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Karyotype.g4
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Karyotype.g4
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/**
* Define a grammar used to parse karyotypes
*
* @author Lin Zhang
* Programmer / Software Development Engineer
* Institute for Informatics
* Washington University School of Medicine in St. Louis
*
* Date: August 30, 2021
*/
grammar Karyotype;
@header {
package compiler;
import java.util.*;
}
@parser::members{
int i = 0;
List<String> sexChrList = new ArrayList<>();
}
row: rowTypeI
| rowTypeII
| (LETTER | .)+ {notifyErrorListeners("-1|This is an incorrect input for karyotype parsing.");}
;
rowTypeI: firstClone (nonclonalClone | clone)* '.'? ;
firstClone
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: ploidy? karyotypeI
;
clone locals [String s = "", int l = 0]
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: '/' ploidy? karyotypeII
| ploidy? karyotypeII
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeII.text;
} else {
$s = $karyotypeII.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a slant line before '" + $s + "'");
}
| tooManySlant ploidy? karyotypeII
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeII.text;
} else {
$s = $karyotypeII.text;
}
$l = $s.length() + $tooManySlant.text.length();
notifyErrorListeners($l + "|Too many slant lines before '" + $s + "'");
}
| incorrectSlant ploidy? karyotypeII
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeII.text;
} else {
$s = $karyotypeII.text;
}
$l = $s.length() + $incorrectSlant.text.length();
notifyErrorListeners($l + "|Incorrect clone separation before '" + $s + "'");
}
;
nonclonalClone locals [String s = "", int l = 0]
@init {i = i + 1;}
: '/' ploidy? karyotypeV
| ploidy? karyotypeV
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeV.text;
} else {
$s = $karyotypeV.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a slant line before '" + $s + "'");
}
| tooManySlant ploidy? karyotypeV
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeV.text;
} else {
$s = $karyotypeV.text;
}
$l = $s.length() + $tooManySlant.text.length();
notifyErrorListeners($l + "|Too many slant lines before '" + $s + "'");
}
| incorrectSlant ploidy? karyotypeV
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeV.text;
} else {
$s = $karyotypeV.text;
}
$l = $s.length() + $incorrectSlant.text.length();
notifyErrorListeners($l + "|Incorrect clone separation before '" + $s + "'");
}
;
rowTypeII: firstStemlineGroup otherStemlineGroup* additionalClone* '.'? ;
firstStemlineGroup: stemlineClone sidelineCloneTypeI sidelineCloneTypeII* sidelineCloneTypeI*
| stemlineClone sidelineCloneTypeI+ sidelineCloneTypeI sidelineCloneTypeII+ sidelineCloneTypeI*
;
otherStemlineGroup: additionalStemlineClone sidelineCloneTypeI+ ;
stemlineClone
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: ploidy? karyotypeI
;
additionalStemlineClone locals [String s = "", int l = 0]
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: '/' ploidy? karyotypeI
| ploidy? karyotypeI
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeI.text;
} else {
$s = $karyotypeI.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a slant line before '" + $s + "'");
}
| tooManySlant ploidy? karyotypeI
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeI.text;
} else {
$s = $karyotypeI.text;
}
$l = $s.length() + $tooManySlant.text.length();
notifyErrorListeners($l + "|Too many slant lines before '" + $s + "'");
}
| incorrectSlant ploidy? karyotypeI
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeI.text;
} else {
$s = $karyotypeI.text;
}
$l = $s.length() + $incorrectSlant.text.length();
notifyErrorListeners($l + "|Incorrect clone separation before '" + $s + "'");
}
;
sidelineCloneTypeI locals [String s = "", int l = 0]
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: '/' ploidy? karyotypeIII
| ploidy? karyotypeIII
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeIII.text;
} else {
$s = $karyotypeIII.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a slant line before '" + $s + "'");
}
| tooManySlant ploidy? karyotypeIII
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeIII.text;
