making atomcache more extensible. Now can be extended by DB-based implementation, rather than file system based.

andreasprlic · andreasprlic · commit 88692567a76f · 2013-03-27T17:57:10.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@10104 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java b/biojava3-structure/src/main/java/org/biojava/bio/structure/align/util/AtomCache.java
@@ -93,7 +93,8 @@ public class AtomCache {
 	boolean autoFetch;
 	boolean isSplit;
 	boolean strictSCOP;
-	FileParsingParameters params;
+	
+	protected FileParsingParameters params;
 
 	private boolean fetchFileEvenIfObsolete;
 
@@ -647,8 +648,10 @@ public Structure getStructure(String name) throws IOException, StructureExceptio
 
 	}
 
-	private Structure loadStructureFromByPdbId(String pdbId)
+	protected Structure loadStructureFromByPdbId(String pdbId)
 			throws StructureException {
+		
+		
 		Structure s;
 		flagLoading(pdbId);
 		try {
@@ -668,6 +671,7 @@ private Structure loadStructureFromByPdbId(String pdbId)
 			throw new StructureException(e.getMessage() + " while parsing " + pdbId,e);
 		}
 		flagLoadingFinished(pdbId);
+		
 		return s;
 	}
 
@@ -924,12 +928,12 @@ private  boolean checkLoading(String name) {
 
 	}
 
-	private  void flagLoading(String name){
+	protected  void flagLoading(String name){
 		if ( ! currentlyLoading.contains(name))	
 			currentlyLoading.add(name);
 	}
 
-	private  void flagLoadingFinished(String name){
+	protected  void flagLoadingFinished(String name){
 		currentlyLoading.remove(name);   
 	}
 

Original file line number	Diff line number	Diff line change
`@@ -93,7 +93,8 @@ public class AtomCache {`
`93`	`93`	`boolean autoFetch;`
`94`	`94`	`boolean isSplit;`
`95`	`95`	`boolean strictSCOP;`
`96`		`- FileParsingParameters params;`
	`96`	`+`
	`97`	`+ protected FileParsingParameters params;`
`97`	`98`
`98`	`99`	`private boolean fetchFileEvenIfObsolete;`
`99`	`100`
`@@ -647,8 +648,10 @@ public Structure getStructure(String name) throws IOException, StructureExceptio`
`647`	`648`
`648`	`649`	`}`
`649`	`650`
`650`		`- private Structure loadStructureFromByPdbId(String pdbId)`
	`651`	`+ protected Structure loadStructureFromByPdbId(String pdbId)`
`651`	`652`	`throws StructureException {`
	`653`	`+`
	`654`	`+`
`652`	`655`	`Structure s;`
`653`	`656`	`flagLoading(pdbId);`
`654`	`657`	`try {`
`@@ -668,6 +671,7 @@ private Structure loadStructureFromByPdbId(String pdbId)`
`668`	`671`	`throw new StructureException(e.getMessage() + " while parsing " + pdbId,e);`
`669`	`672`	`}`
`670`	`673`	`flagLoadingFinished(pdbId);`
	`674`	`+`
`671`	`675`	`return s;`
`672`	`676`	`}`
`673`	`677`
`@@ -924,12 +928,12 @@ private boolean checkLoading(String name) {`
`924`	`928`
`925`	`929`	`}`
`926`	`930`
`927`		`- private void flagLoading(String name){`
	`931`	`+ protected void flagLoading(String name){`
`928`	`932`	`if ( ! currentlyLoading.contains(name))`
`929`	`933`	`currentlyLoading.add(name);`
`930`	`934`	`}`
`931`	`935`
`932`		`- private void flagLoadingFinished(String name){`
	`936`	`+ protected void flagLoadingFinished(String name){`
`933`	`937`	`currentlyLoading.remove(name);`
`934`	`938`	`}`
`935`	`939`