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Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD
[jalview.git]
/
src
/
jalview
/
io
/
IdentifyFile.java
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
b8a4d6a
..
3024039
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-20,6
+20,7
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
import java.io.File;
import java.io.IOException;
import java.io.File;
import java.io.IOException;
@@
-178,7
+179,7
@@
public class IdentifyFile
break;
}
}
break;
}
}
- data = data.toUpperCase();
+ data = data.toUpperCase(Locale.ROOT);
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
@@
-190,6
+191,19
@@
public class IdentifyFile
reply = FileFormat.HMMER3;
break;
}
reply = FileFormat.HMMER3;
break;
}
+ if (data.startsWith("LOCUS"))
+ {
+ reply = FileFormat.GenBank;
+ break;
+ }
+ if (data.startsWith("ID "))
+ {
+ if (data.substring(2).trim().split(";").length == 7)
+ {
+ reply = FileFormat.Embl;
+ break;
+ }
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
@@
-324,7
+338,7
@@
public class IdentifyFile
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
// RNAML, XML
{
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
// RNAML, XML
{
- String upper = data.toUpperCase();
+ String upper = data.toUpperCase(Locale.ROOT);
if (upper.substring(lessThan).startsWith("<HTML"))
{
reply = FileFormat.Html;
if (upper.substring(lessThan).startsWith("<HTML"))
{
reply = FileFormat.Html;