*/
package jalview.io;
+import java.util.Locale;
+
import java.awt.Color;
import java.io.IOException;
import java.util.ArrayList;
// 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;
}
} catch (IOException q)
{
}
- FastaFile parser = new FastaFile(this);
+ // Opening a FastaFile object with the remainder of this object's dataIn.
+ // Tell the constructor to NOT close the dataIn when finished.
+ FastaFile parser = new FastaFile(this, false);
List<SequenceI> includedseqs = parser.getSeqs();
SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);