = "Port Map";
|
||||
public static final String SBOTERM = "SBO Term:";
|
||||
public static final String PORT = "port";
|
||||
public static final String NAME = "Name";
|
||||
public static final String CONSTANT = "boundary";
|
||||
public static final String SPASTIC = "constitutive";
|
||||
public static final String DEGRADES = "degrades";
|
||||
public static final String NORMAL = "normal";
|
||||
public static final String INPUT = "input";
|
||||
public static final String OUTPUT = "output";
|
||||
public static final String INTERNAL = "internal";
|
||||
public static final String TYPE = "Type";
|
||||
public static final String PORTTYPE = "Port Type";
|
||||
public static final String MAX_DIMER_STRING = "N-mer as trascription factor";
|
||||
public static final String INITIAL_STRING = "ns";
|
||||
public static final String PROMOTER = "Promoter";
|
||||
public static final String VARIABLE = "Variable";
|
||||
public static final String PLACE = "Place";
|
||||
public static final String BOOLEAN = "Boolean";
|
||||
public static final String MRNA = "mRNA";
|
||||
public static final String EXPLICIT_PROMOTER = "ExplicitPromoter";
|
||||
public static final String SBMLFILE = "SBML file";
|
||||
public static final String BIOABS = "Biochemical abstraction";
|
||||
public static final String DIMABS = "Dimerization abstraction";
|
||||
public static final String COMPARTMENT = "compartment";
|
||||
public static final String PARAMETER = "parameter";
|
||||
public static final String LOCALPARAMETER = "localParameter";
|
||||
public static final String SBMLSPECIES = "species";
|
||||
public static final String SBMLREACTION = "reaction";
|
||||
public static final String EVENT = "event";
|
||||
public static final String TRANSITION = "transition";
|
||||
public static final String CONSTRAINT = "constraint";
|
||||
public static final String FUNCTION = "functionDefinition";
|
||||
public static final String UNIT = "unitDefinition";
|
||||
public static final String RULE = "rule";
|
||||
public static final String ASSIGNMENT_RULE = "assignmentRule";
|
||||
public static final String INITIAL_ASSIGNMENT = "initialAssignment";
|
||||
public static final String RATE_RULE = "rateRule";
|
||||
public static final String ALGEBRAIC_RULE = "algebraicRule";
|
||||
public static final String GLYPH = "Glyph";
|
||||
public static final String REFERENCE_GLYPH = "ReferenceGlyph";
|
||||
public static final String REACTANT_GLYPH = "ReactantGlyph";
|
||||
public static final String PRODUCT_GLYPH = "ProductGlyph";
|
||||
public static final String MODIFIER_GLYPH = "ModifierGlyph";
|
||||
public static final String TEXT_GLYPH = "TextGlyph";
|
||||
public static final String ENCLOSING_COMPARTMENT = "enclosingCompartment";
|
||||
public static final String DEFAULT_COMPARTMENT = "defaultCompartment";
|
||||
public static final String FAIL = "fail";
|
||||
public static final String FAIL_TRANSITION = "failTransition";
|
||||
public static final String RATE = "rate";
|
||||
public static final String TRIGGER = "trigger";
|
||||
|
||||
public static final String SBOL_PROMOTER = "sbolPromoter";
|
||||
public static final String SBOL_TERMINATOR = "sbolTerminator";
|
||||
public static final String SBOL_RBS = "sbolRBS";
|
||||
public static final String SBOL_CDS = "sbolCDS";
|
||||
public static final String SO_PROMOTER = "SO_0000167";
|
||||
public static final String SO_TERMINATOR = "SO_0000141";
|
||||
public static final String SO_RBS = "SO_0000139";
|
||||
public static final String SO_CDS = "SO_0000316";
|
||||
public static final String SO_AUTHORITY = "purl.obolibrary.org";
|
||||
public static final String SO_AUTHORITY2 = "identifiers.org";
|
||||
public static final String SBOL_COMPONENTDEFINITION = "ComponentDefinition";
|
||||
public static final String SBOL_MODULEDEFINITION = "ModuleDefinition";
|
||||
