+/*
+ * 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;
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;
*/
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
{
for (Pattern p : filters)
{
- if (p.matcher(id.toUpperCase()).matches())
+ if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
{
return true;
}
{
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);
* 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);
}
}
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.
* 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);
}
}