#
#     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 $Id$

{ [ IfSet $TITLE ] } title  $TITLE

$EXCLUDE_RESOLUTION resolution low $EXCLUDE_RESOLUTION_MIN high $EXCLUDE_RESOLUTION_MAX

IF { $MULTI_RUNS == 1 }
LOOP N 1  $NRUNS
1 run $N
LOOP I 1  $RUN_DEFS($N)
CASE  $RUN_MODE($N,$I)
CASEMATCH ALL
 - 1 all
CASEMATCH XTALLIST
 - 1 crystal $RUN_LIST($N,$I)
CASEMATCH XTALRANGE
 - 1 crystal $RUN_IMIN($N,$I) to $RUN_IMAX($N,$I)
CASEMATCH BATCHRANGE
 - 1  $RUN_XCLUDE($N,$I) batch $RUN_IMIN($N,$I) to $RUN_IMAX($N,$I)
CASEMATCH BATCHLIST
 - 1  $RUN_XCLUDE($N,$I) batch $RUN_LIST($N,$I)
CASEMATCH RANGE
 - 1 $RUN_XCLUDE($N,$I) range $RUN_RMIN($N,$I) to $RUN_RMAX($N,$I)
CASEMATCH DATASET
 - 1 dataset $RUN_DATASET($N,$I)
ENDCASE
ENDLOOP
ENDLOOP

$REFERENCE $REFERENCE_RUN reference

LOOP N 1 $NRUNS
LOOP I 1  $RUN_DEFS($N)
CASE $RUN_MODE($N,$I)
CASEMATCH RESOLUTION
1 resolution run $N 
- {[IfSet $RUN_RMIN($N,$I)] } low $RUN_RMIN($N,$I)
- {[IfSet $RUN_RMAX($N,$I)] } high $RUN_RMAX($N,$I)
CASEMATCH SDRANGE
1 exclude run $N sdmin $RUN_RMIN($N,$I)
- {[IfSet $RUN_RMAX($N,$I)]} sdmax $RUN_RMAX($N,$I)
CASEMATCH ABSVALUE
1 exclude run $N absvalue $RUN_RMIN($N,$I)
CASEMATCH RECTANGLE
exclude run $N rectangle $RUN_RMIN($N,$I) $RUN_RMAX($N,$I) $RUN_YMIN($N,$I) $RUN_YMAX($N,$I)
ENDCASE
ENDLOOP
ENDLOOP
ENDIF

# Datasets out
IF { !$MULTI_RUNS }
  IF { $N_FILE_DATASETS <= 1 }
    IF { [StringSame $OUTPUT POLISH] && [StringSame $HARVEST_MODE NOHARVEST] }
      1 # No crystal/dataset information is required
    ELSE
      1 name project $HARVEST_PNAME crystal $HARVEST_XNAME dataset $HARVEST_DNAME
    ENDIF
  ENDIF
  IF { $COMBINE_DATASETS }
    1 name project $HARVEST_PNAME crystal $HARVEST_XNAME dataset $HARVEST_DNAME
  ENDIF
ELSE
  LOOP I 1 $NRUNS
    1 name run $I project $HARVEST_PNAME crystal $RUN_XNAME_OUT($I) dataset $RUN_DNAME_OUT($I)
  ENDLOOP
ENDIF

{!$REFINE } onlymerge
$EXCLUDE_BYSIGMA exclude sdmin $EXCLUDE_BYSIGMA_1 
- {[IfSet $EXCLUDE_BYSIGMA_2]} sdmax $EXCLUDE_BYSIGMA_2
$EXCLUDE_MAXIMUM exclude absmax $EXCLUDE_MAXIMUM_1
1 exclude $EXCLUDE_EMAX 
 - {[StringSame $EXCLUDE_EMAX EMAX]} $EXCLUDE_EMAX_EMAX
 - {[StringSame $EXCLUDE_EMAX EPROB]} $EXCLUDE_EMAX_EPROB

IF  { $EXCLUDE_RECT && $N_EXCLUDE_RECT > 0 }
LOOP I 1 $N_EXCLUDE_RECT
  1 EXCLUDE RECTANGLE $EXCLUDE_XMIN($I) $EXCLUDE_XMAX($I) $EXCLUDE_YMIN($I) $EXCLUDE_YMAX($I)
ENDLOOP
ENDIF

IF { $EXCLUDE_BATCH && $N_EXCLUDE_BATCH > 0 }
LOOP I 1 $N_EXCLUDE_BATCH
 1 exclude batch 
 - { [StringSame $EXCLUDE_BATCH_DEFINE($I) LIST] } $EXCLUDE_BATCH_LIST($I)
 - { [StringSame $EXCLUDE_BATCH_DEFINE($I) RANGE] } $EXCLUDE_BATCH_FIRST($I) to $EXCLUDE_BATCH_LAST($I)
ENDLOOP
ENDIF

