Rapid PHP Editor 歷史版本列表
更新時間：2021-12-03
更新細節：
What's new in this version:
Improvements:
- Animate opening of lists in the Project Manager, action/condition selector and in the Debugger
- Allow usage of custom ICE servers in the P2P extension
- Move scene variables into their own category in actions/conditions/expressions
Extensions, assets and examples:
- Add "Idle object tracker" behavior
- Provides a condition checking if an object did not move for a certain amount of time (configurable, with a configurable tolerance for the movement too)
- New extension "WebSocket client"
- This allows for connecting to a WebSockets server from GDevelop. An extension to create WebSocket servers in GDevelop will follow soon!
- Fix "is inside" in Marching Square extension, add line drawing and hitboxes generation
- Add BehaviorRemapper extension
- This extension allows remapping the default keyboard controls of behaviors in one action.
- Change all default package name to start with com.example
- Useful to trigger a warning in GDevelop if used as is.
- Add an example of a spider throwing a web
Fixed:
- Fix the "separate" action when there are several obstacles
- Previously an object colliding with multiple objects would have been "pushed" too far from the two colliding objects. Now, it gets properly separated, in a much more natural way, avoiding some shaking/flickering on corners or when involving multiple obstacles.
- Fix crash when modifying the operator for an action or condition of a "color" property of a behavior
- Fix debugger actions not hiding properly after opening it
- Fix sounds sometimes not playing after the first time being played
- Fix tweens automatically deleting the object sometimes affecting newly created objects
- Fix the layer of the created object not shown for the "Create object" action in the events sheet
- Fix wrong mention of extensions instead of examples in a text
- Fix tabs in preference dialog disappearing when scrolling in the dialog
更新時間：2021-11-30
更新細節：
What's new in this version:
New Functionality:
- Added a tool for adding enzymes sites to a coding sequence by silent mutation
- Added a tool for removing an enzyme site from a coding sequence by silent mutation
- Added support for custom features types not included in the standard set of GenBank feature types
- Enabled changing the default color of standard Genbank feature types
- Added support for saving and loading Agarose gel simulations as .gel files
- Added support for features within pairwise alignments
- Enabled adding, editing and deleting features in alignments
- Added a features table when viewing pairwise and multiple sequence alignments
- Enabled searching an alignment to find features
- Enhanced Gibson, InFusion and NEBuilder HiFi Assembly simulation tools to allow the vector to be flipped
- Enhanced cloning simulation tools to support adding, removing and re-ordering sequences
- Included controls to filter the set of chosen enzymes based on the number of times and relative location an enzyme cleaves with respect to its recognition sequence
- Enabled setting a default Codon Usage Table
- Added tool for converting ng/uL to nM in the DNA Calculations dialog
- Added base counts to the DNA Calculations dialog
Enhancements:
- Enhanced the 'Blocks of 3' Sequence view format to enable aligning nucleotide triplets with the reading frame
- Support for optionally displaying sequence names alongside the sequences when printing pairwise and multiple sequence alignments
- Switched from "?" to "X/Xaa" in translations to represent ambiguous amino acids
- Added Tm for the selected region in ssDNA sequences
- Added a locking mechanism which sets files as read only to other instances of SnapGene when being edited. Note that the locking mechanism is not available on large files, and has short delay, so is not effective when files are opened simultaneously
- Convert Psi to U when importing or creating a new RNA sequence
- Added support for including binding site locations when exporting primer data
- Added Gateway Cloning destination vectors pEXP3-DEST and pEXP4-DEST, and updated cross-references in descriptions for pEXP-DEST Vectors
- Features and custom numbering are now retained when copying and pasting into the New Protein File dialog, or inserting or replacing residues in a protein sequence
- Added support for pasting copied complementary primer pairs to configure an Agarose Gel lane
- Improved explanation for how to change sequence methylation when an enzyme is blocked during Restriction Cloning
- Added support for adjusting the resolution (ppi) and creating a transparent image when exporting maps from the command line interface
- Included various textual enhancements
Fixed:
- Included Nicking enzymes in the 6+ Cutters enzyme set
- Remove secondary recognition sequence for TaqII as this does not result in cleavage
- Restore last shown enzyme variant when returning to a previously viewed enzyme in the Restriction Enzymes window.
