*/
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
// 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);