Merge branch 'release-1.1'

PavlidisLab · Nov 23, 2021 · f4665bc · f4665bc
2 parents e636cdd + b2bb343
commit f4665bc
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Showing 7 changed files with 166 additions and 112 deletions.
diff --git a/pom.xml b/pom.xml
@@ -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.]]>
@@ -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>

diff --git a/src/ubic/basecode/dataStructure/Link.java b/src/ubic/basecode/dataStructure/Link.java
@@ -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
@@ -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 );
     }
 
 }
diff --git a/src/ubic/basecode/dataStructure/matrix/DoubleMatrix.java b/src/ubic/basecode/dataStructure/matrix/DoubleMatrix.java
@@ -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;
@@ -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" );

diff --git a/src/ubic/basecode/io/reader/DoubleMatrixReader.java b/src/ubic/basecode/io/reader/DoubleMatrixReader.java
@@ -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;
 
@@ -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 );

diff --git a/src/ubic/basecode/io/reader/SparseDoubleMatrixReader.java b/src/ubic/basecode/io/reader/SparseDoubleMatrixReader.java
@@ -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;
@@ -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;