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andreasprlicandreasprlic
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making output less verbose
1 parent 07f244a commit 8ba289d

1 file changed

Lines changed: 12 additions & 13 deletions

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‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestHeaderOnly.java‎

Lines changed: 12 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -40,9 +40,14 @@
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import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
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import org.junit.Assert;
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import org.junit.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class TestHeaderOnly {
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private static final Logger logger = LoggerFactory.getLogger(TestHeaderOnly.class);
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private final String pdbID = "1REP";
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/**
@@ -69,20 +74,14 @@ public void testHeaderOnly() throws StructureException, IOException {
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Structure sPDB = StructureIO.getStructure(pdbID);
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Assert.assertEquals(false, doSeqResHaveAtoms(sPDB));
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for (Chain c : sPDB.getChains()) {
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System.out.println(c.getId() + ":" + getSequenceString(c.getSeqResGroups()));
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}
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// Test 2: with mmCIF
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cache.setUseMmCif(true);
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Structure sCIF = StructureIO.getStructure(pdbID);
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Assert.assertEquals(false, doSeqResHaveAtoms(sCIF));
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83-
for (Chain c : sCIF.getChains()) {
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System.out.println(c.getId() + ":" + getSequenceString(c.getSeqResGroups()));
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}
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}
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/**
@@ -144,7 +143,7 @@ public void testSpeed() {
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}
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long stop = System.nanoTime();
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double diff = (stop - start) / 1000000000.0;
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System.out.println(String.format("[%s] Elapsed time: %.3f s", s.getIdentifier(), diff));
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logger.info(String.format("[%s] Elapsed time: %.3f s", s.getIdentifier(), diff));
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}
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// Test using local files.
@@ -160,28 +159,28 @@ public void testSpeed2() throws StructureException, IOException {
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FileParsingParameters params = new FileParsingParameters();
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params.setHeaderOnly(true); // Flip this true/false to compare parsing speed.
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163-
System.out.println("Testing PDB parsing speed");
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logger.info("Testing PDB parsing speed");
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PDBFileParser pdbpars = new PDBFileParser();
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pdbpars.setFileParsingParameters(params);
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//pdbpars.setLoadChemCompInfo(true);
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long start = System.nanoTime();
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Structure s1 = pdbpars.parsePDBFile(pdbStream) ;
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long stop = System.nanoTime();
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double diff = (stop - start) / 1000000000.0;
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System.out.println(String.format("[%s] Elapsed time: %.3f s", s1.getIdentifier(), diff));
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logger.info(String.format("[%s] Elapsed time: %.3f s", s1.getIdentifier(), diff));
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MMcifParser mmcifpars = new SimpleMMcifParser();
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SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
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consumer.setFileParsingParameters(params);
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mmcifpars.addMMcifConsumer(consumer);
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178-
System.out.println("Testing mmCIF parsing speed");
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logger.info("Testing mmCIF parsing speed");
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start = System.nanoTime();
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mmcifpars.parse(cifStream) ;
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Structure s2 = consumer.getStructure();
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stop = System.nanoTime();
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diff = (stop - start) / 1000000000.0;
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System.out.println(String.format("[%s] Elapsed time: %.3f s", s2.getIdentifier(), diff));
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logger.info(String.format("[%s] Elapsed time: %.3f s", s2.getIdentifier(), diff));
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/* Running from an SSD..
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* PDB .165s (all atom) -> 0.009s (only header) 95% faster.

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