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Merge branch 'develop' into merged_2_11_2_0_to_2_12
[jalview.git]
/
src
/
jalview
/
io
/
StockholmFile.java
diff --git
a/src/jalview/io/StockholmFile.java
b/src/jalview/io/StockholmFile.java
index
a850ff1
..
a4bc631
100644
(file)
--- a/
src/jalview/io/StockholmFile.java
+++ b/
src/jalview/io/StockholmFile.java
@@
-58,8
+58,6
@@
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.models.rna.RNA;
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
/**
* 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
@@
-138,7
+136,7
@@
public class StockholmFile extends AlignFile
pat = "(<|>|\\[|\\]|\\(|\\)|\\{|\\})";
break;
case REGEX_NOT_RNASS:
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*(.*)";
break;
case REGEX_ANNOTATION:
pat = "(\\w+)\\s*(.*)";
@@
-332,7
+330,7
@@
public class StockholmFile extends AlignFile
Regex closeparen = getRegex(REGEX_CLOSE_PAREN);//"(>|\\])", ")");
// // Detect if file is RNA by looking for bracket types
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();
rend.optimize();
p.optimize();
@@
-1204,7
+1202,7
@@
public class StockholmFile extends AlignFile
}
else
{
}
else
{
- key = type2id(aa.label.toLowerCase());
+ key = type2id(aa.label.toLowerCase(Locale.ROOT));
if (key == null)
{
label = aa.label;
if (key == null)
{
label = aa.label;