Revision: 21293
http://sourceforge.net/p/jmol/code/21293
Author: hansonr
Date: 2016-12-01 23:10:35 +0000 (Thu, 01 Dec 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.7.4_2016.12.01"
new feature: fully implemented CIF 2.0 reader
new feature: x = getProperty("cifInfo", "c:/temp/test.cif")
-- reads CIF file data in structured format
-- automatically uses CIF 1.0 or CIF 2.0, as needed.
new feature: CIF reader allows for nonstandard [ .... ] array notation in CIF
1.0 files
-- returned as an unaltered string for CIF 1.x; JSON string in CIF 2.x
Modified Paths:
--------------
trunk/Jmol/src/javajs/api/GenericCifDataParser.java
trunk/Jmol/src/javajs/util/CifDataParser.java
trunk/Jmol/src/javajs/util/Rdr.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2Reader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/api/GenericCifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/api/GenericCifDataParser.java 2016-12-01 15:04:17 UTC
(rev 21292)
+++ trunk/Jmol/src/javajs/api/GenericCifDataParser.java 2016-12-01 23:10:35 UTC
(rev 21293)
@@ -3,7 +3,9 @@
import java.io.BufferedReader;
import java.util.Map;
+import javajs.util.CifDataParser;
+
public interface GenericCifDataParser {
static final int NONE = -1;
@@ -20,21 +22,21 @@
String getFileHeader();
- String getColumnData(int i);
+ Object peekToken() throws Exception;
- String getNextDataToken() throws Exception;
+ Object getTokenPeeked();
+ Object getColumnData(int i);
+
+ Object getNextDataToken() throws Exception;
+
String getNextToken() throws Exception;
- String getTokenPeeked();
-
void parseDataBlockParameters(String[] fields, String key, String data,
int[] key2col, int[] col2key) throws Exception;
- String peekToken() throws Exception;
-
String readLine();
- GenericCifDataParser set(GenericLineReader reader, BufferedReader br);
+ GenericCifDataParser set(GenericLineReader reader, BufferedReader br,
boolean debugging);
String toUnicode(String data);
Modified: trunk/Jmol/src/javajs/util/CifDataParser.java
===================================================================
--- trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-01 15:04:17 UTC
(rev 21292)
+++ trunk/Jmol/src/javajs/util/CifDataParser.java 2016-12-01 23:10:35 UTC
(rev 21293)
@@ -87,20 +87,24 @@
protected int ich;
protected int cch;
protected boolean wasUnquoted;
- private String strPeeked;
+ protected char cterm = '\0';
+ protected String nullString = "\0";
+ protected boolean debugging;
+
+
+ private Object strPeeked;
private int ichPeeked;
private int columnCount;
private String[] columnNames;
- private String[] columnData = new String[KEY_MAX];
+ private Object[] columnData = new Object[KEY_MAX];
private boolean isLoop;
private boolean haveData;
- protected String nullString = "\0";
-
private SB fileHeader = new SB();
private boolean isHeader = true;
- protected char cterm = '\0';
+ protected boolean asObject;
+
/**
* Set the string value of what is returned for "." and "?"
*
@@ -127,7 +131,7 @@
}
@Override
- public String getColumnData(int i) {
+ public Object getColumnData(int i) {
return columnData[i];
}
@@ -151,15 +155,22 @@
*
* @param reader Anything that can deliver a line of text or null
* @param br A standard BufferedReader.
+ * @param debugging
*
*/
@Override
- public CifDataParser set(GenericLineReader reader, BufferedReader br) {
+ public CifDataParser set(GenericLineReader reader, BufferedReader br,
boolean debugging) {
this.reader = reader;
this.br = br;
+ this.debugging = debugging;
return this;
}
+ protected int getVersion() {
+ return 1;
+ }
+
+
/**
*
* @return commented-out section at the start of a CIF file.
@@ -182,14 +193,17 @@
public Map<String, Object> getAllCifData() {
line = "";
String key;
- Map<String, Object> data = null;
+ Map<String, Object> data = null, data0 = null;
Map<String, Object> allData = new Hashtable<String, Object>();
Lst<Map<String, Object>> models = new Lst<Map<String,Object>>();
allData.put("models", models);
+ asObject = (getVersion() >= 2);
+ nullString = null;
+ Lst<Map<String, Object>> saveFrames = new Lst<Map<String, Object>>();
try {
while ((key = getNextToken()) != null) {
if (key.startsWith("global_") || key.startsWith("data_")) {
- models.addLast(data = new Hashtable<String, Object>());
+ models.addLast(data0 = data = new Hashtable<String, Object>());
data.put("name", key);
continue;
}
@@ -198,13 +212,26 @@
continue;
}
if (key.startsWith("save_")) {
- System.out.println("CIF reader ignoring save_");
+ if (key.equals("save_")) {
+ int n = saveFrames.size();
+ if (n == 0) {
+ System.out.println("CIF ERROR ? save_ without corresponding
save_xxxx");
+ data = data0;
+ } else {
+ data = saveFrames.removeItemAt(n - 1);
+ }
+ } else {
+ saveFrames.addLast(data);
+ Map<String, Object> d = data;
+ data = new Hashtable<String, Object>();
+ d.put(key, data);
+ }
continue;
}
if (key.charAt(0) != '_') {
System.out.println("CIF ERROR ? should be an underscore: " + key);
} else {
- String value = getNextToken();
+ Object value = (asObject ? getNextTokenObject() : getNextToken());
if (value == null) {
System.out.println("CIF ERROR ? end of file; data missing: " +
key);
} else {
@@ -215,12 +242,14 @@
} catch (Exception e) {
// ?
