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JAL-1706 fixed to correctly restore the last dialog selection after
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
7dec4ec
..
a4aeac7
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-27,6
+27,7
@@
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@
-1278,7
+1279,7
@@
public class AlignmentUtils
public static AlignmentI makeExonAlignment(SequenceI[] dna,
Set<AlignedCodonFrame> mappings)
{
public static AlignmentI makeExonAlignment(SequenceI[] dna,
Set<AlignedCodonFrame> mappings)
{
- Set<AlignedCodonFrame> newMappings = new HashSet<AlignedCodonFrame>();
+ Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
List<SequenceI> exonSequences = new ArrayList<SequenceI>();
for (SequenceI dnaSeq : dna)
List<SequenceI> exonSequences = new ArrayList<SequenceI>();
for (SequenceI dnaSeq : dna)
@@
-1346,8
+1347,8
@@
public class AlignmentUtils
/*
* Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
*/
/*
* Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
*/
- List<int[]> exonRanges = seqMapping.getMap().getFromRanges();
- for (int[] range : exonRanges)
+ final List<int[]> dnaExonRanges = seqMapping.getMap().getFromRanges();
+ for (int[] range : dnaExonRanges)
{
for (int pos = range[0]; pos <= range[1]; pos++)
{
{
for (int pos = range[0]; pos <= range[1]; pos++)
{
@@
-1389,6
+1390,8
@@
public class AlignmentUtils
.getToRanges(),
3, 1);
newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
.getToRanges(),
3, 1);
newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
+ MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
+ newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
exonSequences.add(exon);
}
exonSequences.add(exon);
}