[Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Phylip PhylipConf.pm, 1.8, 1.9

Jason Stajich jason at pub.open-bio.org
Thu Sep 29 21:21:27 EDT 2005


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phylip
In directory pub.open-bio.org:/tmp/cvs-serv4063/Bio/Tools/Run/Phylo/Phylip

Modified Files:
	PhylipConf.pm 
Log Message:
indent some code


Index: PhylipConf.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** PhylipConf.pm	30 Sep 2005 01:09:30 -0000	1.8
--- PhylipConf.pm	30 Sep 2005 01:21:25 -0000	1.9
***************
*** 77,208 ****
  );
                        
! %Menu = (
!    
!   "3.5"=>{'PROTDIST'=>{'MODEL'  => {
!                                    'CAT'   =>"P\nP\n",
!                                    'KIMURA'=>"P\n",
!                                    },
!                       'GENCODE'=>  {
!                                    'ALLOWED'=>"UMVFY",
!                                    'OPTION' =>"C\n"
!                                    },
!                       'CATEGORY'=>{
!                                    'ALLOWED'=>"CHG",
!                                    'OPTION' =>"A\n"
!                                   },
!                       'PROBCHANGE'=>"E\n",
!                       'TRANS'     =>"T\n",
!                       'FREQ'      =>"F\n",
!                       'SUBMIT'    =>"Y\n",
!                       'MULTIPLE'  =>"M\n",
!                      },
!           'NEIGHBOR'=>{  'TYPE'    =>{
!                                     'UPGMA'=>"N\n"
!                                     },
!                         'OUTGROUP'=>"O\n",
!                         'LOWTRI'  =>"L\n",
!                         'UPPTRI'  =>"R\n",
!                         'SUBREP'  =>"S\n",
!                         'JUMBLE'  =>"J\n",
!                         'SUBMIT'    =>"Y\n",
!                         'MULTIPLE'  =>"M\n",
!                       },
! 
!            'PROTPARS'=>{  'THRESHOLD'=>"T\n",
!                           'JUMBLE'   =>"J\n",
!                           'OUTGROUP' =>"O\n",
!                           'SUBMIT'   =>"Y\n",
!                        },
!                        
!            'SEQBOOT'=>{   'DATATYPE' =>{
!                                         'SEQUENCE'=>"",
!                                         'MORPH'   =>"D\n",
!                                         'REST'    =>"D\nD\n",
!                                         'GENEFREQ'=>"D\nD\nD\n",
!                                        },
!                           'ALLELES'  => "A\n",
!                           'PERMUTE'  => {
!                                         'BOOTSTRAP'=>"",
!                                         'JACKKNIFE'=>"J\n",
!                                         'PERMUTE'  =>"J\nJ\n",
!                                         },
!                           'REPLICATES'=>"R\n",
!                           'SUBMIT'    =>"Y\n",
!                        },
!            'CONSENSE'=>{  
!                           'ROOTED'   => "R\n",
!                           'OUTGROUP' => "O\n",
!                           'SUBMIT'    =>"Y\n",
!                        },
!          },
  	 
