Bug after new checkout fixed

Jlibiada.iml

@@ -52,6 +52,10 @@
     <orderEntry type="library" name="Rapidminer" level="project" />
     <orderEntry type="library" name="BioJava" level="project" />
     <orderEntry type="library" name="Bio" level="project" />
+    <orderEntry type="library" name="BioJava" level="project" />
+    <orderEntry type="library" name="JasperReports" level="project" />
+    <orderEntry type="library" name="MySQL" level="project" />
+    <orderEntry type="library" name="POI" level="project" />
   </component>
 </module>
 

src/libiada/FastChainAlgorithms/FastChain/Calculators/FastAverageGeometryInterval.java

@@ -2,7 +2,7 @@
 
 import libiada.FastChainAlgorithms.FastChain.FastChain;
 import libiada.FastChainAlgorithms.FastChain.FastUniformChain;
-import libiada.FastChainAlgorithms.FastChain.Interfaces.IFastCalculator;
+import libiada.FastChainAlgorithms.FastChain.Interfaces.FastCalculatorBase;
 import libiada.IntervalAnalysis.LinkUp;
 
 /**
@@ -11,7 +11,7 @@
  * Date: 29.07.11
  * Time: 19:01
  */
-public class FastAverageGeometryInterval implements IFastCalculator {
+public class FastAverageGeometryInterval extends FastCalculatorBase {
     @Override
     public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
         double V = FastCalculatorFactory.getVolume().getValue(chain, linkUp);
@@ -21,13 +21,24 @@ public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
 
     @Override
     public double getValue(FastUniformChain chain, LinkUp linkUp) throws Exception {
+        super.getValue(chain, linkUp);
         double V = FastCalculatorFactory.getVolume().getValue(chain, linkUp);
         double n = FastCalculatorFactory.getEventCount().getValue(chain, linkUp);
         return Math.pow(V, 1 / n);
     }
 
     @Override
     public String getName() {
-        return "gelta_g";
+        return "gelta_g" + super.getName();
+    }
+
+    @Override
+    public String getType() {
+        return "double";
+    }
+
+    @Override
+    public String getGroup() {
+        return "Building characteristic";
     }
 }

src/libiada/FastChainAlgorithms/FastChain/Calculators/FastAverageRemoteness.java

@@ -2,7 +2,7 @@
 
 import libiada.FastChainAlgorithms.FastChain.FastChain;
 import libiada.FastChainAlgorithms.FastChain.FastUniformChain;
-import libiada.FastChainAlgorithms.FastChain.Interfaces.IFastCalculator;
+import libiada.FastChainAlgorithms.FastChain.Interfaces.FastCalculatorBase;
 import libiada.IntervalAnalysis.LinkUp;
 
 /**
@@ -11,7 +11,7 @@
  * Date: 29.07.11
  * Time: 19:33
  */
-public class FastAverageRemoteness implements IFastCalculator {
+public class FastAverageRemoteness extends FastCalculatorBase {
     @Override
     public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
         double n = FastCalculatorFactory.getEventCount().getValue(chain, linkUp);
@@ -21,13 +21,24 @@ public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
 
     @Override
     public double getValue(FastUniformChain chain, LinkUp linkUp) throws Exception {
+        super.getValue(chain, linkUp);
         double n = FastCalculatorFactory.getEventCount().getValue(chain, linkUp);
         double gamaut = FastCalculatorFactory.getGamaut().getValue(chain, linkUp);
         return gamaut / n;
     }
 
     @Override
     public String getName() {
-        return "g";
+        return "g" + super.getName();
+    }
+
+    @Override
+    public String getType() {
+        return "double";
+    }
+
+    @Override
+    public String getGroup() {
+        return "Building characteristic";
     }
 }

src/libiada/FastChainAlgorithms/FastChain/Calculators/FastCalculatorFactory.java

@@ -1,6 +1,6 @@
 package libiada.FastChainAlgorithms.FastChain.Calculators;
 
