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-3806 use the covers() test for each selected sequence and the complementary align...
[jalview.git]
/
src
/
jalview
/
util
/
MappingUtils.java
diff --git
a/src/jalview/util/MappingUtils.java
b/src/jalview/util/MappingUtils.java
index
c992243
..
03a32c9
100644
(file)
--- a/
src/jalview/util/MappingUtils.java
+++ b/
src/jalview/util/MappingUtils.java
@@
-36,6
+36,7
@@
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignedCodonFrame;
import jalview.commands.EditCommand.Edit;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
@@
-367,11
+368,11
@@
public final class MappingUtils
{
int mappedStartResidue = 0;
int mappedEndResidue = 0;
{
int mappedStartResidue = 0;
int mappedEndResidue = 0;
-
for (AlignedCodonFrame acf : codonFrames)
{
for (AlignedCodonFrame acf : codonFrames)
{
- Mapping map = acf.getMappingBetween(seq, selected);
- if (map != null)
+ for (SequenceToSequenceMapping map: acf.getMappings())
+ {
+ if (map.covers(selected) && map.covers(seq))
{
/*
* Found a sequence mapping. Locate the start/end mapped residues.
{
/*
* Found a sequence mapping. Locate the start/end mapped residues.
@@
-407,7
+408,7
@@
public final class MappingUtils
mappedGroup.addSequence(seq, false);
break;
}
mappedGroup.addSequence(seq, false);
break;
}
- }
+ }}
}
}
mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
}
}
mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);