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-2360colourSchemeApplicability
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
34fe221
..
ea96b3b
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-60,6
+60,7
@@
import java.util.Map;
import java.util.Map.Entry;
import java.util.NoSuchElementException;
import java.util.Set;
import java.util.Map.Entry;
import java.util.NoSuchElementException;
import java.util.Set;
+import java.util.SortedMap;
import java.util.TreeMap;
/**
import java.util.TreeMap;
/**
@@
-2840,7
+2841,7
@@
public class AlignmentUtils
* @param unmapped
* @return
*/
* @param unmapped
* @return
*/
- static Map<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
+ static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
{
/*
AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
{
/*
@@
-2848,7
+2849,7
@@
public class AlignmentUtils
* {unalignedSequence, characterPerSequence} at that position.
* TreeMap keeps the entries in ascending column order.
*/
* {unalignedSequence, characterPerSequence} at that position.
* TreeMap keeps the entries in ascending column order.
*/
- Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
/*
* record any sequences that have no mapping so can't be realigned
/*
* record any sequences that have no mapping so can't be realigned