more precise comparison of parsing speed between mtf and pdb file formats

andreasprlic · andreasprlic · commit a216f929b07a · 2017-03-29T15:55:35.000-07:00
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java
@@ -95,41 +95,52 @@ public byte[] getByteArrayFromInputStream(InputStream is) throws IOException {
 
     @Test
     public void test3HBX() throws Exception{
-        String pdbId = "3HBX";
+        String pdbId = "3hbx";
+
+        pdbId = pdbId.toUpperCase();
 
         URL url = new URL("https://files.rcsb.org/download/"+pdbId+".pdb.gz");
 
         String pdbFile = convertStreamToString(new GZIPInputStream(url.openStream()));
 
-        long pdbStart = System.currentTimeMillis();
+        long totalTimePDB = 0;
+        long totalTimeMMTF = 0;
+
+        byte[] pdbBytes = pdbFile.getBytes();
 
         PDBFileParser parser = new PDBFileParser();
 
+        URL mmtfURL = new URL("https://mmtf.rcsb.org/v1.0/full/" + pdbId + ".mmtf.gz");
+
+        byte[] mmtfdata = getByteArrayFromInputStream(new GZIPInputStream((mmtfURL.openStream())));
+
         for ( int i =0 ; i< NUMBER_OF_REPEATS ; i++) {
 
-            Structure pdbStructure = parser.parsePDBFile(new ByteArrayInputStream(pdbFile.getBytes()));
-        }
-        long pdbEnd = System.currentTimeMillis();
+            long mmtfStart = System.nanoTime();
+            Structure mmtfStructure = MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
+            long mmtfEnd = System.nanoTime();
 
 
-        URL mmtfURL = new URL("https://mmtf.rcsb.org/v1.0/full/" + pdbId + ".mmtf.gz");
 
+            long pdbStart = System.nanoTime();
+            Structure pdbStructure = parser.parsePDBFile(new ByteArrayInputStream(pdbBytes));
+            long pdbEnd = System.nanoTime();
 
-        byte[] mmtfdata = getByteArrayFromInputStream(new GZIPInputStream((mmtfURL.openStream())));
+            totalTimePDB += (pdbEnd - pdbStart);
 
-        long mmtfStart = System.currentTimeMillis();
 
-        for ( int i =0 ; i< NUMBER_OF_REPEATS ; i++) {
-            Structure mmtfStructure = MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
+            totalTimeMMTF += (mmtfEnd-mmtfStart);
         }
-        long mmtfEnd = System.currentTimeMillis();
 
-        long timeMMTF = (mmtfEnd-mmtfStart);
-        long timePDB = (pdbEnd-pdbStart);
-        logger.warn("average time to parse mmtf: " + (timeMMTF/NUMBER_OF_REPEATS));
-        logger.warn("average time to parse PDB : " + (timePDB/NUMBER_OF_REPEATS));
+
+        long timePDB = (totalTimePDB/NUMBER_OF_REPEATS);
+        long timeMMTF = (totalTimeMMTF/NUMBER_OF_REPEATS);
+
+
+        logger.warn("average time to parse mmtf: " + timeMMTF/(1000*1000) + " ms.");
+        logger.warn("average time to parse PDB : " + timePDB/(1000*1000) + " ms. ");
 //
-        assertTrue( "It should not be the case, but it is faster to parse a PDB file ("+timePDB+" ms.) than MMTF ("+( timeMMTF)+" ms.)!",( timePDB) > ( timeMMTF));
+        assertTrue( "It should not be the case, but it is faster to parse a PDB file ("+timePDB+" ns.) than MMTF ("+( timeMMTF)+" ns.)!",( timePDB) > ( timeMMTF));
 //
     }
 }