public static final String GENETIC_CONSTRUCT_REGEX_DEFAULT =
|
||||
SO_PROMOTER + "(" + SO_RBS + "," + SO_CDS + ")+" + SO_TERMINATOR + "+";
|
||||
public static final String GENETIC_CONSTRUCT_REGEX_PREFERENCE = "biosim.assembly.regex";
|
||||
public static final String SBOL_AUTHORITY_DEFAULT = "http://dummy.org/";
|
||||
public static final String CONSTRUCT_ASSEMBLY_DEFAULT = "False";
|
||||
public static final String CONSTRUCT_ASSEMBLY_PREFERENCE = "biosim.assembly.validation";
|
||||
public static final String CONSTRUCT_VALIDATION_DEFAULT = "False";
|
||||
public static final String CONSTRUCT_VALIDATION_PREFERENCE = "biosim.assembly.validation";
|
||||
public static final String CONSTRUCT_VALIDATION_WARNING_DEFAULT = "False";
|
||||
public static final String CONSTRUCT_VALIDATION_WARNING_PREFERENCE = "biosim.assembly.warning";
|
||||
public static final String CONSTRUCT_VALIDATION_FAIL_STATE_ID = "Sf";
|
||||
public static final String SBOL_ASSEMBLY_PLUS_STRAND = "+";
|
||||
public static final String SBOL_ASSEMBLY_MINUS_STRAND = "-";
|
||||
public static final int MEAN_CDS_LENGTH = 695;
|
||||
public static final int SD_CDS_LENGTH = 268;
|
||||
public static final int MEAN_PROMOTER_LENGTH = 62;
|
||||
public static final int SD_PROMOTER_LENGTH = 23;
|
||||
public static final int RBS_LENGTH = 12;
|
||||
public static final int TERMINATOR_LENGTH = 12;
|
||||
public static final int MEAN_GENE_LENGTH = 781;
|
||||
public static final int SD_GENE_LENGTH = 269;
|
||||
public static final String SBOL_FILE_EXTENSION = ".sbol";
|
||||
public static final String RDF_FILE_EXTENSION = ".rdf";
|
||||
public static final String SBOL_SYNTH_PROPERTIES_EXTENSION = ".sbolsynth.properties";
|
||||
public static final String SBOL_SYNTH_SPEC_PROPERTY = "synthesis.spec";
|
||||
public static final String SBOL_SYNTH_LIBS_PROPERTY = "synthesis.libraries";
|
||||
public static final String SBOL_SYNTH_LIBS_PREFERENCE = "biosim." + SBOL_SYNTH_LIBS_PROPERTY;
|
||||
public static final String SBOL_SYNTH_LIBS_DEFAULT = "";
|
||||
public static final String SBOL_SYNTH_METHOD_PROPERTY = "synthesis.method";
|
||||
public static final String SBOL_SYNTH_METHOD_PREFERENCE = "biosim." + SBOL_SYNTH_METHOD_PROPERTY;
|
||||
public static final String SBOL_SYNTH_EXHAUST_BB = "Exact Branch and Bound";
|
||||
public static final String SBOL_SYNTH_METHOD_DEFAULT = SBOL_SYNTH_EXHAUST_BB;
|
||||
public static final String SBOL_SYNTH_GREEDY_BB = "Greedy Branch and Bound";
|
||||
public static final String SBOL_SYNTH_STRUCTURAL_METHODS = SBOL_SYNTH_EXHAUST_BB + "," + SBOL_SYNTH_GREEDY_BB;
|
||||
|
||||
public static final String SBOL_SYNTH_NUM_SOLNS_PROPERTY = "synthesis.numsolutions";
|
||||
public static final String SBOL_SYNTH_NUM_SOLNS_PREFERENCE = "biosim." + SBOL_SYNTH_NUM_SOLNS_PROPERTY;
|
||||
public static final String SBOL_SYNTH_NUM_SOLNS_DEFAULT = "1";
|
||||
public static final String SBOL_SYNTH_COMMAND = "synthesis_project";
|
||||
|
||||
public static final String BIO = "biochem";
|
||||
public static final String ACTIVATION = "activation";
|
||||
public static final String REPRESSION = "repression";
|
||||
public static final String REGULATION = "regulation";
|
||||
public static final String NOINFLUENCE = "no_influence";
|
||||
|
||||
public static final String SBO_FRAMEWORK = "SBO:0000004";
|
||||
public static final String SBO_MATERIAL_ENTITY = "SBO:0000240";
|
||||
public static final String SBO_INTERACTION = "SBO:0000231";
|
||||
public static final String SBO_PARTICIPANT_ROLE = "SBO:0000003";
|
||||
public static final String SBO_MATHEMATICAL_EXPRESSION = "SBO:0000064";
|
||||
public static final String SBO_PARAMETER = "SBO:0000545";
|
||||
|
||||
// Material entities
|
||||
public static final String SBO_DNA = "SBO:0000251";
|
||||
public static final String SBO_DNA_SEGMENT = "SBO:0000634";
|
||||