-import libiada.FastChainAlgorithms.FastChain.Interfaces.IFastCalculator;
+import libiada.FastChainAlgorithms.FastChain.Interfaces.FastCalculatorBase;
 
 import java.util.HashSet;
 
@@ -11,47 +11,67 @@
  * Time: 0:46
  */
 public class FastCalculatorFactory {
-    public static IFastCalculator getVolume() {
+    public static FastCalculatorBase getVolume() {
         return new FastVolume();
     }
 
-    public static IFastCalculator getHentropy() {
+    public static FastCalculatorBase getHentropy() {
         return new FastHentropy();
     }
 
-    public static IFastCalculator getPropability() {
+    public static FastCalculatorBase getPropability() {
         return new FastPropability();
     }
 
-    public static IFastCalculator getEventCount() {
+    public static FastCalculatorBase getEventCount() {
         return new FastIntervalsCount();
     }
 
-    public static IFastCalculator getGamaut() {
+    public static FastCalculatorBase getGamaut() {
         return new FastGamaut();
     }
 
-    public static IFastCalculator getAverageRemoteness() {
+    public static FastCalculatorBase getAverageRemoteness() {
         return new FastAverageRemoteness();
     }
 
-    public static IFastCalculator getRegularity() {
+    public static FastCalculatorBase getRegularity() {
         return new FastRegularity();
     }
 
-    public static IFastCalculator getLength() {
+    public static FastCalculatorBase getLength() {
         return new FastLength();
     }
 
-    public static IFastCalculator getPositionedPropability(String event, HashSet<Integer> poses, int period) {
+    public static FastCalculatorBase getPositionedPropability(String event, HashSet<Integer> poses, int period) {
         return new FastPositionedPropability(event, poses, period);
     }
 
-    public static IFastCalculator getFastShepherd() {
+    public static FastCalculatorBase getFastShepherd() {
         return new FastShepherd();
     }
 
-    public static IFastCalculator getPositionedEventCount(String event, HashSet<Integer> poses, int period) {
+    public static FastCalculatorBase getPositionedEventCount(String event, HashSet<Integer> poses, int period) {
         return new FastPositionedEventCount(event, poses, period);
     }
+
+    public static FastCalculatorBase getFastTramontanoMacchiato() {
+        return new FastTramontanoMacchiato();
+    }
+
+    public static FastCalculatorBase getGeometryInterval() {
+        return new FastAverageGeometryInterval();
+    }
+
+    public static FastCalculatorBase getBinaryAverageGeomertyInterval(String sym1, String sym2) {
+        return new BinaryFastAverageGeometryInterval(sym1, sym2);
+    }
+
+    public static FastCalculatorBase getBinaryAverageRemoteness(String sym1, String sym2) {
+        return new BinaryFastAverageRemoteness(sym1, sym2);
+    }
+
+    public static FastCalculatorBase getPositionedAverageRemoteness(String event, HashSet<Integer> poses, int period) {
+        return new FastPositionedAverageRemoteness(event, poses, period);
+    }
 }

src/libiada/FastChainAlgorithms/FastChain/Calculators/FastGamaut.java

@@ -2,7 +2,7 @@
 
 import libiada.FastChainAlgorithms.FastChain.FastChain;
 import libiada.FastChainAlgorithms.FastChain.FastUniformChain;
-import libiada.FastChainAlgorithms.FastChain.Interfaces.IFastCalculator;
+import libiada.FastChainAlgorithms.FastChain.Interfaces.FastCalculatorBase;
 import libiada.IntervalAnalysis.LinkUp;
 
 import java.util.Map;
@@ -13,7 +13,7 @@
  * Date: 29.07.11
  * Time: 19:51
  */
-public class FastGamaut implements IFastCalculator {
+public class FastGamaut extends FastCalculatorBase {
     @Override
     public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
         double value = 0;
@@ -25,6 +25,7 @@ public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
 
