The Java Console, Logging and Reporting Bugs

graph_name

+  jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+  
-       /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
       \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa
 # Jalview Launch File
 # Please install the Jalview Desktop from 
-# http://www.jalview.org/getdown/release
+# https://www.jalview.org/getdown/release
 # and then try to open this file again
 jalview.apparg=-open
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta
 jalview.apparg=-annotations
-jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise
+jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise
 jalview.apparg=-colour
 jalview.apparg=Clustal
 
/*
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)

diff --git a/help/help/html/index.html b/help/help/html/index.html
index 442c508..a6bb1b6 100755
--- a/help/help/html/index.html
+++ b/help/help/html/index.html
@@ -45,7 +45,7 @@
   
     For more information, you might also want to take a look at the
     documentation section of the Jalview website (http://www.jalview.org/about/documentation).
+      href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation).
   
   
     If you are using the Jalview Desktop application and are looking for
@@ -54,9 +54,14 @@
     google the online version of these pages. If you don't find what you
     are looking for, or want to report a bug or make a feature request,
     then get in contact over at http://www.jalview.org/community
+      href="https://www.jalview.org/community">https://www.jalview.org/community
+  
+  
+    Logging, troubleshooting and reporting bugs
If
+    something seems to be wrong with your Jalview installation, or you
+    think you've found a problem, take a look at Jalview's
+      logging and bug reporting documentation.
   
-
   
     Citing Jalview
If you use Jalview in your
     work, please cite the Jalview 2 paper in Bioinformatics:
diff --git a/help/help/html/keys.html b/help/help/html/keys.html
index 29b6813..0faa1d5 100755
--- a/help/help/html/keys.html
+++ b/help/help/html/keys.html
@@ -81,7 +81,10 @@
       
JALVIEW_APP_DIR/launcher.log
+  logs.Jalview.level=DEBUG
+  
+  logs.Axis.level=DEBUG
+  
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
-       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
       \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index c83741a..fe4d257 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -1,3 +1,4 @@
+
 
 
+	
+	Development
+        
+          Updated building instructions
+        
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * 
+ * https://ena-docs.readthedocs.io/en/latest/submit/fileprep/flat-file-example.html
+ * https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
+ * 
+ * https://www.ebi.ac.uk/ena/browser/api/embl/X81322.1
+ * https://www.ncbi.nlm.nih.gov/nuccore/X81322.1
+ * 
+   * FT      /note="gene_id=hCG28070.3 
+   * FT      ""foobar"" isoform=CRA_b"
+   * the returned value is
+   * gene_id=hCG28070.3 "foobar" isoform=CRA_b
+   * 
+ * accession, version, sequence, xref
+ * and (for CDS feature) location, protein_id, product, codon_start, translation
+ * 
+   * VERSION     X81322.1
+   * 
+   *   CDS 1-20  // from exon1
+   *   CDS 21-35 // from exon2
+   *   CDS 36-71 // from exon3
+   * 'coalesce' to range 1-71
+   * 
+   * For example:
+   * 1:1 (e.g. gene to CDS):
+   * ranges { [10-20], [31-40] }, wordLengthFrom = wordLength 2 = 1
+   *   for start = 1, end = 9, returns a BitSet with no bits set
+   *   for start = 1, end = 11, returns a BitSet with bits 0-1 set
+   *   for start = 15, end = 35, returns a BitSet with bits 5-15 set
+   * 1:3 (peptide to codon):
+   * ranges { [1-200] }, wordLengthFrom = 1, wordLength 2 = 3
+   *   for start = 9, end = 9, returns a BitSet with bits 24-26 set
+   * 3:1 (codon to peptide):
+   * ranges { [101-150], [171-180] }, wordLengthFrom = 3, wordLength 2 = 1
+   *   for start = 101, end = 102 (partial first codon), returns a BitSet with bit 0 set
+   *   for start = 150, end = 171 (partial 17th codon), returns a BitSet with bit 16 set
+   * 3:1 (circular DNA to peptide):
+   * ranges { [101-150], [21-30] }, wordLengthFrom = 3, wordLength 2 = 1
+   *   for start = 24, end = 40 (spans codons 18-20), returns a BitSet with bits 17-19 set
+   * 

-nodisplay
-open FILE/URL	Specify the alignment file to + open or process by providing additional arguments.
