*/
package jalview.io;
+import java.util.Locale;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.TreeMap;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewportI;
import jalview.util.ParseHtmlBodyAndLinks;
import jalview.util.StringUtils;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-
/**
* Parses and writes features files, which may be in Jalview, GFF2 or GFF3
* format. These are tab-delimited formats but with differences in the use of
*/
public class FeaturesFile extends AlignFile implements FeaturesSourceI
{
- /*
- * map-valued attributes are prefixed with this for output to GFF3;
- * the prefix is removed if found on reading
- */
- public static final String MAP_ATTRIBUTE_PREFIX = "jvmap_";
+ private static final String EQUALS = "=";
private static final String TAB_REGEX = "\\t";
private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
- private static final String NOTE = "Note";
-
protected static final String GFF_VERSION = "##gff-version";
private AlignmentI lastmatchedAl = null;
/**
* Constructor which does not parse the file immediately
*
- * @param file
+ * @param file File or String filename
* @param paste
* @throws IOException
*/
- public FeaturesFile(String file, DataSourceType paste)
+ public FeaturesFile(Object file, DataSourceType paste)
throws IOException
{
super(false, file, paste);
* @param type
* @throws IOException
*/
- public FeaturesFile(boolean parseImmediately, String file,
+ public FeaturesFile(boolean parseImmediately, Object file,
DataSourceType type) throws IOException
{
super(parseImmediately, file, type);
// skip comments/process pragmas
if (line.length() == 0 || line.startsWith("#"))
{
- if (line.toLowerCase().startsWith("##"))
+ if (line.toLowerCase(Locale.ROOT).startsWith("##"))
{
processGffPragma(line, gffProps, align, newseqs);
}
String line;
while ((line = nextLine()) != null)
{
- if (line.toUpperCase().startsWith(ENDFILTERS))
+ if (line.toUpperCase(Locale.ROOT).startsWith(ENDFILTERS))
{
return;
}
if (mf != null)
{
- MapList mapping = mf.mapping.getMap();
for (SequenceFeature sf : mf.features)
{
/*
found.add(sf);
int begin = sf.getBegin();
int end = sf.getEnd();
- int[] range = mf.mapping.getTo() == seq.getDatasetSequence()
- ? mapping.locateInTo(begin, end)
- : mapping.locateInFrom(begin, end);
+ int[] range = mf.getMappedPositions(begin, end);
SequenceFeature sf2 = new SequenceFeature(sf, range[0],
range[1], group, sf.getScore());
complementary.add(sf2);
{
String formatted = StringUtils.urlEncode(value.toString(),
GffHelperI.GFF_ENCODABLE);
- sb.append(key).append("=").append(formatted);
+ sb.append(key).append(EQUALS).append(formatted);
}
}
}
* Formats the map entries as
*
* <pre>
- * jvmap_key={key1=value1,key2=value2,...}
+ * key=key1=value1,key2=value2,...
* </pre>
*
* and appends this to the string buffer
* AbstractMap.toString would be a shortcut here, but more reliable
* to code the required format in case toString changes in future
*/
- sb.append(MAP_ATTRIBUTE_PREFIX).append(key).append("={");
+ sb.append(key).append(EQUALS);
boolean first = true;
for (Entry<?, ?> entry : map.entrySet())
{
sb.append(",");
}
first = false;
- sb.append(entry.getKey().toString()).append("=");
+ sb.append(entry.getKey().toString()).append(EQUALS);
String formatted = StringUtils.urlEncode(entry.getValue().toString(),
GffHelperI.GFF_ENCODABLE);
sb.append(formatted);
}
- sb.append("}");
}
/**