rename the new format to implicant table and add documentation page

build-doc.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # config: set source doc and output
 DOC="doc"

doc/format-cnet.page

@@ -12,7 +12,7 @@
 
     <p>Format used by <link href="https://people.kth.se/~dubrova/bns.html">BNS</link>, a tool for the
 	identification of synchronous attractors. 
-       Models are represented as a list of partial truth tables, similar to the Berkeley Logic Interchange Format.
+       Models are represented as a list of implicants (truth table entries with jokers) for each component, similar to the Berkeley Logic Interchange Format.
     </p>
 
 <code><![CDATA[

doc/format-implicant-tables.page

@@ -0,0 +1,44 @@
+<page xmlns="http://projectmallard.org/1.0/"
+      type="topic"
+      id="format-implicant-tables">
+    <info>
+        <link type="guide" xref="index#formats"/>
+        <link type="guide" xref="formats#list"/>
+        <revision status="draft" date="2018-11-28"/>
+        <desc>Import/Export logical models as lists of implicant tables</desc>
+    </info>
+
+    <title>Implicant tables format</title>
+
+    <p>The implicant tables format supports importing and exporting models a list of implicants 
+       (truth table entries with jokers). Each component of the model is described as a separate 
+       table depending on its own regulators. It is similar to the CNET format but supports
+       multi-valued models and components identifiers are part of the format.
+    </p>
+
+    <p>
+       Each implicant table starts with a line listing the regulators and ending with the ID of the target component.
+       Similarly, each line of the table gives the value of each regulator (or '-' to match any value) and
+       ends with the target value. Lines with a target value of '0' can be skipped.
+       The '#' characters denote line-comments: everything following it on the same line is ignored.
+       Spacing characters are ignored and each value uses a single character (i.e. values higher than 9 are not supported).
+    </p>
+
+    <p>Sample file defining a Boolean model with three components:</p>
+
+<code>
+# Sample model defined as a list of implicant tables
+# [A, B, D]
+
+A : A
+1:1
+
+A : B
+0:1
+
+A B : D
+11:1
+</code>
+
+</page>
+

src/main/antlr4/org/colomoto/biolqm/io/antlr/LTT.g4 → src/main/antlr4/org/colomoto/biolqm/io/antlr/ITNET.g4

@@ -1,4 +1,4 @@
-grammar LTT;
+grammar ITNET;
 
 model:   NEWLINE* table+;
 table:   var* SEP curvar ('[' max ']')? NEWLINE+ line*;

src/main/java/org/colomoto/biolqm/io/truthtable/LogicalTruthTableExport.java → src/main/java/org/colomoto/biolqm/io/implicanttables/ImplicantTableExport.java

@@ -1,45 +1,41 @@
-package org.colomoto.biolqm.io.truthtable;
+package org.colomoto.biolqm.io.implicanttables;
 
 import org.colomoto.biolqm.LogicalModel;
 import org.colomoto.biolqm.NodeInfo;
 import org.colomoto.biolqm.helper.implicants.RestrictedPathSearcher;
 import org.colomoto.biolqm.io.BaseExporter;
 import org.colomoto.mddlib.MDDManager;
-import org.colomoto.mddlib.MDDVariable;
-import org.colomoto.mddlib.PathSearcher;
 
 import java.io.IOException;
 import java.io.Writer;
 import java.util.List;
 
 
 /**
- * Export logical model into cnet truth tables.
+ * Export logical model into lists of implicant tables.
  *
- * @author Hannes Klarner (minor modifications to a file of Aurelien Naldi)
+ * @author Hannes Klarner
+ * @author Aurelien Naldi
  */
-public class LogicalTruthTableExport extends BaseExporter {
+public class ImplicantTableExport extends BaseExporter {
 
-    public LogicalTruthTableExport(LogicalModel model) {
+    public ImplicantTableExport(LogicalModel model) {
         super(model);
     }
 
     public void export() throws IOException {
         MDDManager ddmanager = model.getMDDManager();
-        MDDVariable[] variables = ddmanager.getAllVariables();
-        PathSearcher searcher = new PathSearcher(ddmanager);
-
         int[] functions = model.getLogicalFunctions();
         List<NodeInfo> components = model.getComponents();
 
         Writer writer = streams.writer();
-        writer.write("# Model stored as a collection of truth tables\n");
+        writer.write("# Logical model defined as a collection of implicant tables\n");
         writer.write("# "+components+"\n\n");
 
         RestrictedPathSearcher implicants = new RestrictedPathSearcher(ddmanager);
 
         for (int i=0; i<components.size(); i++) {
-            // Truth table for component i
+            // Implicant table for component i
             NodeInfo ni = components.get(i);
             byte[] implicant = implicants.setNode(functions[i]);
             int[] regulators = implicants.getRegulatorList();

