Merge branch 'develop' into features/JAL-3895_alphafoldcolours

diff --git a/RELEASE b/RELEASE
index c63eaef..5bcf6d0 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_2_Branch
-jalview.version=2.11.2.4
+jalview.version=2.11.2.5

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 1b4156e..3308456 100755 (executable)
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -90,10 +90,10 @@
                        <tocitem text="ClustalX" target="colours.clustal" />
                        <tocitem text="Zappo" target="colours.zappo" />
                        <tocitem text="Taylor" target="colours.taylor" />
-                       <tocitem text="gecos:flower" target="colours.gecos-flower" />
-                       <tocitem text="gecos:blossom" target="colours.gecos-blossom" />
-                       <tocitem text="gecos:sunset" target="colours.gecos-sunset" />
-                       <tocitem text="gecos:ocean" target="colours.gecos-ocean" />
+                       <tocitem text="gecos Flower" target="colours.gecos-flower" />
+                       <tocitem text="gecos Blossom" target="colours.gecos-blossom" />
+                       <tocitem text="gecos Sunset" target="colours.gecos-sunset" />
+                       <tocitem text="gecos Ocean" target="colours.gecos-ocean" />
                        <tocitem text="Hydrophobicity" target="colours.hydro" />
                        <tocitem text="Helix propensity" target="colours.helix" />
                        <tocitem text="Strand propensity" target="colours.strand" />

diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html
index 672910e..e006618 100755 (executable)
--- a/help/help/html/colourSchemes/index.html
+++ b/help/help/html/colourSchemes/index.html
@@ -198,7 +198,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:flower</td>
+                                                       <td>gecos Flower</td>
 
                                                        <td bgcolor="#b18a51"></td>
                                                        <td bgcolor="#83bff1"></td>
@@ -225,7 +225,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:blossom</td>
+                                                       <td>gecos Blossom</td>
                                                        <td bgcolor="#8bc4b4"></td>
                                                        <td bgcolor="#fc9502"></td>
                                                        <td bgcolor="#b5c206"></td>
@@ -251,7 +251,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:sunset</td>
+                                                       <td>gecos Sunset</td>
                                                        <td bgcolor="#fea0fd"></td>
                                                        <td bgcolor="#85746a"></td>
                                                        <td bgcolor="#abc8f5"></td>
@@ -277,7 +277,7 @@ td {
                                                        <td></td>
                                                </tr>
                                                <tr>
-                                                       <td>gecos:ocean</td>
+                                                       <td>gecos Ocean</td>
                                                        <td bgcolor="#c6ca9b"></td>
                                                        <td bgcolor="#0ca0a8"></td>
                                                        <td bgcolor="#0adfc3"></td>

diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html
index 7d4a389..8c4e462 100755 (executable)
--- a/help/help/html/features/seqfetch.html
+++ b/help/help/html/features/seqfetch.html
@@ -99,6 +99,13 @@
       Bioinformatics Institute.<br> Nucleic Acids Res.
       33(1):W25-W28 (2005) <br> <br>
     </li>
+    <li>
+      <a href="https://docs.rfam.org/en/latest/citing-rfam.html#rfam-references">RFAM - a database of RNA families</a>
+    </li>
+    <li>
+      <a href="https://pfam-docs.readthedocs.io/en/latest/citing-pfam.html">PFAM - a database of protein families</a><br/>
+      <a href="https://academic.oup.com/nar/article/49/D1/D344/5958491">Data is provided by the Interpro Web API</a>
+    </li>
   </ul>
 </body>
 </html>

diff --git a/help/markdown/releases/release-2_11_2_5.md b/help/markdown/releases/release-2_11_2_5.md
index c470ee7..a9ea9e4 100644 (file)
--- a/help/markdown/releases/release-2_11_2_5.md
+++ b/help/markdown/releases/release-2_11_2_5.md
@@ -1,13 +1,11 @@
 ---
 version: 2.11.2.5
-date: 2022-10-01
+date: 2022-10-11
 channel: "release"
 ---
 