-props FILE/URL	Use the given Jalview properties diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index e00d390..0ef78f9 100644 --- a/help/help/html/features/commandline.html +++ b/help/help/html/features/commandline.html @@ -38,7 +38,7 @@ Standard installation on Linux/Unix: - /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal + /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal Standard installation on Windows: \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa @@ -65,10 +65,31 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa(put Passing JVM Arguments to Jalview If you need - to modify parameters for Jalview's Java Virtual Machine, then take a - look at the instructions for how to setting - the JVM's maximum memory. + to modify parameters for Jalview's Java Virtual Machine, or + configure system properties, then take a look at the instructions + for how to setting the JVM's + maximum memory. + + Changing Jalview's 'Look and Feel' If you + are experiencing issues with the font size or layout of Jalview's + GUI, you can try changing Jalview's 'Look and feel' by + specifying a custom system property 'laf' on startup (see setting the JVM's memory for + instructions on how to do this for your platform). For the + Jalview standalone executable jar, simply provide one of the + property settings before the -jar argument + + -Dlaf=system (default look and feel for the OS) + -Dlaf=crossplatform (Java's Metal Look and Feel) + -Dlaf=nimbus (Java's alternative Nimbus Look and Feel) + -Dlaf=mac (only has an effect on OSX) + -Dlaf=gtk (only has an effect on Linux) + + The currently configured look and feel is logged to Jalview's console. + Once the look and feel has been changed, it will be stored in + Jalview's .jalview_properties file for future Jalview sessions. + diff --git a/help/help/html/features/groovy.html b/help/help/html/features/groovy.html index ead4436..cc91154 100644 --- a/help/help/html/features/groovy.html +++ b/help/help/html/features/groovy.html @@ -39,7 +39,7 @@ installation of Groovy. Just select Tools→Groovy Console... from the Jalview Desktop's drop-down menu. After a short pause, you should then see the Groovy + href="https://groovy-lang.org/groovyconsole.html">Groovy Console appear. This allows you to interactively execute Groovy scripts whilst Jalview is running. We've also provided a Calculations→Execute Groovy Script button so you can execute the currently loaded @@ -101,7 +101,7 @@ print currentAlFrame.getTitle(); InstallAnywhere version of Jalview, you can find additional groovy scripts in the examples/groovy subfolder of the installation directory. The examples are also available at http://www.jalview.org/examples/groovy. + href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy. Using Groovy to add new Alignment Calculations We've @@ -115,8 +115,8 @@ print currentAlFrame.getTitle(); Creating custom colourschemes You can create your own alignment colourschemes with a groovy script. We've provided two examples: - colourConserved.groovy creates an 'Conserved' colourscheme - similar to the classic GeneDOC shading model. - colourUnconserved.groovy creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink. + colourConserved.groovy creates an 'Conserved' colourscheme - similar to the classic GeneDOC shading model. + colourUnconserved.groovy creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink. diff --git a/help/help/html/features/jvlfiles.html b/help/help/html/features/jvlfiles.html index 27742b3..e23af30 100644 --- a/help/help/html/features/jvlfiles.html +++ b/help/help/html/features/jvlfiles.html @@ -46,12 +46,12 @@ # Jalview Launch File # Please install the Jalview Desktop from -# http://www.jalview.org/getdown/release +# https://www.jalview.org/getdown/release # and then try to open this file again jalview.apparg=-open -jalview.apparg=http://www.jalview.org/examples/jpred_msa.fasta +jalview.apparg=https://www.jalview.org/examples/jpred_msa.fasta jalview.apparg=-annotations -jalview.apparg=http://www.jalview.org/examples/jpred_msa.seq.concise +jalview.apparg=https://www.jalview.org/examples/jpred_msa.seq.concise jalview.apparg=-colour jalview.apparg=Clustal @@ -62,7 +62,7 @@ jalview.apparg=Clustal # Please install the Jalview Desktop from # http://www.jalview.org/getdown/release # and then try to open this file again -appbase=http://www.jalview.org/getdown/archive/2_10_5/ +appbase=https://www.jalview.org/getdown/archive/2_10_5/ For security, the Jalview