} else {
$s = $karyotypeIII.text;
}
$l = $s.length() + $tooManySlant.text.length();
notifyErrorListeners($l + "|Too many slant lines before '" + $s + "'");
}
| incorrectSlant ploidy? karyotypeIII
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeIII.text;
} else {
$s = $karyotypeIII.text;
}
$l = $s.length() + $incorrectSlant.text.length();
notifyErrorListeners($l + "|Incorrect clone separation before '" + $s + "'");
}
;
sidelineCloneTypeII locals [String s = "", int l = 0]
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: '/' ploidy? karyotypeIV
| ploidy? karyotypeIV
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeIV.text;
} else {
$s = $karyotypeIV.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a slant line before '" + $s + "'");
}
| tooManySlant ploidy? karyotypeIV
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeIV.text;
} else {
$s = $karyotypeIV.text;
}
$l = $s.length() + $tooManySlant.text.length();
notifyErrorListeners($l + "|Too many slant lines before '" + $s + "'");
}
| incorrectSlant ploidy? karyotypeIV
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeIV.text;
} else {
$s = $karyotypeIV.text;
}
$l = $s.length() + $incorrectSlant.text.length();
notifyErrorListeners($l + "|Incorrect clone separation before '" + $s + "'");
}
;
additionalClone locals [String s = "", int l = 0]
@init {i = i + 1;}
@after {sexChrList = new ArrayList<>();}
: '/' ploidy? karyotypeI
| ploidy? karyotypeI
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeI.text;
} else {
$s = $karyotypeI.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a slant line before '" + $s + "'");
}
| tooManySlant ploidy? karyotypeI
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeI.text;
} else {
$s = $karyotypeI.text;
}
$l = $s.length() + $tooManySlant.text.length();
notifyErrorListeners($l + "|Too many slant lines before '" + $s + "'");
}
| incorrectSlant ploidy? karyotypeI
{
if ($ploidy.text != null) {
$s = $ploidy.text + $karyotypeI.text;
} else {
$s = $karyotypeI.text;
}
$l = $s.length() + $incorrectSlant.text.length();
notifyErrorListeners($l + "|Incorrect clone separation before '" + $s + "'");
}
;
/** I have seen a karyotype 46,t(X;18)(p11.1;q11.2),t(Y;1)(q11.2;p13) on p.50 of ISCN 2016.
* From Mitleman database, we have seen 46,t(X;14)(p22;q32) or t(Y;14)(p11;q32).
* We may need to allow gender to be missing? (Complicated, but will do.)
*/
karyotypeI locals [int l = 0]
: mosChi? chrNum modalNum? gender regularEvent* cellNum?
| mosChi? chrNum modalNum? r=regularEvent* cellNum?
{
if (sexChrList.size() == 0) {
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $chrNum.text.length();
if ($modalNum.text != null) {
$l = $l + $modalNum.text.length();
}
if ($r.text != null) {
$l = $l + $r.text.length();
}
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing gender in clone # " + i);
}
}
| mosChi? r=regularEvent+ cellNum?
{
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $r.text.length();
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing chromosome numbers and gender");
}
;
karyotypeII locals [int l = 0]
: mosChi? chrNum modalNum? gender regularEvent* cellNum?
| mosChi? chrNum modalNum? idemSpecial regularEvent* cellNum?
| mosChi? idemSpecial r=regularEvent* cellNum?
{
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $idemSpecial.text.length();
if ($r.text != null) {
$l = $l + $r.text.length();
}
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing chromosome numbers");
}
| mosChi? chrNum modalNum? r=regularEvent* cellNum?
{
if (sexChrList.size() == 0) {
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $chrNum.text.length();
if ($modalNum.text != null) {
$l = $l + $modalNum.text.length();
}
if ($r.text != null) {
$l = $l + $r.text.length();
}
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing gender in clone # " + i);
}
}
| mosChi? r=regularEvent+ cellNum?
{
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $r.text.length();
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing chromosome numbers and gender");
}
;
karyotypeIII locals [int l = 0]
: mosChi? chrNum modalNum? slSpecial regularEvent* cellNum?
| mosChi? slSpecial r=regularEvent* cellNum?
