From: gmungoc Date: Tue, 4 Oct 2016 14:12:19 +0000 (+0100) Subject: Merge branch 'bug/JAL-2210_hack_for_Release_2_10' into develop X-Git-Tag: Release_2_10_0~20 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fa2b80f5f3252f1f4801d2048b80a8745b399616;hp=b45b78bfc90750c57a947ba64e47d43de36100f1;p=jalview.git Merge branch 'bug/JAL-2210_hack_for_Release_2_10' into develop --- diff --git a/RELEASE b/RELEASE index 6cd9254..c29c5d5 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ -jalview.release=Release_2_9_0b1_Branch -jalview.version=2.9.0b2 +jalview.release=Release_2_10_Branch +jalview.version=2.10.0 diff --git a/examples/testdata/jal-2005.fa b/examples/testdata/jal-2005.fa new file mode 100644 index 0000000..cc58469 --- /dev/null +++ b/examples/testdata/jal-2005.fa @@ -0,0 +1,16 @@ +>a +QQQ +>b +QQQ +>c +QQQ +>d +QQQ +>e +QQQ +>f +QQQ +>g +QQQ +>h +QQQ diff --git a/examples/testdata/jal-2005.jvf b/examples/testdata/jal-2005.jvf new file mode 100644 index 0000000..8f37849 --- /dev/null +++ b/examples/testdata/jal-2005.jvf @@ -0,0 +1,11 @@ +feature_1 8c25cd + +STARTGROUP Jalview +feature_1 a -1 1 1 feature_1 0.4 +feature_1 a -1 2 2 feature_1 0.6 +feature_1 b -1 1 1 feature_1 0.8 +feature_1 b -1 2 2 feature_1 1.0 +feature_1 c -1 1 1 feature_1 1.5 +feature_1 d -1 1 1 feature_1 2.0 +feature_1 e -1 1 1 feature_1 3.0 +ENDGROUP Jalview diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html index 8c017a9..afee753 100755 --- a/help/html/calculations/sorting.html +++ b/help/html/calculations/sorting.html @@ -82,16 +82,23 @@ sorting.

Sorting according to sequence features
+ Additional sort operations for + alignments containing sequence features are provided in the + Feature + Settings dialog, opened via View→Feature + Settings...

Reversing the Order

Selecting any item from the Sort menu will sort sequences in an ascending order according to the property defining the sort. If the same sort is re-applied, the sequences will be sorted in the inverse - order. In the case of trees and alignment orderings, Jalview will - remember your last choice for sorting the alignment and only apply - the inverse ordering if you select the same tree or alignment - ordering item again.

+ order. In both cases, for sequences which are equivalent under the sort + operation, their order will be preserved (since version 2.10). In + the case of trees and alignment orderings, Jalview will remember + your last choice for sorting the alignment and only apply the + inverse ordering if you select the same tree or alignment ordering + item again.

diff --git a/help/html/colourSchemes/annotationColouring.html b/help/html/colourSchemes/annotationColouring.html index 30b6396..ed0ab3f 100755 --- a/help/html/colourSchemes/annotationColouring.html +++ b/help/html/colourSchemes/annotationColouring.html @@ -39,14 +39,17 @@

Select which annotation to base the colouring scheme on - using the top left selection box.
If the Per-sequence - only tick box is not greyed out, then ticking it will limit the - available annotation rows to just those that are sequence - associated (e.g. T-COFFEE scores and protein disorder predictions), which will colour each sequence - according to its own per-residue scores.
Per-sequence - associated annotation colouring was introduced in Jalview 2.8 + using the top left selection box. Sequence associated alignment + annotation are shown with the seuqence's name appended.
If + the Per-sequence only tick box is not greyed out, + then ticking it will limit the list of available annotation rows + to just the labels for those that are sequence associated. + Annotation rows on each sequence with the same label (e.g. + T-COFFEE scores and protein + disorder predictions) will then be used to colour its + corresponding positions in the alignment.
Per-sequence + associated annotation colouring is currently only available in + the Desktop.
If the "Use Original Colours" box is selected, the colouring scheme will use the colouring scheme present on the diff --git a/help/html/features/columnFilterByAnnotation.html b/help/html/features/columnFilterByAnnotation.html index 2b7d0ec..c53844b 100644 --- a/help/html/features/columnFilterByAnnotation.html +++ b/help/html/features/columnFilterByAnnotation.html @@ -32,7 +32,7 @@ or hidden according to annotation rows on the alignment. The dialog box is opened via "Select→Select/Hide Columns by Annotation...", and different filters are - presented dependent upon the data shown in the selected annotation + then presented for filtering data according to the selected annotation row.
@@ -41,12 +41,20 @@

