Charles 歷史版本列表 Page3

更新時間：2020-10-14
更新細節：

What's new in this version:

New Functionality:
- Enabled visualization of GC content as a color plot in Map view or base colors in Sequence view
- Added support for finding similar DNA sequences with mismatches or indels compared to the search query
- Added support for simulating the migration of supercoiled DNA molecules in agarose gels using TBE, TAE or SB buffer
- Added support for single-stranded DNA (ssDNA) sequences
- Enabled import of Sequencher project files (*.spf)
- Enabled "Undo" for edits in large sequences
- Added DNA ladders from DyneBio
- Added supercoiled MW markers from ELPIS BIOTECH and New England Biolabs
- Added BsmBI-v2 to the list of enzymes available from New England BioLabs
- Added fields for username and email address in the license registration dialog

Enhancements:
- Optimized storage of history for the following operations: Change Methylation, Change Transformation Strain, Set Origin, Flip, Insert/Delete/Replace, Linearize, Circularize
- Updated the supported protein feature types by adding new types (NonStdRes, Protein, Precursor, SecStr, Het, CDS, gene, misc_feature, unsure, variation), promoting Region subtypes to types, and adding new Site and Bond subtypes
- Added a note in Features view to indicate the presence of internal stop codons in a translated feature
- Enhanced the Preferences tools to allow more flexible default options for displaying ORFs
- Enabled carrying over feature qualifiers when creating a protein sequence using "Make Protein" or "Reverse Translate"
- Added the option to merge segments when using "Make Protein" on a multi-segment DNA feature
- Added a "Hide noncutters" check box in the Choose Enzymes dialog
- Enabled importing features from any supported file type when using "Import Features from a SnapGene File"
- Enabled more flexible batch conversion of chromatogram traces to other formats
- Improved search performance for large DNA sequences
- Configured the minimap to show both scrolled areas when two copies of Sequence view are visible
- Updated the format of the Preferences dialog, and added an "Agarose Gels" tab
- Added the option to designate a new collection as the Main Collection
- Enabled saving imported online sequences directly to a collection
- Added shortcuts in a collection Overview for navigating to the DNA Files, Protein Files, or Miscellaneous Files sections
- Enabled symbols to be entered in search queries when searching SnapGene Online Sequences
- Increased the size of the length indicator in the map label at the "Small" font size
- Consolidated all Fisher MW Markers for agarose gels in the Fisher Scientific set
- Configured the Nonredundant Commercial enzyme set to include similar enzymes that differ by methylation sensitivity
- Configured SnapGene to show the Launch dialog on macOS when the SnapGene icon in the Dock is clicked, if no SnapGene windows are open
- Changed the icon for enabling interrupted circle format for a linear DNA sequence in Map view
- Configured the "Export Map" and "Export History" options to be always enabled
- Improved the wording of various menu options and dialogs to provide greater clarity and consistency
- Added a message informing the user that files can be dragged into the list when using Align Multiple Sequences

Fixed:
- Fixed an issue that prevented cloning dialogs from allowing the use of hidden enzymes
- Corrected an issue in "Protein Search" whereby terminal stop codons were not included in the search query
- Ensured that edits in an alignment window do not cause inappropriate scrolling
- Corrected an issue that could prevent alignment of a high-quality sequence trace
- Ensured that the "Find" control in the Enzymes view chooser always shows a message to indicate if the enzyme is not in the chosen set
- Corrected an issue in which U's in overhangs resulting from linearizing were not preserved
- Configured "Select All" in the trace viewer context menu to actually select all
- Ensured that History view reflects changes after editing DNA ends
- Ensured that case changes in the "Find" entry field are preserved when the search is executed
- Ensured that imported RNA alignments are converted to DNA rather than protein alignments
- Corrected the license inactivity countdown to displays seconds rather than milliseconds
- Ensured that the "Accession Number:" label remains next to its entry field in the collection Search dialog
- Ensured that a "Sequence Name" search in the Protein Files area of a collection also searches the map labels and aliases
- Corrected an issue that resulted in alignment and collection windows not showing unsaved changes in the title bar on Windows and Linux
- Ensured more consistent sorting of enzymes in the Choose Enzymes dialog
- Streamlined the substitution matrix options presented when computing pairwise alignments
- Ensured that open alignments can be used as profiles when computing new alignments
- Corrected an issue that could result in the "Kind" column disappearing when viewing a collection
- Ensured that crisp screenshots are shown when detecting updates
- Improved import of the full publication date from PubMed
- Made various stability fixes

更新時間：2020-10-03
更新細節：

更新時間：2020-09-24
更新細節：

更新時間：2020-09-23
更新細節：

What's new in this version:

- This version fixes an issue with pairwise alignments and improves import from NCBI

更新時間：2020-09-23
更新細節：

What's new in this version:

Fixes:
- Corrected a regression with computing pairwise alignments on Windows and Linux
- Improved reliability when importing from NCBI

更新時間：2020-09-17
更新細節：

What's new in this version:

