# # Copyright (C) 1999-2004 Liz Potterton, Peter Briggs # # This code is distributed under the terms and conditions of the # CCP4 Program Suite Licence Agreement as a CCP4 Library. # A copy of the CCP4 licence can be obtained by writing to the # CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK. # #CCP4i_cvs_Id $Id$ #========================================================================== #==_task_window==core procedure. all commands to define graphical interface #========================================================================== #------------------------------------------------------------------------------ proc clustalw_prereq { } { #------------------------------------------------------------------------------ if { ![file exists [FindExecutable clustalw2]] } { return 0 } return 1 } proc clustalw_setup { typedefname arrayname } { upvar #0 $typedefname typedef set typedef(_clustalw_exptype) { menu { \ " DNA Pairwise Alignment" \ " DNA Multiple Alignment" \ "Protein Pairwise Alignment" \ "Protein Multiple Alignment" } { DNAFAST DNAFULL PROTEINFAST PROTEINFULL } } set typedef(_clustalw_outputtype) { menu { "ALN" "GCG" "GDE" "Phylip" "PIR" } { ALN GCG GDE PHYLIP PIR } } set typedef(_clustalw_outorder) { menu { "Input" "Aligned" } { INPUT ALIGNED } } set typedef(_clustalw_score) { menu { "Percent" "Absolute" } { PERCENT ABSOLUTE } } set typedef(_clustalw_pwmatrixn) { menu { "BLOSUM" "PAM" "GONNET" "ID" } { BLOSUM PAM GONNET ID } } set typedef(_clustalw_pwdnamatrixn) { menu { "IUB" "CLUSTALW" } { IUB CLUSTALW } } set typedef(_clustalw_matrixn) { menu { "BLOSUM" "PAM" "GONNET" "ID" } { BLOSUM PAM GONNET ID} } set typedef(_clustalw_dnamatrixn) { menu { "IUB" "CLUSTALW" } { IUB CLUSTALW } } set typedef(_clustalw_outputtreen) { menu { "NJ" "Phylip" "Dist" "Nexus" } { NJ PHYLIP DIST NEXUS } } set typedef(_clustalw_bootlabelsn) { menu { "NODE" "BRANCH" } { NODE BRANCH } } # Check that the CLUSTALW program is available PleaseWait "Looking for the ClustalW program" if { [clustalw_find_program clustalw2] } { # Start the interface return 1 } # Set URL for CLUSTALW homepage set clustalw_url "http://www.ebi.ac.uk/clustalw/" # Make sure we get rid of waiting message PleaseWait set action [ChooseOptionDialog "ClustalW Interface" "ClustalW" \ "The ClustalW program doesn't appear to be available. Without it this interface cannot run. This may be because ClustalW is not on your path, or because the program has not been installed. If you already have ClustalW then you can configure the interface to find it using the options under the \"System Administration\" menu. Otherwise you can download the latest version of ClustalW from $clustalw_url" \ { "Go to website" Dismiss } -default 1 ] # Go to the ClustalW website if ![regexp Dismiss $action] { open_url $clustalw_url -remote } return 0 return 1 } proc clustalw_task_window { arrayname } { global clustalw_var global configure upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Clustalw Interface" "Clustalw" [list "DNA Pairwise Alignment" "DNA Multiple Alignment" "Protein Pairwise Alignment" "Protein Multiple Alignment" "Other Options - Structure Alignments" "Other Options - Phylogenetic Trees" "Output" ]] == 0 } return OpenFolder protocol CreateTitleLine line TITLE CreateLine line label "Conduct" widget EXPTYPE -command "clustalw_set_align $arrayname" CreateLine line \ label "Opening File From... " \ CreateInputFileLine blastin "Select Clustalw Input File 'NO SPACE!'" File INFILE DIR_INFILE CreateLine line \ label "Save File Into..." \ CreateOutputFileLine clustalout "Declare Clustalw Output File 'NO SPACE!'" File OUTFILE DIR_OUTFILE CreateLine line label "Set Output Type" widget OUTPUTTYPE label "and" widget OUTORDER label "with score type" widget SCORE OpenFolder 1 EXPTYPE closed DNAFAST hide CreateLine line widget PWDNAMATRIX label "Set DNA Weight Matrix" widget PWDNAMATRIXN CreateLine line widget KTUPLE label "Set K-TUPLE value" widget KTUPLEN CreateLine line widget TOPDIAGS label "Set number of best diagrams" widget TOPDIAGSN CreateLine line widget PAIRGAP label "Set Gap Penalty" widget PAIRGAPN CreateLine line widget PWGAPOPEN label "Set Gap Opening Penalty" widget PWGAPOPENF CreateLine line widget PWGAPEXT label "Set Gap Extension Penalty" widget PWGAPEXTF OpenFolder 2 EXPTYPE closed DNAFULL hide CreateLine line widget DNAMATRIX label "Set DNA Weight Matrix" widget DNAMATRIXN CreateLine line widget GAPOPEN label "Set Gap opening Penalty" widget GAPOPENF CreateLine line widget GAPEXT