-## New Features
-
 ## Issues Resolved
-- <!-- JAL-4073 --> Pfam Full and Seed alignment retrieval switched to the Interpro Server
+- <!-- JAL-4073 --> Pfam Full and Seed alignment retrieval switched to use http://www.ebi.ac.uk/interpro/api/
 - <!-- JAL-4074 --> URLs reporting Content-Type as application/gzip not being recognized as a gzipped stream
 - <!-- JAL-4063 --> Clustalx colour scheme renamed (back) to Clustal in the GUI
 - <!-- JAL-4014 --> Spanish translations added for gecos colour schemes introduced in 2.11.2.4

diff --git a/help/markdown/whatsnew/whatsnew-2_11_2_5.md b/help/markdown/whatsnew/whatsnew-2_11_2_5.md
new file mode 100644 (file)
index 0000000..d5c4b66
--- /dev/null
+++ b/help/markdown/whatsnew/whatsnew-2_11_2_5.md
@@ -0,0 +1,2 @@
+Jalview 2.11.2.5 is the fifth patch release in the 2.11.2 series. It includes several minor revisions, including a revised Pfam alignment retrieval client based on the Interpro web API, and a fix for a bug where overlapping features of the same type assigned different colours were not shown as coloured differently in the overview window. 
+

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 93001a4..316c1aa 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -39,7 +39,7 @@ import jalview.util.Platform;
 abstract public class Pfam extends Xfam
 {
   public static final String FULL = "full", RP35 = "rp35", RP15 = "rp15",
-          RP75 = "rp75", RP55 = "rp55", SEED = "seed";
+          RP75 = "rp75", RP55 = "rp55", SEED = "seed", UNIPROT = "uniprot";
 
   public String getPfamDownloadURL(String id, String alType)
   {
@@ -53,7 +53,10 @@ abstract public class Pfam extends Xfam
 
   protected String alignmentType;
 
-  private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download";
+  /**
+   * docs are http://www.ebi.ac.uk/interpro/api/
+   */
+  private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$";
 
   static
   {

diff --git a/test/jalview/ws/dbsources/PfamFullTest.java b/test/jalview/ws/dbsources/PfamFullTest.java
index fd59ef3..d03057d 100644 (file)
--- a/test/jalview/ws/dbsources/PfamFullTest.java
+++ b/test/jalview/ws/dbsources/PfamFullTest.java
@@ -38,7 +38,7 @@ public class PfamFullTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "www.ebi.ac.uk/interpro/wwwapi/entry/pfam/ABC/?annotation=alignment:full&download";
+    String path = "www.ebi.ac.uk/interpro/api/entry/pfam/ABC/?annotation=alignment:full";
 
     // with default value for domain
     String url = new PfamFull().getURL(" abc ");
@@ -46,7 +46,7 @@ public class PfamFullTest
 
     // with override in properties
     Cache.setProperty(Pfam.PFAM_BASEURL_KEY,
-            "http://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download");
+            "http://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$");
     url = new PfamFull().getURL(" abc ");
     assertEquals(url, "http://" + path);
   }

diff --git a/test/jalview/ws/dbsources/PfamSeedTest.java b/test/jalview/ws/dbsources/PfamSeedTest.java
index d228c35..3c30086 100644 (file)
--- a/test/jalview/ws/dbsources/PfamSeedTest.java
+++ b/test/jalview/ws/dbsources/PfamSeedTest.java
@@ -38,7 +38,7 @@ public class PfamSeedTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "www.ebi.ac.uk/interpro/wwwapi/entry/pfam/ABC/?annotation=alignment:seed&download";
+    String path = "www.ebi.ac.uk/interpro/api/entry/pfam/ABC/?annotation=alignment:seed";
 
     // with default value for domain
     String url = new PfamSeed().getURL(" abc ");
@@ -46,7 +46,7 @@ public class PfamSeedTest
 
     // with override in properties
     Cache.setProperty(Pfam.PFAM_BASEURL_KEY,
-            "http://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download");
+            "http://www.ebi.ac.uk/interpro/api/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$");
     url = new PfamSeed().getURL(" abc ");
     assertEquals(url, "http://" + path);
   }