!   "3.6"=>{
!       'PROTDIST'=>{
! 	  'MODEL'  => {
! 	      'PMB'        =>"P\n",
! 	      'PAM'        =>"P\nP\n",
! 	      'KIMURA'     =>"P\nP\nP\n",
! 	      'CAT'        =>"P\nP\nP\nP\n",
! 	      'JTT'        =>"Y\n",
! 	  },
! 	  'GENCODE'=>  {
! 	      'ALLOWED'=>"UMVFY",
! 	      'OPTION' =>"U\n",
! 	  },
! 	  'CATEGORY'=> {
! 	      'ALLOWED'=>"CHG",
! 	      'OPTION' =>"A\n",
! 	  },
! 	  'PROBCHANGE'=>"E\n",
! 	  'TRANS'     =>"T\n",
! 	  'FREQ'      =>"F\n",
! 	  'WEIGHTS'   =>"W\n",
! 	  'SUBMIT'    => "Y\n",
! 	  'MULTIPLE'  =>"M\nD\n",
!       },
!       'NEIGHBOR'=>{ 'TYPE'    =>{
! 	  'UPGMA'=>"N\n",
!       },
! 		    'OUTGROUP'=>"O\n",
! 		    'LOWTRI'  =>"L\n",
! 		    'UPPTRI'  =>"R\n",
! 		    'SUBREP'  =>"S\n",
! 		    'JUMBLE'  =>"J\n",
! 		    'SUBMIT'    =>"Y\n",
! 		    'MULTIPLE'  =>"M\n",
! 		},
!       'PROTPARS'=>{  'THRESHOLD'=>"T\n",
! 		     'JUMBLE'   =>"J\n",
! 		     'OUTGROUP' =>"O\n",
! 		     'SUBMIT'   =>"Y\n",
! 		 },
!       'SEQBOOT'=>{   'DATATYPE' =>{
! 	  'SEQUENCE'=>"",
! 	  'MORPH'   =>"D\n",
! 	  'REST'    =>"D\nD\n",
! 	  'GENEFREQ'=>"D\nD\nD\n",
!       },
! 		     'ALLELES'  => "A\n",
! 		     'PERMUTE'  => {
! 			 'BOOTSTRAP'=>"",
! 			 'JACKKNIFE'=>"J\n",
! 			 'PERMUTE'  =>"J\nJ\n",
! 		     },
! 		     'REPLICATES'=>"R\n",
! 		     'SUBMIT'   =>"Y\n",
! 		 },
!       
!       'CONSENSE'=>{  'TYPE'     => {
! 	  'MRE'     =>"",
! 	  'STRICT'  =>"C\n",
! 	  'MR'      =>"C\nC\n",
! 	  'ML'      =>"C\nC\nC\n",
!       },
! 		     'ROOTED'   => "R\n",
! 		     'OUTGROUP' => "O\n",
! 		     'SUBMIT'    =>"Y\n",
! 		 },
!   },
! 	 );
  
  1;
--- 77,214 ----
  );
                        
! %Menu = 
!     (
!      "3.5" => {
! 	 'PROTDIST' => {
! 	     'MODEL'  => {
! 		 'CAT'   =>"P\nP\n",
! 		 'KIMURA'=>"P\n",
! 	     },
! 	     'GENCODE'=>  {
! 		 'ALLOWED'=>"UMVFY",
! 		 'OPTION' =>"C\n",
! 	     },
! 	     'CATEGORY'=>{
! 		 'ALLOWED'=>"CHG",
! 		 'OPTION' =>"A\n",
! 	     },
! 	     'PROBCHANGE'=>"E\n",
! 	     'TRANS'     =>"T\n",
! 	     'FREQ'      =>"F\n",
! 	     'SUBMIT'    =>"Y\n",
! 	     'MULTIPLE'  =>"M\n",
! 	 },
! 	 'NEIGHBOR'=>{  
! 	     'TYPE'    => {
! 		 'UPGMA'=>"N\n",
! 	     },
! 	     'OUTGROUP'=>"O\n",
! 	     'LOWTRI'  =>"L\n",
! 	     'UPPTRI'  =>"R\n",
! 	     'SUBREP'  =>"S\n",
! 	     'JUMBLE'  =>"J\n",
! 	     'SUBMIT'    =>"Y\n",
! 	     'MULTIPLE'  =>"M\n",
! 	 },	 
! 	 'PROTPARS'=>{  
! 	     'THRESHOLD'=>"T\n",
! 	     'JUMBLE'   =>"J\n",
! 	     'OUTGROUP' =>"O\n",
! 	     'SUBMIT'   =>"Y\n",
! 	 },
  	 
