-/*
-
- my $div_ratio_QLA_QRB = $data_struct->{div_ratio_QLA_QRB};
- my $div_ratio_QRA_QLB = $data_struct->{div_ratio_QLB_QRA};
-
- my $per_id_QLA = $data_struct->{per_id_QLA};
- my $per_id_QRB = $data_struct->{per_id_QRB};
- my $per_id_AB = $data_struct->{per_id_AB};
- my $per_id_QA = $data_struct->{per_id_QA};
- my $per_id_QB = $data_struct->{per_id_QB};
- my $per_id_LAB = $data_struct->{per_id_LAB};
- my $per_id_RAB = $data_struct->{per_id_RAB};
- my $per_id_QRA = $data_struct->{per_id_QRA};
- my $per_id_QLB = $data_struct->{per_id_QLB};
- my $per_id_QLB_QRA = $data_struct->{per_id_QLB_QRA};
- my $per_id_QLA_QRB = $data_struct->{per_id_QLA_QRB};
-
- my $win_left_end5 = $data_struct->{win_left_end5};
- my $win_left_end3 = $data_struct->{win_left_end3};
- my $win_right_end5 = $data_struct->{win_right_end5};
- my $win_right_end3 = $data_struct->{win_right_end3};
- my $Q = $data_struct->{query_alignment};
- my $A = $data_struct->{parent_A_alignment};
- my $B = $data_struct->{parent_B_alignment};
- my $BS_A = $data_struct->{BS_A};
- my $BS_B = $data_struct->{BS_B};
-
- my @Q_chars = @{$Q->{align}};
- my @A_chars = @{$A->{align}};
- my @B_chars = @{$B->{align}};
-
- my $query_acc = $Q->{acc};
- my $A_acc = $A->{acc};
- my $B_acc = $B->{acc};
-
- my $break_left = $Q->{seqPos}->[$win_left_end3];
- my $break_right = $Q->{seqPos}->[$win_right_end5];
-
-
- cout << "//\n## CHIMERA\t" << querySeqs[i]->getName() << "\t" << $break_left-$break_right" << endl
- << "\tDIV_QLARB: ". sprintf("%.3f", $div_ratio_QLA_QRB)
- << "\tBS_QLARB: " . sprintf("%.2f", $BS_A)
- << "\tDIV_QRALB: " . sprintf("%.3f", $div_ratio_QRA_QLB)
- << "\tBS_QRALB: " . sprintf("%.2f", $BS_B)
- << "\t$A_acc\t$B_acc"
- << "\tbreakpoint: $break_left-$break_right\n\n";
-
- ## draw illustration:
-
- print " Per_id parents: " . sprintf("%.2f", $per_id_AB) . "\n\n";
- print " Per_id(Q,A): " . sprintf("%.2f", $per_id_QA) . "\n";
- print "--------------------------------------------------- A: $A_acc\n"
- . " " . sprintf("%.2f", $per_id_QLA) . " " . sprintf("%.2f", $per_id_QRA) . "\n"
- . "~~~~~~~~~~~~~~~~~~~~~~~~\\ /~~~~~~~~~~~~~~~~~~~~~~~~ Q: $query_acc\n"
- . "DivR: " . sprintf("%.3f", $div_ratio_QLA_QRB) . " BS: " . sprintf("%.2f", $BS_A) . " |\n"
- . "Per_id(QLA,QRB): " . sprintf("%.2f", $per_id_QLA_QRB) . " |\n"
- . " |\n"
- . " (L-AB: " . sprintf("%.2f", $per_id_LAB) . ") | (R-AB: " . sprintf("%.2f", $per_id_RAB) . ")\n"
- . " WinL:$win_left_end5-$win_left_end3 | WinR:$win_right_end5-$win_right_end3\n"
- . " |\n"
- . "Per_id(QLB,QRA): " . sprintf("%.2f", $per_id_QLB_QRA) . " |\n"
- . "DivR: " . sprintf("%.3f", $div_ratio_QRA_QLB) . " BS: " . sprintf("%.2f", $BS_B) . " |\n"
- . "~~~~~~~~~~~~~~~~~~~~~~~~/ \\~~~~~~~~~~~~~~~~~~~~~~~~~ Q: $query_acc\n"
- . " " . sprintf("%.2f", $per_id_QLB) . " " . sprintf("%.2f", $per_id_QRB) . "\n"
- . "---------------------------------------------------- B: $B_acc\n";
- print " Per_id(Q,B): ". sprintf("%.2f", $per_id_QB) . "\n\n";
-
- my $deltaL = $per_id_QLA - $per_id_QLB;
- my $deltaR = $per_id_QRA - $per_id_QRB;
-
- print "DeltaL: " . sprintf("%.2f", $deltaL) . " DeltaR: " . sprintf("%.2f", $deltaR) . "\n\n";
-
- unless ($printAlignmentsFlag) { return; }
-
-
- ## build the left windows:
- my @Q_left_win = @Q_chars[$win_left_end5..$win_left_end3];
- my @A_left_win = @A_chars[$win_left_end5..$win_left_end3];
- my @B_left_win = @B_chars[$win_left_end5..$win_left_end3];
-
- &print_alignment($A_acc, \@A_left_win,
- $query_acc, \@Q_left_win,
- $B_acc, \@B_left_win);
-
- print "\t\t** Breakpoint **\n\n";
-
- my @Q_right_win = @Q_chars[$win_right_end5..$win_right_end3];
- my @A_right_win = @A_chars[$win_right_end5..$win_right_end3];
- my @B_right_win = @B_chars[$win_right_end5..$win_right_end3];
-
- &print_alignment($A_acc, \@A_right_win,
- $query_acc, \@Q_right_win,
- $B_acc, \@B_right_win);
-
- return;
-}
-
-
-####