Menu
▾
▴
[Treebase-guts] SF.net SVN: treebase:[385] trunk/treebase-core/lib/mesquite
|
From: <rv...@us...> - 2009-12-15 18:42:32
|
Revision: 385
http://treebase.svn.sourceforge.net/treebase/?rev=385&view=rev
Author: rvos
Date: 2009-12-15 18:42:23 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/batchArch/
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/BatchTemplateManager.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ChooseTemplateDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditFileSpecificsDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditTemplatesDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ManageTemplatesDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template
trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/
trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartFromInstructions.class
trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartInstrItemsSource.class
trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/
trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/ExportMatricesBatch.class
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/aBatchArchIntro.class
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplate.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/emb1.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/oneGear.psd
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/snippetNeeded.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.psd
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash2.psd
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateManager.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateeg.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/treeNeeded.gif
trunk/treebase-core/lib/mesquite/batchArch/lib/
trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateManager.class
trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateRecord.class
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/BatchTemplateManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/BatchTemplateManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ChooseTemplateDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ChooseTemplateDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditFileSpecificsDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditFileSpecificsDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditTemplatesDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditTemplatesDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ManageTemplatesDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ManageTemplatesDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,26 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch File Template Manager</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+</HEAD>
+<BODY>
+<H2><TABLE BORDER=4 CELLPADDING=0>
+ <TR>
+ <TD>
+ <H2>Mesquite: Batch File Template Manager</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>September 2003</P>
+
+<p> </p><P>© David Maddison & Wayne Maddison, 2003</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,8 @@
+#MESQUITEINIT BATCHFILE 1
+name = 'Basic NONA tree search'
+explanation = 'Batch file to request NONA to do basic tree search on each data matrix, saving a tree file for each'
+repeat1 = 'proc <name><number>.ss;^nh 100;^namb=;^nemp;^nsv* <name><number>.tre;^nsv/;^ndata -;^nz;'
+end1 = 'proc/;'
+repeat2 = '<name><number>.tre'
+matrixExportFormat = 'NONA, Hennig86, PiWe, WinClada'
+batchFileName1 = 'batch.ss'
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,10 @@
+#MESQUITEINIT BATCHFILE 1
+ name = 'PAUPConstraintTestParsimony'
+ explanation = 'This template produces a batch file to request PAUP to find the most parsimonious trees that match a constraint, and the most parsimonious ones unconstrained, for each matrix. It asks PAUP to write the results to a score file. '
+ start1 = '#NEXUS^nbegin paup;^n log file=''<name>.log'';^n set autoclose nowarnreset tcompress torder=right;^n defaults hs <snippet>search options</snippet>;'
+ repeat1 = ' execute ''<name><number>.nex'';^n set criterion=parsimony;^n constraint theConstraint= <tree>;^n hs enforce noconverse constraint=theConstraint;^n pscore 1/scorefile=''<name>Score.scr'' append;^n hs noenforce;^n pscore 1/scorefile=''<name>Score.scr'' append;'
+ end1 = ' log stop;^nend;'
+ batchFileName1 = PaupCommands.nex
+ start2 = 'MesquiteInstructions^nnumVariables = 2^nnumFiles = 1^nfile1 = ''itemsPerRecord=8 v1=4 v2=8''^nrecordLabel = ''Replicates''^nformula = ''v1-v2''^nlabel1 = ''Constrained treelength''^nlabel2 = ''Unconstrained treelength'''
+ batchFileName2 = MesquiteInstructions
+ matrixExportFormat = NEXUS_file_interpreter
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,8 @@
+#MESQUITEINIT BATCHFILE 1
+ name = Basic_PAUP_tree_search
+ explanation = 'Batch file to request PAUP to do basic tree search on each data matrix, saving a tree file and consensus tree for each. It will also produce consensus trees of the consensus trees from each search.'