New Functionality:
- Added Agilent TapeStation ladders

Fixed:
- Corrected a regression that prevented decoding of features in Gene Construction Kit files
- Corrected a regression that prevented the bacterial transformation strain from being applied to the cloning product
- Fixed an issue with applying the "Limit file history" preference
- Improved detection of Gateway attR1, attR2 and attR4 sites
- Improved the default binding site shown when invoking the Edit Primer dialog for a primer with multiple binding sites
- Corrected an issue with simulating Gateway cloning using att sites that lie across the numerical origin
- Removed an outdated comment regarding PmlI losing activity when stored at -20°C
- Corrected the Import Primers dialog to proceed when Enter/Return is pressed
- Fixed an issue that could result in peak data disappearing when editing Sanger sequence traces
- Corrected a regression that prevented Shift-selecting a range of primers in Primers view
- Removed the "Fixed Line Width" button from the side toolbar in the Anneal Oligos dialog
- Corrected various stability issues when using cloning dialogs
- Ensured that the Sequence view minimap is consistently shown
- Fixed an issue with migrating the chosen enzymes when cloning while using a custom local enzyme set
- Corrected a regression that could cause the Browse Common Features dialog to switch from Sequence to Map view when the displayed feature was changed
- Improved the tooltips for history operations
- Ensured that changing the sequence methylation reliably updates the methylation state in the Description Panel
- Improved the document icon for DNA alignments to include a shadow
- Corrected an issue with splitting the view after having previously done so
- Corrected an issue with using Shift and the Left/Right arrow keys to move selected ranges across an entire gap in an alignment

更新時間：2020-09-17
更新細節：

What's new in this version:

New Functionality:
- Added Agilent TapeStation ladders

Fixed:
- Corrected a regression that prevented decoding of features in Gene Construction Kit files
- Corrected a regression that prevented the bacterial transformation strain from being applied to the cloning product
- Fixed an issue with applying the "Limit file history" preference
- Improved detection of Gateway attR1, attR2 and attR4 sites
- Improved the default binding site shown when invoking the Edit Primer dialog for a primer with multiple binding sites
- Corrected an issue with simulating Gateway cloning using att sites that lie across the numerical origin
- Removed an outdated comment regarding PmlI losing activity when stored at -20°C
- Corrected the Import Primers dialog to proceed when Enter/Return is pressed
- Fixed an issue that could result in peak data disappearing when editing Sanger sequence traces
- Corrected a regression that prevented Shift-selecting a range of primers in Primers view
- Removed the "Fixed Line Width" button from the side toolbar in the Anneal Oligos dialog
- Corrected various stability issues when using cloning dialogs
- Ensured that the Sequence view minimap is consistently shown
- Fixed an issue with migrating the chosen enzymes when cloning while using a custom local enzyme set
- Corrected a regression that could cause the Browse Common Features dialog to switch from Sequence to Map view when the displayed feature was changed
- Improved the tooltips for history operations
- Ensured that changing the sequence methylation reliably updates the methylation state in the Description Panel
- Improved the document icon for DNA alignments to include a shadow
- Corrected an issue with splitting the view after having previously done so
- Corrected an issue with using Shift and the Left/Right arrow keys to move selected ranges across an entire gap in an alignment

更新時間：2020-09-04
更新細節：

更新時間：2020-09-02
更新細節：

更新時間：2020-08-25
更新細節：

What's new in this version:

Features:
- hyperv/disks: Add ability to manage virtual disks for guests

Improvements:
- core: Allow provisioners to be run when a communicator is not available]
- core: Add autocomplete command that allows for install of bash or zsh autocomplete scripts]
- core: Update to childprocess gem to 4.0.0]
- core: Add action to wait for cloud-init to finish running]
- core: Update to net-ssh to 6.0 and net-sftp to 3.0]
- core: Optimize port in use check for faster validation]
- core: Support for Ruby 2.7]
- core: Add synced folder capabilities for mount options and default fstab modification behavior]
- guest/arch: Use systemd-networkd to configure networking for guests]
- guest/haiku: Rsync install for rsync synced folders]
- guest/solaris11: Add guest capability shell_expand_guest_path]
- host/darwin: Add ability to build ISO]
- hosts/linux: Add ability to build ISO]
- hosts/windows: Add ability to build ISO]
- providers/hyperv: Add support for SecureBootTemplate setting on import]
- providers/hyperv: Add support for EnhancedSessionTransportType]
- virtualbox/disks: Add ability to manage virtual dvds for guests]

Bug fixes:
- core: Ensure MapCommandOptions class is required
- core: Fix :all special value on triggers
- core: Ensure network addresses have a valid netmask
- core: Recover local machine metadata in global index
- core: Print CLI help message is ambiguous option provided
- core: Update how /etc/hosts gets updated for darwin, freebsd and openbsd
- core: Capture [3J escape sequence
- core: Treat empty box value as invalid
- core: Allow forwarding ports to unknown addresses
- core: Scrub credentials as whole words
- commands/destroy: Add gracefull option to switch beween gracefully or forcefully shutting down a vm
- communicator/ssh: Raise an error for a nil exit status
- communicator/winrm: Check for nil return from querying for forwarded ports
- config/vm: Add option allow_hosts_modification to allow/disable Vagrant editing the guests /etc/hosts file
- config/vm: Add config option hostname to config.vm.network
- config/vm: Don't ignore NFS synced folders on Windows hosts
- host: Use regular port check for loopback addresses
- host: Allow windows and linux hosts to detach from rdp process
- host/windows: Properly register SMB password validation capability
- guests: Allow setting of hostname according to hostname option for multiple guests
- guest/alpine: Allow setting of hostname according to hostname option
- guest/esxi: Be more permissive with permissions of ssh directory
- guest/linux: Add virtual box shared folders to guest fstab
- guest/suse: Allow setting of hostname according to hostname option
- providers/docker: Ensure new containers don't grab existing bound ports
- providers/hyperv: Fix check for secure boot
- providers/virtualbox: Fix inability to create disk with same name across multiple guests
- provisioners/docker: Allow to specify docker image version using the run option
- provisioners/file: Allow creating empty folders
- provisioners/shell: Ensure Windows shell provisioner gets the correct file extension
- util/powershell: Use correct powershell executable for privileged commands