made tolerances strict by 0.1 | add delay property to SpeciesReferenc…

…e | passes test cases 1121, 1415, 1419
hemilpanchiwala · Jun 28, 2020 · 73ec69f · 73ec69f
1 parent 0677654
commit 73ec69f
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Showing 3 changed files with 17 additions and 3 deletions.
diff --git a/src/main/java/org/simulator/sbml/astnode/SpeciesReferenceValue.java b/src/main/java/org/simulator/sbml/astnode/SpeciesReferenceValue.java
@@ -48,6 +48,12 @@ public class SpeciesReferenceValue extends ASTNodeValue {
    */
   private String id;
 
+  /**
+   * The boolean variable that says whether species reference is constant or
+   * not
+   */
+  private boolean isConstant;
+
   /**
    * @param interpreter
    * @param node
@@ -57,6 +63,7 @@ public class SpeciesReferenceValue extends ASTNodeValue {
   public SpeciesReferenceValue(ASTNodeInterpreter interpreter, ASTNode node, SpeciesReference sr, SBMLValueHolder valueHolder) {
     super(interpreter, node);
     id = sr.getId();
+    isConstant = sr.isConstant();
     this.valueHolder = valueHolder;
   }
 
@@ -65,6 +72,13 @@ public SpeciesReferenceValue(ASTNodeInterpreter interpreter, ASTNode node, Speci
    */
   @Override
   protected void computeDoubleValue(double delay) {
-    doubleValue = valueHolder.getCurrentStoichiometry(id);
+
+    if ((delay == 0d) || (isConstant)){
+      doubleValue = valueHolder.getCurrentStoichiometry(id);
+    } else {
+      double valueTime = interpreter.symbolTime() - delay;
+      doubleValue = valueHolder.computeDelayedValue(valueTime, id, null, null, 0);
+    }
+
   }
 }
diff --git a/src/main/java/org/testsuite/SBMLTestSuiteRunnerWrapper.java b/src/main/java/org/testsuite/SBMLTestSuiteRunnerWrapper.java
@@ -49,7 +49,7 @@ public class SBMLTestSuiteRunnerWrapper {
     public static final String CONCENTRATION = "concentration";
     public static final String ABSOLUTE = "absolute";
     public static final String RELATIVE = "relative";
-    private static final double TOLERANCE_FACTOR = 1E-3;
+    private static final double TOLERANCE_FACTOR = 1E-4;
     private static Logger LOGGER = Logger.getLogger(CompExample.class.getName());
 
     /**

diff --git a/src/test/java/org/simulator/sbml/SBMLTestSuiteTest.java b/src/test/java/org/simulator/sbml/SBMLTestSuiteTest.java
@@ -37,7 +37,7 @@ public class SBMLTestSuiteTest {
     public static final String RELATIVE = "relative";
     private static final Logger logger = LoggerFactory.getLogger(TestUtils.class);
     private static final String SBML_TEST_SUITE_PATH = "SBML_TEST_SUITE_PATH";
-    private static final double TOLERANCE_FACTOR = 1E-3;
+    private static final double TOLERANCE_FACTOR = 1E-4;
     private static final double DELTA = 0.0002d;
 
     public SBMLTestSuiteTest(String path) {