{
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $slSpecial.text.length();
if ($r.text != null) {
$l = $l + $r.text.length();
}
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing chromosome numbers");
}
;
karyotypeIV locals [int l = 0]
: mosChi? chrNum modalNum? sdlSpecial regularEvent* cellNum?
| mosChi? sdlSpecial r=regularEvent* cellNum?
{
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $sdlSpecial.text.length();
if ($r.text != null) {
$l = $l + $r.text.length();
}
if ($cellNum.text != null) {
$l = $l + $cellNum.text.length();
}
notifyErrorListeners($l + "|Missing chromosome numbers");
}
;
karyotypeV: mosChi? (chrNum modalNum? gender ',')?
('n' | 'N') ('o' | 'O') ('n' | 'N') '-'? ('c' | 'C') ('l' | 'L') ('o' | 'O') ('n' | 'N') ('a' | 'A') ('l' | 'L')
(('a' | 'A') ('b' | 'B') ('n' | 'N') (('o' | 'O') ('r' | 'R') ('m' | 'M') ('a' | 'A') ('l' | 'L'))? )?
cellNum? ;
ploidy: modalDesc (('c' | 'C') ('l' | 'L') ('o' | 'O') ('n' | 'N') ('e' | 'E') ':'?)? ;
tooManySlant: '/' '/'+;
incorrectSlant: ('.' | ',' | ';' | '/')+;
modalNum locals [String s = "", int l = 0]
: '<' modalNumContent '>' # correctModalNum
| modalNumContent '>'
{
$s = $modalNumContent.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '<' for a modal number '" + $s + "'");
}
# incorrectModalNum
| '<' modalNumContent
{
$s = $modalNumContent.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '>' for a modal number '" + $s + "'");
}
# incorrectModalNum
| modalNumContent
{
$s = $modalNumContent.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '<>' for a modal number '" + $s + "'");
}
# incorrectModalNum
| incorrectLeftParenthesis modalNumContent incorrectRightParenthesis
{
$s = $modalNumContent.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for a modal number '" + $s + "', expecting '<>'");
}
# incorrectModalNum
;
modalNumContent: POSITIVEDIGIT ('n' | 'N') ;
gender locals [String s = "", int l = 0]
: ',' sexChr orSex c?
| sexChr orSex c?
{
$s = $sexChr.text;
if ($orSex.text != null) {
$s = $s + $orSex.text;
}
if ($c.text != null) {
$s = $s + $c.text;
}
$l = $s.length();
notifyErrorListeners($l + "|Missing a comma before '" + $s + "'");
}
| tooManyComma sexChr orSex c?
{
$s = $sexChr.text;
if ($orSex.text != null) {
$s = $s + $orSex.text;
}
if ($c.text != null) {
$s = $s + $c.text;
}
$l = $s.length() + $tooManyComma.text.length();
notifyErrorListeners($l + "|Too many commas before '" + $s + "'");
}
;
tooManyComma: ',' ','+;
orSex: (('o' | 'O') ('r' | 'R') sexChr)*;
idemSpecial locals [String s = "", int l = 0]
: ',' idemEvent
| idemEvent
{
$s = $idemEvent.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing a comma before '" + $s + "'");
}
| tooManyComma idemEvent
{
$s = $idemEvent.text;
$l = $s.length() + $tooManyComma.text.length();
notifyErrorListeners($l + "|Too many commas before '" + $s + "'");
}
;
slSpecial locals [String s = "", int l = 0]
: ',' slEvent
| slEvent
{
$s = $slEvent.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing a comma before '" + $s + "'");
}
| tooManyComma slEvent
{
$s = $slEvent.text;
$l = $s.length() + $tooManyComma.text.length();
notifyErrorListeners($l + "|Too many commas before '" + $s + "'");
}
;
sdlSpecial locals [String s = "", int l = 0]
: ',' sdlEvent
| sdlEvent
{
$s = $sdlEvent.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing a comma before '" + $s + "'");
}
| tooManyComma sdlEvent
{
$s = $sdlEvent.text;
$l = $s.length() + $tooManyComma.text.length();
notifyErrorListeners($l + "|Too many commas before '" + $s + "'");
}
;
regularEvent locals [String s = "", int l = 0]
: ',' regEvent
| regEvent
{
$s = $regEvent.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing a comma before '" + $s + "'");
}
| tooManyComma regEvent
{
$s = $regEvent.text;
$l = $s.length() + $tooManyComma.text.length();
notifyErrorListeners($l + "|Too many commas before '" + $s + "'");
}
;
incorrectComma: ','+ ;
idemEvent locals [String s = "", int l = 0]
: ('i' | 'I') ('d' | 'D') ('e' | 'E') ('m' | 'M') multiplication?