public static final String SBO_RNA = "SBO:0000250";
|
||||
public static final String SBO_RNA_SEGMENT = "SBO:0000635";
|
||||
public static final String SBO_PROTEIN = "SBO:0000252";
|
||||
public static final String SBO_NONCOVALENT_COMPLEX = "SBO:0000253";
|
||||
public static final String SBO_SIMPLE_CHEMICAL = "SBO:0000247";
|
||||
|
||||
public static final int SBO_ACTIVATION = 459;
|
||||
public static final int SBO_REPRESSION = 20;
|
||||
public static final int SBO_DUAL_ACTIVITY = 595;
|
||||
public static final int SBO_NEUTRAL = 594;
|
||||
public static final int SBO_PROMOTER_MODIFIER = 598;
|
||||
|
||||
public static final int SBO_PROMOTER_BINDING_REGION = 590;
|
||||
public static final int SBO_MRNA = 250;
|
||||
|
||||
public static final int SBO_PETRI_NET_PLACE = 593;
|
||||
public static final int SBO_LOGICAL = 602;
|
||||
public static final int SBO_PETRI_NET_TRANSITION = 591;
|
||||
|
||||
public static final int SBO_INPUT_PORT = 600;
|
||||
public static final int SBO_OUTPUT_PORT = 601;
|
||||
|
||||
public static final int SBO_DEGRADATION = 179;
|
||||
public static final int SBO_DIFFUSION = 185;
|
||||
public static final int SBO_GENETIC_PRODUCTION = 589;
|
||||
public static final int SBO_ASSOCIATION = 177;
|
||||
public static final int SBO_CONSTITUTIVE = 396;
|
||||
public static final int SBO_TRANSCRIPTION = 183;
|
||||
public static final int SBO_TRANSLATION = 184;
|
||||
|
||||
// obsolete
|
||||
public static final int SBO_REGULATION = 19;
|
||||
public static final int SBO_OLD_PROMOTER_SPECIES = 369;
|
||||
public static final int SBO_PROMOTER = 535;
|
||||
public static final int SBO_PROMOTER_SPECIES = 354;
|
||||
public static final int SBO_MRNA_OLD = 278;
|
||||
public static final int SBO_BOOLEAN = 547;
|
||||
public static final int SBO_PLACE = 546;
|
||||
public static final int SBO_TRANSITION = 464;
|
||||
public static final int SBO_PRODUCTION = 183;
|
||||
public static final int SBO_COMPLEX = 526;
|
||||
|
||||
// Model frameworks
|
||||
public static final int SBO_NONSPATIAL_CONTINUOUS = 293;
|
||||
public static final int SBO_SPATIAL_CONTINUOUS = 292;
|
||||
public static final int SBO_NONSPATIAL_DISCRETE = 295;
|
||||
public static final int SBO_SPATIAL_DISCRETE = 294;
|
||||
public static final int SBO_BOOLEAN_LOGICAL = 547;
|
||||
public static final int SBO_FLUX_BALANCE = 624;
|
||||
|
||||
public static final String KISAO_GENERIC = "KISAO:0000000";
|
||||
public static final String KISAO_MONTE_CARLO = "KISAO:0000319";
|
||||
public static final String KISAO_GILLESPIE = "KISAO:0000241";
|
||||
public static final String KISAO_GILLESPIE_DIRECT = "KISAO:0000029";
|
||||
public static final String KISAO_SSA_CR = "KISAO:0000329";
|
||||
public static final String KISAO_EULER = "KISAO:0000030";
|
||||
public static final String KISAO_RUNGE_KUTTA_FEHLBERG = "KISAO:0000086";
|
||||
public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000087";
|
||||
public static final String KISAO_LSODA = "KISAO:0000088";
|
||||
public static final String KISAO_FBA = "KISAO:0000437";
|
||||
public static final String KISAO_MINIMUM_STEP_SIZE = "KISAO:0000485";
|
||||
public static final String KISAO_MAXIMUM_STEP_SIZE = "KISAO:0000467";
|
||||
public static final String KISAO_ABSOLUTE_TOLERANCE = "KISAO:0000211";
|
||||
public static final String KISAO_RELATIVE_TOLERANCE = "KISAO:0000209";
|
||||
public static final String KISAO_SEED = "KISAO:0000488";
|
||||
public static final String KISAO_SAMPLES = "KISAO:0000326";
|
||||
public static final String KISAO_NUMBER_OF_RUNS = "KISAO:0000498";
|
||||
public static final String KISAO_DFBA = "KISAO_0000499";
|
||||
public static final String KISAO_DFBA_SOA = "KISAO:0000500";
|
||||
public static final String KISAO_DFBA_DOA = "KISAO:0000501 ";
|
||||
public static final String KISAO_DFBA_DA = "KISAO:0000501 ";
|
||||
|
||||
public static final String TRUE = "true";
