-jalview.release=Release_2_9_0b1_Branch
-jalview.version=2.9.0b2
+jalview.release=Release_2_10_Branch
+jalview.version=2.10.0
--- /dev/null
+>a
+QQQ
+>b
+QQQ
+>c
+QQQ
+>d
+QQQ
+>e
+QQQ
+>f
+QQQ
+>g
+QQQ
+>h
+QQQ
--- /dev/null
+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
sorting.
</p>
</ul>
- <p>
+ <p><strong>Sorting according to sequence features</strong><br/>
+ Additional sort operations for
+ alignments containing sequence features are provided in the
+ <strong><a href="../features/featuresettings.html#sortbyfeature">Feature
+ Settings</a></strong> dialog, opened via <strong>View→Feature
+ Settings...</strong><p>
<strong>Reversing the Order</strong>
</p>
<p>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.</p>
+ 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.</p>
</body>
</html>
</div>
<ul>
<li>Select which annotation to base the colouring scheme on
- using the top left selection box.<br />If the <strong>Per-sequence
- only</strong> 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 <a
- href="../webServices/proteinDisorder.html"
- >protein disorder predictions</a>), which will colour each sequence
- according to its own per-residue scores.<br /> <em>Per-sequence
- associated annotation colouring was introduced in Jalview 2.8</em>
+ using the top left selection box. Sequence associated alignment
+ annotation are shown with the seuqence's name appended.<br />If
+ the <strong>Per-sequence only</strong> 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 <a href="../webServices/proteinDisorder.html">protein
+ disorder predictions</a>) will then be used to colour its
+ corresponding positions in the alignment.<br /> <em>Per-sequence
+ associated annotation colouring is currently only available in
+ the Desktop.</em>
</li>
<li>If the "Use Original Colours" box is selected,
the colouring scheme will use the colouring scheme present on the
or hidden according to annotation rows on the alignment. The dialog
box is opened <em>via</em> "<strong>Select→Select/Hide
Columns by Annotation...</strong>", 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.
</p>
<table>
<td><img src="AnnotationColumnSelectionWithoutSM.gif"></td>
</tr>
</table>
-
- <p>If an annotation with numeric values is selected, the threshold
+ <p>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.</p>
+ <p>
+ 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.</p>
+ columns matching the query.<br /> <em>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.</em>
+ </p>
<ul>
<li><strong>Search Filter</strong>
<ul>
<body>
<strong>Fetching ENSEMBL Data in Jalview</strong>
- <br /> Jalview Version 2.10 (September 2016) introduced support to
+ <br /> Jalview Version 2.10 (October 2016) introduced support to
retrieve annotated transcripts, peptides and genomic contigs from
<a href="http://www.ensembl.org">ENSEMBL</a>.
<br />
<img src="selectfetchdb.gif" align="left" width="480" height="204"
alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
- <p>Two types of ENSEMBL source are provided. ENSEMBL queries the
- main ENSEMBL site, which only serves data for higher eukaryotes, and
- EnsemblGenomes, which provides access to Ensembl Pathogens, and
- other warehouses.</p>
- <p><strong>General Use</strong><br/> If you have a set of Ensembl
- peptide or transcript IDs, then you can retrieve them
- <em>via</em> the sequence fetcher dialog opened after selecting the
- most appropriate source (either 'ENSEMBL', or Ensembl Genomes).
- However, Jalview's Ensembl client has a couple of additional
- capabilities: </p><p><strong>Retrieving aligned transcripts for a genomic ID</strong>
- </p>
- <p>If a single genomic identifier is entered in the
- Ensembl fetcher, Jalview will return all transcripts and products
- for the locus, and display them in a split view - complete with
- sequence variant annotation.</p>
- <p><strong>Retrieving orthologs for a gene ID</strong></p>
- <p>If a gene ID is entered (e.g. fox1), Jalview will resolve
- Ensembl genomic identifiers for a predefined set of taxa (Mouse,
- Rat, Human, Yeast in Jalview 2.10).
- </p>
+ <p>
+ Two types of ENSEMBL source are provided. ENSEMBL queries the main
+ ENSEMBL warehouse containing data for higher eukaryotes, and
+ EnsemblGenomes, which queries Ensembl Pathogens, and other
+ warehouses.<br />
+ <em>Ensembl support is new in Jalview, and we expect to merge
+ these sources in a future release.</em>
+ </p>
+ <p>
+ <strong>General Use</strong><br /> If you have a set of Ensembl gene
+ or transcript IDs, then you can retrieve them <em>via</em> the
+ sequence fetcher dialog opened after selecting the most appropriate
+ source (either 'ENSEMBL', or Ensembl Genomes). However, Jalview's
+ Ensembl client has a couple of additional capabilities:
+ </p>
+ <p>
+ <strong>Retrieving aligned transcripts for a genomic ID</strong>
+ </p>
+ <p>If a single genomic identifier is entered in the Ensembl
+ fetcher, Jalview will return all transcripts and products for the
+ locus, and display them in a split view - complete with sequence
+ variant annotation.</p>
+ <p>
+ <strong>Retrieving orthologs for a gene ID</strong>
+ </p>
+ <p>
+ If a gene ID is entered (e.g. fox1), Jalview will resolve Ensembl
+ genomic identifiers for a predefined set of taxa (Mouse, Rat, Human,
+ Yeast in Jalview 2.10).<br />
+ </p>
+ <p>
+ <strong><a name="ensemblannotation">Ensembl Sequence
+ Features</a></strong><br /> Jalview 2.10 includes support for the
+ visualisation and transfer genomic and transcriptomic sequence
+ features onto protein product sequences. Retrieval of a genomic
+ locus results in a set of transcripts that are annotated with
+ nucleotide variant information and exonic regions. By default,
+ intronic regions will be hidden.
