Refactored the setters from IReaction to use IAtomContainer*

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Dec 8, 2011 · 04cbb29 · 04cbb29
1 parent 91f8083
commit 04cbb29
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Showing 5 changed files with 22 additions and 17 deletions.
diff --git a/src/main/org/openscience/cdk/Reaction.java b/src/main/org/openscience/cdk/Reaction.java
@@ -111,7 +111,7 @@ public int getProductCount() {
      * Returns a MoleculeSet containing the reactants in this reaction.
      *
      * @return A MoleculeSet containing the reactants in this reaction
-     * @see    #setReactants
+     * @see    org.openscience.cdk.interfaces.IReaction#setReactants
      */
     public IAtomContainerSet getReactants() {
         return reactants;
@@ -120,10 +120,11 @@ public IAtomContainerSet getReactants() {
     /**
      * Assigns a MoleculeSet to the reactants in this reaction.
      *
+     *
      * @param setOfMolecules The new set of reactants
      * @see   #getReactants
      */
-    public void setReactants(IMoleculeSet setOfMolecules) {
+    public void setReactants(IAtomContainerSet setOfMolecules) {
         reactants = setOfMolecules;
 	notifyChanged();
     }
@@ -132,7 +133,7 @@ public void setReactants(IMoleculeSet setOfMolecules) {
      * Returns a MoleculeSet containing the products of this reaction.
      *
      * @return A MoleculeSet containing the products in this reaction
-     * @see    #setProducts
+     * @see    org.openscience.cdk.interfaces.IReaction#setProducts
      */
     public IAtomContainerSet getProducts() {
         return products;
@@ -141,10 +142,11 @@ public IAtomContainerSet getProducts() {
 	/**
      * Assigns a MoleculeSet to the products of this reaction.
      *
+     *
      * @param setOfMolecules The new set of products
      * @see   #getProducts
      */
-    public void setProducts(IMoleculeSet setOfMolecules) {
+    public void setProducts(IAtomContainerSet setOfMolecules) {
         products = setOfMolecules;
 	notifyChanged();
     }

diff --git a/src/main/org/openscience/cdk/debug/DebugReaction.java b/src/main/org/openscience/cdk/debug/DebugReaction.java
@@ -26,7 +26,6 @@
 import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
 import org.openscience.cdk.interfaces.IChemObjectListener;
 import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IMoleculeSet;
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
@@ -162,7 +161,7 @@ public IAtomContainerSet getReactants() {
 		return super.getReactants();
 	}
 
-	public void setReactants(IMoleculeSet reactants) {
+	public void setReactants(IAtomContainerSet reactants) {
 		logger.debug("Setting reactants: ", reactants);
 		super.setReactants(reactants);
 	}
@@ -172,7 +171,7 @@ public IAtomContainerSet getProducts() {
 		return super.getProducts();
 	}
 
-	public void setProducts(IMoleculeSet products) {
+	public void setProducts(IAtomContainerSet products) {
 		logger.debug("Setting products: ", products);
 		super.setProducts(products);
 	}

diff --git a/src/main/org/openscience/cdk/interfaces/IReaction.java b/src/main/org/openscience/cdk/interfaces/IReaction.java
@@ -83,10 +83,11 @@ public enum Direction {
     /**
      * Assigns a IMoleculeSet to the reactants in this reaction.
      *
+     *
      * @param  reactants The new set of reactants
      * @see              #getReactants
      */
-    public void setReactants(IMoleculeSet reactants);
+    public void setReactants(IAtomContainerSet reactants);
 
     /**
      * Returns a IMoleculeSet containing the products of this reaction.
@@ -99,10 +100,11 @@ public enum Direction {
 	/**
      * Assigns a IMoleculeSet to the products of this reaction.
      *
+     *
      * @param products The new set of products
      * @see            #getProducts
      */
-    public void setProducts(IMoleculeSet products);
+    public void setProducts(IAtomContainerSet products);
 
     /**
      * Returns a IMoleculeSet containing the agents in this reaction.

diff --git a/src/main/org/openscience/cdk/silent/Reaction.java b/src/main/org/openscience/cdk/silent/Reaction.java
@@ -109,7 +109,7 @@ public int getProductCount() {
      * Returns a MoleculeSet containing the reactants in this reaction.
      *
      * @return A MoleculeSet containing the reactants in this reaction
-     * @see    #setReactants
+     * @see    org.openscience.cdk.interfaces.IReaction#setReactants
      */
     public IAtomContainerSet getReactants() {
         return reactants;
@@ -118,18 +118,19 @@ public IAtomContainerSet getReactants() {
     /**
      * Assigns a MoleculeSet to the reactants in this reaction.
      *
+     *
      * @param setOfMolecules The new set of reactants
      * @see   #getReactants
      */
-    public void setReactants(IMoleculeSet setOfMolecules) {
+    public void setReactants(IAtomContainerSet setOfMolecules) {
         reactants = setOfMolecules;
     }
 
     /**
      * Returns a MoleculeSet containing the products of this reaction.
      *
      * @return A MoleculeSet containing the products in this reaction
-     * @see    #setProducts
+     * @see    org.openscience.cdk.interfaces.IReaction#setProducts
      */
     public IAtomContainerSet getProducts() {
         return products;
@@ -138,10 +139,11 @@ public IAtomContainerSet getProducts() {
 	/**
      * Assigns a MoleculeSet to the products of this reaction.
      *
+     *
      * @param setOfMolecules The new set of products
      * @see   #getProducts
      */
-    public void setProducts(IMoleculeSet setOfMolecules) {
+    public void setProducts(IAtomContainerSet setOfMolecules) {
         products = setOfMolecules;
     }
 

diff --git a/src/test/org/openscience/cdk/smiles/SmilesParserTest.java b/src/test/org/openscience/cdk/smiles/SmilesParserTest.java
@@ -20,9 +20,6 @@
  */
 package org.openscience.cdk.smiles;
 
-import java.util.Iterator;
-import java.util.List;
-
 import org.junit.Assert;
 import org.junit.Assume;
 import org.junit.Ignore;
@@ -57,6 +54,9 @@
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 import org.openscience.cdk.tools.manipulator.BondManipulator;
 
+import java.util.Iterator;
+import java.util.List;
+
 /**
  * Please see the test.gui package for visual feedback on tests.
  * 
@@ -986,7 +986,7 @@ public void testReactionWithAgents() throws Exception {
 		Assert.assertEquals(2, reaction.getProductCount());
 		Assert.assertEquals(1, reaction.getAgents().getAtomContainerCount());
 
-		Assert.assertEquals(1, reaction.getAgents().getMolecule(0).getAtomCount());
+		Assert.assertEquals(1, reaction.getAgents().getAtomContainer(0).getAtomCount());
 	}