|
||||
public static final String FALSE = "false";
|
||||
public static final String NONE = "none";
|
||||
public static final String OK = "Ok";
|
||||
public static final String CANCEL = "Cancel";
|
||||
|
||||
// public static final String MAX_DIMER_VALUE = "1";
|
||||
// public static final String INITIAL_VALUE = "0";
|
||||
|
||||
|
||||
// public static final String DIMER_COUNT_STRING = "label";
|
||||
// public static final String TYPE_STRING = "label";
|
||||
|
||||
public static final int DEFAULT_SPECIES_WIDTH = 100;
|
||||
public static final int DEFAULT_SPECIES_HEIGHT = 30;
|
||||
public static final int DEFAULT_DNA_WIDTH = 100;
|
||||
public static final int DEFAULT_DNA_HEIGHT = 30;
|
||||
public static final int DEFAULT_RNA_WIDTH = 50;
|
||||
public static final int DEFAULT_RNA_HEIGHT = 20;
|
||||
public static final int DEFAULT_PROTEIN_WIDTH = 40;
|
||||
public static final int DEFAULT_PROTEIN_HEIGHT = 40;
|
||||
public static final int DEFAULT_SMALL_MOLECULE_WIDTH = 20;
|
||||
public static final int DEFAULT_SMALL_MOLECULE_HEIGHT = 20;
|
||||
public static final int DEFAULT_COMPLEX_WIDTH = 100;
|
||||
public static final int DEFAULT_COMPLEX_HEIGHT = 30;
|
||||
public static final int DEFAULT_REACTION_WIDTH = 20;
|
||||
public static final int DEFAULT_REACTION_HEIGHT = 20;
|
||||
public static final int DEFAULT_VARIABLE_WIDTH = 30;
|
||||
public static final int DEFAULT_VARIABLE_HEIGHT = 30;
|
||||
public static final int DEFAULT_RULE_WIDTH = 50;
|
||||
public static final int DEFAULT_RULE_HEIGHT = 50;
|
||||
public static final int DEFAULT_CONSTRAINT_WIDTH = 50;
|
||||
public static final int DEFAULT_CONSTRAINT_HEIGHT = 40;
|
||||
public static final int DEFAULT_EVENT_WIDTH = 75;
|
||||
public static final int DEFAULT_EVENT_HEIGHT = 25;
|
||||
public static final int DEFAULT_TRANSITION_WIDTH = 50;
|
||||
public static final int DEFAULT_TRANSITION_HEIGHT = 20;
|
||||
public static final int DEFAULT_COMPONENT_WIDTH = 80;
|
||||
public static final int DEFAULT_COMPONENT_HEIGHT = 40;
|
||||
public static final int DEFAULT_COMPARTMENT_WIDTH = 250;
|
||||
public static final int DEFAULT_COMPARTMENT_HEIGHT = 250;
|
||||
public static final int DEFAULT_TEXT_WIDTH = 40;
|
||||
public static final int DEFAULT_TEXT_HEIGHT = 10;
|
||||
//public static final String separator = (File.separator.equals("\\")) ? "\\\\" : File.separator;
|
||||
//public static final String separator = File.separator;
|
||||
public static final int SBML_LEVEL = 3;
|
||||
public static final int SBML_VERSION = 2;
|
||||
|
||||
public static String[] splitPath(String path) {
|
||||
String[] subDirs = path.split(Pattern.quote(File.separator));
|
||||
return subDirs;
|
||||
}
|
||||
|
||||
public static String getFilename(String path) {
|
||||
String[] subDirs = splitPath(path);
|
||||
return subDirs[subDirs.length-1];
|
||||
}
|
||||
|
||||
public static String getPath(String path) {
|
||||
return path.substring(0, path.lastIndexOf(File.separator));
|
||||
}
|
||||
|
||||
//Cello Parameters used for dynamical modeling. These parameters are obtained from the Cello paper
|
||||
// and from https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Eco1C1G1T1_collection/1
|
||||
public static final double k_SD_DIM_S = 1.0/300;
|
||||
public static final double k_TF_DIM_S = 1.0/3600;
|
||||
public static final double CELLO_PARAMETER_K = 0.1295;
|
||||
public static final double CELLO_PARAMETER_N = 2.65;
|
||||
public static final double CELLO_PARAMETER_YMAX = 2.829583333;
|
||||
public static final double CELLO_PARAMETER_YMIN = 0.0464125;
|
||||
public static final double CELLO_PARAMETER_ALPHA = 0.408417245;
|
||||
public static final double CELLO_PARAMETER_BETA = 0.432373669;
|
||||
}
|
||||
|
|
|
|||
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Add table
Add a link
Reference in a new issue