improved parameter comments, param annotations, cleanup

src/main/groovy/cz/siret/prank/domain/Dataset.groovy

@@ -215,6 +215,10 @@ class Dataset implements Parametrized {
         return getLoader(attributes.get(PARAM_PREDICTION_METHOD), item)
     }
 
+    /**
+     * Get configured instance of prediction loader.
+     * @param method LBS prediction method name
+     */
     private PredictionLoader getLoader(String method, Item item) {
         PredictionLoader res
         switch (method) {

src/main/groovy/cz/siret/prank/domain/labeling/ModelBasedResidueLabeler.groovy

@@ -18,7 +18,7 @@ import static cz.siret.prank.utils.Formatter.format
 import static cz.siret.prank.utils.Formatter.formatNumbers
 
 /**
- * (not intended o be reused with mode proteins)
+ * (not intended to be reused with mode proteins)
  */
 @Slf4j
 @CompileStatic

src/main/groovy/cz/siret/prank/domain/labeling/ResidueBasedPointLabeler.groovy

@@ -8,7 +8,7 @@ import groovy.util.logging.Slf4j
 import org.biojava.nbio.structure.Atom
 
 /**
- *
+ * Labels points according to nearest residue.
  */
 @Slf4j
 @CompileStatic

src/main/groovy/cz/siret/prank/domain/labeling/ResidueLabeling.groovy

@@ -7,7 +7,7 @@ import groovy.transform.CompileStatic
 import javax.annotation.Nullable
 
 /**
- * Holds partiticular assignment of labels to a set of residues.
+ * Holds particular assignment of labels to a set of residues.
  */
 @CompileStatic
 class ResidueLabeling<L>  {
@@ -15,7 +15,7 @@ class ResidueLabeling<L>  {
     private List<LabeledResidue<L>> labeledResidues
     private Map<Residue.Key, LabeledResidue<L>> labeledMap
 
-    ResidueLabeling(List<LabeledResidue> labeledResidues) {
+    ResidueLabeling(List<LabeledResidue<L>> labeledResidues) {
         this.labeledResidues = labeledResidues
         this.labeledMap = Maps.uniqueIndex(labeledResidues, { it.residue.key })
     }

src/main/groovy/cz/siret/prank/domain/labeling/ResidueLabelings.groovy

@@ -23,7 +23,7 @@ import static cz.siret.prank.utils.Futils.mkdirs
 import static cz.siret.prank.utils.Futils.writeFile
 
 /**
- * Logic for calculating residue lebalings during P2Rank prediction
+ * Logic for calculating residue labelings during P2Rank prediction
  */
 @Slf4j
 class ResidueLabelings implements Parametrized {

src/main/groovy/cz/siret/prank/features/PrankFeatureExtractor.groovy

@@ -37,15 +37,9 @@ class PrankFeatureExtractor extends FeatureExtractor<PrankFeatureVector> impleme
     List<String> atomTableFeatures
     List<String> residueTableFeatures
 
-
     // tied to a protein
     private PointSampler pocketPointSampler
 
-    /**
-     * if set to true extractorFactory will use zero vectors for unknown residues
-     * otherwise throws exception (so the whole pocket can be ignored)
-     */
-    private boolean MASK_UNKNOWN_RESIDUES = params.mask_unknown_residues
     private double NEIGH_CUTOFF_DIST = params.neighbourhood_radius
     private boolean DO_SMOOTH_REPRESENTATION = params.smooth_representation
     private double SMOOTHING_CUTOFF_DIST = params.smoothing_radius
@@ -112,7 +106,6 @@ class PrankFeatureExtractor extends FeatureExtractor<PrankFeatureVector> impleme
         return res
     }
 
-
     @Override
     void prepareProteinPrototypeForPockets() {
         pocketPointSampler = PointSampler.create(protein, trainingExtractor)
@@ -143,7 +136,6 @@ class PrankFeatureExtractor extends FeatureExtractor<PrankFeatureVector> impleme
         this.protein = protein
         this.pocket = pocket
 
