upcoming 1.0.9f

   An update will soon be out (probably in a week or two) with a few bug fixes and some other general updates.  Between starting a new job, moving several states away a baby, and a lack of consistent internet access, it has been a little slow.

pLOT v1.0.9e Minor update

   pLOT v1.0.9e Minor update.  Fixes a graphics bug that on rare occasions caused a circular feature to overextend its length.

pLot 1.0.9e Download Links

This patch requires a full installation of  v1.0.8a.  If updating to 1.0.8a first, please be sure that ALL files are deleted from the Program files/pLOT directory.  *Windows 7+ does not always erase the pLOT.exe and pLOT.dll files on uninstall*
The pLOT.dll is the same one provided in v1.0.9c

pLOT v1.0.9e Patch [Link 1]

  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 or email me explaining the error so that I can implement a fix ASAP.

pLOT v1.0.9d Minor update

   pLOT v1.0.9d Minor update.  Fixes a bug that on rare occasions caused a circular feature to not span its complete length.  Line and Tick Mark graphics now change their widths appropriately on the map like the Box and Arrow features do either from the annotations window or using Ctrl+Left/Right or Shift+Left/Right.

pLot 1.0.9d Download Links

This patch requires a full installation of  v1.0.8a.  If updating to 1.0.8a first, please be sure that ALL files are deleted from the Program files/pLOT directory.  *Windows 7+ does not always erase the pLOT.exe and pLOT.dll files on uninstall*
The pLOT.dll is the same one provided in v1.0.9c

pLOT v1.0.9d Patch [Link 1] [Link 2]

  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 or email me explaining the error so that I can implement a fix ASAP.

pLOT v1.0.9c Minor update

   pLOT v1.0.9c Minor update.  Fixes a bug in the search routines for sequences with gaps that occasionally returned the wrong end value.  Fixes a crash that sometimes occurred in some amino acid search instances.

pLot 1.0.9c Download Links

*This patch requires a full installation of  v1.0.8a.  If installing 1.0.8a first, please be sure that ALL files are deleted from the Program files/pLOT directory.  Windows 7+ does not always erase the pLOT.exe and pLOT.dll files on uninstall*

pLOT v1.0.9c Patch [Link 1] [Link 2]

  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 or email me explaining the error so that I can implement a fix ASAP.

1.0.9b Minor Update

1.0.9b Minor Update

   pLOT 1.0.9b fixes a minor trimming bug that occurs in some cases with the arrows in circular mode.  For once, this bug is not on my end but a documented bug in the graphics library used (whew).  Also a temporary fix for a crash that could occur when a certain search string combination was used.  I've noted that there is a strange bug in returning the locations of the strings as "0" if they start at base 1 of a sequence and contain a gap "-".  This will be addressed soon.

v1.0.9a

  In addition a to few minor fixes, the major addition to pLOT v1.0.9a is the ability to export vector maps to .EPS format in addition to the .BMP format previously available.  This is done through the File/Export Map as Image menu.

Version 1.0.9 will be out shortly (hopefully before Monday).

v1.0.8 Release

   pLOT v1.0.8a is out with two major changes/additions and a few extra shortcut keys.  First, the graphics have been overhauled.  The lines and graphics have been smoothed out (except brackets which are still in progress) and should eliminate the old Floodfill problem.

   pLOT v1.0.7a changes a few things (hopefully for the better).

   First, a new graphic is available.  The Headless Arrow graphic is simply an arrow without those pointy arowheady things protruding.  It is similar to the type of arrow used by some other plasmid mappers.  See below the Cas9 vs AmpR graphics.

pLOT v1.0.7 will be coming out in the next few days!  Along with a few bug fixes, you will be able to specify custom search strings to be retained in a drop-down menu in the search window as well as a few other changes/updates.

    Apparently the file hosting site I've been using went (temporarily?) down without notice.  The links below are updated and go through another file hosting site.

pLot 1.0.6a Download Links

*If you have previously performed a complete installation of pLOT v1.0.4, 

you can download the patch alone.  Otherwise

use the full installation*

Full Installation: pLOT v 1.0.6a Full [Link 1] [Link 2]

Patch Only: pLOT v 1.0.6a Patch Only [Link 1] [Link 2]

   Like the pLOT Facebook Page for up-to-date information on new releases, 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 explaining the error so that I can implement a fix ASAP.

pLOT 1.0.6a

      pLOT 1.0.6a is out.  This patch adds two NEB PFGE ladders for the virtual gels and includes a few minor fixes.  The mouse icon changes when hovering over a feature or label.

pLot 1.0.6a Download Links

*If you have previously performed a complete installation of pLOT v1.0.4, 

you can download the patch alone.  Otherwise

use the full installation*

Full Installation: pLOT v 1.0.6a Full [Link 1] [Link 2]

Patch Only: pLOT v 1.0.6a Patch Only [Link 1] [Link 2]

   Like the pLOT Facebook Page for up-to-date information on new releases, 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 explaining the error so that I can implement a fix ASAP.

