Improve makeValidForR and make it considerably closed to make.names() from R

Author: arteymix

src/ubic/basecode/util/StringUtil.java

@@ -184,6 +184,11 @@ public static boolean isLatinLetter( char c ) {
         return ( c >= 'A' && c <= 'Z' ) || ( c >= 'a' && c <= 'z' );
     }
 
+    private static final String[] R_RESERVED_WORDS = {
+        "if", "else", "repeat", "while", "function", "for", "in", "next", "break",
+        "TRUE", "FALSE", "NULL", "Inf", "NaN", "NA", "NA_integer_", "NA_real_", "NA_character_", "NA_complex_",
+    };
+
     /**
      * Mimics the make.names method in R (character.c) to make valid variables names; we use this for column headers in
      * some output files. This doesn't give the exact sames results as R; we avoid repeated '.'.
@@ -192,17 +197,21 @@ public static boolean isLatinLetter( char c ) {
      * @return modified string
      * @author paul
      */
-    public static String makeValidForR( String s ) {
-
-        // If string starts with a digit or "." and then a digit, prepend an X.
-        if ( s.matches( "^\\.?[0-9].+" ) ) {
-            s = "X" + s;
+    public static String makeValidForR( String colName ) {
+        if ( colName == null ) {
+            return "NA";
         }
-
-        // TODO: check for reserved words. https://stat.ethz.ch/R-manual/R-devel/library/base/html/Reserved.html
-
-        // no dashes or white space or other punctuation. '.' is okay and so is "_", now.
-        return s.replaceAll( "[\\W]+", "." );
+        if ( colName.isEmpty()
+            // starts with a non-letter or non-dot
+            || ( !Character.isAlphabetic( colName.charAt( 0 ) ) && colName.charAt( 0 ) != '.' )
+            // dot followed by a digit
+            || ( colName.charAt( 0 ) == '.' && colName.length() > 1 && Character.isDigit( colName.charAt( 1 ) ) ) ) {
+            return "X" + colName.replaceAll( "[^A-Za-z0-9._]", "." );
+        }
+        if ( StringUtils.equalsAny( colName, R_RESERVED_WORDS ) ) {
+            return colName + ".";
+        }
+        return colName.replaceAll( "[^A-Za-z0-9._]", "." );
     }
 
     /**

test/ubic/basecode/util/StringUtilTest.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
@@ -18,17 +18,16 @@
  */
 package ubic.basecode.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import org.junit.Test;
 
 import java.util.Collection;
 import java.util.HashSet;
 
-import org.junit.Test;
+import static org.junit.Assert.*;
 
 /**
  * @author pavlidis
- * 
+ *
  */
 public class StringUtilTest {
 
@@ -78,20 +77,23 @@ public void testCommonSuffixNone() {
 
     @Test
     public void testMakeRnames() {
-        String actual = StringUtil.makeValidForR( "f33oo dd . [f] a" );
-        assertEquals( "f33oo.dd.f.a", actual );
-        
-        actual = StringUtil.makeValidForR( ".f33oo" );
-        assertEquals( ".f33oo", actual );
-        
-        actual = StringUtil.makeValidForR( "...f33oo" );
-        assertEquals( ".f33oo", actual );
-
-        actual = StringUtil.makeValidForR( "1foo dd . [f] a" );
-        assertEquals( "X1foo.dd.f.a", actual );
-       
-        actual = StringUtil.makeValidForR( ".1foo dd . [f] a" );
-        assertEquals( "X.1foo.dd.f.a", actual );
+        assertFalse( Character.isDigit( '.' ) );
+        assertEquals( "NA", StringUtil.makeValidForR( null ) );
+        assertEquals( "test", StringUtil.makeValidForR( "test" ) );
+        assertEquals( "X", StringUtil.makeValidForR( "X" ) );
+        assertEquals( "X123", StringUtil.makeValidForR( "123" ) );
+        assertEquals( "X", StringUtil.makeValidForR( "" ) );
+        assertEquals( "X..", StringUtil.makeValidForR( "  " ) );
+        assertEquals( "if.", StringUtil.makeValidForR( "if" ) );
+        assertEquals( "TRUE.", StringUtil.makeValidForR( "TRUE" ) );
+        assertEquals( "...", StringUtil.makeValidForR( "..." ) );
+        assertEquals( "..", StringUtil.makeValidForR( ". " ) );
+        assertEquals( "X.2way", StringUtil.makeValidForR( ".2way" ) );
+        assertEquals( "f33oo.dd....f..a", StringUtil.makeValidForR( "f33oo dd . [f] a" ) );
+        assertEquals( ".f33oo", StringUtil.makeValidForR( ".f33oo" ) );
+        assertEquals( "...f33oo", StringUtil.makeValidForR( "...f33oo" ) );
+        assertEquals( "X1foo.dd....f..a", StringUtil.makeValidForR( "1foo dd . [f] a" ) );
+        assertEquals( "X.1foo.dd....f..a", StringUtil.makeValidForR( ".1foo dd . [f] a" ) );
     }
 
 }