- Reduced file size and sped up loading files by omitting features in History view for large ancestral sequences
- Added support for the following non-standard qualifiers for all translatable feature types: calculated_mol_wt, codon, codon_start, exception, protein_id, transl_except, transl_table, translation
- Non-standard qualifiers are now retained when importing and exporting (previously they were converted to /note)
- Added support for /transl_table and /codon_start qualifiers with CDS features in protein sequences
- Fixed an occasional issue on macOS where an empty SnapGene window appears which cannot be closed except by restarting SnapGene
- Disabled subsidiary check boxes when appropriate in Preferences
- Corrected mouse-over effects for Site features with multiple segments
- Fixed an issue that prevented setting a protein point feature type to misc_feature, unsure, or variation.
- Automatically change feature color when changing the type when adding a point feature if the color has not been manually adjusted.
- Fixed an issue where U's were not converted to T's if either end of a linear DNA sequence is modified to be covalently closed.
- Fixed an issue where unsaved files added to the align sequence tools were listed using the wrong name
- Fixed an issue that sometimes prevented run-on translations from being shown in alignments
- Ensured it is always possible to scroll to the last base in DNA files
- Removed inappropriate methylation message which was shown when opening the features tab for some protein files
- Corrected an issue that prevented pliancy from being shown when using the "Choose Alternative Codons" tool
- Corrected various display issues when switching a lane in an agarose gel simulation to using a MW marker
- Fixed an issue that prevented point features from being added to protein sequences
- Require a product name to be specified when using the Mutagenesis tool
- Ensured bases are always visible when history colors are shown
- Always show shared codons in adjacent translated features within Sequence view
- Fixed Align to Reference DNA sequence so that undoing sequences edits no longer hides the aligned sequences
- Reliably display ORF's that wrap around the numerical origin in circular sequences
- Fixed an issue that prevented some keyboard shortcuts from working while the launch dialog was visible on Linux
- Correctly show the Description Panel by default when this preference is toggled on
- Ensured the navigation buttons in the Choose Alternative Codons tool are properly enabled
- Corrected an issue with searching for features in protein sequences when Region features are not shown
- Fixed an issue where qualifier selections in Features view were lost when switching tabs
- Fixed an issue where using undo while viewing an alignment to a reference sequence resulted in expanded aligned sequences being collapsed.
- Fixed issues with Make Protein and Copy Translation with two abutting in-frame translated Features for which a codon spans the feature boundaries
- Fixed lagging selection of checkboxes on windows when importing primers
- Enabled jumping to next/previous regions across the origin using "Next/Previous Aligned Region" buttons
- Clarified dialogs to indicate Java 8 is supported for Vector NTI Express database import
- Fixed the default folder in Preferences > Files for opening being ignored by Open Files
- Corrected an issue that resulted in primer names not being included in default document name when creating a new file from a primer pair selection
- Fixed an issue that prevented using the NEBuilder tool with primers that are separated by less than 50 bp
- Corrected an issue with refreshing the list of sequences after clearing the search control when using the Import SnapGene Online Sequences tool
- Fixed an issue that prevented using preexisting non-overlapping PCR primers for the vector when using the NEBuilder tool
- Corrected an issue that prevented dragging and dropping files onto Agarose Gel windows
- Corrected an issue that prevented shown chosen enzymes when switching between documents in a collection
- Removed unnecessary horizontal lines that remained after removing references in the Edit References window
- Improved default size of the Edit References window
- Corrected an issue with displaying the selection length for selections with sticky overhangs
- Improved stability when making selections in sequences aligned to a reference
- Removed ambiguous codons when using the Insert Codon and Choose Alternative Codons tools
- Improved stability when using Opt-click to close all files
- Improved overall stability and corrected various memory leaks
- Restore selected history operation and display of history colors after undoing hiding an operation.
- Corrected an issue where an erroneous message was shown indicating a purchase was required before installing an available software update.
