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JAL-3251 SequenceToSequenceMapping now SequenceMapping, MappingType++
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
0dfd383
..
f1084a7
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-24,7
+24,6
@@
import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-36,6
+35,7
@@
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceMapping;
import jalview.datamodel.features.SequenceFeatures;
import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyI;
@@
-1107,7
+1107,7
@@
public class AlignmentUtils
SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein);
if (prot != null)
{
SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein);
if (prot != null)
{
- Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
+ Mapping seqMap = mapping.getMappingForSequence(dnaSeq, false);
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap,
alignedCodons);
unmappedProtein.remove(prot);
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap,
alignedCodons);
unmappedProtein.remove(prot);
@@
-1935,7
+1935,7
@@
public class AlignmentUtils
.findMappingsForSequence(proteinProduct, mappings);
for (AlignedCodonFrame acf : mappingsToPeptide)
{
.findMappingsForSequence(proteinProduct, mappings);
for (AlignedCodonFrame acf : mappingsToPeptide)
{
- for (SequenceToSequenceMapping map : acf.getMappings())
+ for (SequenceMapping map : acf.getMappings())
{
Mapping mapping = map.getMapping();
if (mapping != aMapping
{
Mapping mapping = map.getMapping();
if (mapping != aMapping
@@
-2428,7
+2428,8
@@
public class AlignmentUtils
static int computePeptideVariants(SequenceI peptide, int peptidePos,
List<DnaVariant>[] codonVariants)
{
static int computePeptideVariants(SequenceI peptide, int peptidePos,
List<DnaVariant>[] codonVariants)
{
- String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
+ String residue = String
+ .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
int count = 0;
String base1 = codonVariants[0].get(0).base;
String base2 = codonVariants[1].get(0).base;
int count = 0;
String base1 = codonVariants[0].get(0).base;
String base2 = codonVariants[1].get(0).base;