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Merge branch 'bug/JAL-3288splitFrameMenusJava11' into trialMerge
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignedCodonFrame.java
diff --git
a/src/jalview/datamodel/AlignedCodonFrame.java
b/src/jalview/datamodel/AlignedCodonFrame.java
index
ec11fc1
..
26f6e2a
100644
(file)
--- a/
src/jalview/datamodel/AlignedCodonFrame.java
+++ b/
src/jalview/datamodel/AlignedCodonFrame.java
@@
-116,7
+116,7
@@
public class AlignedCodonFrame
*/
public AlignedCodonFrame()
{
*/
public AlignedCodonFrame()
{
- mappings = new ArrayList<SequenceToSequenceMapping>();
+ mappings = new ArrayList<>();
}
/**
}
/**
@@
-179,7
+179,7
@@
public class AlignedCodonFrame
{
// TODO return a list instead?
// return dnaSeqs;
{
// TODO return a list instead?
// return dnaSeqs;
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
for (SequenceToSequenceMapping ssm : mappings)
{
seqs.add(ssm.fromSeq);
for (SequenceToSequenceMapping ssm : mappings)
{
seqs.add(ssm.fromSeq);
@@
-190,7
+190,7
@@
public class AlignedCodonFrame
public SequenceI[] getAaSeqs()
{
// TODO not used - remove?
public SequenceI[] getAaSeqs()
{
// TODO not used - remove?
- List<SequenceI> seqs = new ArrayList<SequenceI>();
+ List<SequenceI> seqs = new ArrayList<>();
for (SequenceToSequenceMapping ssm : mappings)
{
seqs.add(ssm.mapping.to);
for (SequenceToSequenceMapping ssm : mappings)
{
seqs.add(ssm.mapping.to);
@@
-200,7
+200,7
@@
public class AlignedCodonFrame
public MapList[] getdnaToProt()
{
public MapList[] getdnaToProt()
{
- List<MapList> maps = new ArrayList<MapList>();
+ List<MapList> maps = new ArrayList<>();
for (SequenceToSequenceMapping ssm : mappings)
{
maps.add(ssm.mapping.map);
for (SequenceToSequenceMapping ssm : mappings)
{
maps.add(ssm.mapping.map);
@@
-210,7
+210,7
@@
public class AlignedCodonFrame
public Mapping[] getProtMappings()
{
public Mapping[] getProtMappings()
{
- List<Mapping> maps = new ArrayList<Mapping>();
+ List<Mapping> maps = new ArrayList<>();
for (SequenceToSequenceMapping ssm : mappings)
{
maps.add(ssm.mapping);
for (SequenceToSequenceMapping ssm : mappings)
{
maps.add(ssm.mapping);
@@
-225,7
+225,7
@@
public class AlignedCodonFrame
* @param seq
* @return
*/
* @param seq
* @return
*/
- public Mapping getMappingForSequence(SequenceI seq)
+ public Mapping getMappingForSequence(SequenceI seq, boolean cdsOnly)
{
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
{
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
@@
-234,7
+234,11
@@
public class AlignedCodonFrame
{
if (ssm.fromSeq == seqDs || ssm.mapping.to == seqDs)
{
{
if (ssm.fromSeq == seqDs || ssm.mapping.to == seqDs)
{
- return ssm.mapping;
+ if (!cdsOnly || ssm.fromSeq.getName().startsWith("CDS")
+ || ssm.mapping.to.getName().startsWith("CDS"))
+ {
+ return ssm.mapping;
+ }
}
}
return null;
}
}
return null;
@@
-485,7
+489,7
@@
public class AlignedCodonFrame
{
MapList ml = null;
SequenceI dnaSeq = null;
{
MapList ml = null;
SequenceI dnaSeq = null;
- List<char[]> result = new ArrayList<char[]>();
+ List<char[]> result = new ArrayList<>();
for (SequenceToSequenceMapping ssm : mappings)
{
for (SequenceToSequenceMapping ssm : mappings)
{
@@
-524,8
+528,8
@@
public class AlignedCodonFrame
*/
public List<Mapping> getMappingsFromSequence(SequenceI seq)
{
*/
public List<Mapping> getMappingsFromSequence(SequenceI seq)
{
- List<Mapping> result = new ArrayList<Mapping>();
- List<SequenceI> related = new ArrayList<SequenceI>();
+ List<Mapping> result = new ArrayList<>();
+ List<SequenceI> related = new ArrayList<>();
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;