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-2898 show 'stop_gained' variants on peptide sequences
[jalview.git]
/
src
/
jalview
/
analysis
/
Dna.java
diff --git
a/src/jalview/analysis/Dna.java
b/src/jalview/analysis/Dna.java
index
f3088ea
..
ef05a58
100644
(file)
--- a/
src/jalview/analysis/Dna.java
+++ b/
src/jalview/analysis/Dna.java
@@
-161,7
+161,7
@@
public class Dna
int s;
int sSize = selection.size();
int s;
int sSize = selection.size();
- List<SequenceI> pepseqs = new ArrayList<SequenceI>();
+ List<SequenceI> pepseqs = new ArrayList<>();
for (s = 0; s < sSize; s++)
{
SequenceI newseq = translateCodingRegion(selection.get(s),
for (s = 0; s < sSize; s++)
{
SequenceI newseq = translateCodingRegion(selection.get(s),
@@
-213,7
+213,7
@@
public class Dna
if (dnarefs != null)
{
// intersect with pep
if (dnarefs != null)
{
// intersect with pep
- List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> mappedrefs = new ArrayList<>();
DBRefEntry[] refs = dna.getDBRefs();
for (int d = 0; d < refs.length; d++)
{
DBRefEntry[] refs = dna.getDBRefs();
for (int d = 0; d < refs.length; d++)
{
@@
-391,7
+391,7
@@
public class Dna
String seqstring, AlignedCodonFrame acf,
List<SequenceI> proteinSeqs)
{
String seqstring, AlignedCodonFrame acf,
List<SequenceI> proteinSeqs)
{
- List<int[]> skip = new ArrayList<int[]>();
+ List<int[]> skip = new ArrayList<>();
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
// intervals
int skipint[] = null;
ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
// intervals
@@
-544,7
+544,7
@@
public class Dna
skip.add(skipint);
skipint = null;
}
skip.add(skipint);
skipint = null;
}
- if (aa.equals("STOP"))
+ if (aa.equals(ResidueProperties.STOP))
{
aa = STOP_ASTERIX;
}
{
aa = STOP_ASTERIX;
}
@@
-800,7
+800,7
@@
public class Dna
public AlignmentI reverseCdna(boolean complement)
{
int sSize = selection.size();
public AlignmentI reverseCdna(boolean complement)
{
int sSize = selection.size();
- List<SequenceI> reversed = new ArrayList<SequenceI>();
+ List<SequenceI> reversed = new ArrayList<>();
for (int s = 0; s < sSize; s++)
{
SequenceI newseq = reverseSequence(selection.get(s).getName(),
for (int s = 0; s < sSize; s++)
{
SequenceI newseq = reverseSequence(selection.get(s).getName(),