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First version of reactions-to-PRISM converter. 

git-svn-id: https://www.prismmodelchecker.org/svn/prism/prism/trunk@5410 bbc10eb1-c90d-0410-af57-cb519fbb1720
master
Dave Parker 14 years ago
parent
9684963804
commit
06d0fe3c25
2 changed files with 283 additions and 10 deletions
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  1. 53
      prism/src/prism/Reactions2Prism.java
  2. 240
      prism/src/prism/ReactionsText2Prism.java

53
prism/src/prism/Reactions2Prism.java
View File

@ -57,14 +57,14 @@ public class Reactions2Prism
protected ArrayList<Reaction> reactionList; protected ArrayList<Reaction> reactionList;
// Config // Config
/** Maximum amount of each species (unless some initial amount is higher). */ /** Maximum amount of each species (unless some initial amount is higher). */
protected int maxAmount = 100; protected int maxAmount = 100;
// Optional PRISM code header/footer // Optional PRISM code header/footer
protected String prismCodeHeader; protected String prismCodeHeader;
protected String prismCodeFooter; protected String prismCodeFooter;
// Constructors // Constructors
public Reactions2Prism() public Reactions2Prism()
@ -81,7 +81,7 @@ public class Reactions2Prism
{ {
this.maxAmount = maxAmount; this.maxAmount = maxAmount;
} }
/** /**
* Print the currently loaded reaction set model (for testing purposes). * Print the currently loaded reaction set model (for testing purposes).
*/ */
@ -360,8 +360,12 @@ public class Reactions2Prism
sb.append("\t// " + reaction.id); sb.append("\t// " + reaction.id);
if (reaction.name.length() > 0) if (reaction.name.length() > 0)
sb.append(" (" + reaction.name + ")"); sb.append(" (" + reaction.name + ")");
sb.append(": " + reaction.reactionString());
sb.append("\n"); sb.append("\n");
s2 = MathML2Prism.convert(reaction.kineticLaw, renameFrom, renameTo);
if (reaction.kineticLawString != null)
s2 = reaction.kineticLawString;
else
s2 = MathML2Prism.convert(reaction.kineticLaw, renameFrom, renameTo);
sb.append("\t[" + reaction.id + "] " + s2 + " > 0 -> " + s2 + " : true;\n"); sb.append("\t[" + reaction.id + "] " + s2 + " > 0 -> " + s2 + " : true;\n");
} }
sb.append("\nendmodule\n"); sb.append("\nendmodule\n");
@ -429,7 +433,7 @@ public class Reactions2Prism
public String toString() public String toString()
{ {
return id + (name.length() > 0 ? (" (" + name + ")") : "");
return id + (name != null && name.length() > 0 ? (" (" + name + ")") : "");
} }
} }
@ -461,6 +465,7 @@ public class Reactions2Prism
public ArrayList<String> products; public ArrayList<String> products;
public ArrayList<Integer> productStoichs; public ArrayList<Integer> productStoichs;
public Element kineticLaw; public Element kineticLaw;
public String kineticLawString;
public ArrayList<Parameter> parameters; public ArrayList<Parameter> parameters;
public Reaction(String id, String name) public Reaction(String id, String name)
@ -472,6 +477,7 @@ public class Reactions2Prism
products = new ArrayList<String>(); products = new ArrayList<String>();
productStoichs = new ArrayList<Integer>(); productStoichs = new ArrayList<Integer>();
kineticLaw = null; kineticLaw = null;
kineticLawString = null;
parameters = new ArrayList<Parameter>(); parameters = new ArrayList<Parameter>();
} }
@ -482,8 +488,13 @@ public class Reactions2Prism
public void addReactant(String reactant, int stoich) public void addReactant(String reactant, int stoich)
{ {
reactants.add(reactant);
reactantStoichs.add(stoich);
int i = reactants.indexOf(reactant);
if (i == -1) {
reactants.add(reactant);
reactantStoichs.add(stoich);
} else {
reactantStoichs.set(i, reactantStoichs.get(i) + stoich);
}
} }
public void addProduct(String product) public void addProduct(String product)
@ -493,13 +504,25 @@ public class Reactions2Prism
public void addProduct(String product, int stoich) public void addProduct(String product, int stoich)
{ {
products.add(product);
productStoichs.add(stoich);
int i = products.indexOf(product);
if (i == -1) {
products.add(product);
productStoichs.add(stoich);
} else {
productStoichs.set(i, productStoichs.get(i) + stoich);
}
} }
public void setKineticLaw(Element kineticLaw) public void setKineticLaw(Element kineticLaw)
{ {
this.kineticLaw = kineticLaw; this.kineticLaw = kineticLaw;
this.kineticLawString = null;
}
public void setKineticLawString(String kineticLawString)
{
this.kineticLawString = kineticLawString;
this.kineticLaw = null;
} }
public void addParameter(String name, String value) public void addParameter(String name, String value)
@ -528,6 +551,13 @@ public class Reactions2Prism
return productStoichs.get(i); return productStoichs.get(i);
} }
public String reactionString()
{
String s = PrismUtils.joinString(reactants, "+");
s += " -> " + PrismUtils.joinString(products, "+");
return s;
}
public String toString() public String toString()
{ {
String s = ""; String s = "";
@ -539,7 +569,10 @@ public class Reactions2Prism
s += " Reactants stoichiometry: " + productStoichs + "\n"; s += " Reactants stoichiometry: " + productStoichs + "\n";
s += " Products: " + products + "\n"; s += " Products: " + products + "\n";
s += " Products stoichiometry: " + productStoichs + "\n"; s += " Products stoichiometry: " + productStoichs + "\n";
s += " Kinetic law: " + kineticLaw + "\n";
if (kineticLawString != null)
s += " Kinetic law: " + kineticLawString + "\n";
else
s += " Kinetic law: " + kineticLaw + "\n";
s += " Parameters: " + parameters + "\n"; s += " Parameters: " + parameters + "\n";
return s; return s;
} }

