Latest improvements for CLC Sequence Viewer

Bug fixes

• Fixed an issue where the Search for Sequences at NCBI tool did not display the first and last search result in each page of results returned.

New features and improvements

• Tutorial windows are no longer blocked when a wizard is open.
• An exporter has been added to export annotations on sequences or tracks to Generic Feature Format Version 3 (GFF3) format.
• It is now possible to right-click on a table cell and filter table rows based on the value of that cell by choosing options under the new context menu section called  “Table filters”. This change applies to all tables where advanced filtering is available.
• Updated the restriction enzyme list from REBASE.

Bug fixes

• Fixed a problem where launching a tool from the Quick Launch window after sorting led to the wrong tool being started up.
• Fixed an issue with GenBank and EMBL exports where quoting specifications were not being conformed to.
• Fixed an issue where in some cases filtering tables for empty values would not produce any results.
• Fixed an issue where advanced filtering did not work when looking for rows with cells containing multiple values using the filtering term “=” (equals).
• A sporadic java issue that led to errors including the text “java.lang.ClassCastException: sun.awt.image.BufImgSurfaceData cannot be cast to sun.java2d.xr.XRSurfaceData”, has been addressed through an upgrade to java. This issue was primarily seen when using the Workbench remotely on Linux systems.
• Various minor bugfixes.

Retirement

• The GFF exporter has been retired and is no longer available. The new GFF3 exporter should be used instead.

Other notifications

• An option to opt out of providing anonymous usage information to QIAGEN has been added to the Workbench Preferences. We are not yet collecting any usage information so opting in or out does not have any effect at this time.

New features and improvements

• All NCBI server communication is now encrypted. (NCBI will be moving all web services to the HTTPS protocol on September 30, 2016).
• The list of enzymes pre-installed in the workbench has been updated from REBASE.
• The Quick Launch tool is now found under the Toolbox menu instead of the View menu and a button called Launch that brings up this tool has been added to the toolbar.
• The option “is not in list” has been introduced as a new table filtering option.
• The “Sort folder” tool now uses numerical sorting for filenames prefixed with a number.
• New placeholders are available when defining the names of exporter outputs:  {user}, {host}, and for elements of the timestamp of the output object, {year}, {month}, {day}, {hour, {minute}, {second}.
• Placeholders within export output names that were previously available only as digits can now be specified using written names: {input} is a synonym for {1}, {extension} is a synonym for {2} and {counter} is a synonym for {3}.
• GenBank import now also allows for file names with ‘GBFF’ extension.
• Read group details are now shown on the Element Info view of sequence lists.

Bug fixes

• Fixed a rare issue where some annotations could, but did not necessarily, go missing on  sequences with greater than 1000 annotations of a given type on that sequence before the deletion and where the right-click context menu option “Delete selection” was used.
• Fixed a bug in the “Manage Enzymes” wizard that prevented a user from cancelling the action if “Save as new enzyme list” was enabled.
• Fixed an issue with the Import Metadata tool where, if a spreadsheet had already been loaded, then selecting the same spreadsheet again did not reload the spreadsheet content.
• Fixed an issue where it took a long time to open a workbench it it was previouslyclosed when displaying an open table editor that had been sorted.
• Fixed an issue where right-clicking on a graph in a report and choosing to show “Report”, “History” or “Element Info” triggered an error.
• Various minor bugfixes.

Improvements

• All Excel sheets in a document are now imported and each sheet has a table created for its contents.
• The CSV, HTML and Excel table/tabular exporter now use “Inf” and “NaN” values to replace the ambiguous “?”.
• In the wizard for exporting a table in CSV format, when not exporting all columns, it is now possible to cancel or go back to the previous step while selected columns are loading.
• An option has been added to allow the same print settings to be applied to all reports being exported to pdf format in a given export run.
• The “Manage Resources” tab has been removed from the the Plugin Manager.

Changes

• Versions of individual tools are now reported in the history of output objects.
• Export to clc format now truncates very long filenames.
• RPM package installers for Linux are no longer available.
• The ‘Database Fields’ label shown in the ‘Show Element Info‘ view has been renamed to ‘ Local Attribute Fields’.
• The user can no longer uncheck “export all columns” for input objects that do not support this option. This applies to command line functionality as well, where the user will now receive an error if this is attempted.

