[#81] documentation: added java docs and resolved lint wanrings

Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysis.java

-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package cz.fidentis.analyst.procrustes;
 
+import cz.fidentis.analyst.feature.FeaturePoint;
+import cz.fidentis.analyst.procrustes.exceptions.ProcrustesAnalysisException;
+import cz.fidentis.analyst.procrustes.utils.ProcrustesAnalysisUtils;
+import java.util.List;
+
 /**
  *
- * @author kubok
+ * @author Jakub Kolman
  */
 public class ProcrustesAnalysis {
-    
-    public ProcrustesAnalysis() {
+
+    private final List<FeaturePoint> orderedFpList1;
+    private final List<FeaturePoint> orderedFpList2;
+
+    /**
+     * 
+     * @param fpList1
+     * @param fpList2
+     * @throws ProcrustesAnalysisException 
+     */
+    public ProcrustesAnalysis(List<FeaturePoint> fpList1, List<FeaturePoint> fpList2) throws ProcrustesAnalysisException {
+        if (fpList1.size() != fpList2.size()) {
+            throw new ProcrustesAnalysisException("Lists of feature points do not have the same size");
+        }
+        orderedFpList1 = ProcrustesAnalysisUtils.sortByFeaturePointType(fpList1);
+        orderedFpList2 = ProcrustesAnalysisUtils.sortByFeaturePointType(fpList2);
+
+        if (!ProcrustesAnalysisUtils.checkfeaturePointsType(orderedFpList1, orderedFpList2)) {
+            throw new ProcrustesAnalysisException("Lists of feature points do not have the same feature point types");
+        }
+    }
+
+    /**
+     * Calculate scaling ratio of how much the appropriate object corresponding to the second feature
+     * point list has to be scale up or shrunk. 
+     * 
+     * If returned ratioValue is greater 1 then it means that the second object should be scaled up ratioValue times.
+     * If returned ratioValue is smaller 1 than the second object should be shrunk.
+     * 
+     * @return ratioValue
+     */
+    private double calculateScalingValue() {
+        double[] distancesOfList1 = ProcrustesAnalysisUtils.calculateMeanDistancesFromOrigin(orderedFpList1);
+        double[] distancesOfList2 = ProcrustesAnalysisUtils.calculateMeanDistancesFromOrigin(orderedFpList2);
+
+        double[] ratioArray = new double[distancesOfList1.length];
+        double ratioValue = 0;
+
+        for (int i = 0; i < distancesOfList1.length; i++) {
+            ratioArray[i] += distancesOfList1[i] / distancesOfList2[i];
+        }
         
+        for (double ratio: ratioArray) {
+            ratioValue += ratio;
+        }
+
+        return ratioValue / distancesOfList1.length;
     }
-    
+
 }

MeshModel/src/main/java/cz/fidentis/analyst/feature/FeaturePoint.java

 package cz.fidentis.analyst.feature;
 
 import java.io.Serializable;
+import java.util.Objects;
 import javax.vecmath.Point3d;
 
 /**
  *
- * @author Jakub Kolman 
+ * @author Jakub Kolman
  */
 public class FeaturePoint implements Serializable {
 
@@ -14,8 +15,8 @@ public class FeaturePoint implements Serializable {
 
     /**
      * Constructor.
-     * 
-     * @param x Location x 
+     *
+     * @param x Location x
      * @param y Location y
      * @param z Location z
      * @param featurePointType Original type
@@ -24,11 +25,11 @@ public class FeaturePoint implements Serializable {
         this.position = new Point3d(x, y, z);
         this.featurePointType = featurePointType;
     }
-    
+
     public Point3d getPosition() {
         return position;
     }
-    
+
     public double getX() {
         return position.x;
     }
@@ -44,5 +45,42 @@ public class FeaturePoint implements Serializable {
     public FeaturePointType getFeaturePointType() {
         return featurePointType;
     }
-    
+
+    @Override
+    public boolean equals(Object o) {
+        // self check
+        if (this == o) {
+            return true;
+        }
+        // null check
+        if (o == null) {
+            return false;
+        }
+        // type check and cast
+        if (getClass() != o.getClass()) {
+            return false;
+        }
+        FeaturePoint fp = (FeaturePoint) o;
+        // field comparison
+        return Objects.equals(position.x, fp.position.x)
+                && Objects.equals(position.y, fp.position.y)
+                && Objects.equals(position.z, fp.position.z)
+                && Objects.equals(featurePointType.getCode(), fp.featurePointType.getCode())
+                && Objects.equals(featurePointType.getInfo(), fp.featurePointType.getInfo())
+                && Objects.equals(featurePointType.getName(), fp.featurePointType.getName())
+                && Objects.equals(featurePointType.getType(), fp.featurePointType.getType());
+    }
+
+    /**
+     * generated hash code function
+     * 
+     * @return 
+     */
+    @Override
+    public int hashCode() {
+        int hash = 5;
+        hash = 23 * hash + Objects.hashCode(this.position);
+        hash = 23 * hash + Objects.hashCode(this.featurePointType);
+        return hash;
+    }
 }

