git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
[jalview.git]
/
src
/
jalview
/
datamodel
/
Mapping.java
diff --git
a/src/jalview/datamodel/Mapping.java
b/src/jalview/datamodel/Mapping.java
index
ea08d97
..
c4c4a2a
100644
(file)
--- a/
src/jalview/datamodel/Mapping.java
+++ b/
src/jalview/datamodel/Mapping.java
@@
-253,8
+253,7
@@
public class Mapping
* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
- while (alignedBases < truePos
- && alignedColumn < alignedSeq.length)
+ while (alignedBases < truePos && alignedColumn < alignedSeq.length)
{
if (alignedSeq[alignedColumn++] != gap)
{
{
if (alignedSeq[alignedColumn++] != gap)
{
@@
-694,6
+693,7
@@
public class Mapping
*
* @see java.lang.Object#finalize()
*/
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
map = null;
protected void finalize() throws Throwable
{
map = null;
@@
-706,4
+706,14
@@
public class Mapping
return new AlignedCodonIterator(seq, gapChar);
}
return new AlignedCodonIterator(seq, gapChar);
}
+ /**
+ * Readable representation for debugging only, not guaranteed not to change
+ */
+ @Override
+ public String toString()
+ {
+ return String.format("%s %s", this.map.toString(), this.to == null ? ""
+ : this.to.getName());
+ }
+
}
}