Commit 81c8ea6e authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: AlignBox.reverse(), .seq_length

parent 4155cd40
......@@ -51,6 +51,16 @@ AlignBox::AlignBox(string _key, string _color) {
ref_label = "";
}
void AlignBox::reverse() {
int start_ = start;
start = seq_length - end - 1;
end = seq_length - start_ - 1;
int del_left_ = del_left;
del_left = del_right;
del_right = del_left_;
}
int AlignBox::getLength() {
return end - start + 1 ;
}
......
......@@ -104,6 +104,7 @@ class AlignBox
int start;
int end;
int marked_pos; // Marked position, for Cys104 and Phe118/Trp118
int seq_length;
/**
* Alignment positions *compared to reference sequence*
......@@ -116,6 +117,11 @@ class AlignBox
string getSequence(string sequence);
void addToOutput(CloneOutput *clone, int alternative_genes);
/**
* Mirror the AlignBox (over a a sequence length seq_length)
*/
void reverse();
/**
* Returns 'V', 'D', 'J', or possibly '5', '4', '3', '?', depending on the ref_label and on the key
*/
......
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