- Improved the name and icon shown for alignment documents in Window menus
- Fixed an issue that prevented correctly displaying where sequences align to a reference sequence in Map view.
- (Reported by Lauri Lintott)
- Improved the appearance of simulated agarose gels on screen and when exporting to a file
- Improved stability when saving multiple files in a collection
- Improved the appearance of site features in linear maps when printing and copying to the clipboard.
- Ignore collection index conflict flies created by OneDrive.
- (Reported by Andras Solt)
- Fixed an issue that prevented using selected primers to pre-populate controls in PCR-driven cloning dialogs.
- Fixed position where the add/edit/duplicate protein feature dialogs appear
- Improved stability when clicking on Save to Main Collection without a file selected
- Correctly display the sequence name above enzyme sets that are associated with a single sequence in the side toolbar menu
- Stability fixes when using splice to remove intros and new file from selection
- Fixed wrong shortcut showing on Windows in search type combo box for search bar (Meta→Alt)
更新時間：2021-11-05
更新細節：
What's new in this version:
- The NumPy 1.21.4 is a maintenance release that fixes a few bugs discovered after 1.21.3. The most important fix here is a fix for the NumPy header files to make them work for both x86_64 and M1 hardware when included in the Mac universal2 wheels. Previously, the header files only worked for M1 and this caused problems for folks building x86_64 extensions. This problem was not seen before Python 3.10 because there were thin wheels for x86_64 that had precedence. This release also provides thin x86_64 Mac wheels for Python 3.10.
- The Python versions supported in this release are 3.7-3.10. If you want to compile your own version using gcc-11, you will need to use gcc-11.2+ to avoid problems.
更新時間：2021-10-21
更新細節：
What's new in this version:
- The NumPy 1.21.3 is a maintenance release the fixes a few bugs discovered after 1.21.2. It also provides 64 bit Python 3.10.0 wheels
Note a few oddities about Python 3.10:
- There are no 32 bit wheels for Windows, Mac, or Linux
- The Mac Intel builds are only available in universal2 wheels
- The Python versions supported in this release are 3.7-3.10. If you want to compile your own version using gcc-11 you will need to use gcc-11.2+ to avoid problems.
更新時間：2021-08-15
更新細節：
What's new in this version:
- MAINT: set Python version for 1.21.x to <3.11
- BUG: Fix an issue wherein importing numpy.typing could raise
- MAINT: Update Cython version for Python 3.10.
- TST: Bump the python 3.10 test version from beta4 to rc1
- TST: avoid distutils.sysconfig in runtests.py
- MAINT: add missing dunder method to nditer type hints
- BLD, SIMD: Fix testing extra checks when -Werror isn't applicable...
- BUG: Remove logical object ufuncs with bool output
- MAINT: Include .coveragerc in source distributions to support...
- BUG: Fix bad write in masked iterator output copy paths
- ENH: Add support for windows on arm targets
- BUG: add base to templated arguments for platlib
- BUG,DEP: Non-default UFunc signature/dtype usage should be deprecated
- MAINT: Add Python 3.10 to supported versions.
- TST,BUG: Sanitize path-separators when running runtest.py
- BLD: load extra flags when checking for libflame
- BLD: update circleCI docker image
- REL: Prepare for 1.21.2 release
更新時間：2021-07-19
更新細節：
What's new in this version:
- The NumPy 1.21.1 is maintenance release that fixes bugs discovered after the 1.21.0 release and updates OpenBLAS to v0.3.17 to deal with problems on arm64.
- The Python versions supported for this release are 3.7-3.9. The 1.21.x series is compatible with development Python 3.10. Python 3.10 will be officially supported after it is released.
