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
JAL-1645 source formatting and organise imports
[jalview.git]
/
src
/
jalview
/
analysis
/
Dna.java
diff --git
a/src/jalview/analysis/Dna.java
b/src/jalview/analysis/Dna.java
index
5696838
..
9ce00cc
100644
(file)
--- a/
src/jalview/analysis/Dna.java
+++ b/
src/jalview/analysis/Dna.java
@@
-208,9
+208,8
@@
public class Dna
for (int gd = 0; gd < selection.length; gd++)
{
SequenceI dna = selection[gd];
for (int gd = 0; gd < selection.length; gd++)
{
SequenceI dna = selection[gd];
- DBRefEntry[] dnarefs = DBRefUtils
- .selectRefs(dna.getDBRef(),
- jalview.datamodel.DBRefSource.DNACODINGDBS);
+ DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+ jalview.datamodel.DBRefSource.DNACODINGDBS);
if (dnarefs != null)
{
// intersect with pep
if (dnarefs != null)
{
// intersect with pep
@@
-300,8
+299,7
@@
public class Dna
aa.graphHeight = annotation.graphHeight;
if (annotation.getThreshold() != null)
{
aa.graphHeight = annotation.graphHeight;
if (annotation.getThreshold() != null)
{
- aa.setThreshold(new GraphLine(annotation
- .getThreshold()));
+ aa.setThreshold(new GraphLine(annotation.getThreshold()));
}
if (annotation.hasScore)
{
}
if (annotation.hasScore)
{
@@
-446,8
+444,10
@@
public class Dna
aa = gapString;
if (skipint == null)
{
aa = gapString;
if (skipint == null)
{
- skipint = new int[]
- { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
+ skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
+ * cdp[0],
+ * cdp[2]
+ */};
}
skipint[1] = alignedCodon.pos3; // cdp[2];
}
}
skipint[1] = alignedCodon.pos3; // cdp[2];
}
@@
-683,8
+683,7
@@
public class Dna
* range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
* iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
*/
* range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
* iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
*/
- MapList map = new MapList(scontigs, new int[]
- { 1, resSize }, 3, 1);
+ MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
transferCodedFeatures(selection, newseq, map, null, null);
transferCodedFeatures(selection, newseq, map, null, null);
@@
-714,8
+713,7
@@
public class Dna
* @param proteinSeqs
* @return
*/
* @param proteinSeqs
* @return
*/
- protected void insertAAGap(int pos,
- List<SequenceI> proteinSeqs)
+ protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
{
aaWidth++;
for (SequenceI seq : proteinSeqs)
{
aaWidth++;
for (SequenceI seq : proteinSeqs)