+ </p>
+ <p>
+ <strong><a name="variantvis">Variant information on
+ Protein Products</a></strong><br />Jalview can translate genomic variant
+ annotation into protein sequence variant codes for variants
+ intersecting coding regions of a gene. To see this in action, use
+ the <strong>Calculate→Show cross-references</strong> menu to
+ view protein product sequences for the currently displayed (or
+ selected) sequences. The same menu allows you to recover Ensembl
+ exon, transcript and variant information when viewing UniProt
+ sequences.
+ </p>
+ <p>
+ <strong>Viewing more information about variant annotation</strong><br />
+ Variants are highlighted as red sequence features on the protein
+ sequence, with each one reporting all protein sequence variants
+ observed at that position as a result of the genomic variants.
+ Right-clicking a variant allows you to open the Ensembl Variants web
+ page for each variant, via the <strong>Link</strong> submenu.
+ </p>
+ <p>
+ <strong>Work in Progress !</strong><br />In the next few releases,
+ we hope to improve and extend Jalview's support for working with
+ Ensembl. If you have any problems, questions or suggestions then
+ please get in contact with us via the Jalview discussion list.
+ </p>
</body>
</html>
\ No newline at end of file
different names associated with a DOMAIN feature).
</p>
<p>
- <strong>Ordering alignment by features</strong><br> The 'Seq
+ <strong><a name="sortbyfeature">Ordering alignment by features</a></strong><br> The 'Seq
Sort by Score' and 'Seq Sort by Density' buttons will sort the
alignment based on the average score or total number of currently
active features and groups on each sequence. To order the alignment
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>27/9/2016</em></strong>
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>04/10/2016</em></strong>
</div>
</td>
<td><em>General</em>
<ul>
- <li><!-- JAL-2164,JAL-1919,-->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
+ <li><!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
<li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
<li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
<li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
<li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
<li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
<li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
+ <li><!-- JAL-2236 -->Sequence name added to annotation label in select/hide columns by annotation and colour by annotation dialogs</li>
+
</ul> <em>Application</em>
<ul>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
- <li><!-- JAL---></li>
+ <li><!-- JAL-2050-->Automatically hide introns when opening a gene/transcript view</li>
+ <li><!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search dialog</li>
<li><!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>
<li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
<li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
<li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
<li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
- <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
+ <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for record retrieval via ENA rest API</li>
<li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
+ <li><!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster groovy script execution</li>
<li><!-- JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
<li><!-- JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
<li><!-- JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
<li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
<li><!-- JAL-1803 -->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+ <li><!-- JAL-1993 -->Database selection dialog always shown before sequence fetcher is opened</li>
<li><!-- JAL-2183 -->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
<li><!-- JAL-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
<li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+ <li><!-- JAL-2028 -->Displayed columns for PDBe and Uniprot querying stored in preferences</li>
+ <li><!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot search results</li>
+ <li><!-- JAL-1977-->Tooltips shown on database chooser</li>
+ <li><!-- JAL-391 -->Reverse complement function in calculate menu for nucleotide sequences</li>
+ <li>
+ <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+ </li>
+ <li>
+ <!-- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
</ul> <em>Applet</em>
<li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
<li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
<li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
- <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
+ <li><!-- JAL-2067 -->Tidied up links in help file table of contents</li>
<li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
<li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
<li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
<li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
<li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>
<li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
-
+ <li><!-- JAL-2238 -->Cannot create groups on an alignment from from a tree when t-coffee scores are shown</li>
+ <li><!-- JAL-1836,1967 -->Cannot import and view PDB structures with chains containing negative resnums (4q4h)</li>
+ <li><!-- JAL-1998 -->ArithmeticExceptions raised when parsing some structures</li>
+ <li><!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added to Clustal, PIR and PileUp output</li>
+ <li><!-- JAL-2008 -->Reordering sequence features that are not visible causes alignment window to repaint</li>
