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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
util
/
BasicDescriptiveStatistics.java
diff --git
a/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
b/forester/java/src/org/forester/util/BasicDescriptiveStatistics.java
index
538f6a1
..
f3dfb80
100644
(file)
--- 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
// 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;
package org.forester.util;
@@
-50,9
+50,6
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
setDescription( desc );
}
setDescription( desc );
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#addValue(double)
- */
@Override
public void addValue( final double d ) {
_recalc_sigma = true;
@Override
public void addValue( final double d ) {
_recalc_sigma = true;
@@
-66,18
+63,12
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
}
}
}
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#arithmeticMean()
- */
@Override
public double arithmeticMean() {
validate();
return getSum() / getN();
}
@Override
public double arithmeticMean() {
validate();
return getSum() / getN();
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#asSummary()
- */
@Override
public String asSummary() {
if ( getN() > 1 ) {
@Override
public String asSummary() {
if ( getN() > 1 ) {
@@
-89,18
+80,17
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
}
}
}
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#coefficientOfVariation()
- */
@Override
public double coefficientOfVariation() {
validate();
return ( sampleStandardDeviation() / arithmeticMean() );
}
@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();
@Override
public double[] getDataAsDoubleArray() {
validate();
@@
-111,70
+101,48
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
return data_array;
}
return data_array;
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#getMax()
- */
+ @Override
+ public String getDescription() {
+ return _desc;
+ }
+
@Override
public double getMax() {
validate();
return _max;
}
@Override
public double getMax() {
validate();
return _max;
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#getMin()
- */
@Override
public double getMin() {
validate();
return _min;
}
@Override
public double getMin() {
validate();
return _min;
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#getN()
- */
@Override
public int getN() {
return _data.size();
}
@Override
public int getN() {
return _data.size();
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#getSum()
- */
@Override
public double getSum() {
validate();
return _sum;
}
@Override
public double getSum() {
validate();
return _sum;
}
-
@Override
public String getSummaryAsString() {
validate();
final double mean = arithmeticMean();
final double sd = sampleStandardDeviation();
@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() + "]";
}
}
-
@Override
public double getValue( final int index ) {
validate();
return ( ( ( _data.get( index ) ) ).doubleValue() );
}
@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();
@Override
public double median() {
validate();
@@
-197,18
+165,12
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
return median;
}
return median;
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#midrange()
- */
@Override
public double midrange() {
validate();
return ( _min + _max ) / 2.0;
}
@Override
public double midrange() {
validate();
return ( _min + _max ) / 2.0;
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#pearsonianSkewness()
- */
@Override
public double pearsonianSkewness() {
validate();
@Override
public double pearsonianSkewness() {
validate();
@@
-218,47
+180,37
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
return ( ( 3 * ( mean - median ) ) / sd );
}
return ( ( 3 * ( mean - median ) ) / sd );
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#sampleStandardDeviation()
- */
@Override
public double sampleStandardDeviation() {
return Math.sqrt( sampleVariance() );
}
@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() );
}
@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 ) {
@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 ) );
}
}
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() ) );
}
@Override
public double standardErrorOfMean() {
validate();
return ( sampleStandardDeviation() / Math.sqrt( getN() ) );
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#sumDeviations()
- */
@Override
public double sumDeviations() {
validate();
@Override
public double sumDeviations() {
validate();
@@
-273,9
+225,6
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
return _sigma;
}
return _sigma;
}
- /* (non-Javadoc)
- * @see org.forester.util.DescriptiveStatisticsI#toString()
- */
@Override
public String toString() {
if ( getN() < 1 ) {
@Override
public String toString() {
if ( getN() < 1 ) {
@@
-310,6
+259,16
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
return sb.toString();
}
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" );
private void validate() throws ArithmeticException {
if ( getN() < 1 ) {
throw new ArithmeticException( "attempt to get a result from empty data set statistics" );
@@
-347,7
+306,7
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
* Computes the sample standard unit (z-score). Used to compute 'value' in
* terms of standard units. Note that 'value', 'mean' and 'sd' must be all
* from the same sample data.
* Computes the sample standard unit (z-score). Used to compute 'value' in
* terms of standard units. Note that 'value', 'mean' and 'sd' must be all
* from the same sample data.
- *
+ *
* @param value
* a double in the sample for which
* @param mean
* @param value
* a double in the sample for which
* @param mean
@@
-359,19
+318,4
@@
public class BasicDescriptiveStatistics implements DescriptiveStatistics {
public static double sampleStandardUnit( final double value, final double mean, final double sd ) {
return ( value - mean ) / sd;
}
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;
- }
}
}