Merge branch 'feature/JAL-3469clinvarVCF' into spike/clinvar

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index d3afc57..1abe638 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.vcf;
 
 import jalview.analysis.Dna;
@@ -23,13 +43,12 @@ import jalview.util.StringUtils;
 
 import java.io.File;
 import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
@@ -58,17 +77,7 @@ import htsjdk.variant.vcf.VCFInfoHeaderLine;
  */
 public class VCFLoader
 {
-  private static final String ENCODED_COMMA = "%2C";
-
-  private static final String ENCODED_PERCENT = "%25";
-
-  private static final String ENCODED_EQUALS = "%3D";
-
-  private static final String ENCODED_SEMICOLON = "%3B";
-
-  private static final String ENCODED_COLON = "%3A";
-
-  private static final String UTF_8 = "UTF-8";
+  private static final String VCF_ENCODABLE = ":;=%,";
 
   /*
    * Jalview feature attributes for VCF fixed column data
@@ -561,7 +570,7 @@ public class VCFLoader
   {
     for (Pattern p : filters)
     {
-      if (p.matcher(id.toUpperCase()).matches())
+      if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
       {
         return true;
       }
@@ -655,7 +664,7 @@ public class VCFLoader
     {
       try
       {
-      patterns.add(Pattern.compile(token.toUpperCase()));
+      patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
       } catch (PatternSyntaxException e)
       {
         System.err.println("Invalid pattern ignored: " + token);
@@ -904,7 +913,7 @@ public class VCFLoader
          * RuntimeException throwable by htsjdk
          */
         String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
-                map.chromosome, vcfStart, vcfEnd);
+                map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
         Cache.log.error(msg);
       }
     }
@@ -1354,42 +1363,17 @@ public class VCFLoader
       String value = getAttributeValue(variant, key, index);
       if (value != null && isValid(variant, key, value))
       {
-        value = decodeSpecialCharacters(value);
+        /*
+         * decode colon, semicolon, equals sign, percent sign, comma (only)
+         * as required by the VCF specification (para 1.2)
+         */
+        value = StringUtils.urlDecode(value, VCF_ENCODABLE);
         addFeatureAttribute(sf, key, value);
       }
     }
   }
 
   /**
-   * Decodes colon, semicolon, equals sign, percent sign, comma to their decoded
-   * form. The VCF specification (para 1.2) requires these to be encoded where not
-   * used with their special meaning in the VCF syntax. Note that general URL
-   * decoding should not be applied, since this would incorrectly decode (for
-   * example) a '+' sign.
-   * 
-   * @param value
-   * @return
-   */
-  protected static String decodeSpecialCharacters(String value)
-  {
-    /*
-     * avoid regex compilation if it is not needed!
-     */
-    if (!value.contains(ENCODED_COLON) && !value.contains(ENCODED_SEMICOLON)
-            && !value.contains(ENCODED_EQUALS)
-            && !value.contains(ENCODED_PERCENT)
-            && !value.contains(ENCODED_COMMA))
-    {
-      return value;
-    }
-
-    value = value.replace(ENCODED_COLON, ":")
-            .replace(ENCODED_SEMICOLON, ";").replace(ENCODED_EQUALS, "=")
-            .replace(ENCODED_PERCENT, "%").replace(ENCODED_COMMA, ",");
-    return value;
-  }
-
-  /**
    * Answers true for '.', null, or an empty value, or if the INFO type is String.
    * If the INFO type is Integer or Float, answers false if the value is not in
    * valid format.
@@ -1507,12 +1491,7 @@ public class VCFLoader
                * VCF spec requires encoding of special characters e.g. '='
                * so decode them here before storing
                */
-              try
-              {
-                field = URLDecoder.decode(field, UTF_8);
-              } catch (UnsupportedEncodingException e)
-              {
-              }
+              field = StringUtils.urlDecode(field, VCF_ENCODABLE);
               csqValues.put(id, field);
             }
           }