240
prism/src/prism/ReactionsText2Prism.java
View File

@ -0,0 +1,240 @@
//==============================================================================
//
// Copyright (c) 2002-
// Authors:
// * Dave Parker <d.a.parker@cs.bham.ac.uk> (University of Birmingham/Oxford)
//
//------------------------------------------------------------------------------
//
// This file is part of PRISM.
//
// PRISM is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// PRISM is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with PRISM; if not, write to the Free Software Foundation,
// Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
//==============================================================================
package prism;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
/**
* Class to convert a textual description of a set of reactions into PRISM code.
*/
public class ReactionsText2Prism extends Reactions2Prism
{
/**
* Calling point for command-line script:
* e.g. java -cp classes prism.ReactionsText2Prism myfile.txt 100
* (100 denotes (integer) maximum for species population sizes, default is 100)
*/
public static void main(String args[])
{
PrismLog errLog = new PrismPrintStreamLog(System.err);
try {
if (args.length < 1) {
System.err.println("Usage: java -cp classes prism.ReactionsText2Prism <file> [max_amount]");
System.exit(1);
}
ReactionsText2Prism rt2prism = new ReactionsText2Prism(errLog);
try {
if (args.length > 1)
rt2prism.setMaxAmount(Integer.parseInt(args[1]));
} catch (NumberFormatException e) {
throw new PrismException("Invalid max amount \"" + args[1] + "\"");
}
rt2prism.translate(new File(args[0]));
} catch (PrismException e) {
errLog.println("Error: " + e.getMessage() + ".");
}
}
// Enums
private enum SectionType {
SPECIES, PARAMETERS, REACTIONS, RR, R
};
// Constructors
public ReactionsText2Prism()
{
super();
}
public ReactionsText2Prism(PrismLog mainLog)
{
super(mainLog);
}
/**
* Main method: load reactions file, process and send resulting PRISM file to stdout
*/
public void translate(File file) throws PrismException
{
// Read in file
extractModelFromFile(file);
// Generate PRISM code
prismCodeHeader = "// File generated by reactions-to-PRISM conversion\n";
prismCodeHeader += "// Original file: " + file.getPath() + "\n\n";
convertToPRISMCode(System.out);
}
/**
* Build the reaction set model from a parsed SBML file.
*/
private void extractModelFromFile(File file) throws PrismException
{
BufferedReader in;
SectionType secType = null;
String s, s2, ss[], ss2[];
int i, lineNum = 0;
Species species;
Parameter parameter;
Reaction reaction;
String reactionId = null, reactionName = null;
// Initialise storage
speciesList = new ArrayList<Species>();
parameterList = new ArrayList<Parameter>();
reactionList = new ArrayList<Reaction>();
try {
// Open file for reading
in = new BufferedReader(new FileReader(file));
// Read remaining lines
s = in.readLine();
lineNum++;
while (s != null) {
// Skip blank lines
s = s.trim();
if (s.length() > 0) {
// Switch mode on section header
