Current Version: pLOT v1.0.17a


plot



Version: 1.0.17b

New Features:

  • Auto-annotate from library window has been updated and should be faster and better looking than the previous version.
  • Searching for restriction enzyme sites should be faster.  Now, when multiple enzymes share a site sequence, the sequence is only searched for the first enzyme.  Redundant sequences are no longer searched for multiple times.
  • Fix to a restriction site sequence.  Restriction site database format updated to obviate the need for multiple searches for the same sequence.

PLOT DOWNLOAD LINKS

pLOT v1.0.17b full install file [Link]

This update is only available as a full installation file.  It is highly suggested that you uninstall the any prior versions before installing this update.  Please note that on some systems, an error pops up during the install process asking you to abort, retry or ignore.  If this happens, choose the Ignore option.

  Like the pLOT Facebook Page for up-to-date information on new releases, previews of upcoming release features, to report bugs, to suggest new features, or to volunteer as a beta tester.  You can also subscribe to follow this blog for email notification of new posts.  If you experience any bugs or glitches, please feel free to leave a comment, Facebook message, or email me explaining the error so that I can implement a fix ASAP.

 

Older releases

Version: 1.0.17a

New Features:

  • Edit Menu has “Add new feature” menu item (Ctrl+W) to add a new feature from the main menu
  • Auto-annotate from library now opens a window after searching for features and allows the user to select which feature(s) to add.  The name of the feature can be changed from this window prior to adding it to the menu (see image below).

Bug Fixes:

  • Library export saves to .Da2 as default

 

Figure 1.  Auto-Annotations Window

 

 

Version: 1.0.16h

Bug Fixes: Fixes a bug in the Chromatogram Window that causes the scroll bar to function incorrectly under certain circumstances.

pLOT v1.0.16h full install file [Link]

Version: 1.0.16g

Bug Fixes: Fixes to the Copy/paste shortcuts.  Shortcuts should work correctly in the docked tools window textboxes. 

pLOT v1.0.16g full install file [Link]

Version: 1.0.16f

Bug Fixes: Several bugs in the docking window code have been fixed.  Windows should now dock properly again.

pLOT v1.0.16f full install file [Link]

Version: 1.0.16e

Bug Fixes:

  • Fixed a control appearing inappropriately in the Annotations window.
  • Fixed resizing issue in chromatogram window.

pLOT v1.0.16f full install file [Link]

Version: 1.0.16d

New Features

The Restriction Enzyme window now has a new tab to show enzymes with compatible sticky ends.  When an enzyme is selected in the left list, the right list is populated with compatible ended cutters.  Currently this is limited does not take into account degenerate sites but this will be added at a later date.  See figure below the Bug Fix section.

Bug fix

  • A bug in the file saving could result in an error when saving to the root of a drive after saving elsewhere first.  That bug has been fixed.
  • A bug that resulted in pLOT not showing up when Alt+Tab was pressed and the docked Tools window had focus has been fixed.

 

Figure 1.  Compatible Overhang Tab in the Restriction Enzyme Window

PLOT DOWNLOAD LINKS

pLOT v1.0.16d full install file [Link]

This update is only available as a full installation file.  It is highly suggested that you uninstall the any prior versions before installing this update.  Please note that on some systems, an error pops up during the install process asking you to abort, retry or ignore.  If this happens, choose the Ignore option.

  Like the pLOT Facebook Page for up-to-date information on new releases, previews of upcoming release features, to report bugs, to suggest new features, or to volunteer as a beta tester.  You can also subscribe to follow this blog for email notification of new posts.  If you experience any bugs or glitches, please feel free to leave a comment, Facebook message, or email me explaining the error so that I can implement a fix ASAP.

Version: 1.0.16c

Bug fix

  • There was a bug in the chromatogram viewer such that if the user searched for a sequence and clicked on the result, the window would scroll to the incorrect position if the chromatogram had been flipped to the antisense.  That should now be fixed.

 

PLOT DOWNLOAD LINKS

pLOT v1.0.16c full install file [Link]

This update is only available as a full installation file.  It is highly suggested that you uninstall the any prior versions before installing this update.  Please note that on some systems, an error pops up during the install process asking you to abort, retry or ignore.  If this happens, choose the Ignore option.

  Like the pLOT Facebook Page for up-to-date information on new releases, previews of upcoming release features, to report bugs, to suggest new features, or to volunteer as a beta tester.  You can also subscribe to follow this blog for email notification of new posts.  If you experience any bugs or glitches, please feel free to leave a comment, Facebook message, or email me explaining the error so that I can implement a fix ASAP.