IF { $EXCLUDE_DATASET && $N_EXCLUDE_DATASETS > 0 }
LOOP I 1 $N_EXCLUDE_DATASETS
  1 exclude dataset $EXCLUDE_DATASET_NAME($I)
ENDLOOP
ENDIF

IF { !$FINAL_DIF_IS }
  1 partials
 - $IS_CHECK check | nocheck
 - $IS_TEST test $IS_TEST_MIN $IS_TEST_MAX | notest
 - $IS_CORRECT correct $IS_CORRECT_LIMIT
 - $IS_GAP gap | nogap
 - { [IfSet $IS_MAXWIDTH]}  maxwidth $IS_MAXWIDTH
ENDIF

1 intensities $IS_MODE
 - $SCALE_ANOMALOUS  anomalous
 - 1 $IS_PARTIALS
 -- { [StringSame $IS_PARTIALS "SCALE_PARTIALS" ]} $IS_PARTIALS_MINFRAC
IF { ![StringSame $IS_PARTIALS "FULLS" ] && $FINAL_DIF_IS  }
 - $IS_CHECK check | nocheck
 - $IS_TEST test $IS_TEST_MIN $IS_TEST_MAX | notest
 - $IS_CORRECT correct $IS_CORRECT_LIMIT
 - $IS_GAP gap | nogap
 - { [IfSet $IS_MAXWIDTH]}  maxwidth $IS_MAXWIDTH
ENDIF

1 final $FINAL_PARTIALS
 - { [StringSame $FINAL_PARTIALS "SCALE_PARTIALS" ]}  $FINAL_PARTIALS_MINFRAC

IF { ![ StringSame $FINAL_PARTIALS "FULLS" ] && $FINAL_DIF_IS }
 - $FINAL_CHECK check | nocheck
 - $FINAL_TEST test $FINAL_TEST_MIN $FINAL_TEST_MAX | notest
 - $FINAL_CORRECT correct $FINAL_CORRECT_LIMIT
 - $FINAL_GAP  gap | nogap
 - {[IfSet $FINAL_MAXWIDTH]} maxwidth $FINAL_MAXWIDTH
ENDIF

LOOP N 1 $NSCALES
1 scales
 - { ![regexp ALL $SCALES_RUN($N)] }  $SCALES_RUN($N)

CASE $SCALES_MODE($N)
CASEMATCH CONSTANT
 - 1 $SCALES_MODE($N)
CASEMATCH BATCH
 - 1 $SCALES_MODE($N)
CASEMATCH SLOPE
 - 1 $SCALES_MODE($N)
CASEMATCH DETECTOR
 - 1 detector $SCALES_DETECTOR($N) $SCALES_DETECTOR_NX($N) $SCALES_DETECTOR_NY($N)
CASEMATCH ROTATION
 - 1 rotation $SCALES_ROTATION($N) $SCALES_ROTATION_ROT($N)
CASEMATCH ROT&DET
 - 1 detector $SCALES_DETECTOR($N) $SCALES_DETECTOR_NX($N) $SCALES_DETECTOR_NY($N)
 - 1 rotation $SCALES_ROTATION($N) $SCALES_ROTATION_ROT($N)
CASEMATCH SECONDARY
 - 1 rotation $SCALES_ROTATION($N) $SCALES_ROTATION_ROT($N)
 - 1 secondary $SECONDARY_LMAX($N) 
CASEMATCH ABSORPTION
 - 1 rotation $SCALES_ROTATION($N) $SCALES_ROTATION_ROT($N)
 - 1 absorption $SECONDARY_LMAX($N) 
 -- {[IfSet $SURFACE_POLE($N)]} pole $SURFACE_POLE($N)
CASEMATCH SURFACE
 - 1 rotation $SCALES_ROTATION($N) $SCALES_ROTATION_ROT($N)
 - 1 surface $SURFACE_LMAX($N)
 -- {[IfSet $SURFACE_POLE($N)]} pole $SURFACE_POLE($N)
ENDCASE

 - 1 bfactor $SCALES_BFACTOR($N)
 -- { ![StringSame $SCALES_BFACTOR($N) OFF] && ![StringSame $SCALES_BROTATION($N) "NO_TIME" ] } $SCALES_BROTATION($N) $SCALES_BFACTOR_TIME($N)
 - $SCALES_TAILS($N) tails $TAILS_V($N) $TAILS_A0($N) $TAILS_A1($N)

ENDLOOP

$TAILS_FIX_V FIX V | UNFIX V
$TAILS_FIX_A0 FIX A0 | UNFIX A0
$TAILS_FIX_A1 FIX A1 | UNFIX A1
IF { $N_TAIL_LINK  > 0 } 
  LOOP N 1 $N_TAIL_LINK 
    1 $TAIL_LINK($N) 
     - { [StringSame $TAIL_RUN1($N) "ALL"] } all | $TAIL_RUN1($N) to $TAIL_RUN2($N)
  ENDLOOP
ENDIF

