[Gmod-apollo-cmts] CVS: apollo/conf fly.style,1.7,1.8 fly.internal.style,1.1,1.2 synteny-game.style,1.21,1.22 apollo.cfg,1.82,1.83

[Nomi H. <no...@us...>]

Update of /cvsroot/gmod/apollo/conf
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24425

Modified Files:
	fly.style fly.internal.style synteny-game.style apollo.cfg 
Log Message:

mostly just comment changes


Index: fly.style
===================================================================
RCS file: /cvsroot/gmod/apollo/conf/fly.style,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** fly.style	29 Jul 2005 18:02:26 -0000	1.7
--- fly.style	29 Jul 2005 18:11:41 -0000	1.8
***************
*** 29,32 ****
--- 29,33 ----
  
  // Used to pull up gene reports by FBan from annotation info panel
+ //ExternalRefURL "http://www.fruitfly.org/cgi-bin/annot/gene?"
  ExternalRefURL "http://flybase.net/.bin/fbidq.html?"
  

Index: fly.internal.style
===================================================================
RCS file: /cvsroot/gmod/apollo/conf/fly.internal.style,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** fly.internal.style	21 Jul 2005 21:50:15 -0000	1.1
--- fly.internal.style	29 Jul 2005 18:11:41 -0000	1.2
***************
*** 24,31 ****
  UserTranscriptColouring "true"
  
! // This is snarky, but it is doing double duty. If this is set
! // then it serves to both override the ExternalRefUrl and to
! // indicate the general switch to internal only mode
! ProjectRefURL "http://www.fruitfly.org/cgi-bin/annot/mini-search.pl?query="
  
  // 3/08/2005: all requests are routed through fruitfly.org, but
--- 24,28 ----
  UserTranscriptColouring "true"
  
! InternalMode "true"
  
  // 3/08/2005: all requests are routed through fruitfly.org, but

Index: synteny-game.style
===================================================================
RCS file: /cvsroot/gmod/apollo/conf/synteny-game.style,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** synteny-game.style	18 May 2004 20:47:57 -0000	1.21
--- synteny-game.style	29 Jul 2005 18:11:41 -0000	1.22
***************
*** 34,39 ****
  // wants to load (e.g. from a link).
  // These must be filled in for game synteny to be able to load from links
! //SpeciesToDatabase "Drosophila melanogaster -> my-dmel-db"
! //SpeciesToDatabase "Drosophila pseudoobscura -> my-pseudo-db"
  
  // Locked zooming means all species (for now theres just 2) zoom
--- 34,39 ----
  // wants to load (e.g. from a link).
  // These must be filled in for game synteny to be able to load from links
! > SpeciesToDatabase "Drosophila melanogaster -> gadfly3"
! > SpeciesToDatabase "Drosophila pseudoobscura -> gadflydpsef1"
  
  // Locked zooming means all species (for now theres just 2) zoom

Index: apollo.cfg
===================================================================
RCS file: /cvsroot/gmod/apollo/conf/apollo.cfg,v
retrieving revision 1.82
retrieving revision 1.83
diff -C2 -d -r1.82 -r1.83
*** apollo.cfg	21 Jul 2005 21:50:15 -0000	1.82
--- apollo.cfg	29 Jul 2005 18:11:41 -0000	1.83
***************
*** 23,29 ****
  //                        so JavaPath is /usr/lib/java).
  //			  Used by bin/apollo startup script.
! //   Memory             - Max amount of memory Apollo is allowed to use.
! //                        If you're opening many large data files from a
! //                        single Apollo session, you may need to bump this up.
  //   BrowserProgram     - path to your web browser program (e.g. /usr/local/netscape)
  //                        if you don't use the default browser.
--- 23,28 ----
  //                        so JavaPath is /usr/lib/java).
  //			  Used by bin/apollo startup script.
! //   Memory             - Max amount of memory Apollo is allowed to use
! //                        (applies only when you launch Apollo via bin/apollo)
  //   BrowserProgram     - path to your web browser program (e.g. /usr/local/netscape)
  //                        if you don't use the default browser.
***************
*** 46,57 ****
  // Note: if JavaPath is commented out, bin/apollo searches for the Java
  // in your path.  Set JavaPath if you want to use a different Java.
  //JavaPath		"/usr/lib/java"
  
  // Size of the memory stack allocated to Java.  This is not directly used
! // if you've installed Apollo with the installer (though the memory
! // setting for the installer should match this one), but is used if
! // running bin/apollo and is also used for checking whether we're running
  // out of memory.
! Memory 			"512M"
  
  // If AdapterHistoryFile and AutosaveFile are not specified, Apollo will
--- 45,57 ----
  // Note: if JavaPath is commented out, bin/apollo searches for the Java
  // in your path.  Set JavaPath if you want to use a different Java.
+ // Also note:  JavaPath is only used if you run bin/apollo.  If you run the
+ // installed version of Apollo, it decides for itself where to find java.
  //JavaPath		"/usr/lib/java"
  
  // Size of the memory stack allocated to Java.  This is not directly used
! // if you've installed Apollo with the installer, but is used if you're
! // running bin/apollo and is also used for checking whether you're running
  // out of memory.
! Memory 			"800M"
  
  // If AdapterHistoryFile and AutosaveFile are not specified, Apollo will