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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/script Compiler.java,1.19,1.20 Eval.java,1.56,1.57 Token.java,1.24,1.25
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From: Michael T H. <mic...@us...> - 2003-12-12 17:52:58
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script
In directory sc8-pr-cvs1:/tmp/cvs-serv6292/src/org/openscience/jmol/viewer/script
Modified Files:
Compiler.java Eval.java Token.java
Log Message:
added insertion code support to parser
Index: Compiler.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Compiler.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- Compiler.java 12 Dec 2003 14:15:42 -0000 1.19
+++ Compiler.java 12 Dec 2003 17:52:55 -0000 1.20
@@ -171,13 +171,13 @@
ltoken.addElement(new Token(Token.decimal, new Float(value)));
continue;
}
- if (lookingAtSequenceCode()) {
+ if (lookingAtSeqcode()) {
int seqNum =
Integer.parseInt(script.substring(ichToken,
ichToken + cchToken - 1));
char insertionCode = script.charAt(ichToken + cchToken - 1);
- int sequence = PdbGroup.getSequence(seqNum, insertionCode);
- ltoken.addElement(new Token(Token.sequenceCode, sequence));
+ int seqcode = PdbGroup.getSeqcode(seqNum, insertionCode);
+ ltoken.addElement(new Token(Token.seqcode, seqcode, "seqcode"));
continue;
}
if (lookingAtPositiveInteger() ||
@@ -185,7 +185,7 @@
lookingAtNegativeInteger())) {
int val = Integer.parseInt(script.substring(ichToken,
ichToken + cchToken));
- ltoken.addElement(new Token(Token.integer, val));
+ ltoken.addElement(new Token(Token.integer, val, "integer"));
continue;
}
}
@@ -409,7 +409,7 @@
return cchToken > 1; // decimal point plust at least one digit
}
- boolean lookingAtSequenceCode() {
+ boolean lookingAtSeqcode() {
int ichT = ichToken;
char ch = ' ';
while (ichT < cchScript && (ch = script.charAt(ichT)) >= '0' && ch <= '9')
@@ -641,7 +641,11 @@
resNamePattern ::= up to 3 alphanumeric chars with * and ?
- clauseResNumSpec ::= * | {-} integer { - {-} integer}
+ clauseResNumSpec ::= * | clauseSequenceRange
+
+ clauseSequenceRange ::= clauseSequenceCode { - clauseSequenceCode }
+
+ clauseSequenceCode ::= seqcode | {-} integer
clauseChainSpec ::= {:} * | identifier | integer
@@ -743,6 +747,7 @@
return clauseWithin();
case Token.hyphen: // selecting a negative residue spec
case Token.integer:
+ case Token.seqcode:
case Token.asterisk:
case Token.leftsquare:
case Token.identifier:
@@ -832,7 +837,8 @@
}
if (tok == Token.asterisk ||
tok == Token.hyphen ||
- tok == Token.integer) {
+ tok == Token.integer ||
+ tok == Token.seqcode) {
log("I see a residue number");
if (! clauseResNumSpec())
return false;
@@ -923,7 +929,7 @@
log("still here looking at:" + strToken);
// still might be an identifier ... so be careful
- int sequence = -1;
+ int seqcode = -1;
char chain = '?';
if (cchToken > 3) {
// let's take a look at the last character
@@ -940,7 +946,7 @@
try {
int sequenceNum = Integer.parseInt(strResno);
log("I parsed sequenceNum=" + sequenceNum);
- sequence = PdbGroup.getSequence(sequenceNum, ' ');
+ seqcode = PdbGroup.getSeqcode(sequenceNum, ' ');
} catch (NumberFormatException e) {
return generateResidueSpecCode(tokenIdent);
}
@@ -957,12 +963,12 @@
return generateResidueSpecCode(tokenIdent);
}
log(" I see a residue name:" + strUpper3 +
- " sequence=" + sequence +
+ " seqcode=" + seqcode +
" chain=" + chain);
- if (sequence != -1)
+ if (seqcode != -1)
generateResidueSpecCode(new Token(Token.spec_number,
- sequence, "spec_number"));
+ seqcode, "spec_number"));
if (chain != '?')
