fixing a bug with setting the file parsing type in AtomCache. (mmtf and mmcif flags were both always set to true)

andreasprlic · andreasprlic · commit 577e10840a89 · 2016-09-09T17:15:56.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -184,6 +184,10 @@ public AtomCache(UserConfiguration config) {
 		fetchBehavior = config.getFetchBehavior();
 		obsoleteBehavior = config.getObsoleteBehavior();
 		useMmCif = config.getFileFormat().equals( UserConfiguration.MMCIF_FORMAT );
+
+		if ( useMmCif)
+			useMmtf = false;
+
 	}
 
 	/**
@@ -936,6 +940,14 @@ public void setUseMmtf(boolean useMmtf) {
 		
 	}
 
+	/** Returns useMmtf flag
+	 *
+	 * @return true if will load data via mmtf file format
+     */
+	public boolean isUseMmtf(){
+		return this.useMmtf;
+	}
+
 	private boolean checkLoading(String name) {
 		return currentlyLoading.contains(name);
 
@@ -1014,11 +1026,14 @@ public Structure getStructureForPdbId(String pdbId) throws IOException, Structur
 
 		Structure s;
 		if (useMmtf) {
+			logger.debug("loading from mmtf");
 			s = loadStructureFromMmtfByPdbId(pdbId);
 		}
 		else if (useMmCif) {
+			logger.debug("loading from mmcif");
 			s = loadStructureFromCifByPdbId(pdbId);
 		} else {
+			logger.debug("loading from pdb");
 			s = loadStructureFromPdbByPdbId(pdbId);
 		}
 		return s;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
@@ -46,6 +46,7 @@ public class UserConfiguration
 
 	public static final String PDB_FORMAT   = "PDB";
 	public static final String MMCIF_FORMAT = "mmCif";
+	public static final String MMTF_FORMAT  = "mmtf";
 
 	public static final String TMP_DIR = "java.io.tmpdir";
 
@@ -97,7 +98,7 @@ public UserConfiguration(){
 		// note that in initCacheFilePath, we set to the provided one (if readable) or to the same as pdbFilePath
 		cacheFilePath = initCacheFilePath();
 
-		fileFormat = MMCIF_FORMAT;
+		fileFormat = MMTF_FORMAT;
 	}
 
 	private String initPdbFilePath() {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAtomCache.java
@@ -212,4 +212,66 @@ public void testFetchObsolete() throws IOException, StructureException {
 
 	}
 
+
+	@Test
+	public void testSettingFileParsingType(){
+
+		AtomCache cache = new AtomCache();
+
+		//test defaults
+
+		// by default we either use mmtf or mmcif, but not both.
+		assertNotEquals(cache.isUseMmtf(), cache.isUseMmCif());
+
+		// first is mmtf, second is mmcif
+		testFlags(cache,true,false);
+
+		// now change the values
+
+		cache.setUseMmCif(true);
+
+		testFlags(cache,false,true);
+
+		cache.setUseMmtf(true);
+
+		testFlags(cache,true,false);
+
+		// this sets to use PDB!
+		cache.setUseMmCif(false);
+
+		testFlags(cache,false,false);
+
+		// back to defaults
+		cache.setUseMmtf(true);
+
+		testFlags(cache,true,false);
+
+
+		// back to parsing PDB
+		cache.setUseMmtf(false);
+
+		testFlags(cache,false,false);
+
+
+
+	}
+
+
+	/** test the flags for parsing in the atom cache
+	 *
+	 * @param cache
+	 * @param useMmTf
+	 * @param useMmCif
+     */
+	private void testFlags(AtomCache cache ,boolean useMmTf, boolean useMmCif) {
+
+		assertEquals("flag for parsing mmtf is set to " + cache.isUseMmtf() + " but should be " + useMmTf,
+				cache.isUseMmtf(), useMmTf);
+		assertEquals("flag for parsing mmcif is set to " + cache.isUseMmCif() + " but should be set to " + useMmCif,
+				cache.isUseMmCif(), useMmCif);
+
+
+
+	}
+
 }