application will only allow appbase URLs from www.jalview.org. diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html index 58b06db..5a3fe7a 100755 --- a/help/help/html/features/preferences.html +++ b/help/help/html/features/preferences.html @@ -222,17 +222,15 @@ Add Temperature Factor annotation to alignment - if selected, values extracted from the Temperature Factor column for the backbone atoms in the PDB file will be extracted as annotation - lines shown on the alignment. + lines shown on the alignment. Since 2.11.2, scores from the Temperature Column for structures imported via the 3D-Beacons network may be shown instead as model quality or reliability scores. - Default structure viewer - choose Jmol or CHIMERA for + Default structure viewer - choose Jmol, CHIMERA, CHIMERAX or PYMOL for viewing 3D structures. - Path to Chimera program - Optional, as Jalview will search - standard installation paths for Windows, Linux or MacOS. If you have - installed Chimera in a non-standard location, you can specify it - here, by entering the full path to the Chimera executable program. - Double-click this field to open a file chooser dialog. - + Path to Chimera/X/Pymol program - Optional, as Jalview will search + standard installation paths for Windows, Linux or MacOS. If Jalview cannot locate the installation for your selected structure viewer, a dialog will be shown. If you have + installed the chosen viewer in a non-standard location, you can specify it + here, by entering the full path to its executable. For Chimera, locate the path to the chimera program, similarly for ChimeraX and Pymol. Rather than typing in the path, you can also double-click this field to open a file chooser dialog. PDB Fields shown in Search and Structure Summaries - ticks in this table indicate fields shown by default when browsing results diff --git a/help/help/html/features/search.html b/help/help/html/features/search.html index eec68ee..837d7b3 100755 --- a/help/help/html/features/search.html +++ b/help/help/html/features/search.html @@ -36,7 +36,7 @@ td { The search box is displayed by pressing Control and F or selecting "Find..." from the "Search" menu. - + "Find next" will find the next occurrence of the specified and adjust the alignment window view to show it, and "Find all" highlights all matches for a pattern. The @@ -48,18 +48,19 @@ td { of posix and perl style regex - see below for a summary) Gaps are ignored when matching the query to the sequences in the alignment. + Hidden columns can optionally be ignored (since Jalview 2.11) The search is applied to both sequences and their IDs, and optionally also to the description string (since Jalview 2.10) If a region is selected, then search will only - be performed on that region. + be performed on that region. + Tip: to quickly clear the current selection, click the + alignment view you wish to search, then press 'Escape'. - To quickly clear the current selection, press the - "Escape" key. Tick the "Match Case" box to perform a case sensitive search. - To access a previously used + To access a previously used query press the down arrow or click on the button on the right of the text field. @@ -155,12 +156,13 @@ td { stored along with your Jalview user preferences. To open the search history, click on the button to the right of the query field, or press the down arrow key. - - The search history keeps up to 99 queries by default. To clear + + The search history keeps up to 99 queries by default. To clear the history, or modify the size of the history, right-click the text box. - - + + + Other dialogs that provide a query history diff --git a/help/help/html/features/search.png b/help/help/html/features/search.png index 89adb1a..47c18f4 100644 Binary files a/help/help/html/features/search.png and b/help/help/html/features/search.png differ diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html index e726c49..4e9a75f 100755 --- a/help/help/html/features/seqfetch.html +++ b/help/help/html/features/seqfetch.html @@ -72,14 +72,30 @@ "OK" to initiate the retrieval. - If you use the WSDBFetch sequence fetcher services (EMBL, - UniProt, PFAM, and RFAM) in work for publication, please cite: - - Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate - J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez - R. SOAP-based services provided by the European - Bioinformatics Institute. Nucleic Acids Res. 33(1):W25-W28 - (2005) - + If you use the Sequence Fetcher, please remember to cite the + corresponding services (linked to below): + + Ensembl - The + Ensembl REST API + EMBL/EMBLCDS - Provided by the European + Nucleotide Archive's ENA Data API + Note: Versions of Jalview prior to 2.11.1.1 employed the + XML endpoint of the ENA browser, which was retired in August + 2020. + Uniprot - Free Text Search and Retrieval via the Uniprot REST API + PDB - Free Text Search via the PDBe + REST API and retrieval via WSDbFetch + Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate + J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez + R. SOAP-based services provided by the European + Bioinformatics Institute. Nucleic Acids Res. + 33(1):W25-W28 (2005) + + diff --git a/help/help/html/groovy/featuresCounter.html b/help/help/html/groovy/featuresCounter.html index 3b6705b..bd7144e 100644 --- a/help/help/html/groovy/featuresCounter.html +++ b/help/help/html/groovy/featuresCounter.html @@ -43,7 +43,7 @@ Please note: The 2.10.2 feature counting interface is not compatible with earlier versions. http://www.jalview.org/examples/groovy/featuresCounter.groovy + href="https://www.jalview.org/examples/groovy/featuresCounter.groovy">https://www.jalview.org/examples/groovy/featuresCounter.groovy - rendered with hilite.me /* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) diff --git a/help/help/html/index.html b/help/help/html/index.html index 442c508..a6bb1b6 100755 --- a/help/help/html/index.html +++ b/help/help/html/index.html @@ -45,7 +45,7 @@ For more information, you might also want to take a look at the documentation section of the Jalview website (http://www.jalview.org/about/documentation). + href="https://www.jalview.org/about/documentation">https://www.jalview.org/about/documentation). If you are using the Jalview Desktop application and are looking for @@ -54,9 +54,14 @@ google the online version of these pages. If you don't find what you are looking for, or want to report a bug or make a feature request, then get in contact over at http://www.jalview.org/community + href="https://www.jalview.org/community">https://www.jalview.org/community + + + Logging, troubleshooting and reporting bugs If + something seems to be wrong with your Jalview installation, or you + think you've found a problem, take a look at Jalview's + logging and bug reporting documentation. - Citing Jalview If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: diff --git a/help/help/html/keys.html b/help/help/html/keys.html index 29b6813..0faa1d5 100755 --- a/help/help/html/keys.html +++ b/help/help/html/keys.html @@ -81,7 +81,10 @@	Cursor Keys (Arrow Keys)	Cursor	Move cursor around alignment	Move cursor around alignment. Press SHIFT to move + cursor from an aligned region to next gap, or to the next + aligned region when at a gap. +
Cursor Keys (Arrow Keys) diff --git a/help/help/html/logging.html b/help/help/html/logging.html new file mode 100644 index 0000000..0975a47 --- /dev/null +++ b/help/help/html/logging.html @@ -0,0 +1,212 @@ + + + +The Java Console, Logging and Reporting Bugs + + + + The Java Console, Logging and Reporting Bugs + + + Like most programs, Jalview contains bugs, despite our best efforts. + However, Jalview also produces a series of messages during its + operation, often referred to as 'logs'. These logs provide a record + of Jalview's operation. They can also be extremely useful when reporting bugs, since they help the + Jalview developers diagnose and find a workaround for specific + problems that you might encounter. + + + The primary place to look for logs is in the Java + Console which you can open from within Jalview by going to the Tools + menu and checking the box next to Show Java Console. This + option is stored in your Jalview preferences file and so is + remembered across Jalview sessions. + + The Java Console will show you information about what the + Jalview application is doing (often in the background) whilst it is + running. + However, when tracking down problems preventing Jalview from + starting up properly, you need to look at the startup logs - which + are not shown in the Jalview Console. The location of these depends + on how you launched Jalview: + + Jalview Desktop Installation Launch Logs If you are using + a standard desktop version of Jalview installed from one of our + install4j installers, then messages about Jalview's initial launch + can be found in + JALVIEW_APP_DIR/launcher.log + where + JALVIEW_APP_DIR is the directory that Jalview's application + was installed into. + For