blob: 78de49972cc345a9a8b93c8899507c8f2317848d (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
import joelib2.example.FeatureCalculationExample;
import joelib2.feature.util.AtomPropertyDescriptors;
import joelib2.feature.util.SMARTSDescriptors;
import joelib2.io.BasicIOType;
import org.apache.log4j.Category;
public class JoelibFc
{
private static Category logger = Category.getInstance(FeatureCalculationExample.class.getName());
public static final int CONTINUE = 0;
public static final int STOP = 1;
public static final int STOP_USAGE = 2;
private static final double[] RDF_SMOOTHINGFACTORS = { 1.0D, 5.0D, 25.0D, 150.0D };
private static final String NUMERIC = ".numeric";
private static final String NUMERIC_NORMALIZED = ".numeric.normalized";
private boolean calculateAP = true;
private boolean calculateBinarySMARTS = true;
private boolean calculateCountSMARTS = false;
private boolean calculateJCC = true;
private boolean calculateSSKey = true;
private AtomPropertyDescriptors calculatorAP = new AtomPropertyDescriptors();
private SMARTSDescriptors calculatorSMARTS = new SMARTSDescriptors();
private String inputFile;
private BasicIOType inType;
private boolean normalize = false;
private String outputFile;
private BasicIOType outType;
private String[] smartsDescriptions = null;
private String smartsFile;
private String[] smartsPatterns = null;
private String trueDescName = null;
public JoelibFc(String paramString1, String paramString2)
{
FeatureCalculationExample localFeatureCalculationExample = new FeatureCalculationExample();
String[] arrayOfString = new String[2];
arrayOfString[0] = paramString1;
arrayOfString[1] = paramString2;
int i = localFeatureCalculationExample.parseCommandLine(arrayOfString);
localFeatureCalculationExample.initializeSMARTS();
localFeatureCalculationExample.calculateNumericDescriptors();
localFeatureCalculationExample.calculateNormalization();
localFeatureCalculationExample.calculateNominalDescriptors();
}
}
|