+ start1 = '#NEXUS^nbegin paup;^n set autoclose nowarnreset nowarntree nowarntsave;'
+ repeat1 = 'execute ''<name><number>.nex'';^nhs;^nsavetrees file = ''<name><number>.trees'';^ncontree / strict= yes majrule=no treefile = ''CB<name>'' append = yes;'
+ end1 = 'gettrees file = ''CB<name>'' warntree = no allblocks;^nsavetrees file = ''consensus.trees'';^ncontree / strict= yes treefile = ''StrictConsCons.trees'';^ncontree / strict= no majrule=yes treefile = ''MajRuleConsCons.trees'';^nend;'
+ batchFileName1 = paupCommands.nex
+ matrixExportFormat = NEXUS_file_interpreter
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,6 @@
+#MESQUITEINIT BATCHFILE 1
+name = 'Simple List'
+explanation = 'Produces an accessory file consisting of a simple list of the data matrix files'
+repeat1 = '<name><number>.nex'
+matrixExportFormat = 'NEXUS file interpreter'
+batchFileName1 = 'commands.txt'
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartFromInstructions.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartFromInstructions.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartInstrItemsSource.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartInstrItemsSource.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/ExportMatricesBatch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/ExportMatricesBatch.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/aBatchArchIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/aBatchArchIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplate.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplate.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,106 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch Architect: Design of Batch Templates</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</HEAD>
+<BODY bgcolor="#FFFFCC">
+<H2><TABLE BORDER=0 CELLPADDING=4>
+ <TR>
+ <TD> <P><img src="splash.gif" width="164" height="64"></P>
+ </TD>
+ <TD>
+ <H2>Batch Architect: Design of Batch Templates</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<p><a href="index.html">Return to Batch Architect Page</a></p>
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>The Template Editor for editing Batch File templates appears as follows:</P>
+<P align="center"><img src="batchtemplate.gif" width="348" height="408"></P>
+<P> </P>
+<P>The text entered into the "Text for start of batch file" field will
+ be written once, at the start of the file; the text in "Repeated text,
+ written for each replicate" will be written as many times as there are
+ replicates; the text in "Text for end of batch file" will be written
+ at the end of the file. The following codes included in these fields will be
+ replaced in the batch file as follows:</P>
+<ul>
+ <li><name> will be replaced by the text entered in the "base name"
+ field in the Export Matrices & Batch Files or Export Batch Files dialog
+ boxes.</li>
+ <li><tree> will be replaced by the Newick formatted text description of
+ the tree chosen in the Export Matrices & Batch Files or Export Batch Files
+ dialog boxes.</li>
+ <li><snippet></snippet> surrounding the name of a code snippet will
+ be replaced by the text of the code snippet</li>
+ <li><fileExtension> will be replaced by the extension (with dot, if present;
+ e.g., ".nex", ".ss") that Mesquite will write based upon
+ the matrix format. </li>
+ <li><matrixFormat> will be replaced by the name of the matrix format (e.g.,
+ "NEXUS file")</li>
+ <li><random> numValues=n lowerBound=b1 upperBound=b2 type=double|long
+ withReplacement=yes|no </random> will be replaced by n random numbers
+ chosen with a uniform distribution over the range b1 through b2 inclusive,
+ with replacement or not. The numbers are either real numbers (if type=double
+ is chosen) or integers (type=long). For example, <random>numValues=3
+ lowerBound=1 upperBound=100 type=long withReplacement=no</random> entered
+ in the repeated text field might be replaced by "86 42 23" in one
+ replicate, and "5 73 31" in the next replicate. </li>
+</ul>
+<P>For the field "Repeated text, written for each replicate", the following
+ replacement will also be made:</P>
+<ul>
+ <li><number> will be replaced by the number of the replicate</li>
+</ul>
+<P>For example, consider 5 replicates run with a base name of "matrix"
+ for a template with the following specification:</P>
+<P align="center"><img src="templateeg.gif" width="445" height="270"></P>
+<P>A file called "commands.nex" would be created by Mesquite that would
+ look like this:</P>
+<P> </P>
+<pre> #NEXUS
+ begin paup;
+ set autoclose nowarnreset nowarntree nowarntsave;
+ execute 'matrix1.nex';
+ hs;
+ savetrees file = 'maxtrix1.nex';
+
+ execute 'matrix2.nex';
+ hs;
+ savetrees file = 'matrix2.nex';
+
+ execute 'matrix3.nex';
+ hs;
+ savetrees file = 'matrix3.nex';
+
+ execute 'matrix4.nex';
+ hs;
+ savetrees file = 'matrix4.nex';
