Make DoubleMatrixReader thread-safe

The NumberFormat parsing is not synchronized, so it is not safe to use
from multiple threads.

Author: arteymix

src/ubic/basecode/io/reader/DoubleMatrixReader.java

@@ -1,8 +1,8 @@
 /*
  * The baseCode project
- * 
+ *
  * Copyright (c) 2006 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -37,18 +37,12 @@
 
 /**
  * Reader for {@link basecode.dataStructure.matrix.DoubleMatrix}. Lines beginning with "#" or "!" will be ignored.
- * 
+ *
  * @author Paul Pavlidis
- * 
+ *
  */
 public class DoubleMatrixReader extends AbstractMatrixReader<DoubleMatrix<String, String>, Double> {
 
-    private static NumberFormat nf = NumberFormat.getInstance( Locale.ENGLISH );
-    static {
-        if ( nf instanceof DecimalFormat ) {
-            // ( ( DecimalFormat ) nf ).setDecimalSeparatorAlwaysShown( true );
-        }
-    }
     private List<String> colNames;
     private int numHeadings;
 
@@ -87,6 +81,11 @@ public DoubleMatrix<String, String> read( InputStream stream, Collection<String>
     public DoubleMatrix<String, String> read( InputStream stream, Collection<String> wantedRowNames,
             boolean createEmptyRows, int skipColumns, int maxRows ) throws IOException {
 
+        NumberFormat nf = NumberFormat.getInstance( Locale.ENGLISH );
+        if ( nf instanceof DecimalFormat ) {
+            // ( ( DecimalFormat ) nf ).setDecimalSeparatorAlwaysShown( true );
+        }
+
         BufferedReader dis = new BufferedReader( new InputStreamReader( stream ) );
 
         List<DoubleArrayList> MTemp = new Vector<DoubleArrayList>();
@@ -113,7 +112,7 @@ public DoubleMatrix<String, String> read( InputStream stream, Collection<String>
                 continue;
             }
 
-            String rowName = parseRow( row, rowNames, MTemp, wantedRowNames, skipColumns );
+            String rowName = parseRow( row, rowNames, MTemp, wantedRowNames, skipColumns, nf );
 
             if ( rowName == null ) {
                 // signals a blank or skipped row.
@@ -183,7 +182,7 @@ public DoubleMatrix<String, String> read( String filename ) throws IOException {
 
     /**
      * Read a matrix from a file, subject to filtering criteria.
-     * 
+     *
      * @param filename data file to read from (can be compressed)
      * @param wantedRowNames contains names of rows we want to get
      * @return NamedMatrix object constructed from the data file
@@ -277,7 +276,7 @@ protected DoubleMatrix<String, String> createMatrix( List<DoubleArrayList> MTemp
      * @throws IOException
      */
     private String parseRow( String row, Collection<String> rowNames, List<DoubleArrayList> MTemp,
-            Collection<String> wantedRowNames, int skipColumns ) throws IOException {
+            Collection<String> wantedRowNames, int skipColumns, NumberFormat nf ) throws IOException {
 
         if ( row.startsWith( "#" ) || row.startsWith( "!" ) ) {
             return null;

test/ubic/basecode/math/linearmodels/LeastSquaresFitTest.java

@@ -14,40 +14,26 @@
  */
 package ubic.basecode.math.linearmodels;
 
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.text.DecimalFormat;
-import java.text.NumberFormat;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.zip.GZIPInputStream;
-
-import org.apache.commons.math3.distribution.FDistribution;
-import org.junit.Test;
-
 import cern.colt.list.DoubleArrayList;
 import cern.colt.matrix.DoubleMatrix1D;
 import cern.colt.matrix.DoubleMatrix2D;
 import cern.colt.matrix.impl.DenseDoubleMatrix2D;
 import cern.colt.matrix.linalg.Algebra;
 import cern.jet.math.Functions;
-import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix;
-import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D;
-import ubic.basecode.dataStructure.matrix.DoubleMatrix;
-import ubic.basecode.dataStructure.matrix.ObjectMatrix;
-import ubic.basecode.dataStructure.matrix.ObjectMatrixImpl;
-import ubic.basecode.dataStructure.matrix.StringMatrix;
+import org.apache.commons.math3.distribution.FDistribution;
+import org.junit.Test;
+import ubic.basecode.dataStructure.matrix.*;
 import ubic.basecode.io.reader.DoubleMatrixReader;
 import ubic.basecode.io.reader.StringMatrixReader;
-import ubic.basecode.io.writer.MatrixWriter;
 import ubic.basecode.math.DescriptiveWithMissing;
 import ubic.basecode.math.MatrixStats;
 
+import java.util.List;
+import java.util.Map;
+import java.util.zip.GZIPInputStream;
+
+import static org.junit.Assert.*;
+
 /**
  * @author paul
  */

test/ubic/basecode/math/linearmodels/LeastSquaresFitTest2.java

@@ -19,26 +19,21 @@
 
 package ubic.basecode.math.linearmodels;
 
-import static org.junit.Assert.assertArrayEquals;
-import static org.junit.Assert.assertEquals;
-
-import java.text.DecimalFormat;
-import java.text.NumberFormat;
-import java.util.List;
-import java.util.Locale;
-
-import org.junit.Test;
-
 import cern.colt.matrix.DoubleMatrix1D;
 import cern.colt.matrix.DoubleMatrix2D;
+import org.junit.Test;
 import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix;
 import ubic.basecode.dataStructure.matrix.DoubleMatrix;
 import ubic.basecode.dataStructure.matrix.StringMatrix;
 import ubic.basecode.io.reader.DoubleMatrixReader;
 import ubic.basecode.io.reader.StringMatrixReader;
-import ubic.basecode.io.writer.MatrixWriter;
 import ubic.basecode.math.MatrixStats;
 
+import java.util.List;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+
 /**
  * @author paul
  */