Jalview 2.11.0 onwards: + + In Windows this is %APPDATA%\Local\Jalview by + default + + In macOS this is /Applications/Jalview.app/Contents/Resources/app + by default + + In Linux and other Unix OSes this is ~/opt/jalview + by default + + + Jalview Executable Jar Launch Logs If you are using the Jalview executable jar file (also + used by bioconda and OSX homebrew installations) then the default run class ( + jalview.bin.Launcher -- a minimised launcher that will set + memory and linux dpi settings before re-launching + jalview.bin.Jalview), will output logging information to + STDOUT and STDERR. + + + + Java Console and Log Level + + + The Java Console is opened by selecting Tools + → Show Java Console. The visibility of the console is stored + in your preferences, so if you quit Jalview with the console open, + it will be shown the next time you start Jalview. You can close the + console by selecting the same menu option again, or just closing the + console window. + + The Java Console's text display always shows information about + your system and Jalview installation details. The rest are the most + recent messages output during your Jalview session. Some messages + are only captured by the console when it is open, so to get a full + log for debugging a problem, enable the console and then restart + Jalview. + + + You can temporarily control the detail of what appears as output by + selecting a Log level using the drop-down list at the + bottom left of the console. There are several levels to choose from: + The most verbose is TRACE, followed by DEBUG, INFO, WARN. When the + Console is opened, the default level will be chosen (INFO). + + + Note! If you change the log level in the Java + Console, this change will only persist for as long as the console + is open. Once you close the console the log level will revert back + to what it had been when you opened the console (usually INFO). + + Permanently changing Jalview's default log level + You can change the default log level by editing the Jalview + preferences file, .jalview_properties, found in your home + directory (on Windows: %HOMEPATH%, or the folder above 'My + Documents'; on macOS: ~ or /Users/username; on linux/unix: + ~ or /home/username), and setting the property logs.Jalview.level + to the log level you prefer, e.g. + + logs.Jalview.level=DEBUG + + You can also set the property + + logs.Axis.level=DEBUG + + to get debug information for Jalview's JPred service. The Axis log + level cannot be set from within the Java Console. + + + You can also set the logs.jalview.level property to a log level + not usually presented in the Java Console (though restricted to log + levels used by Apache Log4j -- see Log4j + Custom Log Levels for details of the standard log levels + available). Jalview does not currently define any custom log levels. + If you do set the property with a log level that is normally not + visible in the Java Console this should be respected and visibly + selected when you open the console. + + + The Clear button at the bottom of the console will clear + all logging messages except for the initial system information which + is rewritten to the console. + + + The Copy to clipboard button at the bottom right of the + console will copy all of the text in the console to your system + clipboard, ready to paste into another application (e.g. email + composer or issue tracker). + + + Reporting Bugs + + + If you come across a problem in Jalview where something is not + working as described, or how you think it should, you should first + check the Jalview FAQ to + see if this is a known problem and if there is a suggested + workaround. + + + If there is no FAQ answer covering your problem then you can submit + a bug report on the Jalview + Issue Tracker. It is good practice to search the issue tracker + first to see if the issue has already been reported. If an issue + already exists please continue to add your own comments to the issue + which may well help narrow down the problem, if not then you can + create an account and submit a new bug report: + + + Make sure that you set Project to Jalview (JAL), and Issue + Type to Bug or New Feature or Improvement + appropriately. Give a one line summary of the issue in the Summary. + In the Environment text box you can describe the + system you are using. This is usually most easily done by opening + the Java Console, clicking the Clear button, and then + immediately on the Copy to clipboard button, and