- -
If an annotation with numeric values is selected, the threshold +
The drop down menu lists the annotation available on the + alignment. Sequence associated annotation rows will be shown with + the sequence ID appended to the annotation label. It is only + possible to select one row at a time.
+
+ If an annotation with numeric values is selected, the threshold filter option is activated. For other types of annotation, use the text box and secondary structure check boxes (right). The radio buttons at the bottom of the dialog specify the action applied to - columns matching the query.
+ columns matching the query.
Note: annotation + containing only numeric labels (e.g. T-COFFEE column confidence + scores) will not be treated as quantitative data. You will need to + enter search expressions to select columns in this case. +
- Search Filter
  - Export features in Jalview format (again) includes graduated colourschemes
  - More responsive when working with big alignments and lots of hidden columns
  - Hidden column markers not always rendered at right of alignment window
  - Tidied up links in help file table of contents
  - Tidied up links in help file table of contents
  - Feature based tree calculation not shown for DNA alignments
  - Hidden columns ignored during feature based tree calculation
  - Alignment view stops updating when show unconserved enabled for group on alignment
  - Extend selection with columns containing feature not working
  - Pfam format writer puts extra space at beginning of sequence
  - Incomplete sequence extracted from pdb entry 3a6s
  - Cannot create groups on an alignment from from a tree when t-coffee scores are shown
  - Cannot import and view PDB structures with chains containing negative resnums (4q4h)
  - ArithmeticExceptions raised when parsing some structures
  - 'Empty' alignment blocks added to Clustal, PIR and PileUp output
  - 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 + scores associated with features and annotation rows +
  - + amino acid physicochemical conservation + calculation should be case independent +
  - + Remove annotation also updates hidden + 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) +
  - + 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
  - + +
  - + +
  - + +
  Application
  - Cannot save/restore representative sequence from project when only one sequence is represented
  - Disabled 'Best Uniprot Coverage' option in Structure Chooser
  - Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
  - View mapping in structure view shows mappings between sequence and all chains in a PDB file
  - View mapping in structure view shows mappings between sequence and all chains in a PDB file
  - PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type
  - Export complete shown after destination file chooser is cancelled during an image export
  - 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 +
  - + +
  - + +
  Applet
  - Incorrect columns are selected when hidden columns present before start of sequence
  - Missing dependencies on applet pages (JSON jars)
  - + Overview pixel size changes when sequences are hidden in applet +
  - Updated instructions for applet deployment on examples pages. +
  diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index e1b00c4..1743f1c 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -37,16 +37,16 @@
- Ensembl sequence fetcher. Annotated Genes, transcripts and proteinsÂ can be retrieved via Jalview's new Ensembl REST - client. Support for import of Ensembl data also allows: + client. Support for import of Ensembl data allows:
  - Sequence variant data. Jalview - propagates variant annotation imported via Ensembl onto + propagates variant annotation on genomic regions onto transcripts and protein products, complete with associated metadata such as clinical significance.
  - Aligned locus view. Transcripts retrieved for a gene identifier via the Ensembl or EnsemblGenomes sequence databases are automatically aligned to - their reference genome.
- Working with structures.
- UniProt Free Text Search. The new search +
- UniProt Free Text Search. The new search dialog for UniProt allows you to browse and retrieve sequences from UniProt with free-text search and more structured queries
- Reference sequence based alignment - visualisation.. When a reference sequence is defined for the - alignment, the alignment column ruler is now numbered according to - the reference sequence. The reference sequence for alignment views - can also be saved and restored from Jalview projects.
- Reference sequence alignment view.. + Jalview 2.9 introduced support for reference sequences. In 2.10, + when a reference sequence is defined for the alignment, the + alignment column ruler is now numbered according to the reference + sequence. The reference sequence for alignment views can also be + saved and restored from Jalview projects.
- Ensembl and ENA 'show cross-references' + support.The Calculations menu's 'Show cross-references' will now + offer Ensembl as well as EMBLCDS and Uniprot when CDS/Protein + mapping data is available for download or display.