Revision: 21294
http://sourceforge.net/p/jmol/code/21294
Author: hansonr
Date: 2016-12-02 04:55:06 +0000 (Fri, 02 Dec 2016)
Log Message:
-----------
code cleanup and comments
Modified Paths:
--------------
trunk/Jmol/src/javajs/util/CifDataParser.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-01 23:10:35 UTC
(rev 21293)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-02 04:55:06 UTC
(rev 21294)
@@ -688,17 +688,13 @@
setString(readLine());
if (line == null || line.length() == 0)
return line;
- if (doPreProcess(line.charAt(0)))
+ if (line.charAt(0) == ';')
return preprocessString();
if (str.startsWith("###non-st#"))
ich = 10;
return line;
}
- protected boolean doPreProcess(char ch) {
- return ch == ';';
- }
-
/**
* preprocess the string to produce a string with a \1 ... \1 segment
* that will be picked up next, probably from multiline data
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
2016-12-01 23:10:35 UTC (rev 21293)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
2016-12-02 04:55:06 UTC (rev 21294)
@@ -179,36 +179,28 @@
}
/**
- * preprocess operators
- *
+ * final get for quoted object
*/
@Override
- protected boolean doPreProcess(char ch) {
- switch (ch) {
- case '\1': // CIF 1.1 encoded multi-line semicolon-encoded string
- case ';':
- return true;
- default:
- return false;
- }
+ protected Object getQuotedStringOrObject(char ch) {
+ return processQuotedString();
}
/**
- * final get for quoted object
+ * initial processing; returns a string bounded by \1
+ * @throws Exception
*/
@Override
- protected Object getQuotedStringOrObject(char ch) {
- return processQuotedString();
+ protected String preprocessString() throws Exception {
+ line = (ich == 0 ? this.str : this.str.substring(ich));
+ return setString(processSemiString());
}
/**
- * initial processing; returns to string.
+ * Handle all forms of quotation,
+ * including '...', "...", '''...''', """...""", and ;...\n...\n;
+ * @return a string or data structure, depending upon setting asObject
*/
- @Override
- protected String preprocessString() {
- return (String) processQuotedString();
- }
-
private Object processQuotedString() {
String str = null;
char quoteChar = this.str.charAt(ich);
@@ -216,30 +208,22 @@
try {
switch (quoteChar) {
case '\1':
+ // produced from ;....; in a preprocessing stage
str = this.str.substring(1, (ich = this.str.indexOf("\1", ich + 1)));
ich++;
- if (cterm != '\0')
- return (asObject ? str : PT.esc(str));
break;
- case ';':
- line = (ich == 0 ? this.str : this.str.substring(ich));
- str = processSemiString();
- return setString(str);
case '[':
- return readList(ich + 1);
+ return readList();
case ']':
- str = "]";
ich++;
- break;
+ return "]";
case '{':
- return readTable(ich + 1);
+ return readTable();
case '}':
- str = "}";
ich++;
- break;
+ return "}";
case '\'':
case '"':
- //line = this.str.substring(ich);
if (this.str.indexOf("'''") == ich)
tripleChar = "'''";
else if (this.str.indexOf("\"\"\"") == ich)
@@ -247,6 +231,7 @@
int nchar = (tripleChar == null ? 1 : 3);
int pt = ich + nchar;
int pt1 = 0;
+ // read enough lines from the stream to finish this quote.
while ((pt1 = (tripleChar == null ? this.str.indexOf(quoteChar, pt) :
this.str.indexOf(tripleChar, pt))) < 0) {
if (readLine() == null)
@@ -256,19 +241,20 @@
ich = pt1 + nchar;
cch = this.str.length();
str = this.str.substring(pt, pt1);
- if (cterm != '\0')
- return (asObject ? str : PT.esc(str));
break;
}
} catch (Exception e) {
System.out.println("exception in Cif2DataParser ; " + e);
}
- return str;
+ // the global flag cterm can be ']' or '}', indicating that
+ // we are working within a list or table, where we should not
+ // escape the string ever.
+ return (cterm == '\0' || asObject ? str : PT.esc(str));
}
/**
- * sets a multiline semicolon-eclipsed string to be parsed from the
beginning, allowing for
- * CIF 2.0-type prefixed text lines and removing line folding.
+ * Sets a multiline semicolon-eclipsed string to be parsed from the
beginning,
+ * allowing for CIF 2.0-type prefixed text lines and removing line folding.
*
* ;xxxx\comments here
*
@@ -280,18 +266,24 @@
*
* ;
*
- * @return \1....\1 string
- * @throws Exception
+ * @return \1...quote....\1
+ * @throws Exception
*/
protected String processSemiString() throws Exception {
int pt1, pt2;
String str = preprocessSemiString();
// note that this string is already escaped with \1...\1
if (str.indexOf(';') != 1 // "...and it does not begin with a semicolon"
- &&(pt1 = str.indexOf('\\')) > 1 && ((pt2 = str.indexOf('\n')) > pt1 ||
pt2 < 0)) {
+ && (pt1 = str.indexOf('\\')) > 1 // ...and it is followed by a
backslash
+ && ((pt2 = str.indexOf('\n')) > pt1 // ...and theree is no EOL prior
to that
+ || pt2 < 0)
+ ) {
String prefix = str.substring(1, pt1);
+ // (1) Remove the prefix from each line, including the first.
