import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
import java.io.File;
import java.io.IOException;
import org.testng.annotations.BeforeClass;
-import MCview.PDBfile;
+import mc_view.PDBfile;
/**
* This is not a unit test, rather it is a bulk End-to-End scan for sequences
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
if (args == null || args[0] == null)
{
- System.err
- .println("You must provide a PDB directory in the launch argument");
+ System.err.println(
+ "You must provide a PDB directory in the launch argument");
return;
}
public static void testFileParser(String testDir, String[] testFiles)
{
- Set<String> failedFiles = new HashSet<String>();
+ Set<String> failedFiles = new HashSet<>();
int totalSeqScanned = 0, totalFail = 0;
for (String pdbStr : testFiles)
{
try
{
mctest = new PDBfile(false, false, false, testFile,
- AppletFormatAdapter.FILE);
- jtest = new JmolParser(testFile, AppletFormatAdapter.FILE);
+ DataSourceType.FILE);
+ jtest = new JmolParser(testFile, DataSourceType.FILE);
} catch (IOException e)
{
System.err.println("Exception thrown while parsing : " + pdbStr);
int count = 0;
System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned);
- System.out.println("Total sequence passed : "
- + (totalSeqScanned - totalFail));
+ System.out.println(
+ "Total sequence passed : " + (totalSeqScanned - totalFail));
System.out.println("Total sequence failed : " + totalFail);
- System.out
- .println("Success rate: "
- + ((totalSeqScanned - totalFail) * 100)
- / totalSeqScanned + "%");
+ System.out.println("Success rate: "
+ + ((totalSeqScanned - totalFail) * 100) / totalSeqScanned
+ + "%");
System.out.println("\nList of " + failedFiles.size()
+ " file(s) with sequence diffs:");
for (String problemFile : failedFiles)