+
+ execute 'matrix5.nex';
+ hs;
+ savetrees file = 'matrix5.nex';
+ end;
+</pre>
+<P> </P>
+<P>Up to five separate batch files can be specified for any one Batch File Template.</P>
+<p>The "Format of Matrices" choice will be ignored if matrices are not
+ being exported (e.g., if Export Batch Files was chosen).</p>
+<p> </p>
+
+<P>
+
+<HR>
+
+</P>
+
+<P>© David Maddison & Wayne Maddison, 2003</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/emb1.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/emb1.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,165 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch Architect Package</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</HEAD>
+<BODY bgcolor="#FFFFCC">
+<H2>
+ <TABLE BORDER=0 CELLPADDING=4>
+ <TR>
+ <TD>
+<P><img src="splash.gif" width="164" height="64"></P></TD>
+ <TD> <H2>Batch Architect package for the Mesquite system</H2></TD>
+ </TR>
+ </TABLE>
+</H2>
+
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>August 2005</P>
+
+<P>This package of modules supplies basic importing and exporting
+services to Mesquite.</P>
+
+<UL>
+ <LI><A HREF="#overview">Overview</A></LI>
+ <LI><A HREF="#installation">Installation</A></LI>
+ <LI><A HREF="#features">Features</A>
+ <ul>
+ <li><a href="#embf">Export Matrices & Batch Files</a></li>
+ <li><a href="#ebf">Export Batch Files</a></li>
+ <li><a href="#batchtemplates">Batch Templates</a></li>
+ <li><a href="#codesnippets">Code Snippets</a></li>
+ <li><a href="#chartresults">Chart Results via Instruction File</a></li>
+ </ul>
+ </LI>
+ <LI><A HREF="#examples">Examples</A></LI>
+ <LI><A HREF="#citation">Citation</A></LI>
+</UL>
+
+<H3><A NAME=overview></A>Overview</H3>
+
+<P>This package automates the generation of files with repeated elements as well
+ as the processing of files with repeated records.</P>
+<P>One can ask Mesquite to build a "batch" file that can serve as a
+ command file for another program such as PAUP* that does repetitive analyses.
+ For example, one might simulate 100 matrices under a particular model of evolution,
+ and for each of these matrices, include an entry in a batch file that asks PAUP
+ to analyze that matrix, saving tree files for the matrix. At the same time,
+ another batch file might be created that could be used to ask another program
+ to read in, sequentially, each tree file, and conduct a synthetic analysis on
+ them. </P>
+
+<H3><A NAME=installation></A>Installation</H3>
+
+<P>To install the basic Batch Architect package, the "batchArch" directory must
+ be installed in the "mesquite" directory within "Mesquite Folder". It should
+ be present in a basic Mesquite installation.</P>
+
+<H3><A NAME=features id="features"></A>Features</H3>
+<h4><a name="embf"></a>Export Matrices & Batch Files</h4>
+<p>This feature, in the Batch Architect submenu in the Analysis menu, will export
+ multiple matrices and one or more associated batch files. </p>
+<p>In choosing this feature, you will first be led through as serious of dialog
+ boxes in which you will choose how the matrices are to be created. Following
+ your choosing, the Export Matrices & Batch Files dialog box will be presented:</p>
+<p align="center"><img src="emb1.gif" width="336" height="356"></p>
+<p>In this dialog box you are to specify the base name to be used both for the
+ matrices and in the batch file template system. For example, in the example
+ shown, 10 matrices will be created, with names "SimMatrix1", "SimMatrix2",
+ "SimMatrix3", and so on. </p>
+<p>The file names may have extensions added (e.g., ".nex"), depending
+ upon the matrix format to be used (the matrix format is specified in the batch
+ file template). The extension will be added automatically by Mesquite.</p>
+<p>In this dialog you will most importantly also select the batch template to
+ use. A batch template specifies exactly how the batch file or files produced
+ will be structured. To examine or edit the template, use the Edit Templates
+ button. </p>
+<p>Some batch templates contain code that requires "<a href="#codesnippets">code
+ snippets</a>" to be defined. If code snippets are needed by a template,
+ they will be listed in the dialog box. If some are needed but unavailable, the
+ list will appear in red and note them as unavailable:</p>
+<p align="center"><img src="snippetNeeded.gif" width="320" height="48"> </p>
+<p>You can define or edit snippets uing the Edit Snippets button.</p>
+<p>Some batch templates require a tree to be chosen by the user; if so, and you
+ have not yet chosen a tree, "TREE NEEDED" will appear in red in the
+ box beside the Choose Tree button:</p>
+<p align="center"><img src="treeNeeded.gif" width="248" height="24"></p>
+<p>You can then use the Choose Tree button to choose your tree.</p>
+<h4><a name="ebf"></a>Export Batch Files</h4>