更新時間：2021-07-08
更新細節：
What's new in this version:
Fixed:
- Corrected an issue with showing aligned sequences as double-stranded DNA
- Addressed an issue with folders in collections stored on network drives
- Addressed a stability issue with viewing some primers in Sequence view
- Ensured correct reporting of the number of matches when searching ssDNA sequences
- Fixed a regression that prevented the display of some primer binding sites when simplified hybridizations are being shown
- Increased the number of primer binding sites that can be shown in Map view
- Fixed an issue that sometimes prevented showing the first aligned sequence when printing an alignment to a reference sequence
- Corrected an issue with saving aligned reads to an ssDNA sequence
- Improved stability when expanding sequences aligned to a reference DNA sequence
- Improved stability when choosing alternative codons
- Ensured that opened documents are always added to the recent files list
- Fixed an issue that could prevent enzymes from being displayed in older documents in collections
- Ensured that display options are always preserved when duplicating collection documents in a new window
- Removed a blank cascading menu that could appear in the Edit menu when using "Save As"
- Improved stability when dragging trimming handles
- Improved stability when using Opt-click to invoke "Close All Open Files" on macOS
- Improved the appearance of the focus ring for comboboxes on macOS
- Improved the mnemonic shortcut for deleting a restriction fragment on Windows
- Improved the default filename when exporting an alignment
- Improved colors in cloning overviews
- Made various textual corrections
- Prevented unnecessary scrolling when undoing sequence modifications
- Improved stability when using short sequences aligned to a reference DNA sequence
- Improved stability when using "Splice to Remove Introns"
更新時間：2021-06-09
更新細節：
What's new in this version:
Fixed:
- Ensured retention of unchanged alignment name and omission of name controls when using the "Replace" option when redoing an alignment
- Fixed an issue where File → Save did not work after redoing an unsaved alignment
- Preserved the display of preferred codons when switching between DNA and mRNA formats when viewing a codon usage table
- Allocated sufficient space to display the "Size" column in Features view when viewing ssDNA and ssRNA sequences
- Prohibited pasting when multiple files are selected in a collection
- Prevented a crash that would occur after double-clicking when importing SnapGene and Addgene online sequences
- Completely removed the installation folder when uninstalling on Windows
- Enabled "File → Export → Alignment..." and "File → Export → Consensus..." when viewing an alignment
- Made significant stability improvements
- Reduced memory usage
- Improved date formatting on Windows
- Improved button placement in History view
- Fixed an issue that could cause custom common features to be corrupted by using the right-click context menu to edit a common feature
- Removed the "Hybridization Parameters" menu action when viewing an RNA sequence in a collection
- Improved manual adjustment of vertical scaling of sequences traces aligned to a reference sequence
- Fixed an issue that prevented importing from Vector NTI databases on Windows
- Addressed an issue with importing some Vector NTI Express databases
- Fixed an issue in which the text representation of History view did not always refresh immediately when edits were made or undone
- Ensured correct enabling and disabling of the "Edit History" control in History view when the history is modified
- Corrected an issue that allowed duplicate primers with the same name but different sequence case to be imported into a file
- Corrected various issues that could occur when attempting to add features to the common features database, or importing such features, if they were marked as not visible in the original document
- Ensured correct export of common features to the specified folder
- Addressed issues that prevented collections stored on Windows network shares from being listed as recent collections in the File → Open Collection menu
- Improved fonts and text placement in History view
- Improved the message shown if an alignment is selected in a collection
- Corrected an issue that could cause pop-up menus to remain open when the Launch dialog was closed
- Corrected an issue that prevented saving a new file created from a selection from being saved to an open collection
- Ensured remembering of a preference for showing additional binding sites that do not match at the 3' end
- Corrected a regression that prevented imported primers from being restricted to those that have a unique binding site
- Ensured that the chosen enzyme set and enzyme visibility are retained when undoing sequence edits.
