From 21c2deb35c435e6097b0f05c83d21cfdf4929ba2 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 5 Oct 2016 17:53:20 +0100 Subject: [PATCH] JAL-2189 formatting and release notes --- help/html/releases.html | 516 ++++++++++++++++++++++++++++++++++++----------- help/html/whatsNew.html | 21 +- 2 files changed, 413 insertions(+), 124 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index 6eb42bc..f29f708 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -52,91 +52,265 @@ General Application Applet + + +
+ General + Applet - - -
- General -
    -
  • reinstate CTRL-click for opening pop-up menu on OSX
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  • Export features in Jalview format (again) includes graduated colourschemes
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  • More responsive when working with big alignments and lots of hidden columns
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  • Hidden column markers not always rendered at right of alignment window
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  • Tidied up links in help file table of contents
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  • Feature based tree calculation not shown for DNA alignments
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  • Hidden columns ignored during feature based tree calculation
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  • Alignment view stops updating when show unconserved enabled for group on alignment
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  • Cannot insert gaps into sequence when set as reference
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  • Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
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  • Incorrect column numbers in ruler when hidden columns present
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  • Colour by RNA Helices not enabled when user created annotation added to alignment
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  • RNA Structure consensus only computed for '()' base pair annotation
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  • Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
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  • Extend selection with columns containing feature not working
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  • Pfam format writer puts extra space at beginning of sequence
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  • Incomplete sequence extracted from pdb entry 3a6s
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  • Cannot create groups on an alignment from from a tree when t-coffee scores are shown
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  • Cannot import and view PDB structures with chains containing negative resnums (4q4h)
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  • ArithmeticExceptions raised when parsing some structures
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  • 'Empty' alignment blocks added to Clustal, PIR and PileUp output
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  • Reordering sequence features that are not visible causes alignment window to repaint
  • Threshold sliders don't work in graduated colour and colour by annotation row for e-value @@ -151,12 +325,19 @@ columns
  • - FER1_ARATH and FER2_ARATH mislabelled in example file (uniref50.fa, feredoxin.fa, unaligned.fa, exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) + FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
  • - Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled + Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled +
    • +
  • + Quality and Conservation are now shown on + load even when Consensus calculation is disabled
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  • Quality and Conservation are now shown on load even when Consensus calculation is disabled
    • @@ -169,60 +350,151 @@
Application
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  • Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
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  • URLs and links can imported by drag'n'drop on OSX webstart
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  • InstallAnywhere distribution fails when launching Chimera
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  • Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
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  • Cannot save project when view has a reference sequence defined
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  • Columns are suddenly selected in other alignments and views when revealing hidden columns
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  • Hide columns not mirrored in complement view in a cDNA/Protein splitframe
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  • Cannot save/restore representative sequence from project when only one sequence is represented
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  • Disabled 'Best Uniprot Coverage' option in Structure Chooser
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  • Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
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  • View mapping in structure view shows mappings between sequence and all chains in a PDB file
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  • PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
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  • Export complete shown after destination file chooser is cancelled during an image export
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  • Error when querying PDB Service with sequence name containing special characters
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  • Manual PDB structure querying should be case insensitive
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  • Large tooltips with broken HTML formatting don't wrap
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  • Figures exported from wrapped view are truncated so L looks like I in consensus annotation
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  • Export features should only export the currently displayed features for the current selection or view
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  • Enable 'Get Cross-References' in menu after fetching cross-references
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  • Mouseover of a copy of a sequence is not followed in the structure viewer
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  • Titles for individual alignments in splitframe not restored from project
  • - missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default + +
    • +
  • + Corrupt preferences for SVG, EPS & HTML + output when running on non-gb/us i18n platforms +
    • +
  • + URLs and links can imported by drag'n'drop + on OSX webstart +
    • +
  • + InstallAnywhere distribution fails when + launching Chimera +
    • +
  • + Jalview very slow to launch via webstart + (also hotfix for 2.9.0b2) +
    • +
  • + Cannot save project when view has a + reference sequence defined
  • - amino acid physicochemical conservation is case dependent + Columns are suddenly selected in other + alignments and views when revealing hidden columns
  • - RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems) + Hide columns not mirrored in complement + view in a cDNA/Protein splitframe
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  • Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references
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  • - No progress bar shown during export of alignment as HTML + Cannot save/restore representative + sequence from project when only one sequence is + represented
  • - Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records. + Disabled 'Best Uniprot Coverage' option + in Structure Chooser
  • - Structures not always superimposed after multiple structures are shown for one or more sequences. + Modifying 'Ignore Gaps' on consensus or + structure consensus didn't refresh annotation panel
  • - Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled. + View mapping in structure view shows + mappings between sequence and all chains in a PDB file
  • - Cannot specify chain code when entering specific PDB id for sequence + PDB and Uniprot FTS + dialogs format columns correctly, don't display array + data, sort columns according to type
  • - File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled. + Export complete shown after destination + file chooser is cancelled during an image export
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  • Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence
  • - Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report + Error when querying PDB Service with + sequence name containing special characters +
    • +
  • + Manual PDB structure querying should be + case insensitive +
    • +
  • + Large tooltips with broken HTML + formatting don't wrap +
    • +
  • + Figures exported from wrapped view are + truncated so L looks like I in consensus annotation +
    • +
  • + Export features should only export the + currently displayed features for the current selection or + view +
    • +
  • + Enable 'Get Cross-References' in menu + after fetching cross-references +
    • +
  • + Mouseover of a copy of a sequence is not + followed in the structure viewer +
    • +
  • + Titles for individual alignments in + splitframe not restored from project +
    • +
  • + missing autocalculated annotation at + trailing end of protein alignment in transcript/product + splitview when pad-gaps not enabled by default +
    • +
  • + amino acid physicochemical conservation + is case dependent +
    • +
  • + RSS reader doesn't stay hidden after last + article has been read (reopened issue due to + internationalisation problems) +
    • +
  • + Only offer PDB structures in structure + viewer based on sequence name, PDB and Uniprot + cross-references +
    • + +
  • + No progress bar shown during export of + alignment as HTML +
    • +
  • + Improved warning messages when + DB Ref Fetcher fails to match, or otherwise updates + sequence data from external database records. +
    • +
  • + Structures not always superimposed after + multiple structures are shown for one or more sequences. +
    • +
  • + Reference sequence characters should not + be replaced with '.' when 'Show unconserved' format option + is enabled. +
    • +
  • + Cannot specify chain code when entering + specific PDB id for sequence +
    • +
  • + File->Export->.. as doesn't work when + 'Export hidden sequences' is enabled, but 'export hidden + columns' is disabled. +
    • +
  • + Best Quality option in structure chooser + selects lowest rather than highest resolution structures + for each sequence +
    • +
  • + Incorrect start and end reported for PDB + to sequence mapping in 'View Mappings' report
  • @@ -235,12 +507,21 @@
Applet
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  • Incorrect columns are selected when hidden columns present before start of sequence
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  • Missing dependencies on applet pages (JSON jars)
  • - Overview pixel size changes when sequences are hidden in applet + Incorrect columns are selected when + hidden columns present before start of sequence +
    • +
  • + Missing dependencies on applet pages + (JSON jars)
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  • Updated instructions for applet deployment on examples pages. +
  • + Overview pixel size changes when + sequences are hidden in applet +
    • +
  • + Updated instructions for applet + deployment on examples pages.
@@ -282,7 +563,7 @@
  • Updated Spanish translations of localized text for 2.9
    • Application -