JAL-2446 merged to spike branch

[jalview.git] / src / jalview / ext / ensembl / EnsemblRestClient.java

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index ab3b197..2437588 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -57,13 +57,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   /*
    * update these constants when Jalview has been checked / updated for
-   * changes to Ensembl REST API
+   * changes to Ensembl REST API (ref JAL-2105)
    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
    * @see http://rest.ensembl.org/info/rest?content-type=application/json
    */
-  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.8";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "4.8";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
@@ -76,6 +76,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
 
+  private static final Regex PROTEIN_REGEX = new Regex(
+          "(ENS)([A-Z]{3}|)P[0-9]{11}$");
+
   private static final Regex TRANSCRIPT_REGEX = new Regex(
           "(ENS)([A-Z]{3}|)T[0-9]{11}$");
 
@@ -125,6 +128,18 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   /**
    * Answers true if the query matches the regular expression pattern for an
+   * Ensembl protein stable identifier
+   * 
+   * @param query
+   * @return
+   */
+  public boolean isProteinIdentifier(String query)
+  {
+    return query == null ? false : PROTEIN_REGEX.search(query);
+  }
+
+  /**
+   * Answers true if the query matches the regular expression pattern for an
    * Ensembl gene stable identifier
    * 
    * @param query
@@ -513,9 +528,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
       if (laterVersion)
       {
-        System.err.println(String.format(
-                "Expected %s REST version %s but found %s, see %s",
-                getDbSource(), expected, version, REST_CHANGE_LOG));
+        System.err
+                .println(String
+                        .format("EnsemblRestClient expected %s REST version %s but found %s, see %s",
+                                getDbSource(), expected, version,
+                                REST_CHANGE_LOG));
       }
       info.restVersion = version;
     } catch (Throwable t)