README

   1 NAME
   2 Javacyc.java
   3
   4 ABSTRACT
   5 A Java interface for Pathway Tools software. Pathway Tools software
   6 needs to run a special socket server program for Javacyc to work.
   7
   8 SYNOPSIS
   9 Javacyc is a Java interface for Pathway Tools software.
  10         Javacyc cyc = new Javacyc("ARA");
  11         ArrayList pathways = cyc.allPathways();
  12
  13 VERSION
  14 Version 0.2 August 1, 2004
  15
  16 HISTORY
  17 Version History:
  18         0.1 June 6, 2003 initial version
  19         0.2 August 1, 2004 fixed a socket close bug in the C code
  20
  21 INSTALLATION
  22 The Javacyc class uses native methods in order to access AF_UNIX sockets for
  23 interprocess communication.  Javacyc can be installed by using the included
  24 makefile.
  25
  26 If you choose not to use the makefile, below is an example of how to
  27 compile Javacyc.  The example assumes that the path to the Java directory is
  28 /usr/java and that the platform is solaris:
  29         javac UnixDomainSocket.java
  30         javah UnixDomainSocket
  31         gcc -c -fPIC -I/usr/java/include -I/usr/java/include/solaris/ UnixDomainSoceket.c
  32         gcc -shared -o libunixdomainsocket.so UnixDomainSocket.o
  33         javac Javacyc.java
  34
  35 IMPORTANT NOTE:  In order for Javacyc to work, ensure that the environment
  36 variable, LD_LIBRARY_PATH, includes the directory where libunixdomainsocket.so
  37 is located.
  38
  39 DESCRIPTION
  40 Javacyc is a Java class for accessing internal Pathway Tools functions.
  41 For a description of what the individual functions do, please refer to the
  42 Pathway Tools documentation at http://bioinformatics.ai.sri.com/ptools .
  43
  44 Note that optional parameters of all functions are not supported in Javacyc.
  45
  46 Limitations:
  47 Javacyc does not implement GFP objects in Java.  It sends snippets of code to
  48 Pathway Tools through a socket connection.  Only one connection may be opened
  49 at any given time.  The returned values are of type boolean, String, ArrayList,
  50 and ArrayLists that contain ArrayLists for functions that return multiple
  51 lists.  A list of available functions is given below.
  52
  53 GFP functions: (More information on these functions can be found at:
  54 http://www.ai.sri.com/~gfp/spec/paper/node63.html )
  55         get-slot-values
  56         get-slot-value
  57         get-class-slot-slotvalue
  58         get-class-all-instances
  59         instance-all-instance-of-p
  60         member-slot-value-p
  61         current-kb
  62         put-slot-values
  63         put-slot-value
  64         add-slot-value
  65         replace-slot-value
  66         remove-slot-value
  67         coercible-to-frame-p
  68         class-all-type-of-p
  69         get-instance-direct-types
  70         get-instance-all-types
  71         get-frame-slots
  72         put-instance-types
  73         save-kb
  74         revert-kb
  75         find-indexed-frame
  76
  77 Pathway Tools functions: (More information on these functions can be found at
  78 http://bioinformatics.ai.sri.com/ptools/ptools-fns.html)
  79         select-organism
  80         all-pathways
  81         all-orgs
  82         all-rxns
  83         genes-of-reaction
  84         substrates-of-reaction
  85         products-of-reaction
  86         enzymes-of-reaction
  87         reaction-reactants-and-products
  88         get-predecessors
  89         get-successors
  90         get-reaction-list
  91         genes-of-pathway
  92         enzymes-of-pathway
  93         compounds-of-pathway
  94         substrates-of-pathway
  95         all-transcription-factors
  96         transcription-factor?
  97         all-cofactors
  98         all-modulators
  99         monomers-of-protein
 100         components-of-protein
 101         genes-of-protein
 102         reactions-of-enzyme
 103         enzyme?
 104         transporter?
