Clearing ChemComp cache whenever provider changes

sbliven · sbliven · commit cbde02da997b · 2016-02-09T15:23:44.000+01:00
This avoids requiring the user to manually clear the cache, so the cache no longer
needs to be publically exposed.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.java
@@ -57,10 +57,8 @@ public static ChemComp getChemComp(String recordName){
 		logger.debug("Chem comp "+recordName+" read from provider "+chemCompProvider.getClass().getCanonicalName());
 		cc = chemCompProvider.getChemComp(recordName);
 		
-		// If chemCompProvider fails don't try to cache null & one letter code may be null.
-		if (null != cc && !cc.isEmpty()){
-			cache.put(recordName, cc);
-		}
+		// Note that this also caches null or empty responses
+		cache.put(recordName, cc);
 		return cc;
 	}
 
@@ -79,6 +77,8 @@ public static ChemComp getChemComp(String recordName){
 	public static void setChemCompProvider(ChemCompProvider provider) {
 		logger.debug("Setting new chem comp provider to "+provider.getClass().getCanonicalName());
 		chemCompProvider = provider;
+		// clear cache
+		cache.clear();
 	}
 
 	public static ChemCompProvider getChemCompProvider(){
@@ -154,9 +154,4 @@ public  static String getOneLetterCode(ChemComp cc){
 		return oneLetter;
 	}
 
-	public static SoftHashMap<String, ChemComp> getCache() {
-		return cache;
-	}
-
-
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/model/ChemComp.java
@@ -594,7 +594,7 @@ public static ChemComp getEmptyChemComp(){
 		ChemComp comp = new ChemComp();
 
 		comp.setOne_letter_code("?");
-		comp.setThree_letter_code("???");
+		comp.setThree_letter_code("???"); // Main signal for isEmpty()
 		comp.setPolymerType(PolymerType.unknown);
 		comp.setResidueType(ResidueType.atomn);
 		return comp;
@@ -606,7 +606,7 @@ public static ChemComp getEmptyChemComp(){
 	 */
 	public boolean isEmpty() {
 		// Is this the best flag for it being empty?
-		return id == null || getThree_letter_code().equals("???");
+		return id == null || getThree_letter_code() == null || getThree_letter_code().equals("???");
 	}
 
 }
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ChemCompTest.java
@@ -117,10 +117,6 @@ public void testPRR(){
 	@Test
     public void testChangingProviders(){
 
-		//reset the cache
-		SoftHashMap<String, ChemComp> cache = ChemCompGroupFactory.getCache();
-		cache.clear();
-		
 		// test for issue #145
 
         String chemID = "MEA";
@@ -134,7 +130,7 @@ public void testChangingProviders(){
 
         assertTrue(" is not mea" , cc.getId().equals(chemID));
         
-        assertNull(cc.getThree_letter_code());
+        assertTrue(cc.isEmpty());
 
         // now we change to download chem comp provider
 
@@ -151,7 +147,6 @@ public void testChangingProviders(){
         
         
         // now testing in opposite order
-        cache.clear();
 
         // first we test with download chem comp provider
 
