From 75410e6a6e9d981f4667cd38b637102670ea54a0 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 24 Sep 2010 11:27:02 +0200
Subject: [PATCH] added cname.rnum.aname shortcut to query language
The shortcut doesn't work when
- cname is an empty string, numeric or any special character not
allow in identifiers
- the aname starts with a number. This is due to the fact, that the
"." is both used as a decimal point in floating point numbers and
as a separator between chain, residue number and atom name. When
parsing a numerical token, we have deal with trailing "."
appropriately and stop parsing when the next character is not
numeric. However, when the character following the "." is numeric,
we also treat it as part of the numeric value.
---
modules/mol/base/src/impl/query_impl.cc | 55 ++++++++++++++++++++++++-
modules/mol/base/src/impl/query_impl.hh | 3 +-
2 files changed, 55 insertions(+), 3 deletions(-)
diff --git a/modules/mol/base/src/impl/query_impl.cc b/modules/mol/base/src/impl/query_impl.cc
index 5c930c961..92b004346 100644
--- a/modules/mol/base/src/impl/query_impl.cc
+++ b/modules/mol/base/src/impl/query_impl.cc
@@ -107,19 +107,24 @@ QueryToken QueryLexer::LexQuotedStringLiteral()
QueryToken QueryLexer::LexNumericToken() {
Range range(current_, 0);
static String allowed_chars("_");
- bool dot_present=false, is_string=false;
+ bool dot_present=false, is_string=false, last_was_dot=false;
//TODO Better checking for duplicate -
while(current_<query_string_.size()){
if (isdigit(query_string_[current_]) || query_string_[current_]=='-') {
current_++;
+ last_was_dot=false;
} else if (query_string_[current_]=='.') {
if (dot_present) {
is_string=true;
break;
}
dot_present = true;
+ last_was_dot=true;
current_++;
} else {
+ if (last_was_dot) {
+ break;
+ }
is_string=isalnum(query_string_[current_]) ||
allowed_chars.find_first_of(query_string_[current_])!=String::npos;
break;
@@ -128,6 +133,11 @@ QueryToken QueryLexer::LexNumericToken() {
range.Length=current_-range.Loc;
if (!is_string) {
if (dot_present) {
+ if (last_was_dot) {
+ current_--;
+ return QueryToken(Range(range.Loc, range.Length-1),
+ tok::IntegralValue);
+ }
return QueryToken(range, tok::FloatingValue);
} else {
return QueryToken(range, tok::IntegralValue);
@@ -173,7 +183,10 @@ QueryToken QueryLexer::LexToken() {
return QueryToken(Range(current_-1, 1), tok::Coma);
case ':':
current_++;
- return QueryToken(Range(current_-1, 1), tok::Colon);
+ return QueryToken(Range(current_-1, 1), tok::Colon);
+ case '.':
+ current_++;
+ return QueryToken(Range(current_-1, 1), tok::Dot);
case '{':
current_++;
return QueryToken(Range(current_-1, 1), tok::LeftCurlyBrace);
@@ -605,6 +618,44 @@ Node* QueryImpl::ParsePropValueExpr(QueryLexer& lexer) {
String s=query_string_.substr(sname.GetRange().Loc,sname.GetRange().Length);
Prop property=PropertyFromString(s);
QueryToken op=lexer.NextToken();
+
+ // this block deals with the cname.rnum.aname shortcut.
+ if (op.GetType()==tok::Dot) {
+ QueryToken cname=sname;
+ QueryToken rnum=lexer.NextToken();
+ if (!this->Expect(tok::IntegralValue, "residue number", rnum)) {
+ return NULL;
+ }
+ if (!this->Expect(tok::Dot, "'.'", lexer.NextToken())) {
+ return NULL;
+ }
+ QueryToken aname=lexer.NextToken();
+ if (!this->Expect(tok::Identifier, "atom name", aname)) {
+ return NULL;
+ }
+ LogicOP lop=inversion_stack_.back() ? LOP_OR : LOP_AND;
+ CompOP cop=inversion_stack_.back() ? COP_NEQ : COP_EQ;
+ ParamType cname_val(query_string_.substr(cname.GetValueRange().Loc,
+ cname.GetValueRange().Length).c_str());
+ Prop cname_prop(Prop::CNAME, Prop::STRING, Prop::CHAIN);
+ SelNode* cname_node=new SelNode(cname_prop, cop, cname_val);
+ ParamType aname_val(query_string_.substr(aname.GetValueRange().Loc,
+ aname.GetValueRange().Length).c_str());
+ Prop aname_prop(Prop::ANAME, Prop::STRING, Prop::ATOM);
+ SelNode* aname_node=new SelNode(aname_prop, cop, aname_val);
+ ParamType rnum_val(atoi(query_string_.substr(rnum.GetValueRange().Loc,
+ rnum.GetValueRange().Length).c_str()));
+ Prop rnum_prop(Prop::RNUM, Prop::INT, Prop::RESIDUE);
+ SelNode* rnum_node=new SelNode(rnum_prop, cop, rnum_val);
+ LogicOPNode* and_one=new LogicOPNode(lop);
+ LogicOPNode* and_two=new LogicOPNode(lop);
+ and_one->SetLHS(and_two);
+ and_one->SetRHS(cname_node);
+ and_two->SetLHS(rnum_node);
+ and_two->SetRHS(aname_node);
+ lexer.NextToken();
+ return and_one;
+ }
if (property.id>=Prop::CUSTOM) {
property.id=(Prop::ID)(Prop::CUSTOM+num_gen_prop_++);
EntityPropertyMapper epm=EntityPropertyMapper(s.substr(2), property.level);
diff --git a/modules/mol/base/src/impl/query_impl.hh b/modules/mol/base/src/impl/query_impl.hh
index d9a28760a..02915d391 100644
--- a/modules/mol/base/src/impl/query_impl.hh
+++ b/modules/mol/base/src/impl/query_impl.hh
@@ -45,7 +45,8 @@ namespace tok {
IntegralValue,
FloatingValue,
Colon,
- Coma,
+ Coma,
+ Dot,
And,
Or,
Not,
--
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