import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.models.rna.RNA;
-// import org.apache.log4j.*;
-
/**
* This class is supposed to parse a Stockholm format file into Jalview There
* are TODOs in this class: we do not know what the database source and version
pat = "(<|>|\\[|\\]|\\(|\\)|\\{|\\})";
break;
case REGEX_NOT_RNASS:
- pat = "^[^<>[\\](){}A-DF-Za-df-z]*$";
+ pat = "^[^<>[\\](){}ADFJ-RUVWYZadfj-ruvwyz]*$"; // update 2.11.2
break;
case REGEX_ANNOTATION:
pat = "(\\w+)\\s*(.*)";
Regex closeparen = getRegex(REGEX_CLOSE_PAREN);//"(>|\\])", ")");
// // Detect if file is RNA by looking for bracket types
- // Regex detectbrackets = getRegex("(<|>|\\[|\\]|\\(|\\))");
+// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
}
else
{
- key = type2id(aa.label.toLowerCase());
+ key = type2id(aa.label.toLowerCase(Locale.ROOT));
if (key == null)
{
label = aa.label;