MeshModel/src/main/java/cz/fidentis/analyst/feature/FeaturePointType.java

@@ -13,6 +13,14 @@ public class FeaturePointType implements Serializable {
     private final String info;
     private final String code;
 
+    /**
+     * Constructor
+     * 
+     * @param type
+     * @param name
+     * @param info
+     * @param code 
+     */
     public FeaturePointType(int type, String name, String info, String code) {
         this.type = type;
         this.name = name;

MeshModel/src/main/java/cz/fidentis/analyst/feature/provider/FeaturePointTypeProvider.java

@@ -10,7 +10,7 @@ import java.util.Map;
  * 
  * @author Jakub Kolman
  */
-public class FeaturePointTypeProvider {
+public final class FeaturePointTypeProvider {
 
     private final Map<Integer, FeaturePointType> featurePointTypesById;
     private final Map<String, FeaturePointType> featurePointTypesByCode;
@@ -21,7 +21,8 @@ public class FeaturePointTypeProvider {
      */
     private static class InstanceHolder {
 
-        public static FeaturePointTypeProvider instance = new FeaturePointTypeProvider();
+        public static final FeaturePointTypeProvider INSTANCE = new FeaturePointTypeProvider();
+    
     }
 
     /**
@@ -39,7 +40,7 @@ public class FeaturePointTypeProvider {
      * @return
      */
     public static FeaturePointTypeProvider getInstance() {
-        return InstanceHolder.instance;
+        return InstanceHolder.INSTANCE;
     }
 
     /**

MeshModel/src/main/java/cz/fidentis/analyst/feature/utils/FileResourcesUtils.java

 package cz.fidentis.analyst.feature.utils;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.util.List;
 
-
+/**
+ * Deprecated class
+ * 
+ * @author Jakub Kolman
+ */
 public class FileResourcesUtils {
 
-
+    /**
+     * main method
+     * 
+     * @param args
+     * @throws IOException
+     * @throws URISyntaxException 
+     */
     public static void main(String[] args) throws IOException, URISyntaxException {
 
         FileResourcesUtils app = new FileResourcesUtils();
@@ -28,8 +44,13 @@ public class FileResourcesUtils {
 
     }
 
-    // get a file from the resources folder
-    // works everywhere, IDEA, unit test and JAR file.
+    /**
+     * get a file from the resources folder
+     * works everywhere, IDEA, unit test and JAR file.
+     * 
+     * @param fileName
+     * @return 
+     */
     public InputStream getFileFromResourceAsStream(String fileName) {
 
         // The class loader that loaded the class
@@ -45,12 +66,14 @@ public class FileResourcesUtils {
 
     }
 
-    /*
-        The resource URL is not working in the JAR
-        If we try to access a file that is inside a JAR,
-        It throws NoSuchFileException (linux), InvalidPathException (Windows)
-
-        Resource URL Sample: file:java-io.jar!/json/file1.json
+    /**
+     * The resource URL is not working in the JAR If we try to access a file
+     * that is inside a JAR, It throws NoSuchFileException (linux),
+     * InvalidPathException (Windows)
+     *
+     * Resource URL Sample: file:java-io.jar!/json/file1.json
+     *
+     * @param fileName
      */
     private File getFileFromResource(String fileName) throws URISyntaxException {
 
@@ -67,17 +90,35 @@ public class FileResourcesUtils {
 
     }
 
-    // get a file from the resources folder
-    // works everywhere, IDEA, unit test and JAR file.
+    /**
+     * get a file from the resources folder works everywhere, IDEA, unit test
+     * and JAR file.
+     *
+     * @param path
+     * @param fileName
+     * @return
+     * @throws FileNotFoundException
+     */
     public InputStream getFileAsStream(String path, String fileName) throws FileNotFoundException {
         return new FileInputStream(getFile(path, fileName));
     }
 
+    /**
+     * get File from path, file name
+     *
+     * @param path
+     * @param fileName
+     * @return
+     */
     private File getFile(String path, String fileName) {
         return new File(path, fileName);
     }
 
-    // print input stream
+    /**
+     * print input stream
+     *
+     * @param is
+     */
     private static void printInputStream(InputStream is) {
         try (InputStreamReader streamReader
                 = new InputStreamReader(is, StandardCharsets.UTF_8);