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JAL-1551 formatting
[jalview.git]
/
src
/
jalview
/
io
/
IdentifyFile.java
diff --git
a/src/jalview/io/IdentifyFile.java
b/src/jalview/io/IdentifyFile.java
index
ed67af8
..
c21127e
100755
(executable)
--- a/
src/jalview/io/IdentifyFile.java
+++ b/
src/jalview/io/IdentifyFile.java
@@
-20,6
+20,8
@@
*/
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;
@@
-31,12
+33,14
@@
import java.io.IOException;
*/
public class IdentifyFile
{
*/
public class IdentifyFile
{
-
- public FileFormatI identify(Object file, DataSourceType protocol) throws FileFormatException
+
+ public FileFormatI identify(Object file, DataSourceType protocol)
+ throws FileFormatException
{
// BH 2018
{
// BH 2018
- return (file instanceof File ? identify((File) file, protocol) : identify((String) file, protocol));
-
+ return (file instanceof File ? identify((File) file, protocol)
+ : identify((String) file, protocol));
+
}
public FileFormatI identify(File file, DataSourceType sourceType)
}
public FileFormatI identify(File file, DataSourceType sourceType)
@@
-165,8
+169,8
@@
public class IdentifyFile
if (source.inFile != null)
{
String fileStr = source.inFile.getName();
if (source.inFile != null)
{
String fileStr = source.inFile.getName();
- if (fileStr.contains(".jar")
- || fileStr.contains(".zip") || fileStr.contains(".jvp"))
+ if (fileStr.contains(".jar") || fileStr.contains(".zip")
+ || fileStr.contains(".jvp"))
{
// possibly a Jalview archive (but check further)
reply = FileFormat.Jalview;
{
// possibly a Jalview archive (but check further)
reply = FileFormat.Jalview;
@@
-178,13
+182,26
@@
public class IdentifyFile
break;
}
}
break;
}
}
- data = data.toUpperCase();
+ data = data.toUpperCase(Locale.ROOT);
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
reply = FileFormat.ScoreMatrix;
break;
}
if (data.startsWith(ScoreMatrixFile.SCOREMATRIX))
{
reply = FileFormat.ScoreMatrix;
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;
@@
-319,7
+336,7
@@
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;
@@
-452,6
+469,11
@@
public class IdentifyFile
return true;
}
return true;
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
for (int i = 0; args != null && i < args.length; i++)
public static void main(String[] args)
{
for (int i = 0; args != null && i < args.length; i++)
@@
-475,5
+497,4
@@
public class IdentifyFile
}
}
}
}
-
}
}