1. We recommend including the Java Virtual Machine (JVM) for a more robust installation.
   This will not affect any of your other Java applications or Web browsers as it is used only with ProtPlot.
2. The distribution includes:
   • The ProtPlot Java stand-alone application,
   • A set of PRP samples data derived from http://cgap.nci.nih.gov/ DB.
   • Support files for your operating system - possibly including the JVM which you may optionally download.

1. Procedure for downloading and installing ProtPlot on your computer

2. You start the download process when you click on the installer for your computer platform. (You may alternatively use the default installer discussed below.) Follow the directions it provides as you download the installer. It also provides instructions in the "View" hyperlink adjacent to the operating system you selected that tells you what to do after you finished the download. Part of the installation consists of telling the installer where you want to 1) put the executable installer (a temporary directory where you have lots of room is a good choice), and 2) the "installation" directory where you will typically leave the distribution after the installer unpacks it.

We use the commercial InstallAnywhere^(TM) program to create the installers. It provides installers for:

• Windows 95/98/NT/2000/XP
• Mac OS (OS8 and OS9, OS-X)
• Solaris
• HP-UX
• Linux
• Unix
• Other Java enabled platforms

1.3 Downloading just the ProtPlot.jar file after initial install

1.4 Starting ProtPlot Using a ".prpstate" startup state file

If you are on a Macintosh system, then start ProtPlot and then run the startup .prpstate file you want by going to the (File menu | State | Change state) command. Then browse your disk and then open up the startup state file of interest.

If you are on a Unix system, then you supply the state startup file explicitly in the command line. You might consider adding the "installation" directory to your UNIX $PATH or $path variable to have UNIX automatically find the executable binary.

  cd installation-directory/
  ProtPlot.bin myLastSession.prpstate

1. The MacOS installer is available, but may not work with older versions of MacOS. In addition, there may be problems if file names are longer than 32 characters. For now, the solution is to use short file names. There may also be problems if your data files have embedded carriage returns in addition to line feeds. For now, the solution is to strip the CRs out of the data file.

2. On Solaris, and possibly other Unix systems, you may have problems with the stack limits. Do a "man limit" to read about the command for your particular Unix shell. We have found that the following seems to work. For the Unix C-shell (csh), add the following to your .cshrc startup file.

      limit stacksize unlimited
   

   In addition, we have set the default stack size that ProtPlot uses to 96Mbytes. If your computer has less physical memory, it will page. You may also increase this number as well if you have more memory and want to use it. The solution is to edit the ProtPlot.lax file found where you installed ProtPlot. Change the two instances of memory allocation from 96000000 to a smaller number that is less than your actual memory size.
3. On Solaris, if you download the version with the JVM, unless your Solaris system has been updated recently, it may not be able to find the libCrun.so.xxx version required by the JVM. Try downloading the non-JVM version or update your Solaris system.
4. If you have problems with the Sun installer, you may need to update your Solaris OS system patch set. It is not a single patch. It is the latest Recommended Patch Cluster from Sun. We STRONGLY recommend having your SysAdmin do this for you if you have not done this before. Point your Web browser to:

     http://sunsolve.Sun.COM/pub-cgi/show.pl?target=patches/patch-access
   

   and choose the appropriate patch set for the version of Solaris (2.6, 7, or 8) that you are running. Do not choose any of the x86 versions unless you are running Solaris x86. Click on either the Download HTTP option or Download FTP option, and click the GO button to download the patch set.

1.7 Sun Solaris (or other Unix system) Memory Problems

  % ProtPlot
 
  Stack size of 97664 Kb exceeds current limit of 8192 Kb.
  (Stack sizes are rounded up to a multiple of the system page size.)
  See limit(1) to increase the stack size limit.

1.8 ProtPlot LAX file

Default Lax settings
The Lax file is a startup file generated by InstallAnywhere when we packaged ProtPlot. It is used when ProtPlot starts up on your computer. We currently set the memory limits to 96Mbytes. If you have more memory, you can edit the Lax file to have it use more memory.

 
  #   LAX.NL.JAVA.OPTION.JAVA.HEAP.SIZE.MAX
  #   -------------------------------------
  lax.nl.java.option.java.heap.size.max=96000000
 
 
  #   LAX.NL.JAVA.OPTION.NATIVE.STACK.SIZE.MAX
  #   ----------------------------------------
  lax.nl.java.option.native.stack.size.max=96000000