X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Futil%2FBasicDescriptiveStatistics.java;h=057b388dfce1b8d59f755d66377aa7409a9db4cd;hb=256204975bca8c5e5c00a9728caff30c52bd65cc;hp=4d73ffb9675fdcafb6d4fd9a1b7c3785ed8ea370;hpb=321da767c9d9eb4e5f40f656e16005ff9244fd4d;p=jalview.git

diff --git a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
index 4d73ffb..057b388 100644
--- a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
+++ b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
@@ -23,7 +23,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.util;
 
@@ -45,9 +45,11 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         init();
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#addValue(double)
-     */
+    public BasicDescriptiveStatistics( final String desc ) {
+        init();
+        setDescription( desc );
+    }
+
     @Override
     public void addValue( final double d ) {
         _recalc_sigma = true;
@@ -61,18 +63,12 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         }
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#arithmeticMean()
-     */
     @Override
     public double arithmeticMean() {
         validate();
         return getSum() / getN();
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#asSummary()
-     */
     @Override
     public String asSummary() {
         if ( getN() > 1 ) {
@@ -84,18 +80,17 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         }
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#coefficientOfVariation()
-     */
     @Override
     public double coefficientOfVariation() {
         validate();
         return ( sampleStandardDeviation() / arithmeticMean() );
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getDataAsDoubleArray()
-     */
+    @Override
+    public List<Double> getData() {
+        return _data;
+    }
+
     @Override
     public double[] getDataAsDoubleArray() {
         validate();
@@ -106,74 +101,48 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return data_array;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getMax()
-     */
+    @Override
+    public String getDescription() {
+        return _desc;
+    }
+
     @Override
     public double getMax() {
         validate();
         return _max;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getMin()
-     */
     @Override
     public double getMin() {
         validate();
         return _min;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getN()
-     */
     @Override
     public int getN() {
         return _data.size();
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getSum()
-     */
     @Override
     public double getSum() {
         validate();
         return _sum;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getSummaryAsString()
-     */
     @Override
     public String getSummaryAsString() {
         validate();
         final double mean = arithmeticMean();
         final double sd = sampleStandardDeviation();
-        return "" + mean + ( ( char ) 177 ) + sd + " [" + getMin() + "..." + getMax() + "]";
+        return "" + mean + ( ( char ) 177 ) + sd + " [" + getN() + "] [" + getMin() + "-" + getMax() + "]";
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#getValue(int)
-     */
     @Override
     public double getValue( final int index ) {
         validate();
         return ( ( ( _data.get( index ) ) ).doubleValue() );
     }
 
-    private void init() {
-        _data = new ArrayList<Double>();
-        _sum = 0.0;
-        _min = Double.MAX_VALUE;
-        _max = -Double.MAX_VALUE;
-        _sigma = 0.0;
-        _recalc_sigma = true;
-        _desc = "";
-    }
-
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#median()
-     */
     @Override
     public double median() {
         validate();
@@ -196,18 +165,12 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return median;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#midrange()
-     */
     @Override
     public double midrange() {
         validate();
         return ( _min + _max ) / 2.0;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#pearsonianSkewness()
-     */
     @Override
     public double pearsonianSkewness() {
         validate();
@@ -217,47 +180,37 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return ( ( 3 * ( mean - median ) ) / sd );
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sampleStandardDeviation()
-     */
     @Override
     public double sampleStandardDeviation() {
         return Math.sqrt( sampleVariance() );
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sampleStandardUnit(double)
-     */
     @Override
     public double sampleStandardUnit( final double value ) {
         validate();
         return BasicDescriptiveStatistics.sampleStandardUnit( value, arithmeticMean(), sampleStandardDeviation() );
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sampleVariance()
-     */
     @Override
     public double sampleVariance() {
         validate();
         if ( getN() < 2 ) {
-            throw new ArithmeticException( "attempt to calculate sample variance for less then two values" );
+            return 0;
         }
         return ( sumDeviations() / ( getN() - 1 ) );
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#standardErrorOfMean()
-     */
+    @Override
+    public void setDescription( final String desc ) {
+        _desc = desc;
+    }
+
     @Override
     public double standardErrorOfMean() {
         validate();
         return ( sampleStandardDeviation() / Math.sqrt( getN() ) );
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#sumDeviations()
-     */
     @Override
     public double sumDeviations() {
         validate();
@@ -272,9 +225,6 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return _sigma;
     }
 
-    /* (non-Javadoc)
-     * @see org.forester.util.DescriptiveStatisticsI#toString()
-     */
     @Override
     public String toString() {
         if ( getN() < 1 ) {
@@ -309,6 +259,16 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
         return sb.toString();
     }
 
+    private void init() {
+        _data = new ArrayList<Double>();
+        _sum = 0.0;
+        _min = Double.MAX_VALUE;
+        _max = -Double.MAX_VALUE;
+        _sigma = 0.0;
+        _recalc_sigma = true;
+        _desc = "";
+    }
+
     private void validate() throws ArithmeticException {
         if ( getN() < 1 ) {
             throw new ArithmeticException( "attempt to get a result from empty data set statistics" );
@@ -358,19 +318,4 @@ public class BasicDescriptiveStatistics implements DescriptiveStatistics {
     public static double sampleStandardUnit( final double value, final double mean, final double sd ) {
         return ( value - mean ) / sd;
     }
-
-    @Override
-    public List<Double> getData() {
-        return _data;
-    }
-
-    @Override
-    public void setDescription( final String desc ) {
-        _desc = desc;
-    }
-
-    @Override
-    public String getDescription() {
-        return _desc;
-    }
 }