- Ensured that bold is correctly used to highlight unique cutters after undoing sequence edits
- Reduced the file size when exporting maps and history as PNG images
- Improved the toggling of enzyme visibility when repeatedly clicking check boxes in Enzymes view
- Fixed an issue that prevented looking up an enzyme by right-clicking in the Enzyme or Sites column in Enzymes view
- Fixed an issue that incorrectly suggested a sequence trace has unsaved edits after using File → Save As
更新時間：2021-05-14
更新細節：
What's new in this version:
New Functionality:
- Added support for viewing features in multiple sequence alignments
- Enhanced History view with a Text format tab, and with an option to show the entire history
- Added support for RNA sequences as .rna files
- Enabled viewing files of all types simultaneously in a Collection using a new "All Files" area
- Enabled gaps to be displayed every 10th base for protein sequences, and every 10th or 3rd base for nucleotide sequences
- Added support for filling in DNA ends of annealed oligos to create a double-stranded DNA sequence
- Added support for annotating primers that anneal at the 5’ end but not the 3’ end
- Enabled viewing and printing chromatogram files in a wrapped multi-line format
- Improved the conversion of .geneious nucleotide and protein sequences and alignments
- Added DNA Ladders from Ecogen, TIANGEN, and Vazyme
Enhancements:
- Extended the range for the minimum required 3' match for primers from 25 to 35 bases
- Enabled export of alignments to rich text format .rtf files
- Enhanced the visualization of mutagenesis simulations and mutagenic primers
- Enhanced the response to mousing over a primer so that the binding site is now highlighted in gray
- Added support for /protein_id qualifiers for mat_peptide features
- Enabled printing to PDF on macOS when no printers are installed
- Added an indicator in the selection bar to show "DNA" or "RNA" as the sequence type
- Enhanced enzyme, feature, and primer label layout in Map view for linear sequences
- Added clickable "contact support" links to messages that pop up in various places
- Made terminator features directional in the common features database
- Added the keyboard shortcuts Cmd+1 / Cmd+2 / Cmd+3 for switching between tabs in chromatogram windows
- Enhanced cursor placement, highlighting, and trace data tooltips when the mouse cursor is between bases
- Changed the "Replace" button label in Collections to "Bulk Edit" for improved clarity and accuracy
- Improved primer binding sites to avoid bulges if a 5' N tail is present in the primer sequence
- Updated the MAFFT aligner to version 7.471
- Updated the Parasail aligner to version 2.4.2
- Added a shortcut (Shift + Spacebar) for scrolling one page up in multiple sequence alignments
- Streamlined toolbar on macOS
Fixed:
- Rationalized the View menu to show options relevant to the file type
- Removed the "Browse..." menu action that had no effect in the "Import Primers from a SnapGene File" dialog
- Adjusted the tooltips for buttons in the "Find" bar to make them more consistent with other tooltips
- Changed the heading in the Collection search dialog for Protein Files to say "Names" rather than "Names & Numbers"
- Ensured that only a single /mod_base qualifier is allowed for modified_base features
- Added a ruler for protein sequences when viewing in compact format
- Fixed a bug with selection of the last item in Features, Primers, and Enzymes views
- Implemented immediate update of the version listed on the account administrator page after SnapGene is updated
- Corrected a regression in which sequence selection was lost after clicking in the Description Panel
- Corrected a regression with enzyme site selection in Lines mode of Enzymes view
- Ensured consistent display of the selection when switching to Sequence view
- Fixed an issue in which spaces were not shown after commas on macOS Big Sur
- Fixed a non-functional "Choose Enzymes..." command in the "Choose enzyme set" dropdown menu
- Corrected a regression that caused overtyping of characters in the primer name fields of the Simulate Agarose Gel dialog
- Ensured correct refreshing of primer binding sites when changing hybridization parameters
- Prevented truncation of 3' overhangs that extend beyond the end of a circular sequence
- Prevented input of an invalid location in the Go To dialog for sequences aligned to a reference DNA sequence
- Fixed some tabs that displayed as white text on a white background on macOS Big Sur
- Ensured that features are not lost from inserts in cloning operations when windows are opened or closed
- Corrected the color of the gray bar below the list box in the Collection interface
- Prevented "< Please choose >" from being propagated from the Anneal Oligos dialog to the oligo names in the resulting history
- Ensured that in the Anneal Oligos dialog, a double-click on a compatible enzyme is needed to transfer focus to the Restriction Enzymes dialog
- Configured the pull-down menus in the Anneal Oligos dialog to refresh when documents are opened or closed
