# # Copyright (C) 2014 David Waterman # # 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 $Id$ # ====================================================================== # blend.tcl -- # # CCP4Interface # # ======================================================================= #--------------------------------------------------------------------- proc blend_setup { typedefVar arrayname } { #--------------------------------------------------------------------- upvar #0 $typedefVar typedef upvar #0 $arrayname array global tcl_platform # A trick to put Rscript.exe in the path on Windows if it isn't already if { ([regexp -nocase windows $tcl_platform(os)]) && ([FindExecutable "Rscript.exe" ] == "") } { if { ![catch { exec cmd.exe /c ftype RWorkspace } result] } { set path_to_r [file nativename [file dirname [lindex [split $result \"] 1] ] ] set ::env(PATH) "$path_to_r;$::env(PATH)" } } # Check that R is installed on this system if { ( [FindExecutable "Rscript" ] == "" ) && ( [FindExecutable "Rscript.exe" ] == "" ) } { WarningMessage "Dependency Error: BLEND requires R. Please go to http://cran.r-project.org/" return 0 } DefineMenu _blend_mode [ list "Analysis" \ "Synthesis" \ "Combination" ] \ [ list ANALYSIS SYNTHESIS COMBINATION ] DefineMenu _blend_anomalous_flag [ list "ON" \ "OFF" ] return 1 } #-------------------------------------------------------------- proc blend_browse { arrayname path_type} { #-------------------------------------------------------------- # Use the file browser to select a directory of datasets upvar #0 $arrayname array if { [SelectFile filename -directory] } { # Update the parameters in the window if { $path_type == "HKL_SOURCE" } { set array(HKL_SOURCE) $filename } if { $path_type == "PREV_RUNDIR" } { # The browser can return either a filename or a directory # name - make sure we get the leading directory in the # former case if { [file isdirectory $filename] } { set dirname $filename } else { set dirname [file dirname $filename] } set array(PREV_RUNDIR) $dirname } } return } #-------------------------------------------------------------- proc blend_view { arrayname } { #-------------------------------------------------------------- # Display the the list of input files in a text viewer upvar #0 $arrayname array if { [file isfile $array(HKL_SOURCE)] } { DisplayTextFile $array(HKL_SOURCE) } } #-------------------------------------------------------------- proc blend_run { arrayname } { #-------------------------------------------------------------- upvar #0 $arrayname array # Why is it the Titlecase version and not ALLCAPS? if { $array(BLEND_MODE) == "Analysis" } { if { $array(HKL_SOURCE) == "none" } { WarningMessage "Input Error: You must choose a source of integrated datasets as input!" return 0 } } if { $array(BLEND_MODE) == "Synthesis" } { if { $array(PREV_RUNDIR) == "none" } { WarningMessage "Input Error: You must supply the path to a previous run of Blend!" return 0 } } if { $array(BLEND_MODE) == "Combination" } { if { $array(PREV_RUNDIR) == "none" } { WarningMessage "Input Error: You must supply the path to a previous run of Blend!" return 0 } } return 1 } #--------------------------------------------------------------------- proc CombDatasets { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ message "Enter the identifying number of a dataset to include" \ label "Include dataset number" \ widget INC_DATASETS \ label "in combination" } #--------------------------------------------------------------------- proc CombClusters { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ message "Enter the identifying number of a cluster to include" \ label "Include cluster number" \ widget INC_CLUSTERS \ label "in combination" } #--------------------------------------------------------------------- proc ExclDatasets { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ message "Enter the identifying number of a dataset to exclude" \ label "Exclude dataset number" \ widget EXC_DATASETS \ label "from combination" } #--------------------------------------------------------------------- proc DefRuns { arrayname counter } { #--------------------------------------------------------------------- CreateLine line \ message "Define Runs by Batch ranges" \ label "Define Run" \ widget RUNS \ label "from Batch" \ widget RUN_BATCH_LO \ label "to Batch" \ widget RUN_BATCH_HI \ } # procedure to draw task window #--------------------------------------------------------------------- proc blend_task_window { arrayname } { #--------------------------------------------------------------------- global configure upvar #0 $arrayname array if { [CreateTaskWindow $arrayname \ "Run BLEND for multiple dataset analysis/combination" "BLEND" \ [ list "Options" \ ] ] == 0 } return SetProgramHelpFile "blend" set array(INITIALISED) 0 #=PROTOCOL============================================================== OpenFolder protocol CreateTitleLine line TITLE #=FILES================================================================= OpenFolder file CreateLine line \ message "Select the mode for BLEND to run" \ label "Program Mode:" \ widget BLEND_MODE #CreateOutputFileLine line \ # "Enter output PDB file name (XYZOUT)" \ # "PDB out" \ # XYZOUT DIR_XYZOUT #=Options for analysis mode only======================================== OpenSubFrame frame \ -toggle_display BLEND_MODE open [list ANALYSIS] CreateLine line \ message "Dataset source" \ label "Directory or file list of integrated datasets" \ widget HKL_SOURCE -oblig \ -width 50 set browse [button $line.browse -text "Browse" \ -command "blend_browse $arrayname HKL_SOURCE"] $browse configure -font $configure(FONT_SMALL) set view [button $line.view -text "View" \ -command "blend_view $arrayname"] $view configure -font $configure(FONT_SMALL) pack $browse $view -after $line.e2 -side left CloseSubFrame #=Options for synthesis mode only======================================== OpenSubFrame frame \ -toggle_display BLEND_MODE open [list SYNTHESIS] CreateLine line \ message "Previous run directory" \ label "Path to an earlier Blend run directory" \ widget PREV_RUNDIR -oblig \ -width 50 set browse [button $line.browse -text "Browse" \ -command "blend_browse $arrayname PREV_RUNDIR"] $browse configure -font $configure(FONT_SMALL) pack $browse -after $line.e2 -side left CreateLine line \ label "Enter heights from the dendrogram to define merging groups" \ CreateLine line \ message "Enter a height taken from the dendrogram" \ label "Upper height cutoff" \ widget DEND_HEIGHT1 \ label "Lower height cutoff" \ widget DEND_HEIGHT2 \ label "(optional)" CloseSubFrame #=Options for combination mode only====================================== OpenSubFrame frame \ -toggle_display BLEND_MODE open [list COMBINATION] CreateLine line \ message "Previous run directory" \ label "Path to an earlier Blend run directory" \ widget PREV_RUNDIR -oblig \ -width 50 set browse [button $line.browse -text "Browse" \ -command "blend_browse $arrayname PREV_RUNDIR"] $browse configure -font $configure(FONT_SMALL) pack $browse -after $line.e2 -side left CreateLine line \ message "Enter identifying numbers of datasets you want to combine" \ label "Specify datasets to include in combination" \ -italic CreateExtendingFrame N_INC_DATASETS CombDatasets \ "Add an integer to include that dataset in combination" \ "Add item"\ [list INC_DATASETS ] CreateLine line \ message "Enter identifying numbers of clusters you want to combine" \ label "Specify clusters to include in combination" \ -italic CreateExtendingFrame N_INC_CLUSTERS CombClusters \ "Add an integer to include that cluster in combination" \ "Add item"\ [list INC_CLUSTERS ] CreateLine line \ message "Enter identifying numbers of datasets you want to exclude" \ label "Specify datasets to exclude from combination" \ -italic CreateExtendingFrame N_EXC_DATASETS ExclDatasets \ "Add an integer to exclude that dataset from combination" \ "Add item"\ [list EXC_DATASETS ] CloseSubFrame #=Message to report mode of operation================================== OpenSubFrame frame \ -toggle_display BLEND_MODE open [list ANALYSIS] CreateLine line \ label "Run blend in analysis mode" \ -italic CloseSubFrame OpenSubFrame frame \ -toggle_display BLEND_MODE open [list SYNTHESIS] CreateLine line \ label "Run blend in synthesis mode" \ -italic CloseSubFrame OpenSubFrame frame \ -toggle_display BLEND_MODE open [list COMBINATION] CreateLine line \ label "Run blend in combination mode" \ -italic CloseSubFrame #=Folder to select special options================================== OpenFolder 1 closed OpenSubFrame frame \ -toggle_display BLEND_MODE open [list ANALYSIS] CreateLine line \ message "Set radfrac" \ widget SET_RADFRAC -width 4 \ label "Tolerated fraction of damaged average intensity" \ widget RADFRAC CreateLine line \ message "Set I/sigI" \ widget SET_ISIGI -width 4 \ label "I/sigI resolution cut-off" \ widget ISIGI CreateLine line \ message "Select to use I descriptors" \ widget USE_IDESC -width 4 \ label "Use intensity averages rather than cell parameters as descriptors" #widget CPARWT CreateLine line \ message "Set Laue group" \ widget SET_LAUEGROUP -width 4 \ label "Choose the Laue group " \ widget LAUEGROUP CloseSubFrame OpenSubFrame frame \ -toggle_display BLEND_MODE open [list SYNTHESIS COMBINATION] CreateLine line \ label "Control execution of Pointless" \ CreateLine line \ message "Set dataref" \ widget SET_DATAREF -width 4 \ label "Input index of a reference dataset in case of alternative indexing" \ widget DATAREF CreateLine line \ message "Set space group" \ widget SET_SPACEGROUP -width 4 \ label "Impose" \ widget SPACEGROUP \ label "as final space group" CreateLine line \ message "Set tolerance" \ widget SET_TOLERANCE -width 4 \ label "Tolerated unit cell difference (degrees)" \ widget TOLERANCE CreateLine line \ label "Control execution of Aimless" \ CreateLine line \ message "Set resolution" \ widget SET_RESOLUTION -width 4 \ label "Set resolution limits. Low:" \ widget LO_RES \ label "Set resolution limits. High:" \ widget HI_RES \ CreateLine line \ message "Set ANOMALOUS ON/OFF" \ widget SET_ANOMALOUS -width 4 \ label "Set value of ANOMALOUS keyword to" \ widget ANOMALOUS CreateLine line \ message "Set SCALES" \ widget SET_SCALES -width 4 \ label "Set value of SCALES keyword to" \ widget SCALES CreateLine line \ message "Set EXCLUDE BATCH" \ widget SET_EXC_BATCH -width 4 \ label "Set value of EXCLUDE BATCH keyword to" \ widget EXC_BATCH CreateLine line \ message "Set SDCORR" \ widget SET_SDCORR -width 4 \ label "Set value of SDCORRECTION keyword to" \ widget SDCORR CreateLine line \ label "Define Runs by Batch ranges" \ -italic CreateExtendingFrame N_RUNS DefRuns \ "Enter definitions for Runs" \ "Add Run"\ [list RUNS RUN_BATCH_LO RUN_BATCH_HI ] CloseSubFrame }