then + pasting the clipboard into the text box. + + + You can then give more detailed information about how to recreate + the problem in the Description text box. If you want to + attach any screenshots or example alignment files that demonstrate + the problem then you can drag them to the Create Issue dialog in + your browser, or use the Attachment browse facility to + locate them on your computer. + + + + To help the Jalview team with diagnosing a particular issue, it is + really helpful if you can also add more detailed logs output whilst + re-creating the problem. To do this, open the Java Console, click + the Clear button and select TRACE in the Log level + drop down list. Whilst leaving the console open, perform the + task in Jalview that re-creates the problem. Then you can + copy the debug information in the Java Console by clicking on the Copy + to clipboard button and then paste that into the Description, or a + Comment of your issue. + + + + For other queries or comments about Jalview, remember you can + contact the Jalview team using email via the + Jalview + discussion list, on Twitter @Jalview, or for technical + discussions, via the Jalview developer's chatroom at + https://gitter.im/jalview/developers. + + + + diff --git a/help/help/html/memory.html b/help/help/html/memory.html index 0374dcb..7d6fb85 100755 --- a/help/help/html/memory.html +++ b/help/help/html/memory.html @@ -80,7 +80,7 @@ arguments, but you must put the jvl file first, e.g. /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa Alternatively, you can use the standard Jalview command line arguments with or without the jvl file (first), e.g. - /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal You can use command line arguments to control memory + /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal You can use command line arguments to control memory settings in Windows and macOS too: In Windows you must use, e.g. \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa In macOS you can use the macOS open command like this: diff --git a/help/help/html/releases.html b/help/help/html/releases.html index c83741a..fe4d257 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -1,3 +1,4 @@ + + + Development + + Updated building instructions +	+ + + Occupancy calculation is incorrect for + alignment columns with over -1+2^32 gaps (breaking filtering + and display) + + + Caps on Hi-DPI scaling to prevent crazy + scale factors being set with buggy window-managers (linux + only) + + Development + + Fixed non-fatal gradle errors during build + +
2.11.1 .4 + 09/03/2021	Improved control of + Jalview's use of network services via jalview_properties + + + New .jalview_properties token controlling + launch of the news browser (like -nonews argument) + + + New .jalview_properties token controlling + download of linkout URLs from + www.jalview.org/services/identifiers + + + New .jalview_properties token controlling + download of BIOJSHTML templates + + + New 'Discover Web Services' option to + trigger a one off JABAWS discovery if autodiscovery was + disabled + +	+ + + Intermittent deadlock opening structure in + Jmol + + New Known defects + + + Protein Cross-Refs for Gene Sequence not + always restored from project (since 2.10.3) + + + Selections from tree built from CDS aren't + propagated to Protein alignment (since 2.11.1.3) + + +
2.11.1 .3 + 29/10/2020	+ + + +	+ + + Find doesn't always highlight all matching + positions in a sequence (bug introduced in 2.11.1.2) + + + Alignments containing one or more protein + sequences can be classed as nucleotide + + + CDS alignment doesn't match original CDS + sequences after alignment of protein products (known defect + first reported for 2.11.1.0) + + + No tooltip or popup menu for genomic + features outwith CDS shown overlaid on protein + + + Overlapping CDS in ENA accessions are not + correctly mapped by Jalview (e.g. affects viral CDS with + ribosomal slippage, since 2.9.0) + + + Spliced transcript CDS sequences don't show + CDS features + + + Selections in CDS sequence panel don't + always select corresponding protein sequences + + + Make groups from selection for a + column selection doesn't always ignore hidden columns + + Installer + + + Space character in Jalview install path on + Windows prevents install4j launching getdown + + Development + + + Fixed typos and specified compatible gradle + version numbers in doc/building.md + + +
