Merge branch 'bug/JAL-3218scalePanelPopups' into develop

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index e64c51a..617ab21 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -64,9 +64,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @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 = "9.0";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "10.0";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "9.0";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "10.0";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 8296985..3b71823 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -42,7 +42,8 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   // domain properties default values:
   protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
 
-  protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = "https://rest.ensemblgenomes.org";
+  // ensemblgenomes REST service merged to ensembl 9th April 2019
+  protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
 
   /*
    * accepts ENSG/T/E/P with 11 digits

diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index 2e51bce..1d7d1c9 100644 (file)
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -143,6 +143,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
   {
     textarea.setDocument(textarea.getEditorKit().createDefaultDocument());
     textarea.setText(text);
+    textarea.setCaretPosition(0);
   }
 
   @Override

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 29d4ec7..a28be2c 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -21,7 +21,6 @@
 package jalview.ws;
 
 import jalview.ext.ensembl.EnsemblGene;
-import jalview.ext.ensembl.EnsemblGenomes;
 import jalview.ws.dbsources.EmblCdsSource;
 import jalview.ws.dbsources.EmblSource;
 import jalview.ws.dbsources.Pdb;
@@ -49,7 +48,7 @@ public class SequenceFetcher extends ASequenceFetcher
   public SequenceFetcher()
   {
     addDBRefSourceImpl(EnsemblGene.class);
-    addDBRefSourceImpl(EnsemblGenomes.class);
+    // addDBRefSourceImpl(EnsemblGenomes.class);
     addDBRefSourceImpl(EmblSource.class);
     addDBRefSourceImpl(EmblCdsSource.class);
     addDBRefSourceImpl(Uniprot.class);