| ('i' | 'I') ('d' | 'D') ('e' | 'E') ('m' | 'M') incorrectComma multiplication
{
$s = $multiplication.text;
$l = $s.length() + 4 + $incorrectComma.text.length();
notifyErrorListeners($l + "|No comma should be used between 'idem' and '" + $s + "'");
}
;
slEvent locals [String s1 = "", String s2 = "", int l = 0]
: slMark multiplication?
| slMark incorrectComma multiplication
{
$s1 = $slMark.text;
$s2 = $multiplication.text;
$l = $s1.length() + $s2.length() + $incorrectComma.text.length();
notifyErrorListeners($l + "|No comma should be used between '" + $s1 + "' and '" + $s2 + "'");
}
;
slMark: ('s' | 'S') ('l' | 'L') integer? ;
sdlEvent locals [String s1 = "", String s2 = "", int l = 0]
: sdlMark multiplication?
| sdlMark incorrectComma multiplication
{
$s1 = $sdlMark.text;
$s2 = $multiplication.text;
$l = $s1.length() + $s2.length() + $incorrectComma.text.length();
notifyErrorListeners($l + "|No comma should be used between '" + $s1 + "' and '" + $s2 + "'");
}
;
sdlMark: ('s' | 'S') ('d' | 'D') ('l' | 'L') integer? ;
regEvent: regEventType (('o' | 'O') ('r' | 'R') regEventType)+ # multipleInterpretationRegularEvent
| regEventType # simpleRegularEvent
;
regEventType: prefixPlus? ('r' | 'R') suffix? ',' QUES? dminNum? ('d' | 'D') ('m' | 'M') ('i' | 'I') ('n' | 'N') suffix? # undecodedSpecialEvent
| aberration # aberrationEvent
| undecoded # undecodedEvent
| gainLossChr # gainLossChrEvent
;
/** Note: The multiplication sign should not be used to denote multiple copies of normal chromosomes.
* For example, we have 48,XX,del(6)(q13q23)x2,+7,+7 on p.80 of ISCN 2016.
*/
gainLossChr locals [String s = "", int l = 0]
: prefixPlus gainChr (c | inh)?
{
$s = $gainChr.text.toUpperCase();
if ($s.contains("X")) {sexChrList.add("X");}
if ($s.contains("Y")) {sexChrList.add("Y");}
}
# gainChrEvent
| prefixMinus lossChr (c | inh)?
{
$s = $lossChr.text.toUpperCase();
if ($s.contains("X")) {sexChrList.add("X");}
if ($s.contains("Y")) {sexChrList.add("Y");}
}
# lossChrEvent
| undeterminedPrefix gainChr? (c | inh)?
{
$s = $gainChr.text;
$l = $undeterminedPrefix.text.length();
if ($c.text != null) {
$l = $l + $c.text.length();
}
if ($inh.text != null) {
$l = $l + $inh.text.length();
}
if ($s != null) {
$l = $l + $s.length();
notifyErrorListeners($l + "|Cannot use both '-' and '+' for the gain/loss aberration of chromosome '" + $gainChr.text + "'");
} else {
notifyErrorListeners($l + "|Cannot use both '-' and '+' for the gain/loss aberration and missing chromosome information");
}
}
# gainLossChrError
| (prefixPlus | prefixMinus)
{
if ($prefixPlus.text != null) {
$l = $prefixPlus.text.length();
}
if ($prefixMinus.text != null) {
$l = $prefixMinus.text.length();
}
notifyErrorListeners($l + "|Missing chromosome information of the gain/loss aberration");
}
# gainLossChrError
;
undecoded: prefixPlus? ('r' | 'R') suffix?
| prefixPlus ('m' | 'M') ('a' | 'A') ('r' | 'R') integer suffix?
| prefixPlus marNum? ('m' | 'M') ('a' | 'A') ('r' | 'R') suffix?
| QUES? dminNum? ('d' | 'D') ('m' | 'M') ('i' | 'I') ('n' | 'N') suffix?
| ('i' | 'I') ('n' | 'N') ('c' | 'C')
;
aberration locals [String s = "", int l = 0]
: prefix? mosChi? derId derChrList derBreakpointsList? rearrangementElement* suffix?