2.11.1 .2 + 25/09/2020	+ + +	+ + + Fresh install of Jalview 2.11.1.1 reports + "Encountered problems opening + https://www.jalview.org/examples/exampleFile_2_7.jvp" + + +
2.11.1 .1 - 13/07/2020	- - + + Shift+arrow keys navigate to next gap or + residue in cursor mode + + + Support import of VCF 4.3 by updating + HTSJDK from 2.12 to 2.23 + + + IntervalStore library updated to v.1.1: + optimisations and improvements suggested by Bob Hanson and + improved compatibility with JalviewJS + + + Retrieve GZipped stockholm formatted + alignments from Pfam and Rfam + + + Recognise GZipped content for URLs and File + import (no longer based on .gz extension) + + + Updated Spanish Translation for 2.11.1 + + + Migrate EMBL record retrieval to use latest + ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and + EMBL flat file + + + Improved warning messages, debug logging + and fixed Retry action when Jalview encounters errors when + saving or making backup files. + + + Enhanced Jalview Java Console: + + Jalview's logging level can be configured + Copy to Clipboard Buttion + + + + Improved support for Hi-DPI (4K) screens + when running on Linux (Requires Java 11+) + + Launching Jalview + + + Configure Jalview Desktop's look and feel + through a system property + + + Improved built-in documentation and command + line help for configuring Jalview's memory + +	- Escape does not clear highlights on the alignment (Since Jalview 2.10.3) - + + Conservation and Quality tracks are shown + but not calculated and no protein or DNA score models are + available for tree/PCA calculation when launched with + Turkish language locale + + + Escape does not clear highlights on the + alignment (Since Jalview 2.10.3) + + + Alt+Left or Right arrow in cursor mode + doesn't slide selected sequences, just sequence under cursor + + + Alt+Up/Down in cursor mode doesn't move + sequence under the cursor + + + Peptide-to-CDS tracking broken when + multiple EMBL gene products shown forÂ a single contig + + + Errors encountered when processing variants + from VCF files yield "Error processing VCF: Format specifier + '%s'" on the console + + + Count of features not shown can be wrong + when there are both local and complementary features mapped + to the position under the cursor + + + Sequence ID for reference sequence is + clipped when Right align Sequence IDs enabled + + + Slider with negative range values not + rendered correctly in VAqua4 (Since 2.10.4) + + + Single quotes not displayed correctly in + internationalised text for some messages and log output + + + Find doesn't report matches that span + hidden gapped columns + + + Resolved memory leaks in Tree and PCA + panels, Alignment viewport and annotation renderer. + + + Jalview ignores file format parameter + specifying output format when exporting an alignment via the + command line + + + Windows 10: For a minority of users, if + backups are not enabled, Jalview sometimes fails to + overwrite an existing file and raises a warning dialog. (in + 2.11.0, and 2.11.1.0, the workaround is to try to save the + file again, and if that fails, delete the original file and + save in place.) + + + Cannot process alignments from HTTPS urls + via command line + + + References to http://www.jalview.org in + program and documentation + + Launching Jalview + + + Jalview application fails when launched the + first time for a version that has different jars to the + previous launched version. + + Developing Jalview + + + Fixed issue with cleaning up old coverage + data, causing cloverReport gradle task to fail with an + OutOfMemory error. + + + Migrated the Jalview Version Checker to + monitor the release channel + + New Known defects + + + CDS shown in result of submitting proteins + in a CDS/Protein alignment to a web service is wrong when + proteins share a common transcript sequence (e.g. + genome of RNA viruses) + + + Co-located features exported and re-imported + are ordered differently when shown on alignment and in + tooltips. (Also affects v2.11.1.0) + + + Drag and drop of alignment file onto + alignment window when in a HiDPI scaled mode in Linux only + works for the top left quadrant of the alignment window + + + Stale build data in jalview standalone jar + builds (only affects 2.11.1.1 branch) + + + Sequence ID colourscheme not re-applied + when alignment view restored from project (since Jalview 2.11.0) + + + Duplicate CDS sequences are generated when + protein products for certain ENA records are repeatedly + shown via Calculate->Show Cross Refs + +