 105         containers-of
 106         modified-forms
 107         modified-containers
 108         top-containers
 109         reactions-of-protein
 110         regulon-of-protein
 111         transcription-units-of-protein
 112         regulator-proteins-of-transcription-unit
 113         enzymes-of-gene
 114         all-products-of-gene
 115         reactions-of-gene
 116         pathways-of-gene
 117         chromosome-of-gene
 118         transcription-units-of-gene
 119         transcription-unit-promoter
 120         transcription-unit-genes
 121         transcription-unit-binding-sites
 122         transcription-unit-transcription-factors
 123         transcription-unit-terminators
 124         all-transported-chemicals
 125         reactions-of-compounds
 126         full-enzyme-name
 127         enzyme-activity-name
 128
 129 EXAMPLE
 130 /**
 131    A program to test Javacyc.
 132 */
 133
 134 import java.util.ArrayList;
 135 import java.io.*;
 136
 137 public class JavacycTest
 138 {
 139     public static void printLists(ArrayList list)
 140     {
 141         for (int i = 0; i < list.size(); i++)
 142         {
 143             Object obj = list.get(i);
 144             if (obj instanceof String)
 145             {
 146                 String str = (String)obj;
 147                 System.out.println(str);
 148             }
 149             else if (obj instanceof ArrayList)
 150             {
 151                 System.out.println("*begin inner list*");
 152                 ArrayList aList = (ArrayList)obj;
 153                 printLists(aList);
 154                 System.out.println("*end inner list*");
 155             }
 156             else
 157             {
 158                 System.out.println("WARNING THIS SHOULD NOT HAPPEN!");
 159             }
 160         }
 161     }
 162
 163     public static void main(String[] args) throws IOException
 164     {
 165         Javacyc cyc = new Javacyc("ARA");
 166         BufferedReader in = new BufferedReader(
 167            new InputStreamReader(System.in));
 168
 169         // test a function that returns a boolean
 170         System.out.println("Testing a function that returns a boolean: "
 171                            + "coercible-to-frame-p");
 172         System.out.print("Enter a value for frame: ");
 173         String thing = in.readLine();
 174         boolean result1 = cyc.coercibleToFrameP(thing);
 175         if (result1)
 176         {
 177             System.out.println("The result: true\n");
 178         }
 179         else
 180         {
 181             System.out.println("The result: false\n");
 182         }
 183
 184         // test a function that returns a string
 185         System.out.println("Testing a function that returns a string: "
 186                            + "full-enzyme-name");
 187         System.out.print("Enter a value for enzyme: ");
 188         String enzyme = in.readLine();
 189         String result2 = cyc.fullEnzymeName(enzyme);
 190         System.out.println("The result: " + result2 +"\n");
 191
 192         // test a function that returns an ArrayList
 193         System.out.println("Testing a function that returns an ArrayList: "
 194                            + "genes-of-pathway 'PWY-581");
 195         ArrayList result3 = cyc.genesOfPathway("PWY-581");
 196         System.out.println("The returned values: ");
 197         for (int i = 0; i < result3.size(); i++)
 198         {
 199             String rxn = (String)result3.get(i);
 200             System.out.println(rxn);
 201         }
 202
 203         // test a function that returns multiple lists
 204         System.out.println("\nTesting a function that returns multiple"
 205                            + " lists: reaction-reactants-and-products");
 206         System.out.print("Enter a value for reaction: ");
 207         String rxn = in.readLine();
 208         System.out.print("Enter a value for pathway: ");
 209         String pwy = in.readLine();
 210         ArrayList result4 = cyc.reactionReactantsAndProducts(rxn, pwy);
 211         System.out.println("The returned values: ");
 212         printLists(result4);
 213     }
 214 }
 215
 216 TROUBLESHOOTING
 217 Please send bug reports and comments to curator@arabidopsis.org
 218
 219 LICENSE
 220 Javacyc, a Java interface for Pathway Tools software
 221 Copyright (c) 2003 by Thomas Yan, The Arabidopsis Information Resource (TAIR)
 222 and the Carnegie Institution of Washingtion.
 223
 224 This library is free software; you can redistribute it and/or
 225 modify it under the terms of version 2.1 of the GNU Lesser General
 226 Public License as published by the Free Software Foundation.
 227
 228 This library is distributed in the hope that it will be useful,
 229 but WITHOUT ANY WARRANTY; without even the implied warranty of
 230 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 231 Lesser General Public License for more details:
 232
 233 http://www.opensource.org/licenses/lgpl-license.html
 234 http://www.gnu.org/copyleft/lesser.html
 235
 236 To obtain a written copy of the GNU Lesser General Public License,
 237 please write to the Free Software Foundation, Inc., 59 Temple Place,
 238 Suite 330, Boston, MA  02111-1307 USA
 239
 240
 241 Javacyc uses native methods to access AF_UNIX sockets provided by J-BUDS,
 242 which was released by Echogent Systems under the GNU Lesser General Public
 243 License.  See the JBUDS_COPYRIGHT for details.
 244
 245 AUTHOR
 246 Thomas Yan
 247
 248 ACKNOWLEDGMENTS
 249 Many thanks to Lukas Mueller and Danny Yoo.