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Should fix 825: import cadnano - domains that end on deletions #826

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Should fix 825: import cadnano - domains that end on deletions #826

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30 changes: 30 additions & 0 deletions lib/src/state/design.dart
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Original file line number Diff line number Diff line change
Expand Up @@ -2125,6 +2125,23 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
else
start = old_base;

bool running = true;
while(running){
switch(Design._cadnano_v2_import_extract_end_deletions(vstrands[old_helix]['skip'], start,end)){
case -1:{
start = start + 1;
}
break;
case 1:{
end = end-1;
}
break;
case 0:{
running = false;
}
}
}

domains.add(Domain(
is_scaffold: strand_type == 'scaf',
helix: old_helix,
Expand Down Expand Up @@ -2174,6 +2191,19 @@ abstract class Design with UnusedFields implements Built<Design, DesignBuilder>,
return to_return;
}


/// Routines which finds cadnano skips that correspond to domain ends. Returns -1 if they appear at the start, +1 if they appear at the end, or 0 if there are no end deletions.
static int _cadnano_v2_import_extract_end_deletions(List<dynamic> skip_table, int start, int end){
if ((skip_table[start] == -1)){
return -1;
}
if (skip_table[end] == -1){
return 1;
} else {
return 0;
}
}

/// Routines which converts cadnano skips to scadnano insertions
static List<Insertion> _cadnano_v2_import_extract_insertions(List<dynamic> loop_table, int start, int end) {
List<Insertion> to_return = [];
Expand Down