}
+ asObject = false;
try {
if (br != null)
br.close();
} catch (Exception e) {
// ?
}
+ nullString = "\0";
return allData;
}
@@ -236,17 +265,23 @@
private void getAllCifLoopData(Map<String, Object> data) throws Exception {
String key;
Lst<String> keyWords = new Lst<String>();
- while ((key = peekToken()) != null && key.charAt(0) == '_') {
- key = fixKey(getTokenPeeked());
+ Object o;
+ while ((o = peekToken()) != null && o instanceof String && ((String)
o).charAt(0) == '_') {
+ key = fixKey((String) getTokenPeeked());
keyWords.addLast(key);
data.put(key, new Lst<String>());
}
columnCount = keyWords.size();
if (columnCount == 0)
return;
- while (getData())
+ isLoop = true;
+ int n = 0;
+ while (getData()) {
for (int i = 0; i < columnCount; i++)
- ((Lst<String>)data.get(keyWords.get(i))).addLast(columnData[i]);
+ ((Lst<Object>)data.get(keyWords.get(i))).addLast(columnData[i]);
+ n++;
+ }
+ isLoop = false;
}
@Override
@@ -300,7 +335,7 @@
String str;
SB ret = (doReport ? new SB() : null);
int n = 0;
- while ((str = peekToken()) != null && str.charAt(0) == '_') {
+ while ((str = (String) peekToken()) != null && str.charAt(0) == '_') {
if (ret != null)
ret.append(str).append("\n");
getTokenPeeked();
@@ -309,7 +344,7 @@
if (n == 0)
n = columnCount; // end-of-label-section skip
int m = 0;
- while ((str = getNextDataToken()) != null) {
+ while ((str = (String) getNextDataToken()) != null) {
if (ret == null)
continue;
ret.append(str).append(" ");
@@ -327,10 +362,20 @@
@Override
public String getNextToken() throws Exception {
wasUnquoted = true;
+ return (String) getNextTokenProtected();
+ }
+
+ /**
+ *
+ * @return the next token of any kind, or null
+ * @throws Exception
+ */
+ public Object getNextTokenObject() throws Exception {
+ wasUnquoted = true;
return getNextTokenProtected();
}
- protected String getNextTokenProtected() throws Exception {
+ protected Object getNextTokenProtected() throws Exception {
return (getNextLine() ? nextStrToken() : null);
}
@@ -343,16 +388,19 @@
* @throws Exception
*/
@Override
- public String getNextDataToken() throws Exception {
- String str = peekToken();
- if (str == null)
+ public Object getNextDataToken() throws Exception {
+ Object o = peekToken();
+ if (o == null)
return null;
- if (wasUnquoted)
+ if (wasUnquoted && o instanceof String) {
+ String str = (String) o;
if (str.charAt(0) == '_' || str.startsWith("loop_")
|| str.startsWith("data_")
+ || str.startsWith("save_")
|| str.startsWith("stop_")
|| str.startsWith("global_"))
return null;
+ }
return getTokenPeeked();
}
@@ -364,7 +412,7 @@
* @throws Exception
*/
@Override
- public String peekToken() throws Exception {
+ public Object peekToken() throws Exception {
if (!getNextLine())
return null;
int ich = this.ich;
@@ -386,7 +434,7 @@
* @return the token last acquired; may be null
*/
@Override
- public String getTokenPeeked() {
+ public Object getTokenPeeked() {
ich = ichPeeked;
return strPeeked;
}
@@ -486,6 +534,7 @@
public void parseDataBlockParameters(String[] fields, String key,
String data, int[] key2col, int[] col2key)
throws Exception {
isLoop = (key == null);
+ Object o;
String s;
if (fields == null) {
// for reading full list of keys, as for matrices
@@ -501,18 +550,18 @@
int pt, i;
if (isLoop) {
while (true) {
- s = peekToken();
- if (s == null) {
+ o = peekToken();
+ if (o == null) {
// we are PREMATURELY done; reset
columnCount = 0;
break;
}
// end of the loop is a new token not starting with underscore
- if (s.charAt(0) != '_')
+ if (!(o instanceof String) || ((String) o).charAt(0) != '_')
break;
pt = columnCount++;
- s = fixKey(getTokenPeeked());
+ s = fixKey((String) getTokenPeeked());
if (fields == null) {
// just make a linear model, saving the list
columnNames[col2key[pt] = key2col[pt] = pt] = s;
@@ -530,14 +579,14 @@
// end of the loop is a new token not starting with underscore
pt = columnCount++;
if (key == null) {
- key = getTokenPeeked();
+ key = (String) getTokenPeeked();