+<p>This is similar to the Export Matrices & Batch Files feature expect that
+ no matrices are exported. This can be used to generate batch files for already
+ existing matrices, for example, or to automate processes other than the analyses
+ of matrices.</p>
+<h4><a name="batchtemplates"></a>Batch Templates</h4>
+<P>Batch templates contain the instructions telling Mesquite how to construct
+ the batch files. They are managed in the Batch Template Manager window, which
+ allow ones to create, duplicate, edit, rename, or delete templates:</P>
+<P align="center"><img src="templateManager.gif" width="275" height="237"></P>
+<P>You can also load templates from template files; this allows you to move templates
+ between copies of Mesquite. For example, if you create a template on one computer,
+ it will be stored as a single text file in the BatchTemplates in the Mesquite_Prefs
+ directory in the Mesquite_Support_Files directory on your disk. You can then
+ move that file to another computer, and load it into Mesquite on that computer
+ using the Load button. </P>
+<P>Selecting a template in the Batch File Template Manager and pressing "View"
+ (if it is a pre-defined template) or "Edit..." (if it is a user-defined
+ template) will bring forth the Batch Template Editor, in which the template
+ can be viewed or edited:</P>
+<P align="center"><img src="batchtemplate.gif" width="348" height="408"></P>
+<P>See the page on <a href="batchtemplates.html">Designing Batch Templates</a>
+ for details on the formats used. Batch templates can be edited using the submenu
+ in Mesquite's Edit menu, or from the Export Matrices & Batch Files or Export
+ Batch Files dialog boxes.</P>
+<P>The pre-defined templates can be viewed and duplicated, but not renamed or
+ edited. Their duplicates can be renamed and edited.</P>
+<h4><a name="codesnippets"></a>Code Snippets</h4>
+<P>Code snippets are designed as file-specific elements that are to be used in
+ place of tagged elements in the batch templates. For example, if in a batch
+ template the following text appeared:</P>
+<pre> exec setParameterValues;
+ <snippet>search command</snippet>
+ display all;</pre>
+<p>then within the Mesquite file you could store a code snippet called "search
+ command" whose contents would be inserted in place of the above text when
+ the batch file was created. If the text of "search command" was</p>
+<pre> hsearch nreps=100 addseq=random swap=tbr;</pre>
+<P>then the batch file, when written, would contain</P>
+<pre> exec setParameterValues;
+ hsearch nreps=100 addseq=random swap=tbr;
+ display all;
+
+</pre>
+<p>Batch templates can be edited using the Batch File Templates submenu in Mesquite's
+ Edit menu, or from the Export Matrices & Batch Files or Export Batch Files
+ dialog boxes.</p>
+<h4><a name="chartresults"></a>Chart Results via Instruction File</h4>
+<P>If you have a text file on disk containing tab-delimited data, you can design
+ a Mesquite Instruction file that will give Mesquite enough information about
+ the data file to allow Mesquite to read it. See <a href="instructions.html">Instructions
+ File Format</a> for details about the way Mesquite Instruction files are to
+ be structured.</P>
+<P>Some of the batch templates distributed with Mesquite have instruction files
+ defined within them.</P>
+<H3><a name=examples></a>Examples</H3>
+<p>See the <a href="../../../docs/mesquite/RandomSimul/RandomSimul.html">Simulations
+ and Randomizations</a> page of the Mesquite manual for examples.</p>
+<H3>Citation</H3>
+
+<P> Maddison, D.R., & W.P. Maddison. 2005. Batch Architect: automation of
+ simulations and replicated analyses. A package of modules for Mesquite. Version
+ 1.06.</P>
+
+<P>
+
+<HR>
+
+</P>
+
+<P>© David Maddison & Wayne Maddison, 2005</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,130 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch Architect: Instructions File Format</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</HEAD>
+<BODY bgcolor="#FFFFCC">
+<H2>
+ <TABLE BORDER=0 CELLPADDING=4>
+ <TR>
+ <TD> <P><img src="splash.gif" width="164" height="64"></P>
+ </TD>
+ <TD> <H2>Batch Architect: Instruction File Format</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<p><a href="index.html">Return to Batch Architect Page</a></p>
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>A Mesquite Instruction File is a text file describing the contents of one or
+ more other text files containing data. The Instruction File gives enough details
+ about the other text files to allow Mesquite to be able to read it. </P>
+<h4>Structure of the data file to be read</h4>
+<P>The data file that is to be described by the Instructions File must consist
+ of a series of records, each record represented by the same number of elements,
+ and each element must be separated by either a tab or a new line or carriage