! 	 'SEQBOOT'=>{   
! 	     'DATATYPE' =>{
! 		 'SEQUENCE'=>"",
! 		 'MORPH'   =>"D\n",
! 		 'REST'    =>"D\nD\n",
! 		 'GENEFREQ'=>"D\nD\nD\n",
! 	     },
! 	     'ALLELES'  => "A\n",
! 	     'PERMUTE'  => {
! 		 'BOOTSTRAP'=>"",
! 		 'JACKKNIFE'=>"J\n",
! 		 'PERMUTE'  =>"J\nJ\n",
! 	     },
! 	     'REPLICATES'=>"R\n",
! 	     'SUBMIT'    =>"Y\n",
! 	 },
! 	 'CONSENSE'=>{  
! 	     'ROOTED'   => "R\n",
! 	     'OUTGROUP' => "O\n",
! 	     'SUBMIT'    =>"Y\n",
! 	 },
!      },	 
!      "3.6"=>{
! 	 'PROTDIST'=>{
! 	     'MODEL'  => {
! 		 'PMB'        =>"P\n",
! 		 'PAM'        =>"P\nP\n",
! 		 'KIMURA'     =>"P\nP\nP\n",
! 		 'CAT'        =>"P\nP\nP\nP\n",
! 		 'JTT'        =>"Y\n",
! 	     },
! 	     'GENCODE'=>  {
! 		 'ALLOWED'=>"UMVFY",
! 		 'OPTION' =>"U\n",
! 	     },
! 	     'CATEGORY'=> {
! 		 'ALLOWED'=>"CHG",
! 		 'OPTION' =>"A\n",
! 	     },
! 	     'PROBCHANGE'=>"E\n",
! 	     'TRANS'     =>"T\n",
! 	     'FREQ'      =>"F\n",
! 	     'WEIGHTS'   =>"W\n",
! 	     'SUBMIT'    => "Y\n",
! 	     'MULTIPLE'  =>"M\nD\n",
! 	 },
! 	 'NEIGHBOR' => { 
! 	     'TYPE'    => {
! 		 'UPGMA'=>"N\n",
! 	     },
! 	     'OUTGROUP'=>"O\n",
! 	     'LOWTRI'  =>"L\n",
! 	     'UPPTRI'  =>"R\n",
! 	     'SUBREP'  =>"S\n",
! 	     'JUMBLE'  =>"J\n",
! 	     'SUBMIT'    =>"Y\n",
! 	     'MULTIPLE'  =>"M\n",
! 	 },
! 	 'PROTPARS' => {  
! 	     'THRESHOLD'=>"T\n",
! 	     'JUMBLE'   =>"J\n",
! 	     'OUTGROUP' =>"O\n",
! 	     'SUBMIT'   =>"Y\n",
! 	 },
! 	 'SEQBOOT'=>{   
! 	     'DATATYPE' => {
! 		 'SEQUENCE'=> "",
! 		 'MORPH'   =>"D\n",
! 		 'REST'    =>"D\nD\n",
! 		 'GENEFREQ'=>"D\nD\nD\n",
! 	     },
! 	     'ALLELES'  => "A\n",
! 	     'PERMUTE'  => {
! 		 'BOOTSTRAP'=>"",
! 		 'JACKKNIFE'=>"J\n",
! 		 'PERMUTE'  =>"J\nJ\n",
! 	     },
! 	     'REPLICATES'=>"R\n",
! 	     'SUBMIT'   =>"Y\n",
! 	 },      
! 	 'CONSENSE'=>{  
! 	     'TYPE'     => {
! 		 'MRE'     =>"",
! 		 'STRICT'  =>"C\n",
! 		 'MR'      =>"C\nC\n",
! 		 'ML'      =>"C\nC\nC\n",
! 	     },
! 	     'ROOTED'   => "R\n",
! 	     'OUTGROUP' => "O\n",
! 	     'SUBMIT'    =>"Y\n",
! 	 },
!      },
!      );
  
  1;



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