Genographer Help


Displays a sized and straightened gel image reconstructed from lanes. Bins can be set and viewed as a bunch of traces or as a graph. The bins will be automatically scored, and the scoring can be manually edited. The scoring can be exported as a text file for use with other programs, such as MapMaker.


Using the Program

Importing Files

Select "File|Import..." to select the lanes to import. This will bring up the Import Dialog Box. Select the type of file to import from the box in the lower left. (See "Import Formats Supported" in Program Features.) Then select the files to import. Warning, the lists are not alphabetized, so one may have to search for the entry. Double clicking on a directory will cause that directory to be displayed. Sometimes, moving up a directory will not work the first time. Simply try again and if that does not work, contact the author. Double clicking on a file will add it to the list of files to be imported and has the same effect as clicking "Add". Note, sometimes it may be quicker to "Add All" of the files in a directory and then remove the unwanted ones.


When print is selected from the menu, or the "Print" button is clicked, the current display will be printed (gel, thumbnail, etc.). However, the program seems to have trouble printing the gel, at least in the cases it was tested for. The gel seems to print out as a black and white image instead of a greyscale image. Therefore, printing of the gel is not recommended. Instead, the gel image should be exported and printed with a graphics program to obtain a hard copy of it.


The program currently supports the exporting of the gel and the analysis views only. The gel is exported as a PNG image, which can be read by some graphics programs. (Thanks to VisualTek for the code for the image.) Only the gel itself will be exported, so the bins will not show up in the exported image. The analysis is exported as a simple text file, containing whatever text is on the screen, including an modifications made by the user.

New, Open, and Save

The program can save a gel to a file. This will save all of the bins, and scorings as well as the current intensity, etc. The same file can then be opened again later. Also, opening a file is MUCH faster than importing the lanes every time, so it is heighly recommended. A new project can be started by clicking on new. Warning: Unlike most programs today, Genographer will not ask if you want to save a file before exiting, or starting a new one, or openning another one.

Controlling the Lanes

The program does not offer much in the way of determining how the lanes are ordered in the gel. It can be done though. The order is determined by the order in the Import Dialog. For example, if the experiment has two physical gels with common samples, placing the common samples next to eachother in the file list will cause the lanes to appear next to eachother. Also more lanes can always be added to a gel at any time. Finally, lanes can be deleted by selecting them (double-click on the lane tab) and then seleting "Lane|Delete Marked Lanes".

Component Descriptoin

Switch between the different views by clicking on the buttons on the left side of the screen, or by selecting an item from the "View" menu.


Icons Appear in Wrong Spot

Sometimes the image for a button will display in the wrong spot. The cause of this problem is currently unknown, but reselecting the view should fix the problem. For example, when viewing the gel, click on the "Gel" button on the left to fix the problem.


Displaying the gel can take a lot of memory. In many cases, the program will not have enough memory to display an image. (A 32-lane gel at 200% will take 4MB, while the same gel at 400% take 16MB.) If the program is being run with the JRE from sun, the amount of memory is limited to 16MB by default. This can be increased by running the jre like this: jre -mxnumberm -cp intallpath genographer, where number is the new maximum amount of memory and installpath is the location of the program files. This should be somewhat less than the total memory available on the system. Remember, that things like the operating system will be using some of the memory on the computer. The "m" after the number stands for megabytes, use "k" if you want to specify kilobytes. However, you can also simply adjust the sizes displayed and then the program will use less memory and perform quicker.

Null Pointers

This error should not usually appear. If it can be reproduced, please inform the author. It will also be helpful to have the stack trace. Click the stack trace button when the error occurs and record the information. The information will appear on the shell/DOS-Prompt that started the program. If you can't find it, let the author know.


Program Features

Installing and Running

Source Code Documentation

The source code is available only if one choose to download the source code. It is available at If not, contact the author, see about. A no-frames version is also available.

About Genographer (Copyright/License)