[Jsbml-svn] SF.net SVN: jsbml:[2474] trunk

[<and...@us...>]

Revision: 2474
          http://sourceforge.net/p/jsbml/code/2474
Author:   andreas-draeger
Date:     2016-01-25 20:54:22 +0000 (Mon, 25 Jan 2016)
Log Message:
-----------
Added forgotten methods to directly obtain object instances (getXXXInstance() and isSetXXXInstance()) and made isSetSpeciesInstance() in SimpleSpeciesReference more consistent with the rest of the code.

Modified Paths:
--------------
    trunk/core/src/org/sbml/jsbml/SimpleSpeciesReference.java
    trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java
    trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java

Modified: trunk/core/src/org/sbml/jsbml/SimpleSpeciesReference.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SimpleSpeciesReference.java	2016-01-25 04:12:26 UTC (rev 2473)
+++ trunk/core/src/org/sbml/jsbml/SimpleSpeciesReference.java	2016-01-25 20:54:22 UTC (rev 2474)
@@ -57,7 +57,7 @@
   }
 
   /**
-   * Creates a SimpleSpeciesReference instance. 
+   * Creates a SimpleSpeciesReference instance.
    * 
    * @param level the SBML level
    * @param version the SBML version
@@ -89,7 +89,7 @@
   }
 
   /**
-   * Creates a SimpleSpeciesReference instance. 
+   * Creates a SimpleSpeciesReference instance.
    * @param id
    */
   public SimpleSpeciesReference(String id) {
@@ -98,7 +98,7 @@
 
   /**
    * Creates a SimpleSpeciesReference instance.
-   *  
+   * 
    * @param id
    * @param level the SBML level
    * @param version the SBML version
@@ -108,7 +108,7 @@
   }
 
   /**
-   * Creates a SimpleSpeciesReference instance. 
+   * Creates a SimpleSpeciesReference instance.
    * 
    * @param id
    * @param name
@@ -189,8 +189,7 @@
    *         {@link SimpleSpeciesReference} as id is not {@code null}.
    */
   public boolean isSetSpeciesInstance() {
-    Model m = getModel();
-    return m != null ? m.getSpecies(speciesID) != null : false;
+    return getSpeciesInstance() != null;
   }
 
   /* (non-Javadoc)

Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java	2016-01-25 04:12:26 UTC (rev 2473)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java	2016-01-25 20:54:22 UTC (rev 2474)
@@ -26,6 +26,7 @@
 
 import org.sbml.jsbml.AbstractNamedSBase;
 import org.sbml.jsbml.LevelVersionError;
+import org.sbml.jsbml.Model;
 import org.sbml.jsbml.PropertyUndefinedError;
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.UniqueNamedSBase;
@@ -203,10 +204,29 @@
    * @return the value of reaction
    */
   public String getReaction() {
-    return reaction;
+    return isSetReaction() ? reaction : "";
   }
 
   /**
+   * @return
+   */
+  public Reaction getReactionInstance() {
+    if (isSetReaction()) {
+      Model m = getModel();
+      return (m != null) ? m.getReaction(getReaction()) : null;
+    }
+    return null;
+  }
+
+  /**
+   * 
+   * @return
+   */
+  public boolean isSetReactionInstance() {
+    return getReactionInstance() != null;
+  }
+
+  /**
    * Returns whether reaction is set
    *
    * @return whether reaction is set

Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java	2016-01-25 04:12:26 UTC (rev 2473)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java	2016-01-25 20:54:22 UTC (rev 2474)
@@ -23,6 +23,7 @@
 import java.util.Map;
 
 import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.Model;
 import org.sbml.jsbml.UniqueNamedSBase;
 
 /**
@@ -148,6 +149,26 @@
     return "";
   }
 
+  /**
+   * 
+   * @return
+   */
+  public GeneProduct getGeneProductInstance() {
+    if (isSetGeneProduct()) {
+      Model m = getModel();
+      return (m != null) ?(GeneProduct) m.findNamedSBase(getGeneProduct()) : null;
+    }
+    return null;
+  }
+
+  /**
+   * 
+   * @return
+   */
+  public boolean isSetGeneProductInstance() {
+    return getGeneProductInstance() != null;
+  }
+
   /* (non-Javadoc)
    * @see java.lang.Object#hashCode()
    */

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