Revision: 21296
http://sourceforge.net/p/jmol/code/21296
Author: hansonr
Date: 2016-12-02 05:30:58 +0000 (Fri, 02 Dec 2016)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/CifDataParser.java
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-02 05:13:45 UTC
(rev 21295)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-02 05:30:58 UTC
(rev 21296)
@@ -14,8 +14,10 @@
/**
*
-* A special tokenizer class for dealing with quoted strings in CIF files.
+* A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
*
+* Subclassed by org.jmol.adapters.readers.cif.Cif2DataParser
+*
* Greek letters implemented in Jmol 13.3.9 and only for
* titles and space groups. All other mark ups ignored.
*
@@ -72,6 +74,10 @@
public class CifDataParser implements GenericCifDataParser {
+ protected int getVersion() {
+ return 1;
+ }
+
/**
* The maximum number of columns (data keys) passed to the parser or found
in the file
* for a given loop_ or category.subkey listing.
@@ -82,16 +88,61 @@
private GenericLineReader reader;
private BufferedReader br;
- protected String line;
+ /**
+ * from buffered reader
+ */
+ protected String line;
+
+ /**
+ * working string (buffer)
+ *
+ */
protected String str;
+
+ /**
+ * pointer to current character on str
+ */
protected int ich;
+
+ /**
+ * length of str
+ *
+ */
protected int cch;
+
+ /**
+ * whether we are processing an unquoted value or key
+ */
protected boolean wasUnquoted;
+
+ /**
+ * optional token terminator; in CIF 2.0 could be } or ]
+ */
protected char cterm = '\0';
+
+ /**
+ * string to return for CIF data value . and ?
+ */
protected String nullString = "\0";
+
+ /**
+ * A flag to create and return Java objects, not strings.
+ * Used only by Jmol scripting x = getProperty("cifInfo", filename).
+ */
+ protected boolean asObject;
+
+
+ /**
+ * debugging flag passed from reader; unused
+ *
+ */
protected boolean debugging;
+ /**
+ * private processing fields
+ *
+ */
private Object strPeeked;
private int ichPeeked;
private int columnCount;
@@ -99,12 +150,14 @@
private Object[] columnData = new Object[KEY_MAX];
private boolean isLoop;
private boolean haveData;
- private SB fileHeader = new SB();
+
+ /**
+ * comments at the top of a file, including #\#CIF_2.0, for example
+ */
+ private SB fileHeader = new SB();
private boolean isHeader = true;
- protected boolean asObject;
-
/**
* Set the string value of what is returned for "." and "?"
*
@@ -148,7 +201,7 @@
/**
* A Chemical Information File data parser.
*
- * Should be called immediately upon construction.
+ * set() should be called immediately upon construction.
*
* Two options; one of reader or br should be null, or reader will be
* ignored. Just simpler this way...
@@ -166,11 +219,7 @@
return this;
}
- protected int getVersion() {
- return 1;
- }
-
/**
*
* @return commented-out section at the start of a CIF file.
@@ -426,6 +475,13 @@
return strPeeked;
}
+ /**
+ * grab a new line if necessary and prepare it
+ * if it starts with ";"
+ *
+ * @return updated this.str
+ * @throws Exception
+ */
private boolean getNextLine() throws Exception {
while (!strHasMoreTokens())
if (prepareNextLine() == null)
@@ -685,6 +741,8 @@
* that full multiline string. Uses \1 to indicate that
* this is a special quotation.
*
+ *
+ *
* @return the next line or null if EOF
* @throws Exception
*/
@@ -700,9 +758,12 @@
}
/**
- * preprocess the string to produce a string with a \1 ... \1 segment
- * that will be picked up next, probably from multiline data
+ * Preprocess the string on a line starting with a semicolon
+ * to produce a string with a \1 ... \1 segment
+ * that will be picked up in the next round
+ *
* @return escaped part with attached extra data
+ * @throws Exception
*/
protected String preprocessString() throws Exception {
return setString(preprocessSemiString());
@@ -774,8 +835,8 @@
/**
* In CIF 2.0, this method turns a String into an Integer or Float
- * Method is only used in CIF 2.0.
- * @param s
+ * In CIF 1.0 (here) just return the unchanged value.
+ * @param s unquoted string
* @return unchanged value
*/
protected Object unquoted(String s) {
@@ -810,26 +871,29 @@
}
/**
- * CIF 1.1 only, with addition of SIMPLE arrays due to the fact that
+ * CIF 1.0 only, with addition of SIMPLE arrays due to the fact that
* the MagCIF format includes one data value of that type even though it is
not a CIF 2.0 file.
*
- * @param ch current character being ponted to
+ * This is just a rudimentary hack to allow simple [....] in magCIF files.
+ * See Cif2DataParser for the real thing.
+ *
+ * @param ch current character being pointed to
* @return a String data object
*/
protected Object getQuotedStringOrObject(char ch) {
int ichStart = ich;
boolean isArray = (ch == '[');
char chClosingQuote = (isArray ? ']' : ch);
- boolean previousCharacterWasQuote = false;
+ boolean wasQuote = false;
while (++ich < cch) {
ch = str.charAt(ich);
- // CIF 1.0 rules require that the closing ' or "" be followed by space
or tab
- if (previousCharacterWasQuote && (ch == ' ' || ch == '\t'))
+ // CIF 1.0 rules require that the closing ' or "" be followed by space
or tab
+ if (wasQuote && (ch == ' ' || ch == '\t'))
break;
- previousCharacterWasQuote = (ch == chClosingQuote);
+ wasQuote = (ch == chClosingQuote);
}
if (ich == cch || isArray) {
- if (previousCharacterWasQuote && !isArray) // close quote was last char
of string
+ if (wasQuote && !isArray) // close quote was last char of string
return str.substring(ichStart + 1, ich - 1);
// reached the end of the string without finding closing ', or we have
[...]
return str.substring(ichStart, ich);
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