Java doc

3 files changed, 112 insertions, 37 deletions

diff --git a/java/ApplyCDKDescriptors.class b/java/ApplyCDKDescriptors.class
index dd00864..c5ee8a4 100644
--- a/java/ApplyCDKDescriptors.class
+++ b/java/ApplyCDKDescriptors.class
diff --git a/java/ApplyCDKDescriptors.java b/java/ApplyCDKDescriptors.java
index f872026..85a1abd 100644
--- a/java/ApplyCDKDescriptors.java
+++ b/java/ApplyCDKDescriptors.java
@@ -28,40 +28,52 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
 import org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor;
 import org.openscience.cdk.smiles.SmilesGenerator;
 
-public class ApplyCDKDescriptors
-{
 
-  public ApplyCDKDescriptors(String inpath, String outpath, String descNamesStr) throws java.io.IOException 
-  { 
+/**
+ * ApplyCDKDescriptors.java
+ * Purpose: Calculate CDK descriptors in CSV format from input SDF files
+ * For ease of use, the design is completely static, i.e. no member functions
+ * Calling the constructor executes the algorithm
+ *
+ * @author Martin Guetlein, Andreas Maunz
+ * @version 1.0 20/9/2012
+ */
+public class ApplyCDKDescriptors {
+	private static DescriptorEngine ENGINE = new DescriptorEngine(DescriptorEngine.MOLECULAR);
+
+
+ /**
+  * Constructor, executing the algorithm
+  *
+  * @param: string The path to the input SDF file
+  * @param: string The path to the output CSV file
+  */
+  public ApplyCDKDescriptors(String inpath, String outpath, String descNamesStr) throws java.io.IOException  { 
     getDescriptorCSV(inpath,outpath,descNamesStr);
   }
 
-	private static DescriptorEngine ENGINE = new DescriptorEngine(DescriptorEngine.MOLECULAR);
-
-	private static int getSize(IMolecularDescriptor descriptor)
-	{
-		IDescriptorResult r = descriptor.getDescriptorResultType();
-		if (r instanceof DoubleArrayResultType)
-			return ((DoubleArrayResultType) r).length();
-		else if (r instanceof IntegerArrayResultType)
-			return ((IntegerArrayResultType) r).length();
-		else
-			return 1;
-	}
 
-	private static String getName(IDescriptor descriptor)
+ /**
+  * Example main
+  *
+  */
+	public static void main(String args[]) throws java.io.IOException 
 	{
-		return ENGINE.getDictionaryTitle(descriptor.getSpecification()).trim();
+		String inpath = "hamster_3d.sdf";
+    String outpath = "hamster_desc.csv";
+    getDescriptorCSV(inpath,outpath,"");
 	}
 
-	//public static void main(String args[]) throws java.io.IOException 
-	//{
-	//	String inpath = "hamster_3d.sdf";
-  //  String outpath = "hamster_desc.csv";
-  //  getDescriptorCSV(inpath,outpath,"");
-	//}
 
- public static void getDescriptorCSV(String sdfInputPath, String csvOutputPath, String descNamesStr) throws java.io.IOException  {
+ /**
+  * Calculate descriptors. Omits IPMolecularLearningDescriptor
+  *
+  * @param string path to SDF input file
+  * @param string path to CSV output file
+  * @param string comma-seperated list of descriptor names (if empty, all descriptors will be calculated)
+  */
+ public static void getDescriptorCSV(String sdfInputPath, String csvOutputPath, String descNamesStr) throws java.io.IOException  
+ {
     List<IMolecule> mols = readMolecules(sdfInputPath);
 		System.err.println("read " + mols.size() + " compounds");
 		List<IDescriptor> descriptors = ENGINE.getDescriptorInstances();
@@ -110,24 +122,45 @@ public class ApplyCDKDescriptors
  }
 
