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JAL-3725 restrict mapped virtual feature location to mapped region
[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
6732e82
..
ab2c00a
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-25,6
+25,8
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.util.Locale;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Sequence;
@@
-68,6
+70,8
@@
public class JPredFile extends AlignFile
/**
* Creates a new JPredFile object.
*
/**
* Creates a new JPredFile object.
*
+ * BH allows File or String
+ *
* @param inFile
* DOCUMENT ME!
* @param sourceType
* @param inFile
* DOCUMENT ME!
* @param sourceType
@@
-76,7
+80,7
@@
public class JPredFile extends AlignFile
* @throws IOException
* DOCUMENT ME!
*/
* @throws IOException
* DOCUMENT ME!
*/
- public JPredFile(String inFile, DataSourceType sourceType)
+ public JPredFile(Object inFile, DataSourceType sourceType)
throws IOException
{
super(inFile, sourceType);
throws IOException
{
super(inFile, sourceType);
@@
-361,10
+365,9
@@
public class JPredFile extends AlignFile
}
/**
}
/**
- * DOCUMENT ME!
*
* @param args
*
* @param args
- * DOCUMENT ME!
+ * @j2sIgnore
*/
public static void main(String[] args)
{
*/
public static void main(String[] args)
{
@@
-408,7
+411,7
@@
public class JPredFile extends AlignFile
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
// check that no stray annotations have been added at the end.
{
SequenceI sq = seqs.elementAt(j - 1);
- if (sq.getName().toUpperCase().startsWith("JPRED"))
+ if (sq.getName().toUpperCase(Locale.ROOT).startsWith("JPRED"))
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);
{
annotSeqs.addElement(sq);
seqs.removeElementAt(--j);