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Merged
merged 5 commits into from
Nov 23, 2021
Merged

Release 1.1 #13

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a09c43b
update for next development version
arteymix Oct 22, 2021
dfdb3ed
add method for counting nearly identical values but ignoring NAs
ppavlidis Nov 10, 2021
d091071
update versions for release
arteymix Nov 23, 2021
45b36b1
Fix number parsing and formatting when using different system locale
arteymix Nov 23, 2021
b2bb343
Update Apache POI to 5.1.0
arteymix Nov 23, 2021
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4 changes: 2 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<name>baseCode</name>
<groupId>baseCode</groupId>
<artifactId>baseCode</artifactId>
<version>1.0.32</version>
<version>1.1</version>
<inceptionYear>2003</inceptionYear>
<description>
<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
Expand Down Expand Up @@ -49,7 +49,7 @@
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>5.0.0</version>
<version>5.1.0</version>
</dependency>
<dependency>
<groupId>colt</groupId>
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3 changes: 2 additions & 1 deletion src/ubic/basecode/dataStructure/Link.java
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Expand Up @@ -19,6 +19,7 @@
package ubic.basecode.dataStructure;

import java.text.NumberFormat;
import java.util.Locale;

/**
* Implements comparable, which sorts by the 'x' coordinate and then secondarily by the 'y' coordinate. (This behavior
Expand Down Expand Up @@ -96,7 +97,7 @@ public int hashCode() {
*/
@Override
public String toString() {
return super.toString() + "\t" + NumberFormat.getInstance().format( this.weight );
return super.toString() + "\t" + NumberFormat.getInstance( Locale.ENGLISH ).format( this.weight );
}

}
7 changes: 2 additions & 5 deletions src/ubic/basecode/dataStructure/matrix/DoubleMatrix.java
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Expand Up @@ -18,10 +18,7 @@
*/
package ubic.basecode.dataStructure.matrix;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.*;

import cern.colt.list.DoubleArrayList;
import cern.colt.matrix.DoubleMatrix1D;
Expand Down Expand Up @@ -188,7 +185,7 @@ public final String toString() {
if ( Double.isNaN( value ) ) {
buf.append( "\t" );
} else {
buf.append( "\t" + String.format( "%.4g", value ) );
buf.append( "\t" + String.format( Locale.ENGLISH, "%.4g", value ) );
}
}
buf.append( "\n" );
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8 changes: 2 additions & 6 deletions src/ubic/basecode/io/reader/DoubleMatrixReader.java
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Expand Up @@ -26,11 +26,7 @@
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.text.ParseException;
import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import java.util.*;

import org.apache.commons.lang3.StringUtils;

Expand All @@ -47,7 +43,7 @@
*/
public class DoubleMatrixReader extends AbstractMatrixReader<DoubleMatrix<String, String>, Double> {

private static NumberFormat nf = NumberFormat.getInstance();
private static NumberFormat nf = NumberFormat.getInstance( Locale.ENGLISH );
static {
if ( nf instanceof DecimalFormat ) {
// ( ( DecimalFormat ) nf ).setDecimalSeparatorAlwaysShown( true );
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14 changes: 2 additions & 12 deletions src/ubic/basecode/io/reader/SparseDoubleMatrixReader.java
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Expand Up @@ -22,17 +22,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.*;

import ubic.basecode.dataStructure.matrix.DoubleMatrix;
import ubic.basecode.dataStructure.matrix.SparseDoubleMatrix;
Expand Down Expand Up @@ -179,7 +169,7 @@ public DoubleMatrix<String, String> readJW( InputStream stream ) throws IOExcept

BufferedReader dis = new BufferedReader( new InputStreamReader( stream ) );

Scanner ff = new Scanner( dis );
Scanner ff = new Scanner( dis ).useLocale( Locale.ENGLISH );

int index = 0;
int amount = 0;
Expand Down
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