     @Override
     public double getValue(FastUniformChain chain, LinkUp linkUp) throws Exception {
+        super.getValue(chain, linkUp);
         double result = 0;
         for (Map.Entry<Integer, Integer> entry : chain.getCommonIntervals().entrySet()) {
             result += entry.getValue() * Math.log10(entry.getKey()) / Math.log10(2);
@@ -59,6 +60,16 @@ public double getValue(FastUniformChain chain, LinkUp linkUp) throws Exception {
 
     @Override
     public String getName() {
-        return "G";
+        return "G" + super.getName();
+    }
+
+    @Override
+    public String getType() {
+        return "double";
+    }
+
+    @Override
+    public String getGroup() {
+        return "Building characteristic";
     }
 }

src/libiada/FastChainAlgorithms/FastChain/Calculators/FastHentropy.java

@@ -2,7 +2,7 @@
 
 import libiada.FastChainAlgorithms.FastChain.FastChain;
 import libiada.FastChainAlgorithms.FastChain.FastUniformChain;
-import libiada.FastChainAlgorithms.FastChain.Interfaces.IFastCalculator;
+import libiada.FastChainAlgorithms.FastChain.Interfaces.FastCalculatorBase;
 import libiada.IntervalAnalysis.LinkUp;
 
 /**
@@ -11,24 +11,36 @@
  * Date: 29.07.11
  * Time: 2:46
  */
-public class FastHentropy implements IFastCalculator {
+public class FastHentropy extends FastCalculatorBase {
     @Override
     public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
         double result = 0;
         for (int i = 0; i < chain.alphabetPower(); i++) {
-            result -= getValue(chain.getFastUniformChain(i), linkUp);
+            result += getValue(chain.getFastUniformChain(i), linkUp);
         }
+        event = null;
         return result;
     }
 
     @Override
     public double getValue(FastUniformChain chain, LinkUp linkUp) throws Exception {
+        super.getValue(chain, linkUp);
         double p = FastCalculatorFactory.getPropability().getValue(chain, linkUp);
-        return p * (Math.log10(p) / Math.log10(2));
+        return -p * (Math.log10(p) / Math.log10(2));
     }
 
     @Override
     public String getName() {
-        return "H";
+        return "H" + super.getName();
+    }
+
+    @Override
+    public String getType() {
+        return "double";
+    }
+
+    @Override
+    public String getGroup() {
+        return "Propability";
     }
 }

src/libiada/FastChainAlgorithms/FastChain/Calculators/FastIntervalsCount.java

@@ -1,9 +1,9 @@
 package libiada.FastChainAlgorithms.FastChain.Calculators;
 
 import libiada.FastChainAlgorithms.FastChain.FastChain;
+import libiada.FastChainAlgorithms.FastChain.FastIntervalsChain;
 import libiada.FastChainAlgorithms.FastChain.FastUniformChain;
-import libiada.FastChainAlgorithms.FastChain.Interfaces.IFastCalculator;
-import libiada.FastChainAlgorithms.FastChain.UtilClasses.FastIntervalsChain;
+import libiada.FastChainAlgorithms.FastChain.Interfaces.FastCalculatorBase;
 import libiada.IntervalAnalysis.LinkUp;
 
 /**
@@ -12,20 +12,32 @@
  * Date: 29.07.11
  * Time: 19:06
  */
-public class FastIntervalsCount implements IFastCalculator {
+public class FastIntervalsCount extends FastCalculatorBase {
     @Override
     public double getValue(FastChain chain, LinkUp linkUp) throws Exception {
         return getCommonValue(chain, linkUp);
     }
 
     @Override
     public double getValue(FastUniformChain chain, LinkUp linkUp) throws Exception {
+        super.getValue(chain, linkUp);
+        event = chain.getEvent();
         return getCommonValue(chain, linkUp);
     }
 
     @Override
     public String getName() {
-        return "n";
+        return "Intervals count" + super.getName();
+    }
+
+    @Override
+    public String getType() {
+        return "int";
+    }
+
+    @Override
+    public String getGroup() {
+        return "Building characteristic";
     }
 
     private double getCommonValue(FastIntervalsChain chain, LinkUp linkUp) throws Exception {