1.0.5d fixes a bug in redrawing annotated features after doing a full-sequence reverse/complement conversion.  This was just a graphics glitch and files/annotations had previously saved correctly so no need to worry about that =)

*Please note that you should have installed 1.0.4 in order to apply this patch*

pLOT v 1.0.5d
pLOT v1.0.4 this is required to use the 1.0.5d patch

It seems there was an error occurring when a new sequence was entered.  This is now fixed in this patch.  Apologies for the issue.

pLOT v1.0.5c Patch

Version 1.0.5b is a minor update that changes the spacing in the circular map to a more evenly spaced form where groups of labels are more centered on the middle of the group.  It also fixes a bug that occurred sometimes when only a single label was being drawn on the linear map.

Old Spacing

New Spacing

pLOT v1.0.5a is out!  This update:

• Fixes a bug that caused enzymes to not be shown after a gel is displayed.
• Linear plots now show labels written vertically and spaced correctly as opposed to the previous, uglier horizontal texts.  See image below!
• Since some annotated sequences are short relative to the whole sequence and thus don't take up much space on the map, clicking on them can be difficult at times.  Additionally, annotations behind others cannot be clicked on either.  To fix this, labels for annotations are now clickable and bring up the same options/menus/etc... as if you had clicked on the feature itself on the map.  Many thanks to my fellow labmate "NL" for this suggestion.

Known Bugs & future fixes:

• There is still a FloodFill bug where most of the map will get colored if you view a linear sequence where an arrow graphic spans the origin.
• I'm not thrilled with the spacing of labels in the circular map and will be implementing a change soon to make the spacing more even.
• Editing base pairs through the edit menu can result in shifts in the sequence without shifting the bp at which annotations begin.  This will be fixed shortly but it is recommended that you do not use this feature to add or subtract base pairs from the sequence, simply to change existing ones.  Use the "Insert/Delete Sequence" from the Edit-> Sequence menu.

As always, feel free to like the pLOT Facebook Page for up-to-date information on new releases, to report bugs, or to suggest new features.

Download Links
*This is an update for the executable only provided you have v1.0.4a previously installed.  Decompress the executable and place it in the pLOT directory, overwriting the old version*

pLOT v1.0.5a Update See 1.0.5b post
pLOT Sample Files
pLOT Manual v1.0 (Very rough draft)

Incoming!

pLOT version 1.0.5a is set to come out soon (before the weekend at the latest, probably in a day or two).  This patch changes the text direction in linear plots from the previous horizontal form (which was ugly, imho) to vertical.  Because some short-sequence features can take up very little space, clicking on them can be challenging in some situations.  To solve this, clicking the labels for the annotated feature will now do the same thing as if you clicked on the feature itself.  My thanks to my fellow labbie "NL" who made this suggestion!  As always, feel free to like the pLOT Facebook Page for up-to-date information on new releases, to report bugs, or to suggest new features.

Small bug fix

A small bug was found in the code for selecting multi-enzyme mixes that resulted in new mixes not adding correctly (previously saved ones were fine).  This bug is fixed and the pLOT.exe can be downloaded here if you've previously installed v1.0.4.  The 1.0.4 complete installation file in the previous post has been updated.  I apologize for any inconvenience.

pLOT 1.0.4a Fix

pLOT v1.0.4

   Version 1.0.4 represents quite a bit of under-the-hood modifications for speed and efficiency as well as the addition of quite a few new features.

Version 1.0.4 is due to be released in a few days.  This update will consist of a number of minor fixes, speed improvements and new features.  Stay tuned!

pLOT v1.0.3a is now released.  This update allows the customization of colors for primer labels as well as a number of minor fixes (listed in the change log section).

* If you downloaded v1.0.2, please update to 1.0.2b, which fixes a bug in the search routine *

pLOT version 1.0.2b is now out.  Aside from a few fixes (listed below) this release includes the automates search for primers in your sequence.  The display of primers on the map can be toggled on and off by clicking on the "Display Primers" button.  Primers are displayed in bold, italicized dark orange font (color customization will be available in upcoming releases).

pLOT v1.0.1 Update Release

  pLOT update to v1.0.1 is now available.  This update allows gaps to be part of sequences in your Annotations Library and search strings (amino acid and DNA versions).  This results in a more flexible search and auto-annotations than you would get using "N" or "X" as ambiguous DNA bases or amino acids respectively and allow matching of sequences with variable lengths.  Gaps are represented by a "-" for both DNA and amino acid sequences.  An importable Annotations Library add-on file is also available with a few sequences to demonstrate this.

pLOT v1.0 Released!

   Today marks the release of pLOT v1.0.  pLOT is a plasmid mapping program for Windows-based PCs that I had initially been developing for my own personal use over the past year (and some change) and later decided to release for free for public use.