{
$s = $derChrList.text.toUpperCase();
if ($s.contains("X")) {sexChrList.add("X");}
if ($s.contains("Y")) {sexChrList.add("Y");}
}
# derAberration
| prefix? mosChi? id chrList breakpointsList? suffix?
{
$s = $chrList.text.toUpperCase();
if ($s.contains("X")) {sexChrList.add("X");}
if ($s.contains("Y")) {sexChrList.add("Y");}
}
# basicAberration
| prefix? mosChi? idUncertainChr uncertainChr suffix?
{
$s = $uncertainChr.text.toUpperCase();
if ($s.contains("X")) {sexChrList.add("X");}
if ($s.contains("Y")) {sexChrList.add("Y");}
}
# uncertainBasicAberration
| prefix? mosChi? derId comma=','+ derChrList derBreakpointsList? r=rearrangementElement* suffix?
{
if ($prefix.text != null) {
$l = $l + $prefix.text.length();
}
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $derId.text.length();
$l = $l + $comma.text.length();
$l = $l + $derChrList.text.length();
if ($r.text != null) {
$l = $l + $r.text.length();
}
if ($suffix.text != null) {
$l = $l + $suffix.text.length();
}
if ($derBreakpointsList.text != null) {
$l = $l + $derBreakpointsList.text.length();
notifyErrorListeners($l + "|Incorrect comma before '" + $derChrList.text + $derBreakpointsList.text + "'");
} else {
notifyErrorListeners($l + "|Incorrect comma before '" + $derChrList.text + "'");
}
}
# derAberrationError
| prefix? mosChi? id comma=','+ chrList breakpointsList? suffix?
{
if ($prefix.text != null) {
$l = $l + $prefix.text.length();
}
if ($mosChi.text != null) {
$l = $l + $mosChi.text.length();
}
$l = $l + $id.text.length();
$l = $l + $comma.text.length();
$l = $l + $chrList.text.length();
if ($suffix.text != null) {
$l = $l + $suffix.text.length();
}
if ($breakpointsList.text != null) {
$l = $l + $breakpointsList.text.length();
notifyErrorListeners($l + "|Incorrect comma before '" + $chrList.text + $breakpointsList.text + "'");
} else {
notifyErrorListeners($l + "|Incorrect comma before '" + $chrList.text + "'");
}
}
# basicAberrationError
;
rearrangementElement: rearrangement # normalRearrangement
| rearrangement (('o' | 'O') ('r' | 'R') rearrangement)+ # multipleInterpretationRearrangement
;
rearrangement locals [int l = 0]
: QUES? rId rChrList rBreakpointsList?
| QUES? rId comma=','+ rChrList rBreakpointsList?