-        this.MASK_UNKNOWN_RESIDUES = proteinPrototype.MASK_UNKNOWN_RESIDUES
         this.headerAdditionalFeatures = proteinPrototype.headerAdditionalFeatures
         this.pocketPointSampler    = proteinPrototype.pocketPointSampler
         this.extraFeaturesHeader   = proteinPrototype.extraFeaturesHeader
@@ -156,10 +148,6 @@ class PrankFeatureExtractor extends FeatureExtractor<PrankFeatureVector> impleme
         this.surfaceLayerAtoms = proteinPrototype.surfaceLayerAtoms
         this.properties = proteinPrototype.properties
         this.smoothRepresentations = proteinPrototype.smoothRepresentations
-
-
-
-
     }
 
     @Override

src/main/groovy/cz/siret/prank/features/api/FeatureRegistry.groovy

@@ -1,5 +1,9 @@
 package cz.siret.prank.features.api
 
+
+import cz.siret.prank.features.api.FeatureCalculator
+import cz.siret.prank.features.api.ResidueToAtomicFeatWrapper
+import cz.siret.prank.features.api.ResidueToSasFeatWrapper
 import cz.siret.prank.features.implementation.AAIndexFeature
 import cz.siret.prank.features.implementation.Asa2Feature
 import cz.siret.prank.features.implementation.AsaFeature

src/main/groovy/cz/siret/prank/features/api/ResidueToAtomicFeatWrapper.groovy

@@ -5,7 +5,7 @@ import cz.siret.prank.domain.Residue
 import org.biojava.nbio.structure.Atom
 
 /**
- *
+ * Maps a residue features to atom feature
  */
 class ResidueToAtomicFeatWrapper extends AtomFeatureCalculator {
 

src/main/groovy/cz/siret/prank/features/api/ResidueToSasFeatWrapper.groovy

@@ -10,7 +10,7 @@ import groovy.transform.CompileStatic
 import org.biojava.nbio.structure.Atom
 
 /**
- * Mapping Closest Residue to SAS
+ * Mapping Closest Residue to SAS point
  */
 @CompileStatic
 class ResidueToSasFeatWrapper extends SasFeatureCalculator {

src/main/groovy/cz/siret/prank/features/api/SasFeatureCalculationContext.groovy

@@ -6,7 +6,7 @@ import cz.siret.prank.geom.Atoms
 import groovy.transform.CompileStatic
 
 /**
- * Context for calculation of SAS feature.
+ * Context for calculation of a SAS feature.
  */
 @CompileStatic
 class SasFeatureCalculationContext {

src/main/groovy/cz/siret/prank/program/params/ModelParam.groovy

@@ -0,0 +1,13 @@
+package cz.siret.prank.program.params
+
+/**
+ * Marks parameters of the prediction model (including feature extraction params) i.e. algorithm params.
+ * The notion of "model" here is seen wholesomely as a pocket prediction model = the whole algorithm, which includes feature extraction, classification and aggregation to binding sites.
+ *
+ * These are the parameters that must be the same in training and prediction phase.
+ *
+ * Currently annotation serves only documentation purposes.
+ */
+@interface ModelParam {
+
+}

src/main/groovy/cz/siret/prank/program/params/RuntimeParam.groovy

@@ -0,0 +1,11 @@
+package cz.siret.prank.program.params
+
+/**
+ * Marks parameters of the program execution (training or prediction phase)
+ * i.e. parameters not directly related to the prediction algorithm itself.
+ *
+ * Currently annotation serves only documentation purposes.
+ */
+@interface RuntimeParam {
+
+}

src/main/groovy/cz/siret/prank/utils/CutoffAtomsCallLog.java

@@ -7,7 +7,7 @@ import java.util.List;
 import java.util.stream.Collectors;
 
 /**
- *
+ * Utility for debugging and profiling cutoffAtoms methods
  */
 public class CutoffAtomsCallLog {
 

src/main/groovy/cz/siret/prank/utils/ProcessRunner.groovy

@@ -6,7 +6,7 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 
 /**
- *
+ * Encapsulates system (command line) process
  */
 @Slf4j
 @CompileStatic