Two convenience methods to make dealing with BODR data a lot easier

Change-Id: I1c29e2d1b412a898bf01ecc2a4d0bb3a145249cd Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Aug 2, 2013 · c4c63dd · c4c63dd
1 parent d5b5947
commit c4c63dd
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diff --git a/src/main/org/openscience/cdk/config/IsotopeFactory.java b/src/main/org/openscience/cdk/config/IsotopeFactory.java
@@ -169,6 +169,51 @@ public IIsotope[] getIsotopes(String symbol) {
         return list.toArray(new IIsotope[list.size()]);
     }
 
+    /**
+	 * Gets a array of all isotopes known to the IsotopeFactory.
+	 *
+	 * @return         An array of all isotopes
+	 */
+    @TestMethod("testGetIsotopes")
+    public IIsotope[] getIsotopes() {
+    	ArrayList<IIsotope> list = new ArrayList<IIsotope>();
+    	for (IIsotope isotope : isotopes) {
+            try {
+                IIsotope clone = (IIsotope) isotope.clone();
+                list.add(clone);
+            } catch (CloneNotSupportedException e) {
+                logger.error("Could not clone IIsotope: ", e.getMessage());
+                logger.debug(e);
+            }
+    	}
+    	return list.toArray(new IIsotope[list.size()]);
+    }
+
+    /**
+	 * Gets an array of all isotopes matching the searched exact mass within
+	 * a certain difference.
+	 *
+	 * @param  exactMass  search mass
+	 * @param  difference mass the isotope is allowed to differ from the search mass
+	 * @return            An array of all isotopes
+	 */
+    @TestMethod("testGetIsotopes_double_double")
+    public IIsotope[] getIsotopes(double exactMass, double difference) {
+    	ArrayList<IIsotope> list = new ArrayList<IIsotope>();
+    	for (IIsotope isotope : isotopes) {
+    		if (Math.abs(isotope.getExactMass() - exactMass) <= difference) {
+    			try {
+    				IIsotope clone = (IIsotope) isotope.clone();
+    				list.add(clone);
+    			} catch (CloneNotSupportedException e) {
+    				logger.error("Could not clone IIsotope: ", e.getMessage());
+    				logger.debug(e);
+    			}
+    		}
+    	}
+    	return list.toArray(new IIsotope[list.size()]);
+    }
+
     /**
      * Get isotope based on element symbol and mass number.
      *

diff --git a/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java b/src/test/org/openscience/cdk/config/IsotopeFactoryTest.java
@@ -157,6 +157,25 @@ public void testGetIsotopes_String() throws Exception {
 		Assert.assertEquals(8, list.length);
 	}    
 
+    @Test
+    public void testGetIsotopes() throws Exception {
+		IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
+        IIsotope[] list = isofac.getIsotopes();
+		Assert.assertTrue(list.length > 200);
+	}    
+
+    @Test
+    public void testGetIsotopes_double_double() throws Exception {
+		IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
+        IIsotope[] list = isofac.getIsotopes(87.90, 0.01);
+//        should return:
+//        Isotope match: 88Sr has mass 87.9056121
+//        Isotope match: 88Y has mass 87.9095011
+		Assert.assertEquals(2, list.length);
+		Assert.assertEquals(88, list[0].getMassNumber().intValue());
+		Assert.assertEquals(88, list[1].getMassNumber().intValue());
+	}    
+
     @Test
     public void testIsElement_String() throws Exception {
 		IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());