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josemduartejosemduarte
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Fixing test and clean up
1 parent 3d0274b commit 9afde8f

2 files changed

Lines changed: 8 additions & 51 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -516,7 +516,6 @@ public static void addSeqRes(Chain modelChain, String sequence) {
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group = getSeqResGroup(singleLetterCode, chainType);
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addGroupAtId(seqResGroups, group, i);
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seqResGroups.set(i, group);
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}
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}
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‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfPerformance.java‎

Lines changed: 8 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -44,54 +44,14 @@ public class TestMmtfPerformance {
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private static final int NUMBER_OF_REPEATS = 10;
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// Returns the contents of the file in a byte array.
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public static byte[] getBytesFromFile(File file) throws IOException {
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// Get the size of the file
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long length = file.length();
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// You cannot create an array using a long type.
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// It needs to be an int type.
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// Before converting to an int type, check
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// to ensure that file is not larger than Integer.MAX_VALUE.
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if (length > Integer.MAX_VALUE) {
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// File is too large
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throw new IOException("File is too large!");
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}
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// Create the byte array to hold the data
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byte[] bytes = new byte[(int)length];
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// Read in the bytes
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int offset = 0;
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int numRead = 0;
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InputStream is = new FileInputStream(file);
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try {
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while (offset < bytes.length
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&& (numRead=is.read(bytes, offset, bytes.length-offset)) >= 0) {
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offset += numRead;
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}
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} finally {
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is.close();
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}
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// Ensure all the bytes have been read in
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if (offset < bytes.length) {
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throw new IOException("Could not completely read file "+file.getName());
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}
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return bytes;
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}
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static String convertStreamToString(java.io.InputStream is) {
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private static String convertStreamToString(java.io.InputStream is) {
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try (
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java.util.Scanner s = new java.util.Scanner(is)){
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return s.useDelimiter("\\A").hasNext() ? s.next() : "";
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}
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}
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public byte[] getByteArrayFromInputStream(InputStream is) throws IOException {
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private byte[] getByteArrayFromInputStream(InputStream is) throws IOException {
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ByteArrayOutputStream buffer = new ByteArrayOutputStream();
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int nRead;
@@ -104,7 +64,6 @@ public byte[] getByteArrayFromInputStream(InputStream is) throws IOException {
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buffer.flush();
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return buffer.toByteArray();
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}
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@Test
@@ -128,31 +87,30 @@ public void test3HBX() throws Exception{
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byte[] mmtfdata = getByteArrayFromInputStream(new GZIPInputStream((mmtfURL.openStream())));
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// first make sure chemcomp cache is warmed up (chemcomp files are parsed). Like that we count the parsing time without the influence of chemcomp parsing
91+
MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
92+
parser.parsePDBFile(new ByteArrayInputStream(pdbBytes));
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for ( int i =0 ; i< NUMBER_OF_REPEATS ; i++) {
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long mmtfStart = System.nanoTime();
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MmtfActions.readFromInputStream(new ByteArrayInputStream(mmtfdata));
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long mmtfEnd = System.nanoTime();
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long pdbStart = System.nanoTime();
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parser.parsePDBFile(new ByteArrayInputStream(pdbBytes));
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long pdbEnd = System.nanoTime();
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totalTimePDB += (pdbEnd - pdbStart);
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totalTimeMMTF += (mmtfEnd-mmtfStart);
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}
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long timePDB = (totalTimePDB/NUMBER_OF_REPEATS);
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long timeMMTF = (totalTimeMMTF/NUMBER_OF_REPEATS);
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logger.warn("average time to parse mmtf: " + timeMMTF/(1000*1000) + " ms.");
155-
logger.warn("average time to parse PDB : " + timePDB/(1000*1000) + " ms. ");
112+
logger.info("average time to parse mmtf: " + timeMMTF/(1000*1000) + " ms.");
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logger.info("average time to parse PDB : " + timePDB/(1000*1000) + " ms. ");
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assertTrue( "It should not be the case, but it is faster to parse a PDB file ("+timePDB+" ns.) than MMTF ("+( timeMMTF)+" ns.)!",( timePDB) > ( timeMMTF));
158116

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