+ // (2) If the remaining part of the first line starts with two
backslashes then remove the first of them;
+ // otherwise remove the whole first line.
+ str = PT.rep(str, "\n" + prefix, "\n");
// remove just the next \ if it is there, or the first full line
- str = PT.rep(str, "\n" + prefix, "\n");
str = "\1" + str.substring(str.charAt(pt1 + 1) == '\\' ? pt1 + 1 : pt2 <
0 ? str.length() - 1 : pt2 + 1);
// Note: Jmol's CIF 1.0 CifReader does not already recognize "\\\n" as a
line folding indicator.
}
@@ -299,46 +291,69 @@
return fixLineFolding(str);
}
- public Object readList(int ichStart) throws Exception {
- String str = "";
- ich = ichStart;
- int n = 0;
+ /**
+ * Read a CIF 2.0 list structure, converting it to either a JSON string or to
+ * a Java data structure
+ *
+ * @return a string or data structure, depending upon setting asObject
+ * @throws Exception
+ */
+ public Object readList() throws Exception {
+ ich++;
+ // save the current globals cterm and nullString,
+ // and restore them afterward.
+ // nullString is what is returned for '.' and '?';
+ // for the Jmol CifReader only, this needs to be "\0"
char cterm0 = cterm;
cterm = ']';
- Lst<Object> lst = (asObject ? new Lst<Object>() : null);
String ns = nullString;
nullString = null;
+ Lst<Object> lst = (asObject ? new Lst<Object>() : null);
+ int n = 0;
+ String str = "";
while (true) {
- Object s = (asObject ? getNextTokenObject() : getNextToken());
- if (s == null || s.equals("]"))
+ // Iteratively pick up all the objects until the closing bracket
+ // This is akin to an array "deep copy"
+ Object value = (asObject ? getNextTokenObject() : getNextToken());
+ if (value == null || value.equals("]"))
break;
if (asObject) {
- lst.addLast(s);
- continue;
+ lst.addLast(value);
+ } else {
+ if (n++ > 0)
+ str += ",";
+ str += value;
}
- if (n++ > 0)
- str += ",";
- str += s;
}
cterm = cterm0;
- str = "[" + str + "]";
- if (cterm == '\0' && debugging)
- Logger.debug("CIF2 list: " + str);
nullString = ns;
- return (asObject ? lst : str);
+ return (asObject ? lst : "[" + str + "]");
}
- public Object readTable(int ichStart) throws Exception {
- String str = "";
- int n = 0;
- ich = ichStart;
+ /**
+ * Read a CIF 2.0 table into either a JSON string
+ * or a java data structure
+ *
+ * @return an Object or String, depending upon settings
+ * @throws Exception
+ */
+ public Object readTable() throws Exception {
+ ich++;
+ // save the current globals cterm and nullString,
+ // and restore them afterward.
+ // nullString is what is returned for '.' and '?';
+ // for the Jmol CifReader only, this needs to be "\0"
char cterm0 = cterm;
cterm = '}';
- String ns = nullString;
+ String ns = nullString;
nullString = null;
Map<String, Object> map = (asObject ? new Hashtable<String, Object>()
: null);
+ int n = 0;
+ String str = "";
while (true) {
+ // Iteratively pick up all the objects until the closing bracket
+ // This is akin to a map "deep copy"
String key = getNextToken();
if (key == null || key.equals("}"))
break;
@@ -347,21 +362,22 @@
if (asObject) {
map.put(key, getNextTokenObject());
} else {
- String value = getNextToken();
if (n++ > 0)
str += ",";
- str += key + ":" + value;
+ str += key + " : " + getNextToken();
}
}
cterm = cterm0;
- str = "{" + str + "}";
nullString = ns;
- if (cterm == '\0' && debugging)
- Logger.debug("CIF2 table: " + str);
- return (asObject ? map : str);
+ return (asObject ? map : "{" + str + "}");
}
+ /** used by readTable
+ *
+ * @param ich buffer pointer
+ * @return true if whitespace or colon
+ */
private boolean isSpaceOrColon(int ich) {
if (ich < cch)
switch (line.charAt(ich)) {
@@ -374,16 +390,23 @@
return false;
}
+ /**
+ * Handle unquoted value as Integer or Float if we can.
+ *
+ */
@Override
protected Object unquoted(String s) {
if (cterm == '\0' && !asObject)
return s;
int n = s.length();
if (n > 0) {
+ // look for a leading character in the set {0123456789.-}
char c = s.charAt(0);
if (PT.isDigit(c) || c == '-' || c == '.' && n > 1) {
+ // trim off (10) in 1.345(10)
+ // other implementers may want to handle this some other way
int pt = s.indexOf('(');
- // trim off (10) in 1.345(10)
+ // guess type
boolean isFloat = (s.indexOf(".") >= 0);
if (n > 1 && pt > 0 && s.indexOf(')', pt + 1) == n - 1)
s = s.substring(0, pt);
@@ -410,7 +433,8 @@
/**
* allow white space between \ and \n
- * @param str
+ *
+ * @param str already enclosed in \1.....\1
* @return fixed line
*/
private String fixLineFolding(String str) {
@@ -438,11 +462,7 @@
if (pt < eol)
str = str.substring(0, pt) + str.substring(eol + 1);
}
- if (debugging)
- Logger.debug("CIF2 folded: " + str.replace("\1", "~~"));
return str;
}
-
-
}
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