{
if ($QUES.text != null) {
$l = $l + $QUES.text.length();
}
$l = $l + $rId.text.length();
$l = $l + $comma.text.length();
$l = $l + $rChrList.text.length();
if ($rBreakpointsList.text != null) {
$l = $l + $rBreakpointsList.text.length();
notifyErrorListeners($l + "|Incorrect comma before '" + $rChrList.text + $rBreakpointsList.text + "'");
} else {
notifyErrorListeners($l + "|Incorrect comma before '" + $rChrList.text + "'");
}
}
;
derChrList locals [String s = "", int l = 0]
: '(' derChrListElements ')' # correctDerChrList
| derChrListElements ')'
{
$s = $derChrListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for derivative chromosome list '" + $s + "'");
}
# incorrectDerChrList
| '(' derChrListElements
{
$s = $derChrListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for derivative chromosome list '" + $s + "'");
}
# incorrectDerChrList
| derChrListElements
{
$s = $derChrListElements.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for derivative chromosome list '" + $s + "'");
}
# incorrectDerChrList
| incorrectLeftParenthesis derChrListElements incorrectRightParenthesis
{
$s = $derChrListElements.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for derivative chromosome list '" + $s + "', expecting '()'");
}
# incorrectDerChrList
;
derChrListElements
: derChr (';' derChr)*
| incorrectDerChrListElements
{
notifyErrorListeners($incorrectDerChrListElements.text.length() + "|Incorrect use of separators inside derivative chromosome list '" + $incorrectDerChrListElements.text + "', expecting ';'");
}
;
incorrectDerChrListElements: derChr ((';'|',') derChr)+ ;
incorrectLeftParenthesis: ('['|'{'|'<'|'(')*;
incorrectRightParenthesis: (']'|'}'|'>'|')')*;
derBreakpointsList locals [String s = "", int l = 0]
: '(' derBreakpointsListElements ')' # correctDerBreakpointsList
| derBreakpointsListElements ')'
{
$s = $derBreakpointsListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for derivative breakpoints list '" + $s + "'");
}
# incorrectDerBreakpointsList
| '(' derBreakpointsListElements
{
$s = $derBreakpointsListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for derivative breakpoints list '" + $s + "'");
}
# incorrectDerBreakpointsList
| derBreakpointsListElements
{
$s = $derBreakpointsListElements.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for derivative breakpoints list '" + $s + "'");
}
# incorrectDerBreakpointsList
| incorrectLeftParenthesis derBreakpointsListElements incorrectRightParenthesis
{
$s = $derBreakpointsListElements.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for derivative breakpoints list '" + $s + "', expecting '()'");
}
# incorrectDerBreakpointsList
;
derBreakpointsListElements
: derBreakpointsInOneChr (';' derBreakpointsInOneChr)*
| incorrectDerBreakpointsListElements
{
notifyErrorListeners($incorrectDerBreakpointsListElements.text.length() + "|Incorrect use of separators inside breakpoints list '" + $incorrectDerBreakpointsListElements.text + "', expecting ';'");
}
;
incorrectDerBreakpointsListElements: derBreakpointsInOneChr ((';'|',') derBreakpointsInOneChr)+ ;
derBreakpointsInOneChr: derBreakpoints # normalDerBreakpoints
| derBreakpoints (('o' | 'O') ('r' | 'R') derBreakpoints)+ # multipleInterpretationDerBreakpoints
;
chrList locals [String s = "", int l = 0]
: '(' chrListElements ')' # correctChrList
| chrListElements ')'
{
$s = $chrListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for chromosome list '" + $s + "'");
}
# incorrectChrList
| '(' chrListElements
{
$s = $chrListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for chromosome list '" + $s + "'");
}
# incorrectChrList
| chrListElements
{
$s = $chrListElements.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for chromosome list '" + $s + "'");
}
# incorrectChrList
| incorrectLeftParenthesis chrListElements incorrectRightParenthesis
{
$s = $chrListElements.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for chromosome list '" + $s + "', expecting '()'");
}
# incorrectChrList
;
chrListElements
: chr (';' chr)*
| incorrectChrListElements
{
notifyErrorListeners($incorrectChrListElements.text.length() + "|Incorrect use of separators inside chromosome list '" + $incorrectChrListElements.text + "', expecting ';'");
}
;
incorrectChrListElements: chr ((';'|',') chr)+ ;