if (s.charAt(0) == '@') {
s2 = s.substring(1);
if (s2.equals("species")) {
secType = SectionType.SPECIES;
} else if (s2.equals("parameters")) {
secType = SectionType.PARAMETERS;
} else if (s2.equals("reactions")) {
secType = SectionType.REACTIONS;
} else if (s2.startsWith("rr=")) {
secType = SectionType.RR;
// Extract reaction id/name
s2 = s2.substring(3);
i = s2.indexOf(' ');
reactionId = s2.substring(0, i > 0 ? i : s2.length());
reactionName = i > 0 ? s2.substring(i + 1).replaceAll("\"", "") : "";
} else if (s2.startsWith("r=")) {
secType = SectionType.R;
// Extract reaction id/name
s2 = s2.substring(2);
i = s2.indexOf(' ');
reactionId = s2.substring(0, i > 0 ? i : s2.length());
reactionName = i > 0 ? s2.substring(i + 1).replaceAll("\"", "") : "";
} else {
throw new PrismException("@" + s2 + " section not supported");
}
} else {
switch (secType) {
// Species list
case SPECIES:
ss = s.split("=");
if (ss.length != 2)
throw new PrismException("invalid species definition \"" + s + "\"");
// Get id
String speciesId = ss[0];
// Get init amount/name
s2 = ss[1].trim();
i = s2.indexOf(' ');
String sInit = s2.substring(0, i > 0 ? i : s2.length());
String speciesName = i > 0 ? s2.substring(i + 1).replaceAll("\"", "") : null;
int initialAmount = Integer.parseInt(sInit);
species = new Species(speciesId, speciesName, initialAmount);
speciesList.add(species);
break;
// Parameter list
case PARAMETERS:
ss = s.split("=");
if (ss.length == 1) {
// Get id (value undefined)
String paramId = ss[0];
parameter = new Parameter(paramId, null);
} else if (ss.length == 2) {
// Get id and value
String paramId = ss[0];
parameter = new Parameter(paramId, ss[1]);
} else {
throw new PrismException("invalid parameter definition \"" + s + "\"");
}
parameterList.add(parameter);
break;
// Reaction
case RR:
case R:
ss = s.split("->");
if (ss.length != 2)
throw new PrismException("invalid reaction definition \"" + s + "\"");
// Create reaction object with earlier info
reaction = new Reaction(reactionId, reactionName);
// Get reactants
ss2 = ss[0].trim().split("\\+");
for (String reactant : ss2) {
reaction.addReactant(reactant, 1);
}
// Get products
ss2 = ss[1].trim().split("\\+");
for (String product : ss2) {
reaction.addProduct(product, 1);
}
// Next line
s = in.readLine();
if (s == null)
throw new PrismException("missing line in reaction definition");
s = s.trim();
// Get kinetic law
// TODO: reversible case
reaction.setKineticLawString(s);
lineNum++;
reactionList.add(reaction);
break;
// Anything else: skip
default:
}
}
}
// read next line
s = in.readLine();
lineNum++;
}
// close file
in.close();
} catch (IOException e) {
throw new PrismException("File I/O error reading from \"" + file + "\"");
} catch (NumberFormatException e) {
throw new PrismException("Error detected at line " + lineNum + " of file \"" + file + "\"");
} catch (PrismException e) {
throw new PrismException("Error detected (" + e.getMessage() + ") at line " + lineNum + " of file \"" + file + "\"");
}
}
}
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