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JAL-1705 derive transcript sequences from gene sequence/GFF; handle CDS
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
ExonerateHelper.java
diff --git
a/src/jalview/io/gff/ExonerateHelper.java
b/src/jalview/io/gff/ExonerateHelper.java
index
e373861
..
f7805fd
100644
(file)
--- a/
src/jalview/io/gff/ExonerateHelper.java
+++ b/
src/jalview/io/gff/ExonerateHelper.java
@@
-41,7
+41,7
@@
public class ExonerateHelper extends Gff2Helper
*
* @param seq
* the sequence with which this feature is associated
*
* @param seq
* the sequence with which this feature is associated
- * @param sf
+ * @param gffColumns
* the sequence feature with ATTRIBUTES property containing any
* additional attributes
* @param align
* the sequence feature with ATTRIBUTES property containing any
* additional attributes
* @param align
@@
-167,7
+167,7
@@
public class ExonerateHelper extends Gff2Helper
mapToSequence);
/*
mapToSequence);
/*
- * exonerate GFF has the strand of the target in column 7 rather
+ * exonerate GFF has the strand of the target in column 7
* (differs from GFF3 which has it in the Target descriptor)
*/
String strand = gff[STRAND_COL];
* (differs from GFF3 which has it in the Target descriptor)
*/
String strand = gff[STRAND_COL];
@@
-304,7
+304,7
@@
public class ExonerateHelper extends Gff2Helper
* Tests whether the GFF data looks like it was generated by exonerate, and is
* a format we are willing to handle
*
* Tests whether the GFF data looks like it was generated by exonerate, and is
* a format we are willing to handle
*
- * @param sf
+ * @param columns
* @return
*/
public static boolean recognises(String[] columns)
* @return
*/
public static boolean recognises(String[] columns)