{
for (String base : alleles.split(","))
{
- if (!base1.equalsIgnoreCase(base))
+ if (!base1.equals(base))
{
- String codon = base.toUpperCase() + base2.toLowerCase()
- + base3.toLowerCase();
- String canonical = base1.toUpperCase() + base2.toLowerCase()
- + base3.toLowerCase();
+ String codon = base + base2 + base3;
if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon, canonical))
+ codon))
{
count++;
}
{
for (String base : alleles.split(","))
{
- if (!base2.equalsIgnoreCase(base))
+ if (!base2.equals(base))
{
- String codon = base1.toLowerCase() + base.toUpperCase()
- + base3.toLowerCase();
- String canonical = base1.toLowerCase() + base2.toUpperCase()
- + base3.toLowerCase();
+ String codon = base1 + base + base3;
if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon, canonical))
+ codon))
{
count++;
}
{
for (String base : alleles.split(","))
{
- if (!base3.equalsIgnoreCase(base))
+ if (!base3.equals(base))
{
- String codon = base1.toLowerCase() + base2.toLowerCase()
- + base.toUpperCase();
- String canonical = base1.toLowerCase() + base2.toLowerCase()
- + base3.toUpperCase();
+ String codon = base1 + base2 + base;
if (addPeptideVariant(peptide, peptidePos, residue, var,
- codon, canonical))
+ codon))
{
count++;
}
* @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,
- String residue, DnaVariant var, String codon, String canonical)
+ String residue, DnaVariant var, String codon)
{
/*
* get peptide translation of codon e.g. GAT -> D
{
return false;
}
- String desc = canonical + "/" + codon;
+ String desc = codon;
String featureType = "";
if (trans.equals(residue))
{
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
assertEquals("stop_gained", sf.getType());
- assertEquals("Aaa/Taa", sf.getDescription());
+ assertEquals("TAA", sf.getDescription());
assertEquals("var3", sf.getValue("ID"));
assertEquals("Bad", sf.getValue("clinical_significance"));
assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
+ "TAA var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
sf.links.get(0));
assertEquals(dbSnp, sf.getFeatureGroup());
assertEquals(1, sf.getBegin());
assertEquals(1, sf.getEnd());
assertEquals("synonymous_variant", sf.getType());
- assertEquals("aaA/aaG", sf.getDescription());
+ assertEquals("AAG", sf.getDescription());
assertEquals("var4", sf.getValue("ID"));
assertEquals("None", sf.getValue("clinical_significance"));
assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ sf.links.get(0));
+ assertEquals(cosmic, sf.getFeatureGroup());
+
+ // AAA -> AAG synonymous
+ sf = sfs.get(4);
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("synonymous_variant", sf.getType());
+ assertEquals("AAG", sf.getDescription());
+ assertEquals("var4", sf.getValue("ID"));
+ assertEquals("None", sf.getValue("clinical_significance"));
+ assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "AAG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
sf.links.get(0));
assertEquals(cosmic, sf.getFeatureGroup());
assertEquals(2, sf.getBegin());
assertEquals(2, sf.getEnd());
assertEquals("synonymous_variant", sf.getType());
- assertEquals("ttT/ttC", sf.getDescription());
+ assertEquals("TTC", sf.getDescription());
assertEquals("var6", sf.getValue("ID"));
assertNull(sf.getValue("clinical_significance"));
assertEquals("ID=var6", sf.getAttributes());
assertEquals(1, sf.links.size());
assertEquals(
- "ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ "TTC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
sf.links.get(0));
assertEquals(dbSnp, sf.getFeatureGroup());