+ return. For example, you might have a file with various numbers given for each
+ of a series of five trees. The data for each tree might be on a single line,
+ and there might be three numbers per tree. There would thus be five records
+ (corresponding to the five trees), and each record would have exactly three
+ numbers. </P>
+<h4>Instruction File format</h4>
+<P>The format of the instruction file is currently very primitive and simple;
+ eventually, it will be altered to use standard languages such as XML, and allow
+ more flexibility, but for the moment it is formatted as follows.</P>
+<ol>
+ <li> The first line must be "MesquiteInstructions"<br>
+ </li>
+ <li>The second line gives the number of data elements to be read in and stored
+ for each record. Currently the maximum number of elements to
+ be stored is 12. There can be many more elements per record, but if there
+ are more than the maximum number, some of them will not be able to be stored
+ by Mesquite. The form of this line is<br>
+ <br>
+ numVariables = <number of elements to be read and stored><br>
+ </li>
+ <li>The third line describes how many files are to be read. The current maximum
+ is 2. If more than one file is to be read, the two files need not have the
+ same format.<br>
+ </li>
+ <li>The next lines specify the layout of each file to be read, using the format:<br>
+ <br>
+ file1 = 'itemsPerRecord=<number of elements total in each record> v1=<element
+ number of first variable> v2=<element number of second variable>...'<br>
+ <br>
+ For the second file, use <br>
+ <br>
+ file2 = ...<br>
+ </li>
+ <li>An optional line can be included specifying the name to be applied to the
+ records:<br>
+ <br>
+ recordLabel = <label for records><br>
+ </li>
+ <li>An optional line can be included specifying a simple formula to manipulate
+ the data, of the form:<br>
+ <br>
+ formula = 'v1-v2'<br>
+ <br>
+ The formula can consist of nothing more than two variables with one of the
+ standard four operators (+, -, *, /).<br>
+ <br>
+ If a formula is defined, you can label it with<br>
+ <br>
+ formulaLabel = <label for formula><br>
+ </li>
+ <li>Optional lines can then be give naming each of the variables that has been
+ stored:<br>
+ <br>
+ label1 = <label for variable 1><br>
+ label2 = <label for variable 2><br>
+ </li>
+</ol>
+<p>For each of these parts of the description, the <specification> part
+ must consist of a single token; thus, if you wish to label something with multiple
+ words, surround them by single quotes, as in 'Gamma Shape'.</p>
+<h4>Example</h4>
+<P>Imagine that you wished to ask PAUP* to estimate the value of the gamma shape
+ parameter and proportion of invariant characters for a series of trees. The
+ PAUP* commands you might give are:<br>
+</P>
+<pre> lset basefreq=empirical nst=1 pinvar=estimate rates=gamma shape=estimate;
+ lscoreall/scorefile='score';</pre>
+<P>The start of the score file that would be generated would look something like
+ this:</P>
+<pre> Tree -lnL p-inv gamma shape
+ 1 8430.14114160 0.59050567 1.075992
+ 2 8410.59386351 0.57306194 0.991805
+ 3 7922.53719113 0.64386747 1.401232</pre>
+<p>The first step would be to strip the first line out of the score file, to yield:</p>
+<pre> 1 8430.14114160 0.59050567 1.075992
+ 2 8410.59386351 0.57306194 0.991805
+ 3 7922.53719113 0.64386747 1.401232</pre>
+<p>Each record has four items. If you wished Mesquite to read in only the estimate
+ of the porportion of invariable characters and the gamma shape parameters, then
+ you will want Mesquite to read in the third and fourth item in each record.
+ The MesquiteInstructions file for processing this might then be:</p>
+<pre> MesquiteInstructions
+ numVariables = 2
+ numFiles = 1
+ file1 = 'itemsPerRecord=4 v1=3 v2=4'
+ recordLabel = 'Replicates'
+ label1 = 'proportion invariable
+ label2 = 'gamma shape'</pre>
+<p> </p>
+
+<P>
+
+<HR>
+
+</P>
+
+<P>© David Maddison & Wayne Maddison, 2005</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/oneGear.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/oneGear.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/snippetNeeded.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/snippetNeeded.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash2.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash2.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateManager.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateManager.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateeg.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateeg.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/treeNeeded.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/treeNeeded.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateRecord.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateRecord.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