generateResidueSpecCode(new Token(Token.spec_chain, chain, "spec_chain"));
return true;
@@ -974,40 +980,44 @@
tokenNext();
return true;
}
- boolean negativeInt1 = false;
+ return clauseSequenceRange();
+ }
+
+ boolean clauseSequenceRange() {
+ if (! clauseSequenceCode())
+ return false;
if (tokPeek() == Token.hyphen) {
tokenNext();
- negativeInt1 = true;
+ int seqcodeMin = seqcode;
+ if (! clauseSequenceCode())
+ return false;
+ return generateResidueSpecCode(new Token(Token.spec_number_range,
+ seqcodeMin,
+ new Integer(seqcode)));
}
- Token tokenInt1 = tokenNext();
- if (tokenInt1.tok != Token.integer)
- return resnumSpecificationExpected();
- int sequenceNum = negativeInt1 ? -tokenInt1.intValue : tokenInt1.intValue;
- log("sequenceNum=" + sequenceNum);
- int sequence = PdbGroup.getSequence(sequenceNum, ' ');
- if (tokPeek() != Token.hyphen)
- return generateResidueSpecCode(new Token(Token.spec_number,
- sequence, "spec_number"));
- log("seems to be a range");
- tokenNext(); // throw away range hyphen
- // now look for negative int hyphen
- boolean negativeInt2 = false;
- if (tokPeek() == Token.hyphen) {
+ return generateResidueSpecCode(new Token(Token.spec_number,
+ seqcode, "seqcode"));
+ }
+
+ int seqcode;
+
+ boolean clauseSequenceCode() {
+ boolean negative = false;
+ int tokPeek = tokPeek();
+ if (tokPeek == Token.hyphen) {
tokenNext();
- negativeInt2 = true;
+ negative = true;
+ tokPeek = tokPeek();
}
- Token tokenInt2 = tokenNext();
- if (tokenInt2.tok != Token.integer)
- return resnumSpecificationExpected();
- int sequenceNumLast =
- (negativeInt2 ? -tokenInt2.intValue : tokenInt2.intValue);
- log("sequenceNumLast=" + sequenceNumLast);
-
- int sequenceLast = PdbGroup.getSequence(sequenceNumLast, ' ');
-
- return generateResidueSpecCode(new Token(Token.spec_number_range,
- sequence,
- new Integer(sequenceLast)));
+ if (tokPeek == Token.seqcode)
+ seqcode = tokenNext().intValue;
+ else if (tokPeek == Token.integer)
+ seqcode = PdbGroup.getSeqcode(tokenNext().intValue, ' ');
+ else
+ return false;
+ if (negative)
+ seqcode = -seqcode;
+ return true;
}
boolean clauseChainSpec() {
Index: Eval.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Eval.java,v
retrieving revision 1.56
retrieving revision 1.57
diff -u -r1.56 -r1.57
--- Eval.java 12 Dec 2003 12:24:26 -0000 1.56
+++ Eval.java 12 Dec 2003 17:52:55 -0000 1.57
@@ -782,7 +782,7 @@
PdbAtom pdbatom = frame.getAtomAt(i).getPdbAtom();
if (pdbatom == null)
continue;
- if (number == pdbatom.getSequence())
+ if (number == pdbatom.getSeqcode())
bsResno.set(i);
}
return bsResno;
@@ -795,7 +795,7 @@
PdbAtom pdbatom = frame.getAtomAt(i).getPdbAtom();
if (pdbatom == null)
continue;
- int atomResno = pdbatom.getSequence();
+ int atomResno = pdbatom.getSeqcode();
if (atomResno >= resnoMin && atomResno <= resnoLast)
bsResidue.set(i);
}
@@ -976,7 +976,7 @@
int getResno(Atom atom) {
PdbAtom pdbatom = atom.getPdbAtom();
- return (pdbatom == null) ? -1 : pdbatom.getSequence();
+ return (pdbatom == null) ? -1 : pdbatom.getSeqcode();
}
int getTemperature(Atom atom) {
Index: Token.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Token.java,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- Token.java 12 Dec 2003 14:15:42 -0000 1.24
+++ Token.java 12 Dec 2003 17:52:55 -0000 1.25
@@ -59,7 +59,7 @@
final static int integer = 2;
final static int decimal = 3;
final static int string = 4;
- final static int sequenceCode = 5;
+ final static int seqcode = 5;
final static int unknown = 6;
final static int keyword = 7;
final static int whitespace = 8;
@@ -69,7 +69,7 @@
final static String[] astrType = {
"nada", "identifier", "integer", "decimal", "string",
- "sequence", "unknown", "keyword"
+ "seqcode", "unknown", "keyword"
};
final static int command = (1 << 8);
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