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package jalview.ext.jmol; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.DataSourceType; |
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import java.io.File; |
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import java.io.IOException; |
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import java.util.HashSet; |
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import java.util.Set; |
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import java.util.Vector; |
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import org.testng.annotations.BeforeClass; |
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import mc_view.PDBfile; |
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@author |
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| 0% |
Uncovered Elements: 48 (48) |
Complexity: 8 |
Complexity Density: 0.2 |
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public class JmolVsJalviewPDBParserEndToEndTest |
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{ |
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| 0% |
Uncovered Elements: 2 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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@param |
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| 0% |
Uncovered Elements: 10 (10) |
Complexity: 3 |
Complexity Density: 0.38 |
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public static void main(String[] args)... |
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{ |
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if (args == null || args[0] == null) |
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{ |
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System.err |
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.println("You must provide a PDB directory in the launch argument"); |
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return; |
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} |
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String testDir = args[0]; |
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System.out.println("PDB directory : " + testDir); |
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File pdbDir = new File(testDir); |
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String testFiles[] = pdbDir.list(); |
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testFileParser(testDir, testFiles); |
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} |
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| 0% |
Uncovered Elements: 33 (33) |
Complexity: 4 |
Complexity Density: 0.13 |
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public static void testFileParser(String testDir, String[] testFiles)... |
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{ |
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Set<String> failedFiles = new HashSet<>(); |
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int totalSeqScanned = 0, totalFail = 0; |
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for (String pdbStr : testFiles) |
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{ |
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String testFile = testDir + "/" + pdbStr; |
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PDBfile mctest = null; |
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JmolParser jtest = null; |
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try |
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{ |
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mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE); |
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jtest = new JmolParser(testFile, DataSourceType.FILE); |
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} catch (IOException e) |
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{ |
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System.err.println("Exception thrown while parsing : " + pdbStr); |
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} |
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Vector<SequenceI> seqs = jtest.getSeqs(); |
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Vector<SequenceI> mcseqs = mctest.getSeqs(); |
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for (SequenceI sq : seqs) |
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{ |
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try |
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{ |
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String testSeq = mcseqs.remove(0).getSequenceAsString(); |
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if (!sq.getSequenceAsString().equals(testSeq)) |
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{ |
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++totalFail; |
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System.err.println("Test Failed for " + pdbStr + ". Diff:"); |
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System.err.println(sq.getSequenceAsString()); |
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System.err.println(testSeq); |
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failedFiles.add(pdbStr); |
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} |
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++totalSeqScanned; |
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} catch (Exception e) |
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{ |
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e.printStackTrace(); |
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} |
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} |
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} |
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int count = 0; |
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System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned); |
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System.out.println("Total sequence passed : " |
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+ (totalSeqScanned - totalFail)); |
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System.out.println("Total sequence failed : " + totalFail); |
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System.out |
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.println("Success rate: " |
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+ ((totalSeqScanned - totalFail) * 100) |
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/ totalSeqScanned + "%"); |
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System.out.println("\nList of " + failedFiles.size() |
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+ " file(s) with sequence diffs:"); |
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for (String problemFile : failedFiles) |
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{ |
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System.out.println(++count + ". " + problemFile); |
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} |
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} |
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} |