+ <li>
+ <!-- JAL-2006 -->Threshold sliders don't work in
+ graduated colour and colour by annotation row for e-value
+ scores associated with features and annotation rows
+ </li>
+ <li>
+ <!-- JAL-1797 -->amino acid physicochemical conservation
+ calculation should be case independent
+ </li>
+ <li>
+ <!-- JAL-2173 -->Remove annotation also updates hidden
+ columns
+ </li>
+ <li>
+ <!-- JAL-2234 -->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)
+ </li>
+ <li>
+ <!-- JAL-2065 -->Null pointer exceptions and redraw problems when reference sequence defined and 'show non-conserved' enabled
+ </li>
+ <li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
</ul>
<em>Application</em>
<ul>
<li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
<li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
<li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
- <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>
+ <li><!-- JAL-1962 -->View mapping in structure view shows mappings between sequence and all chains in a PDB file</li>
+ <li><!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS dialogs format columns correctly, don't display array data, sort columns according to type</li>
+ <li><!-- JAL-1975 -->Export complete shown after destination file chooser is cancelled during an image export </li>
+ <li><!-- JAL-2025 -->Error when querying PDB Service with sequence name containing special characters</li>
+ <li><!-- JAL-2024 -->Manual PDB structure querying should be case insensitive</li>
+ <li><!-- JAL-2104 -->Large tooltips with broken HTML formatting don't wrap</li>
+ <li><!-- JAL-1128 -->Figures exported from wrapped view are truncated so L looks like I in consensus annotation</li>
+ <li><!-- JAL-2003 -->Export features should only export the currently displayed features for the current selection or view</li>
+ <li><!-- JAL-2036 -->Enable 'Get Cross-References' in menu after fetching cross-references</li>
+ <li><!-- JAL-2032 -->Mouseover of a copy of a sequence is not followed in the structure viewer</li>
+ <li><!-- JAL-2163 -->Titles for individual alignments in splitframe not restored from project</li>
+ <li>
+ <!-- JAL-2145 -->missing autocalculated annotation at trailing end of protein alignment in transcript/product splitview when pad-gaps not enabled by default
+ </li>
+ <li>
+ <!-- JAL-1797 -->amino acid physicochemical conservation is case dependent
+ </li>
+ <li>
+ <!-- JAL-1448 -->RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+ </li>
+ <li><!-- JAL-1960 -->Only offer PDB structures in structure viewer based on sequence name, PDB and Uniprot cross-references</li>
+
+ <li>
+ <!-- JAL-1976 -->No progress bar shown during export of alignment as HTML
+ </li>
+ <li>
+ <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+ </li>
+ <li>
+ <!-- JAL-2213 -->Structures not always superimposed after multiple structures are shown for one or more sequences.
+ </li>
+ <li>
+ <!-- JAL-1370 -->Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ </li>
+ <li>
+ <!-- JAL-1823 -->Cannot specify chain code when entering specific PDB id for sequence
+ </li>
+ <li>
+ <!-- JAL-1944 -->File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ </li>
+ <li><!--JAL-2026-->Best Quality option in structure chooser selects lowest rather than highest resolution structures for each sequence</li>
+ <li>
+ <!-- JAL-1887 -->Incorrect start and end reported for PDB to sequence mapping in 'View Mappings' report
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+
<!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
</ul>
<em>Applet</em>
<ul>
<li><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
+ <li><!-- JAL-1986 -->Missing dependencies on applet pages (JSON jars)</li>
+ <li>
+ <!-- JAL-1947 -->Overview pixel size changes when sequences are hidden in applet
+ </li>
+ <li><!-- JAL-1996 -->Updated instructions for applet deployment on examples pages.
+ </li>
</ul>
</div>
</td>
<li><strong>Ensembl sequence fetcher.</strong> Annotated Genes,
transcripts and proteins can be retrieved via Jalview's new <a
href="features/ensemblsequencefetcher.html">Ensembl REST
- client</a>. Support for import of Ensembl data also allows:
+ client</a>. Support for import of Ensembl data allows:
<ul>
<li><strong>Sequence variant data.</strong> 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.</li>
<li><strong>Aligned locus view.</strong> Transcripts
retrieved for a gene identifier via the Ensembl or
EnsemblGenomes sequence databases are automatically aligned to
- their reference genome.</li>
+ their reference genome, and introns hidden from the view.</li>
</ul></li>
<li><strong>Working with structures.</strong>
<ul>
now downloads data from the EMBL-EBI's PDBe site as <a href="features/mmcif.html">mmCIF</a>.
This allows very large structures to be imported, such as the HIV virus capsid assembly.</li>
</ul></li>
- <li><strong>UniProt Free Text Search</strong>. The new search
+ <li><strong>UniProt Free Text Search.</strong> The new search
dialog for UniProt allows you to browse and retrieve sequences
from UniProt with free-text search and more structured queries</li>
- <li><strong>Reference sequence based alignment
- visualisation.</strong>. 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.</li>
- <li></li>
+ <li><strong>Reference sequence alignment view.</strong>.
+ 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.</li>
+ <li><strong>Ensembl and ENA 'show cross-references'
+ support.</strong>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.</li>
</ul>
</body>
git://source.jalview.org / jalview.git / commitdiff