Merge branch 'master' into cmpdfixcmpdfix

1 files changed, 48 insertions, 0 deletions

diff --git a/java/JoelibFc.java b/java/JoelibFc.java
new file mode 100644
index 0000000..78de499
--- /dev/null
+++ b/java/JoelibFc.java
@@ -0,0 +1,48 @@
+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();
+  }
+}