From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 7 Mar 2022 20:12:04 +0000 (+0000)
Subject: Merge branch 'develop' into releases/Release_2_11_2_Branch
X-Git-Tag: Release_2_11_2_0~5
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=caa5930cf71ef14a4af891f2c17aa4a6e0f72bcf;hp=9d2d74b49cd06966eaad8796c87386be1e296057

Merge branch 'develop' into releases/Release_2_11_2_Branch
---

diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index d5e5dec..e3a2a05 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -100,6 +100,16 @@ li:before {
             <!-- JAL-3863 -->Support for Canonical Uniprot IDs
           </li>
           <li>
+            <!-- JAL-3881 -->Sequence IDs split on '_' as well as other
+            non-alphanumerics when discovering database references with
+            'Fetch DB Refs'
+          </li>
+          <li>
+            <!-- JAL-3884 -->Suppressed harmless exceptions output to
+            Console whilst discovering database references for a
+            sequence
+          </li>
+          <li>
             <!-- JAL-3204 -->Updated Jalview bindings for Uniprot XML
             schema
           </li>
@@ -119,6 +129,10 @@ li:before {
             textbox
           </li>
           <li>
+            <!-- JAL-3632 JAL-3633 -->support for HTTP/S access via
+            proxies that require authentication
+          </li>
+          <li>
             <!-- JAL-3837 -->GPL license info on splash screen and About
             text
           </li>
@@ -152,7 +166,10 @@ li:before {
             macOS, Linux/Unix, Windows and documentation in Help.  Installer wizard has option
             to add this to PATH, or link to it in your PATH.
           </li>
-
+          <li>
+            <!-- JAL-3633 -->Getdown launcher inherits HTTP/S proxy
+            configuration from jalview_properties
+          </li>
         </ul> <em>JalviewJS</em>
         <ul>
           <li>
@@ -257,6 +274,10 @@ li:before {
             <!-- JAL-3275 -->Can open multiple Preferences panels
           </li>
           <li>
+            <!-- JAL-3633 -->Properly configure HTTPS proxy settings
+            from Preferences
+          </li>
+          <li>
             <!-- JAL-3949 -->Standard out logging broken: messages only
             routing to stderr and appear as a raw template
           </li>
@@ -302,6 +323,14 @@ li:before {
           </li>
 
         </ul>
+        <em>Known Issues</em>
+        <ul>
+          <li>
+            <!-- JAL-3764 -->Display of RESNUM sequence features are not
+            suppressed when structures associated with a sequence are
+            viewed with an external viewer (Regression from 2.11.1 series)
+          </li>
+        </ul>
       </td>
     </tr>
     <tr>
@@ -544,6 +573,12 @@ li:before {
             <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
             when running on Linux (Requires Java 11+)
           </li>
+          <li>
+            <!-- JAL-1842 JAL-3509 -->RESNUM sequence features (the
+            green ones) are not automatically displayed when associated
+            structures are displayed or for sequences retrieved from the
+            PDB.
+          </li>
         </ul> <em>Launching Jalview</em>
         <ul>
           <li>
@@ -624,6 +659,11 @@ li:before {
             save in place.)
           </li>
           <li>
+            <!-- JAL-3509 -->Dragging a PDB file onto an alignment with
+            sequence features displayed causes displayed features to be
+            hidden.
+          </li>
+          <li>
             <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
             via command line
           </li>
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index fec31b8..023f591 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -273,7 +273,7 @@ label.viewer_path = Path to {0} program
 label.viewer_path_tip = Jalview will first try any path entered here, else standard installation locations.<br>Double-click to browse for file.
 label.invalid_viewer_path = Path not found or not executable
 label.viewer_missing = Structure viewer not found.<br/>Please enter the path to the executable (if installed),<br/>or download and install the program.
-label.open_viewer_failed = Error opening {0} - is it installed?\nCheck configured path in the Preferences' Structure tab 
+label.open_viewer_failed = Error opening {0} - is it installed?\nCheck configured path in Structure tab of Jalview''s Preferences 
 label.min_colour = Minimum Colour
 label.max_colour = Maximum Colour
 label.no_colour = No Colour
@@ -403,7 +403,7 @@ label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be
 label.couldnt_load_file = Couldn't load file
 label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
 label.no_pdb_id_in_file = No PDB Id in File
-label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
+label.couldnt_read_pasted_text = Couldn''t read the pasted text {0}
 label.error_parsing_text = Error parsing text
 label.input_alignment_from_url = Input Alignment From URL
 label.input_alignment = Input Alignment
@@ -855,7 +855,7 @@ label.invalid_name = Invalid name
 label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
 label.proxy_authorization_failed = Proxy Authorization Failed
 label.internal_jalview_error = Internal Jalview Error
-label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located.
+label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn''t be located.
 label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\!
 label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown
 label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!
@@ -969,7 +969,7 @@ error.cannot_set_arguments_to_jabaws_param_set = Cannot set arguments to a JabaW
 error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1})
 error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0}
 error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset!
-error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!"
+error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can''t locate either oldname ({0}) or presetName ({1}) in the datastore!"
 error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore
 error.cannot_set_source_file_for = Cannot set source file for {0}
 error.mismatch_service_instance_preset = Probable mismatch between service instance and preset!
@@ -977,7 +977,7 @@ error.cannot_set_params_for_ws_preset = Cannot set Parameters for a Jaba Web ser
 error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets
 error.no_aacon_service_found = No AACon service found
 error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain!
-error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8.
+error.couldnt_encode_as_utf8 = Couldn''t encode {0} as UTF-8.
 error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented
 error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process
 error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
@@ -1034,18 +1034,18 @@ error.implementation_error_reset_called_for_invalid_source = Implementation Erro
 exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3})
 label.mapped = mapped
 exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns
-exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0}
+exception.couldnt_parse_concise_annotation_for_prediction = Couldn''t parse concise annotation for prediction profile.\n{0}
 exception.newfile = NewickFile\: {0}\n
 label.no_tree_read_in = No Tree read in
-exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0})
-exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0})
+exception.rnaml_couldnt_access_datasource = Couldn''t access datasource ({0})
+exception.ranml_couldnt_process_data = Couldn''t process data as RNAML file ({0})
 exception.ranml_invalid_file = Invalid RNAML file ({0})
 exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
 exception.pfam_no_sequences_found = No sequences found (PFAM input)
 exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
 exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
 exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
-exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
+exception.couldnt_store_sequence_mappings = Couldn''t store sequence mappings for {0}
 exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
 exception.browser_not_found = Exception in finding browser: {0}
 exception.browser_unable_to_locate = Unable to locate browser: {0}
@@ -1077,7 +1077,7 @@ warn.service_not_supported = Service not supported!
 warn.input_is_too_big = Input is too big!
 warn.invalid_job_param_set = Invalid job parameter set!
 warn.oneseq_msainput_selection = The current selection only contains a single sequence. Do you want to submit all sequences for alignment instead ?   
-info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0}
+info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn''t support this program.\n{0}
 info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0}
 info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n
 info.no_jobs_ran = No jobs ran