breakpointsList locals [String s = "", int l = 0]
: '(' breakpointsListElements ')' # correctBreakpointsList
| breakpointsListElements ')'
{
$s = $breakpointsListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for breakpoints list '" + $s + "'");
}
# incorrectBreakpointsList
| '(' breakpointsListElements
{
$s = $breakpointsListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for breakpoints list '" + $s + "'");
}
# incorrectBreakpointsList
| breakpointsListElements
{
$s = $breakpointsListElements.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for breakpoints list '" + $s + "'");
}
# incorrectBreakpointsList
| incorrectLeftParenthesis breakpointsListElements incorrectRightParenthesis
{
$s = $breakpointsListElements.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for breakpoints list '" + $s + "', expecting '()'");
}
# incorrectBreakpointsList
;
breakpointsListElements
: breakpointsInOneChr (';' breakpointsInOneChr)*
| incorrectBreakpointsListElements
{
notifyErrorListeners($incorrectBreakpointsListElements.text.length() + "|Incorrect use of separators inside breakpoints list '" + $incorrectBreakpointsListElements.text + "', expecting ';'");
}
;
incorrectBreakpointsListElements: breakpointsInOneChr ((';'|',') breakpointsInOneChr)+ ;
breakpointsInOneChr: breakpoints # normalBreakpoints
| breakpoints (('o' | 'O') ('r' | 'R') breakpoints)+ # multipleInterpretationBreakpoints
;
rChrList locals [String s = "", int l = 0]
: '(' chrListElements ')' # correctRChrList
| chrListElements ')'
{
$s = $chrListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for chromosome list '" + $s + "'");
}
# incorrectRChrList
| '(' chrListElements
{
$s = $chrListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for chromosome list '" + $s + "'");
}
# incorrectRChrList
| chrListElements
{
$s = $chrListElements.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for chromosome list '" + $s + "'");
}
# incorrectRChrList
| incorrectLeftParenthesis chrListElements incorrectRightParenthesis
{
$s = $chrListElements.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for chromosome list '" + $s + "', expecting '()'");
}
# incorrectRChrList
;
rBreakpointsList locals [String s = "", int l = 0]
: '(' breakpointsListElements ')' # correctRBreakpointsList
| breakpointsListElements ')'
{
$s = $breakpointsListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for breakpoints list '" + $s + "'");
}
# incorrectRBreakpointsList
| '(' breakpointsListElements
{
$s = $breakpointsListElements.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for breakpoints list '" + $s + "'");
}
# incorrectRBreakpointsList
| breakpointsListElements
{
$s = $breakpointsListElements.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for breakpoints list '" + $s + "'");
}
# incorrectRBreakpointsList
| incorrectLeftParenthesis breakpointsListElements incorrectRightParenthesis
{
$s = $breakpointsListElements.text;
$l = $s.length();
if ($incorrectLeftParenthesis.text != null) {
$l = $l + $incorrectLeftParenthesis.text.length();
}
if ($incorrectRightParenthesis.text != null) {
$l = $l + $incorrectRightParenthesis.text.length();
}
notifyErrorListeners($l + "|Wrong bracket format for breakpoints list '" + $s + "', expecting '()'");
}
# incorrectRBreakpointsList
;
idUncertainChr: ('a' | 'A') ('d' | 'D') ('d' | 'D')
| ('d' | 'D') ('e' | 'E') ('l' | 'L')
| (('p' | 'P') ('s' | 'S') ('u' | 'U'))? ('i' | 'I') ('d' | 'D') ('i' | 'I') ('c' | 'C')
| ('d' | 'D') ('u' | 'U') ('p' | 'P')
| ('t' | 'T') ('r' | 'R') ('p' | 'P')
| ('q' | 'Q') ('d' | 'D') ('p' | 'P')
| ('h' | 'H') ('s' | 'S') ('r' | 'R')
| ('i' | 'I') ('n' | 'N') ('s' | 'S')
| ('i' | 'I') ('n' | 'N') ('v' | 'V')
| ('i' | 'I')
;
uncertainChr locals [String s = "", int l = 0]
: '(' uncertainChrContent ')' # correctUncertainChr
| uncertainChrContent ')'
{
$s = $uncertainChrContent.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing '(' for an uncertain chr '" + $s + "'");
}
# incorrectUncertainChr
| '(' uncertainChrContent
{
$s = $uncertainChrContent.text;
$l = $s.length() + 1;
notifyErrorListeners($l + "|Missing ')' for an uncertain chr '" + $s + "'");
}
# incorrectUncertainChr
| uncertainChrContent
{
$s = $uncertainChrContent.text;
$l = $s.length();
notifyErrorListeners($l + "|Missing '()' for an uncertain chr '" + $s + "'");
}