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JAL-2897 more informative description on synonymous variants
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentUtils.java
diff --git
a/src/jalview/analysis/AlignmentUtils.java
b/src/jalview/analysis/AlignmentUtils.java
index
aa1a98b
..
5e11446
100644
(file)
--- a/
src/jalview/analysis/AlignmentUtils.java
+++ b/
src/jalview/analysis/AlignmentUtils.java
@@
-2430,11
+2430,14
@@
public class AlignmentUtils
{
for (String base : alleles.split(","))
{
{
for (String base : alleles.split(","))
{
- if (!base1.equals(base))
+ if (!base1.equalsIgnoreCase(base))
{
{
- String codon = base + base2 + base3;
+ String codon = base.toUpperCase() + base2.toLowerCase()
+ + base3.toLowerCase();
+ String canonical = base1.toUpperCase() + base2.toLowerCase()
+ + base3.toLowerCase();
if (addPeptideVariant(peptide, peptidePos, residue, var,
if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon))
+ codon, canonical))
{
count++;
}
{
count++;
}
@@
-2456,11
+2459,14
@@
public class AlignmentUtils
{
for (String base : alleles.split(","))
{
{
for (String base : alleles.split(","))
{
- if (!base2.equals(base))
+ if (!base2.equalsIgnoreCase(base))
{
{
- String codon = base1 + base + base3;
+ String codon = base1.toLowerCase() + base.toUpperCase()
+ + base3.toLowerCase();
+ String canonical = base1.toLowerCase() + base2.toUpperCase()
+ + base3.toLowerCase();
if (addPeptideVariant(peptide, peptidePos, residue, var,
if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon))
+ codon, canonical))
{
count++;
}
{
count++;
}
@@
-2482,11
+2488,14
@@
public class AlignmentUtils
{
for (String base : alleles.split(","))
{
{
for (String base : alleles.split(","))
{
- if (!base3.equals(base))
+ if (!base3.equalsIgnoreCase(base))
{
{
- String codon = base1 + base2 + base;
+ String codon = base1.toLowerCase() + base2.toLowerCase()
+ + base.toUpperCase();
+ String canonical = base1.toLowerCase() + base2.toLowerCase()
+ + base3.toUpperCase();
if (addPeptideVariant(peptide, peptidePos, residue, var,
if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon))
+ codon, canonical))
{
count++;
}
{
count++;
}
@@
-2509,10
+2518,13
@@
public class AlignmentUtils
* @param residue
* @param var
* @param codon
* @param residue
* @param var
* @param codon
+ * the variant codon e.g. aCg
+ * @param canonical
+ * the 'normal' codon e.g. aTg
* @return true if a feature was added, else false
*/
static boolean addPeptideVariant(SequenceI peptide, int peptidePos,
* @return true if a feature was added, else false
*/
static boolean addPeptideVariant(SequenceI peptide, int peptidePos,
- String residue, DnaVariant var, String codon)
+ String residue, DnaVariant var, String codon, String canonical)
{
/*
* get peptide translation of codon e.g. GAT -> D
{
/*
* get peptide translation of codon e.g. GAT -> D
@@
-2527,7
+2539,7
@@
public class AlignmentUtils
{
return false;
}
{
return false;
}
- String desc = codon;
+ String desc = canonical + "/" + codon;
String featureType = "";
if (trans.equals(residue))
{
String featureType = "";
if (trans.equals(residue))
{