IF { $N_SURFACE_LINK  > 0 }
  LOOP N 1 $N_SURFACE_LINK
    1 $SURFACE_LINK($N)
     - { [StringSame $SURFACE_RUN1($N) "ALL"] } all | $SURFACE_RUN1($N) to $SURFACE_RUN2($N)
  ENDLOOP
ENDIF

CASE $INITIAL_MODE
CASEMATCH RUN
1 initial
  LOOP N 1 $NRUNS
   - 1 run $N $INITIAL_VALUE($N)
  ENDLOOP
CASEMATCH MEAN
 1 initial $INITIAL_MODE
CASEMATCH UNITY
 1 initial $INITIAL_MODE
CASEMATCH RESTORE
 1 restore $RESTORE_FILE
ENDCASE

{ $TIE_ROTATION } tie rotation $TIE_ROTATION_SD
{ $TIE_DETECTOR } tie detector $TIE_DETECTOR_SD
{ $TIE_SURFACE } tie surface $TIE_SURFACE_SD
{ $TIE_BFACTOR } tie bfactor $TIE_BFACTOR_SD
{ $TIE_A1 } tie a1 $TIE_A1_SD

IF { $SMOOTHING || $PROB_LIMIT }
1 smoothing
 - $SMOOTHING time $SMOOTHING_TIME rotation $SMOOTHING_ROTATION detector $SMOOTHING_DETECTOR
 - $PROB_LIMIT prob_limit $PROB_LIMIT_TIME $PROB_LIMIT_DETECTOR $PROB_LIMIT_ROTATION
ENDIF

1 cycles $CYCLES converge $CONVERGE reject $REJECT
 - $CYCLE_UNIT_WEIGHT weight unit
$SKIP skip $SKIP_NREFLECTIONS for $SKIP_NCYCLES
{ [IfSet $FILTER_DAMP ] } filter 1.0e-6  $FILTER_DAMP

$REJECT_CRITERIA reject scale
 - $REJECT_BYRUN byrun
 - 1 $REJECT_SDMAX $REJECT_SDMAX2
$REJECT_CRITERIA reject merge
 - $MERGE_REJECT_BYRUN  byrun
 - 1 $MERGE_REJECT_SDMAX $MERGE_REJECT_SDMAX2
 - 1 all $MERGE_REJECT_ALL

$ANOMALOUS_ON anomalous on 
- $IF_ANOMALOUS_MATCH  match $ANOMALOUS_MATCH
 -- {[StringSame $ANOMALOUS_MATCH SYMMETRY]} $ANOMALOUS_MATCH_SYM
 -- {[IfSet $ANOMALOUS_PHIDIF] } phidif $ANOMALOUS_PHIDIF

1 output $OUTPUT
CASE $OUTPUT
CASEMATCH UNMERGED
 - { !$OUTPUT_REDUCED }  original
 - $UNMERGED_TOGETHER together
CASEMATCH SEPARATE
 - $OUTPUT_REFERENCE reference | noreference
 - $OUTPUT_OUTLIERS omit outliers
 LOOP N 1 $NRUNS
 - $OUTPUT_PARTIALS($N) omit partials run $N
 ENDLOOP
CASEMATCH POSTREF
 - $OUTPUT_REFERENCE reference | noreference
 - $OUTPUT_OUTLIERS omit outliers
 LOOP N 1 $NRUNS
 - $OUTPUT_PARTIALS($N) omit partials run $N
 ENDLOOP
CASEMATCH POLISH
 - 1 UNMERGED
ENDCASE

$USE_CORNERCORRECT CORNERCORRECT $CORNERCORRECT_FILE

IF $SD_CORRECT 
LOOP N 1 $NSDS
1 SDCORRECTION
 - { ![StringSame $SD_RUNS($N) ALL ] } $SD_RUNS($N)
 - $SD_ADJUST($N) adjust | noadjust
 - $SD_REFINE($N) refine | norefine
 - 1 $SD_APPLY($N) 
 - { [IfSet $SD_FAC($N) ] } $SD_FAC($N)
 -- { [IfSet $SD_B($N) ] } $SD_B($N) 
 -- 1 $SD_ADD($N)
ENDLOOP
ELSE
1 sdcorrection noadjust
ENDIF

1 print $PRINT $OVERLAP
{ !$INSCALE } inscale off

IF { $ACCEPT_OVERLOADS || $ACCEPT_PKRATIO }
  1 ACCEPT
  - $ACCEPT_OVERLOADS OVERLOADS
  - $ACCEPT_PKRATIO PKRATIO $PKRATIO
ENDIF

AT { [FileJoin [GetEnvPath CCP4I_TOP] templates harvest.com ] }