 

Version: 1.0.16b 

PLOT DOWNLOAD LINKS

pLOT v1.0.16b full install file [Link]

Updates

  • The toolbar at the top of the screen for editing some of the properties of features has been replaced by a dockable toolbar that has fields for all of the properties.  Changes are committed as the user makes them.  A Revert button resets the feature properties to what they were at the time you clicked on it.  Ctrl+T shows or hides the Tool bar.  Double clicking the title bar or The clicking the restore button docks/undocks the bar.

Bug fix

  • A bug that could cause the program to crash when the split window was detached has been fixed.
  • A bug that sometimes showed the text color in the Sequence editor window has been fixed.

Figure 1.  The Dockable toolbar and split window in docked positions.

Figure 2.  The toolbar and split window undocked

 

Version: 1.0.16a

Sequence Editor Updates

  • The Sequence Editor window now displays feature colors as background highlighting instead of as the text color to make light colored feature sequences easy to read.

Annotations Editor Updates

  • The Annotations Grid interface has been updated.  Tab or escape while editing now correctly exits edit mode.  Clicking the Delete or Backspace erases the contents of the cell.
  • Clicking the Hide/Show cell for a feature graphic or label automatically toggles without dropdown boxes.
  • Fixed bug that caused SGrid to crash if feature was added when no others were present

Restriction Enzyme Window Updates

  • Partial word search in the RE Window over the single enzyme selection list. Pressing enter adds the enzyme to the list.
  • In the Enzyme Mix tab, clicking the name of a previously added mix causes the enzymes in the list to be highlighted in the selection list box to make it easy to add or change the mix without having to select all of the enzymes manually every time.

Main Window and Misc. Updates

  • The old toolbar in the main window has been replaced with a movable toolbar.
  • pLOT now has embedded high resolution icons.  pLOT files should show in the new icon image instead of the old pixelated one.
  • If a primer binds to more than one place in the sequence, hovering over one of the primer’s labels causes all of the labels to highlight to make it easy to see instances of multiple binding sites.
  • The Virtual Gel window now has a statusbar at bottom to display the band length the mouse is hovering over.
  • A bug in opening .pl2 format that resulted in empty features being added is fixed.

 

The New Toolbar

Updated Sequence Editor Window

1.0.15n

  • The Annotations window uses an updated Grid/Worksheet like interface (See picture below)
  • Fixed a bug in the Zoom in/out  so that the map no longer shows shifted during the zooming
  • A bug in the last release causing the categories dropdown box in the Library Editor window to not display the menu on right click has been fixed
  • Primers Window now accepts CSV format files for importing primers as well as the previously accepted tab.

1.0.15m

  • A bug in the “Convert Primer to Feature” menu item has been fixed.
  • Double clicking on the main window when no files are loaded now opens up the Enter Sequence window.
  • Homing nuclease names have been fixed and now show up correctly in the list box in the RE window. They had incorrectly showed a special character after the name.
  • Copying to the clipboard as pLOT Feature Format is now the default for copying to the clipboard.
  • The copy to clipboard format has been tweaked. The pLOT feature details are now retained for pLOT while pasting to non-pLOT programs such as text editors will pass only the raw sequence.
  • Copying bands from the gel window uses the new CB format.

1.0.15l

  • Fixed an issue with the items “Move to First” and “Move to Last” in the drawing order in the Feature’s popup menu.
  • Fixed the restriction site for BcnI

1.0.15k

  • Fixed an issue with a crash when loading the chromatogram viewer

Added features (1.0.15i/j)

  • Customizable menu systems with option to change color and style in the Preferences window.  This menu system is a slightly modified version of a menu library written by Steve McMahon.  All credit for the menu code goes to him.
  • Copying a feature to the clipboard can now be done using the additional “as pLOT Format” option.  Pasting the copied data to the pLOT View/Edit window inserts the sequence and the feature annotation information as well.  Pasting the data to the New window likewise retains the feature annotation information.
  • The mouse wheel is now recognized for zooming in or out.  Using the mouse wheel while holding down the Control key changes the zoom.  When zoomed in, using the mouse wheel will scroll the map up or down in the window.
  • The Feature’s popup menu now includes “Move to the First” and “Move to Last” which will move the feature to the top or bottom of the drawing order.

Bug fixes in version 1.0.15i

  • This update fixes a bug that could cause pLOT to retrieve feature names from .pl2 formatted files.
  • A bug in the Zoom in code has been fixed and the map should now scale appropriately.

Leave a Reply

Your email address will not be published. Required fields are marked *