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JAL-1705 regular expression updates, tests, other refactoring
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSequenceFetcher.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index
67c5e63
..
9a4952e
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@
-12,9
+12,13
@@
import com.stevesoft.pat.Regex;
*/
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
{
*/
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
{
- // TODO modify to accept other species e.g. ENSMUSTnnn
+ /*
+ * accepts ENSG/T/E/P with 11 digits
+ * or ENSMUSP or similar for other species
+ * or CCDSnnnnn.nn with at least 3 digits
+ */
private static final Regex ACCESSION_REGEX = new Regex(
private static final Regex ACCESSION_REGEX = new Regex(
- "(ENSP|ENST|ENSG|CCDS)[0-9.]{3,}$");
+ "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
/*
* possible values for the 'feature' parameter of the /overlap REST service
/*
* possible values for the 'feature' parameter of the /overlap REST service