- Ensured that the specified font size is used when printing the Description Panel
- Fixed an issue with the folder location used when exporting standard common features
- Improved scrolling performance in Enzymes view
- Fixed the default file name chosen when exporting a single file from a Collection
- Improved the reliability of displaying the warning in the Print dialog on Windows about printing to PDF
- Ensured that tabbed window controls on macOS are reliably shown
- Improved the background color display in Map view
- Fixed issue in which keywords could be used as the construct name for some GenBank/GenPept files
- Improved the opening of SeqBuilder files
- Addressed issues with importing references from another file
- Improved the quality when exporting maps at high resolutions
- Updated Map, Sequence, and other views when protein sequences are zoomed
- Implemented hiding of zoom controls in a collection when switching from a long sequence that supports zooming to a shorter one that does not
- Prevented unnecessary display of a message about unsupported qualifiers during NCBI import when the content includes nonstandard qualifiers (e.g., /UniProtKB_evidence) that are deliberately converted to /note qualifiers
- Corrected an issue in which some line breaks in /note qualifiers were not preserved when opening GenBank or GenPept files
- Addressed a potential stability issue when viewing protein files
- Fixed copying of maps and histories on macOS, and improved the quality when pasting such content into applications such as Microsoft Word or PowerPoint on macOS
- Improved the message shown when attempting to use a sequence over 1 Mbp to compute a pairwise alignment
- Ensured correct identification of macOS Big Sur when sending anonymous user statistics
- Ensured correct display of a trace file icon in the Windows menu
- Fixed various issues with specifying and displaying the /collection_date qualifier
- Addressed an issue that could result in sequence characters moving slightly after periods of no mouse activity on Windows and Linux
- Simplified the choice of a destination folder during import into a collection by making the "Add" button the default
- Improved the display of feature names on Windows during pliancy and selection
- Fixed the Redo shortcut on Linux
- Improved margins and alignment in various windows and dialogs
- Improved the default placement of a window created via File → Open when no document was previously open
- Improved stability while viewing collections
- Avoided duplication of DNA documents in the Window menu after converting to single- or double-stranded format
- Corrected the shortcut for Overlap Extension PCR of two fragments
- Ensured that if the side toolbar button is used to show alignments and there are no currently aligned sequences, the software asks which files to import to align to the reference sequence
- Corrected an issue in which unmodified alignment documents sometimes indicated unsaved changes
- Corrected issues with dragging collection files onto other applications
- Fixed a crash when saving an alignment to a collection
- Disabled "Actions → Convert to Single-Stranded..." when viewing alignments
- Corrected an issue that prevented conversion of a feature translation to upper- or lowercase if the last selected codon was located at the end of the sequence
- Fixed a bug in which an open document might not be listed in the Window menu or in the lists of open documents in cloning dialogs, while the launch dialog would remain visible
- Fixed an issue that could result in two copies of the application running on macOS
- Ensured correct rendering of multi-region Site features that span multiple rows in Sequence view
- Addressed a stability issue when exporting and opening the alignment consensus
- Removed the dead "Browse..." action in the source menu when importing features from BED, GFF3, or GTF files
- Ensured that "Primers → Sort Primer List..." executes the desired sort
- Updated outdated web links to online resources
- Ensured correct residue numbering for Smith-Waterman (local) pairwise alignments
更新時間：2021-05-11
更新細節：
What's new in this version:
- bug: Correct datetime64 missing type overload for datetime.date...
- maint: Remove __all__ in favor of explicit re-exports
- bld: Strip extra newline when dumping gfortran version on MacOS
- bug: fix segfault in object/longdouble operations
- maint: Use towncrier build explicitly
- maint: Relax certain integer-type constraints
- maint: Remove unsafe unions and ABCs from return-annotations
- maint: Allow more recursion depth for scalar tests.
- bug: Initialize the full nditer buffer in case of error
- bld: remove unnecessary flag -faltivec on macOS
- maint, CI: treats _SIMD module build warnings as errors through...
- bug: for MINGW, threads.h existence test requires GLIBC > 2.12
- bug: Make changelog recognize gh- as a PR number prefix.
- rel, DOC: Prepare for the NumPy 1.20.3 release.
- bug: Fix failing mypy test in 1.20.x.