Bug fixes

• Fixed a frame offset bug that occurred when translating reverse complemented CDS regions into protein sequences.
• The “Search for sequences at NCBI” tool would in some cases fail to download nucleotide sequences with the error message “The following sequences were not downloaded correctly: …”.
• Fixed a bug that caused the Excel importer to use column names as cell values of the first row.
• Fixed an issue where open tabs were not correctly ordered after splitting view horizontally or vertically using the View menu or keyboard shortcuts.
• Fixed an issue so that double clicking on clc:// urls on Mac OS X now opens the data element in a view in an installed CLC Workbench.
• A Workbench Data Location pointing at a file on the system instead of a folder will now appear as unavailable in the Workbench Navigation area instead of throwing an error.
• Fixed a bug where it was possible to type non-number characters into a number field when starting up a job in the Workbench.
• An error was previously thrown when encountering blank annotation-values. Blank values are now ignored.
• Fixed an error that could appear when moving the mouse over annotations in a sequence annotation table.
• Fix an issue that could lead to an error when a job status description changed while a full description was being generated.
• Fixed an issue where, when the option to “Skip these updates” was checked in the plugin update information window, this information was not saved. This led to the same plugin update information being presented after each Workbench restart if the plugins were not updated.
• Fixed an error that occurred when pressing the Print button in the Help dialog (Mac OS X only).
• Fixed an issue where the text area in error dialogs did not expand vertically when the dialog was expanded.
• Fixed a rare issue that could be triggered by switching editor view with a double click.

Plugin updates and fixes

All plugins need to installed in the new Workbench for compatibility reasons.

Changes to freely available plugins

• Batch rename: Fixed an issue where a warning was displayed for entries not modified.

New features and improvements

• Tooltips on leaves of phylogenetic trees now display a description of the attached sequence.
• One can now select “EST” as database when using the Search for Sequences at NCBI tool.
• The output of the Reverse Complement Sequence now gets the suffix -RC attached to the name of the input instead of -1 before.
• 3D molecule viewer improvements:
  • Molecular surfaces can now be transparent
  • A clipping plane can cut into surfaces and secondary structure
  • Options for creating atom groups and visualizing hydrogen bonds have been improved

Bug fixes

• Fixed an issue where some filtering operations, such as “doesn’t contain” did not act correctly when filtering table cells that contained multiple pieces of information.
• Fixed an issue where annotations that spanned the ends of a circular sequence would be incorrectly placed in the Circular Sequence View.
• Fixed a bug that caused the workbench to freeze if certain sequences were displayed in circular view with radial rendering of labels.
• Fixed an issue where some filtering operations, such as “doesn’t contain” did not act correctly when filtering table cells that contained multiple pieces of information.
• Fixed an issue that prevented a root folder on Windows drives from being used as a File Location.
• Fixed an issue where updating an existing installation on Windows would result in the .vmoptions file being deleted, which makes the Workbench run with the default Java configuration.

New features and improvements

• A 3D Molecule Viewer is now available for visualization of protein, RNA, DNA, and small molecules.
• Improved reporting of errors related to low disk space.

Bug fixes

• Fixed problem with links and text in tables that were being cut off when succeeding a link.
• Restriction site analysis: The values “Cut position(s)” column of the restriction site analysis table now behaves like numbers instead of text, meaning sorting and filtering works.

• A problem with saved table settings that sometimes did not work has been fixed. The bug fix includes a more robust/generic way of saving table settings with different columns. To fix this problem, existing saved table settings should first be loaded on an object where it works (i.e. has the same columns as when it was saved); and then the table settings should be saved with the old name to overwrite the settings.

• Metadata for phylogenetic trees: A bug has been fixed with import of metadata containing column names with colons.

• Fixed error when showing protein translations of annotations shorter than 3 bases.

New features and improvements

• The unused “Workflows” button has been removed from the toolbar.
• Local Search enabled from the menu bar now includes filtering on “Path”.
• Advanced filtering on tables now includes the option to filter for a space, comma or semi-colon delimited lists of terms.
• Zoom tools redesign: The “Zoom to selection” feature is now also available for sequences, sequence lists, alignments, and read mappings.
• Saving/applying side-panel settings for tables now works for different tables that share some columns.
• Copy operations can now be stopped.
• Import of Example Data and imports done through dragging files into the workbench and dropping them in the Navigation Area will no longer block the user interface while executing. Instead, the import happens as a background process that can be monitored and controlled via the Processes tab in the lower left corner.
• CLC workbenches now support high resolution displays such as Apple retina displays of all data shown in the View Area (including tooltips).
• More informative naming of coding region translations produced by the tool Translate to Protein. The name for a coding region translation consists of the name of the input sequence followed by the annotation type and finally the annotation name.

Changes

• Due to upgrade to Java 7,  Windows Server 2003 and OSX 10.5.8, 10.6 are no longer supported by Oracle. Hence, the system requirements are now: Linux, Windows Vista, Windows 7, Windows 8 or Windows Server 2008, or Mac OS X 10.7 or later.