From: Jim Procter Date: Fri, 14 Oct 2022 15:38:56 +0000 (+0100) Subject: Merge branch 'develop' into features/JAL-3895_alphafoldcolours X-Git-Tag: Release_2_11_3_0~23^2~50^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f05e348630e97e1d86d222bd22bab09d6bf0fb06;hp=0d3cbb0cb96f079d5dd499301ba8733297a22c91;p=jalview.git Merge branch 'develop' into features/JAL-3895_alphafoldcolours --- diff --git a/RELEASE b/RELEASE index c63eaef..5bcf6d0 100644 --- 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 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -90,10 +90,10 @@ - - - - + + + + diff --git a/help/help/html/colourSchemes/index.html b/help/help/html/colourSchemes/index.html index 672910e..e006618 100755 --- a/help/help/html/colourSchemes/index.html +++ b/help/help/html/colourSchemes/index.html @@ -198,7 +198,7 @@ td { - gecos:flower + gecos Flower @@ -225,7 +225,7 @@ td { - gecos:blossom + gecos Blossom @@ -251,7 +251,7 @@ td { - gecos:sunset + gecos Sunset @@ -277,7 +277,7 @@ td { - gecos:ocean + gecos Ocean diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html index 7d4a389..8c4e462 100755 --- a/help/help/html/features/seqfetch.html +++ b/help/help/html/features/seqfetch.html @@ -99,6 +99,13 @@ Bioinformatics Institute.
Nucleic Acids Res. 33(1):W25-W28 (2005)

+
  • + RFAM - a database of RNA families +
    • +
  • + PFAM - a database of protein families
    + Data is provided by the Interpro Web API +
    • 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 --- 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 -- Pfam Full and Seed alignment retrieval switched to the Interpro Server +- Pfam Full and Seed alignment retrieval switched to use http://www.ebi.ac.uk/interpro/api/ - URLs reporting Content-Type as application/gzip not being recognized as a gzipped stream - Clustalx colour scheme renamed (back) to Clustal in the GUI - 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 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 --- 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 --- 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 --- 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); }