label "Set Gap Extension Penalty" widget GAPEXTF CreateLine line widget ENDGAPS label "No End Gap Separation Penalty" CreateLine line widget GAPDIST label "Set Gap Separation Penalty Range" widget GAPDISTN CreateLine line widget NOPGAP label "No residue-specific gaps" CreateLine line widget NOHGAP label "No Hydrophilic gaps" CreateLine line widget HGAPRESIDUES label "List Hydrophilic Residues" CreateLine line widget TRANSWEIGHT label "Set Transitions Weighting" widget TRANSWEIGHTF OpenFolder 3 EXPTYPE closed PROTEINFAST hide CreateLine line widget PWMATRIX label "Set Protein Weight Matrix" widget PWMATRIXN CreateLine line widget KTUPLE label "Set K-TUPLE value" widget KTUPLEN CreateLine line widget TOPDIAGS label "Set number of best diagrams" widget TOPDIAGSN CreateLine line widget PAIRGAP label "Set Gap Penalty" widget PAIRGAPN CreateLine line widget PWGAPOPEN label "Set Gap Opening Penalty" widget PWGAPOPENF CreateLine line widget PWGAPEXT label "Set Gap Extension Penalty" widget PWGAPEXTF OpenFolder 4 EXPTYPE closed PROTEINFULL hide CreateLine line widget MATRIX label "Set Protein Weight Matrix" widget MATRIXN CreateLine line widget GAPOPEN label "Set Gap opening Penalty" widget GAPOPENF CreateLine line widget GAPEXT label "Set Gap Extension Penalty" widget GAPEXTF CreateLine line widget ENDGAPS label "No End Gap Separation Penalty" CreateLine line widget GAPDIST label "Set Gap Separation Penalty Range" widget GAPDISTN CreateLine line widget NOPGAP label "No residue-specific gaps" CreateLine line widget NOHGAP label "No Hydrophilic gaps" CreateLine line widget HGAPRESIDUES label "List Hydrophilic Residues" CreateLine line widget TRANSWEIGHT label "Set Transitions Weighting" widget TRANSWEIGHTF OpenFolder 5 closed CreateLine line widget HELIXGAP label "Set gap penalty for helix core residues" label "n=" widget HELIXGAPN CreateLine line widget STRANDGAP label "Set gap penalty for strand core residues" label "n=" widget STRANDGAPN CreateLine line widget LOOPGAP label "Set gap penalty for loop regions" label "n=" widget LOOPGAPN CreateLine line widget TERMINALGAP label "Set gap penalty for structure termini" label "n=" widget TERMINALGAPN CreateLine line widget HELIXENDIN label "Set number of residues inside helix treated as termini" widget HELIXENDINN CreateLine line widget HELIXENDOUT label "Set number of residues outside helix treated as termini" widget HELIXENDOUTN CreateLine line widget STRANDENDIN label "Set number of residues inside strand treated as termini" widget STRANDENDINN CreateLine line widget STRANDENDOUT label "Set number of residues outside strand treated as termini" widget STRANDENDOUTN OpenFolder 6 closed CreateLine line widget OUTPUTTREE label "Output Phylogenetic Tree in" widget OUTPUTTREEN label "Format" CreateLine line widget SEED label "Set seed number for bootstraps" widget SEEDN CreateLine line widget KIMURA label "Use Kimura's Correction" CreateLine line widget TOSSGAPS label "Ignore positions with gaps" CreateLine line widget BOOTLABELS label "Set position of bootstrap values in tree display" widget BOOTLABELSN OpenFolder 7 open CreateText outputaln " " -scroll set array(OUTPUTALN) $outputaln } proc clustalw_set_align { arrayname } { upvar #0 $arrayname array if { $array(EXPTYPE) == "Protein Multiple Alignment" } { set array(ALIGN) 1 set array(TYPE) "PROTEIN" } if { $array(EXPTYPE) == " DNA Multiple Alignment" } { set array(ALIGN) 1 set array(TYPE) "DNA" } if { $array(EXPTYPE) == "Protein Pairwise Alignment" } { set array(ALIGN) 0 set array(TYPE) "PROTEIN" } if { $array(EXPTYPE) == " DNA Pairwise Alignment" } { set array(ALIGN) 0 set array(TYPE) "DNA" } return 1 } proc clustalw_run { arrayname } { upvar #0 $arrayname array set align $array(ALIGN) set infile [GetFullFileName [FileRootName $array(INFILE)] $array(DIR_INFILE)] set outfile [GetFullFileName [FileRootName $array(OUTFILE)] $array(DIR_OUTFILE)] return 1 } proc clustalw_review { arrayname job_id } { upvar #0 $arrayname array if { [ReadFile [GetFullFileName0 $arrayname OUTFILE] alignment] } { AppendTextWindow $array(OUTPUTALN) $alignment } else { AppendTextWindow $array(OUTPUTALN) "Program failed! Check log file." } } #----------------------------------------------------------------------- proc clustalw_find_program { program } { #----------------------------------------------------------------------- # Search for the clustalw executable, to make sure that the program # will run if { ![file exists [FindExecutable $program]] } { return 0 } return 1 }