src/main/java/org/colomoto/biolqm/io/implicanttables/ImplicantTableFormat.java

@@ -0,0 +1,28 @@
+package org.colomoto.biolqm.io.implicanttables;
+
+import org.colomoto.biolqm.LogicalModel;
+import org.colomoto.biolqm.io.AbstractFormat;
+import org.colomoto.biolqm.io.LogicalModelFormat;
+import org.colomoto.biolqm.service.MultivaluedSupport;
+import org.kohsuke.MetaInfServices;
+
+@MetaInfServices(LogicalModelFormat.class)
+public class ImplicantTableFormat extends AbstractFormat {
+
+    public static final String ID = "itnet";
+
+    public ImplicantTableFormat() {
+        super(ID, "Implicant Table format", MultivaluedSupport.MULTIVALUED);
+    }
+
+    @Override
+    public ImplicantTableExport getExporter(LogicalModel model) {
+        return new ImplicantTableExport(model);
+    }
+
+
+    @Override
+    public ImplicantTableImport getLoader() {
+        return new ImplicantTableImport();
+    }
+}

src/main/java/org/colomoto/biolqm/io/truthtable/LogicalTruthTableImport.java → src/main/java/org/colomoto/biolqm/io/implicanttables/ImplicantTableImport.java

@@ -1,4 +1,4 @@
-package org.colomoto.biolqm.io.truthtable;
+package org.colomoto.biolqm.io.implicanttables;
 
 import org.antlr.v4.runtime.ANTLRInputStream;
 import org.antlr.v4.runtime.CharStream;
@@ -7,8 +7,8 @@
 import org.colomoto.biolqm.LogicalModelImpl;
 import org.colomoto.biolqm.NodeInfo;
 import org.colomoto.biolqm.io.BaseLoader;
-import org.colomoto.biolqm.io.antlr.LTTLexer;
-import org.colomoto.biolqm.io.antlr.LTTParser;
+import org.colomoto.biolqm.io.antlr.ITNETLexer;
+import org.colomoto.biolqm.io.antlr.ITNETParser;
 import org.colomoto.biolqm.io.antlr.ErrorListener;
 import org.colomoto.mddlib.MDDManager;
 import org.colomoto.mddlib.MDDManagerFactory;
@@ -20,27 +20,27 @@
 import java.util.Map;
 
 
-public class LogicalTruthTableImport extends BaseLoader {
+public class ImplicantTableImport extends BaseLoader {
 
     @Override
     protected LogicalModel performTask() throws Exception {
 
         CharStream input = new ANTLRInputStream(streams.reader());
-        CommonTokenStream tokens = new CommonTokenStream( new LTTLexer(input) );
-        LTTParser parser = new LTTParser( tokens );
+        CommonTokenStream tokens = new CommonTokenStream( new ITNETLexer(input) );
+        ITNETParser parser = new ITNETParser( tokens );
         ErrorListener errors = new ErrorListener();
         parser.addErrorListener(errors);
-        LTTParser.ModelContext mtx = parser.model();
+        ITNETParser.ModelContext mtx = parser.model();
 
         // Peak forward to create all components and prepare the MDD manager
-        List<LTTParser.TableContext> tables = mtx.table();
+        List<ITNETParser.TableContext> tables = mtx.table();
         int nbvar = tables.size();
         List<NodeInfo> components = new ArrayList<>(nbvar);
         Map<String,Integer> id2index = new HashMap<>();
         MDDVariableFactory mvf = new MDDVariableFactory();
         int max = 5;
         for (int idx=0 ; idx<nbvar ; idx++) {
-            LTTParser.TableContext ttx = tables.get(idx);
+            ITNETParser.TableContext ttx = tables.get(idx);
             String id = ttx.curvar().getText();
             id2index.put(id, idx);
             byte curmax = 1;
@@ -61,27 +61,27 @@ protected LogicalModel performTask() throws Exception {
 
         // Load all functions
         int[] functions = new int[nbvar];
-        for (LTTParser.TableContext ttx: mtx.table()) {
+        for (ITNETParser.TableContext ttx: mtx.table()) {
             int curComponent = id2index.get( ttx.curvar().getText() );
-            List<LTTParser.VarContext> regulatorIDs = ttx.var();
+            List<ITNETParser.VarContext> regulatorIDs = ttx.var();
             int[] regulators = new int[regulatorIDs.size()];
             int i = 0;
-            for (LTTParser.VarContext vtx: regulatorIDs) {
+            for (ITNETParser.VarContext vtx: regulatorIDs) {
                 regulators[i++] = id2index.get(vtx.getText());
             }
 
-            List<LTTParser.LineContext> ttlines = ttx.line();
+            List<ITNETParser.LineContext> ttlines = ttx.line();
             List<byte[]> states = new ArrayList<>( ttlines.size());
             int count = regulators.length;
-            for (LTTParser.LineContext ltx: ttlines) {
+            for (ITNETParser.LineContext ltx: ttlines) {
                 int targetValue = Integer.parseInt( ltx.target().getText() );
                 if (targetValue == 0) {
                     continue;
                 }
 
                 String line = ltx.ttline().getText().trim();
                 if (line.length() != count) {
-                    throw new RuntimeException("Wrong number of values in truth table line: "+line.length() +" expected "+ count);
+                    throw new RuntimeException("Wrong number of values in implicant table line: "+line.length() +" expected "+ count);
                 }
 
                 byte[] vals = new byte[count];

src/main/java/org/colomoto/biolqm/io/implicanttables/package-info.java

@@ -0,0 +1,5 @@
+/**
+ * Implicant table format.
+ * This package contains import/export support for models defined as a list of implicant tables.
+ */
+package org.colomoto.biolqm.io.implicanttables;