 
+ /**
+  * Get SMILES code for a molecule
+  *
+  * @param IMolecule The molecule
+  * @return string The SMILES code
+  */
  public static String getSmiles(IMolecule m)
-  {
-    Map<Object, Object> props = m.getProperties();
-    for (Object key : props.keySet()) {
-      if (key.toString().equals("STRUCTURE_SMILES") || key.toString().equals("SMILES"))
-        return props.get(key).toString();
-    }
-    SmilesGenerator g = new SmilesGenerator();
-    return g.createSMILES(m);
-  }
+ {
+   Map<Object, Object> props = m.getProperties();
+   for (Object key : props.keySet()) {
+     if (key.toString().equals("STRUCTURE_SMILES") || key.toString().equals("SMILES"))
+       return props.get(key).toString();
+   }
+   SmilesGenerator g = new SmilesGenerator();
+   return g.createSMILES(m);
+ }
+
 
+ /**
+  * Compute descriptor values, convert to list
+  *
+  * @param List<IMolecule> The molecules
+  * @param IMoleculeDescriptor The descriptor
+  * @return List<Double[]> The descriptor values as list
+  */
 	public static List<Double[]> computeLists(List<IMolecule> mols, IMolecularDescriptor desc )
 	{
-    //System.out.println("computing descriptor " + getName(desc));
+    System.out.println("computing descriptor " + getName(desc));
     List<Double[]> values = computeDescriptors(mols, (IMolecularDescriptor) desc);
     return values;
 	}
 
+
+ /**
+  * Read in molecules, using any supported format
+  *
+  * @param string The input file
+  * @return Vector<IMolecule> The molecules
+  */
 	public static List<IMolecule> readMolecules(String filepath)
 	{
 		Vector<IMolecule> mols = new Vector<IMolecule>();
@@ -179,6 +212,14 @@ public class ApplyCDKDescriptors
 		return mols;
 	}
 
+
+ /**
+  * Compute descriptors
+  *
+  * @param List<IMolecule> The molecules
+  * @param IMoleculeDescriptor The descriptor
+  * @return List<Double[]> The results as list
+  */
 	public static List<Double[]> computeDescriptors(List<IMolecule> mols, IMolecularDescriptor descriptor)
 	{
 		List<Double[]> vv = new ArrayList<Double[]>();
@@ -227,4 +268,35 @@ public class ApplyCDKDescriptors
 
 		return vv;
 	}
+
+
+ /**
+  * Get length of result for a given descriptor
+  *
+  * @param IMolecularDescriptor The descriptor
+  * @return int The length
+  */
+	private static int getSize(IMolecularDescriptor descriptor) 
+  {
+		IDescriptorResult r = descriptor.getDescriptorResultType();
+		if (r instanceof DoubleArrayResultType)
+			return ((DoubleArrayResultType) r).length();
+		else if (r instanceof IntegerArrayResultType)
+			return ((IntegerArrayResultType) r).length();
+		else
+			return 1;
+	}
+
+
+ /**
+  * Get name for a given descriptor
+  *
+  * @param IMolecularDescriptor The descriptor
+  */
+	private static String getName(IDescriptor descriptor) 
+  {
+		return ENGINE.getDictionaryTitle(descriptor.getSpecification()).trim();
+	}
+
+
 }
diff --git a/pc.rb b/pc.rb
index 2ef95bb..14a1e76 100644
--- a/pc.rb
+++ b/pc.rb
@@ -79,8 +79,11 @@ post '/pc/AllDescriptors' do
 
   task = OpenTox::Task.create("PC descriptor calculation for dataset ", @uri) do |task|
     Rjb.load(nil,["-Xmx64m"]) # start vm
-    byteArray = Rjb::import('java.io.ByteArrayOutputStream'); printStream = Rjb::import('java.io.PrintStream'); 
-    out = byteArray.new() ; Rjb::import('java.lang.System').out = printStream.new(out) # joelib is too verbose
+    byteArray = Rjb::import('java.io.ByteArrayOutputStream')
+    printStream = Rjb::import('java.io.PrintStream')
+    out = byteArray.new() 
+    Rjb::import('java.lang.System').out = printStream.new(out) # suppress java output
+    Rjb::import('java.lang.System').err = printStream.new(out) # suppress java output
     s = Rjb::import('JoelibFc') # import main class
     t = Rjb::import('ApplyCDKDescriptors')