Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS

diff --git a/RELEASE b/RELEASE
index cfbbf93..a5d5f52 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
 jalview.release=releases/Release_2_11_3_Branch
-jalview.version=2.11.3.0
+jalview.version=2.11.3.1

diff --git a/help/markdown/releases/release-2_11_3_1.md b/help/markdown/releases/release-2_11_3_1.md
new file mode 100644 (file)
index 0000000..70fc3cb
--- /dev/null
+++ b/help/markdown/releases/release-2_11_3_1.md
@@ -0,0 +1,19 @@
+---
+version: 2.11.3.1
+date: 2023-11-22
+channel: "release"
+---
+
+## New Features
+
+- <!-- JAL-4243 --> bio.tools record for jalview updated and synced with json in source release
+
+## Issues Resolved
+
+- <!-- JAL-4340 --> Getdown does not preserve executable permission of jalview.sh file when it gets updated
+- <!-- JAL-4347 --> Single position features from Uniprot are incorrectly parsed as non-positional features
+- <!-- JAL-4345 --> Double clicking in PAE annotation to select column groups doesn't always select group under the mouse
+- <!-- JAL-4348 --> ChimeraX 1.3 and Chimera 1.16.2 are not automatically found
+
+### New Known Issues
+

diff --git a/help/markdown/whatsnew/whatsnew-2_11_3_1.md b/help/markdown/whatsnew/whatsnew-2_11_3_1.md
new file mode 100644 (file)
index 0000000..5f7f2c0
--- /dev/null
+++ b/help/markdown/whatsnew/whatsnew-2_11_3_1.md
@@ -0,0 +1 @@
+The 2.11.3.1 addresses patches critical bugs in the Uniprot parser and PAE annotation row selection mechanism. It also ensures the jalview command line tool is marked as executable on OSX and other systems, and that jalview autodetects recent versions of Chimera and ChimeraX.
\ No newline at end of file

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
index f7dba79..85d0def 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java
@@ -69,14 +69,16 @@ public class StructureManager
    * May 2020: 1.14 is Chimera latest, anticipating a few more...
    * 0.93 is ChimeraX latest, 1.0 expected soon
    */
-  private static String[] CHIMERA_VERSIONS = new String[] { "1.16.2",
-      "1.16.1", "1.16", "1.15.2", "1.15.1", "1.15", "1.14.2", "1.14.1",
-      "1.14", "1.13.1", "1.13", "1.12.2", "1.12.1", "1.12", "1.11.2",
-      "1.11.2", "1.11.1", "1.11" };
+  private static String[] CHIMERA_VERSIONS = new String[] { "1.18",
+      "1.17.4", "1.17.3", "1.17.2", "1.17.1", "1.17", "1.16.2", "1.16.1",
+      "1.16", "1.15.2", "1.15.1", "1.15", "1.14.2", "1.14.1", "1.14",
+      "1.13.1", "1.13", "1.12.2", "1.12.1", "1.12", "1.11.2", "1.11.2",
+      "1.11.1", "1.11" };
 
   // Missing 1.1 as this has known bug see JAL-2422
-  private static String[] CHIMERAX_VERSIONS = new String[] { "1.3", "1.2.5",
-      "1.0", "0.93", "0.92", "0.91", "0.9" };
+  private static String[] CHIMERAX_VERSIONS = new String[] { "1.7", "1.6.1",
+      "1.6", "1.5", "1.4", "1.3", "1.2.5", "1.0", "0.93", "0.92", "0.91",
+      "0.9" };
 
   static final String[] defaultStructureKeys = { "Structure", "pdb",
       "pdbFileName", "PDB ID", "structure", "biopax.xref.PDB", "pdb_ids",

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index e1193c9..68ceff0 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -677,7 +677,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
             {
               SequenceI rseq = clicked.sequenceRef;
               BitSet grp = new BitSet();
-              grp.or(matrix.getGroupsFor(currentX));
+              grp.or(matrix.getGroupsFor(forCurrentX.getPosition()));
               // TODO: cXci needs to be mapped to real groups
               for (int c = fr; c <= to; c++)
               {

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index b125ba5..69ee379 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -298,7 +298,7 @@ public class Uniprot extends DbSourceProxyImpl
         if (location.getPosition() != null)
         {
           if (location.getPosition().getPosition() == null
-                  || !"unknown".equals(location.getPosition().getStatus()))
+                  || "unknown".equals(location.getPosition().getStatus()))
           {
             Console.warn(
                     "Ignoring single position feature with uncertain location "

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index f2d3b66..a95d520 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -242,6 +242,13 @@ public class UniprotTest
     // FIXME: Jim needs to specify what (promoted) means !! - or perhaps we just
     // ignore it !
     assertEquals("1 (promoted)", (res.get(0).getVersion()));
+
+    List<SequenceFeature> features = seq.getFeatures().findFeatures(41, 41,
+            "sequence variant");
+    // verify single position features are parsed correctly JAL-4347
+    assertNotNull(features);
+    assertEquals(3, features.size());
+
   }
 
   /**

diff --git a/utils/biotools/Jalview.json b/utils/biotools/Jalview.json
index 69aa95c..760eaa7 100644 (file)
--- a/utils/biotools/Jalview.json
+++ b/utils/biotools/Jalview.json
@@ -5,7 +5,7 @@
   "biotoolsID": "Jalview",
   "biotoolsCURIE": "biotools:Jalview",
   "version": [
-    "2.11.2.7"
+    "2.11.3.0"
   ],
   "relation": [
     {
@@ -233,11 +233,12 @@
           ]
         }
       ],
-      "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\n\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);"
+      "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);"
     }
   ],
   "toolType": [
-    "Desktop application"
+    "Desktop application",
+    "Command-line tool"
   ],
   "topic": [
     {
@@ -255,6 +256,9 @@
     "Mac"
   ],
   "license": "GPL-3.0",
+  "collectionID": [
+    "ELIXIR-UK"
+  ],
   "maturity": "Mature",
   "cost": "Free of charge",
   "accessibility": "Open access",
@@ -363,7 +367,7 @@
         "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench",
         "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).",
         "date": "2009-05-07T00:00:00Z",
-        "citationCount": 5999,
+        "citationCount": 6209,
         "authors": [
           {
             "name": "Waterhouse A.M."
@@ -403,7 +407,7 @@
   ],
   "owner": "ben_s",
   "additionDate": "2019-02-13T17:01:40Z",
-  "lastUpdate": "2023-07-22T09:24:44.755337Z",
+  "lastUpdate": "2023-11-16T19:51:39.349417Z",
   "editPermission": {
     "type": "group",
     "authors": [