data = getNextToken();
}
Integer iField = htFields.get(fixKey(key));
i = (iField == null ? NONE : iField.intValue());
if ((col2key[pt] = i) != NONE)
columnData[key2col[i] = pt] = data;
- if ((s = peekToken()) == null || !s.startsWith(str0))
+ if ((o = peekToken()) == null || !(o instanceof String) || !((String)
o).startsWith(str0))
break;
key = null;
}
@@ -700,13 +749,13 @@
*
* @return null if no more tokens, "\0" if '.' or '?', or next token
*/
- protected String nextStrToken() {
+ private Object nextStrToken() {
if (ich == cch)
return null;
char ch = str.charAt(ich);
if (isQuote(ch)) {
wasUnquoted = false;
- return (String) getQuotedStringOrObject(ch);
+ return getQuotedStringOrObject(ch);
}
int ichStart = ich;
wasUnquoted = true;
@@ -720,7 +769,7 @@
return unquoted(s);
}
- protected String unquoted(String s) {
+ protected Object unquoted(String s) {
return s;
}
Modified: trunk/Jmol/src/javajs/util/Rdr.java
===================================================================
--- trunk/Jmol/src/javajs/util/Rdr.java 2016-12-01 15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/javajs/util/Rdr.java 2016-12-01 23:10:35 UTC (rev 21293)
@@ -67,7 +67,7 @@
}
public static Map<String, Object> readCifData(GenericCifDataParser parser,
BufferedReader br) {
- return parser.set(null, br).getAllCifData();
+ return parser.set(null, br, false).getAllCifData();
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
2016-12-01 15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2DataParser.java
2016-12-01 23:10:35 UTC (rev 21293)
@@ -1,6 +1,12 @@
package org.jmol.adapter.readers.cif;
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.util.Logger;
+
import javajs.util.CifDataParser;
+import javajs.util.Lst;
import javajs.util.PT;
/**
@@ -9,10 +15,25 @@
*
* see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html
*
+ * Will deliver JSON versions of the data while file reading and Java List/Map
structures when
+ * called by
+ *
+ * x = getProperty("cifInfo", filename)
+ *
+ * Validated using the test-data suite by John Bollinger
(john.bollin...@stjude.org)
+ * found at https://github.com/COMCIFS/cif_api
+ *
* @author Bob Hanson hans...@stolaf.edu
*/
public class Cif2DataParser extends CifDataParser {
+
+ @Override
+ protected int getVersion() {
+ return 2;
+ }
+
+
// 3.1. Character set and encoding
//
// - UTF-8
@@ -144,7 +165,7 @@
@Override
protected boolean isQuote(char ch) {
switch (ch) {
- case '\1': // CIF 1.1 encoded multi-line semicolon-encoded string
+ case '\1': // preprocessed CIF 1.1 encoded multi-line semicolon-encoded
string
case '\'':
case '\"':
case '[':
@@ -158,7 +179,7 @@
}
/**
- * preprocess all operators
+ * preprocess operators
*
*/
@Override
@@ -177,7 +198,7 @@
*/
@Override
protected Object getQuotedStringOrObject(char ch) {
- return processQuotedString(false);
+ return processQuotedString();
}
/**
@@ -185,10 +206,10 @@
*/
@Override
protected String preprocessString() {
- return processQuotedString(true);
+ return (String) processQuotedString();
}
- private String processQuotedString(boolean isPreprocessing) {
+ private Object processQuotedString() {
String str = null;
char quoteChar = this.str.charAt(ich);
String tripleChar = null;
@@ -196,50 +217,47 @@
switch (quoteChar) {
case '\1':
str = this.str.substring(1, (ich = this.str.indexOf("\1", ich + 1)));
+ ich++;
if (cterm != '\0')
- str = PT.esc(str);
- ich++;
+ return (asObject ? str : PT.esc(str));
break;
case ';':
line = (ich == 0 ? this.str : this.str.substring(ich));
str = processSemiString();
return setString(str);
case '[':
- str = readListAsJSON(ich + 1);
- break;
+ return readList(ich + 1);
case ']':
str = "]";
ich++;
break;
case '{':
- str = readTableAsJSON(ich + 1);
- break;
+ return readTable(ich + 1);
case '}':
str = "}";
ich++;
break;
case '\'':
case '"':
- line = this.str.substring(ich);
- if (line.indexOf("'''") == 0)
+ //line = this.str.substring(ich);
+ if (this.str.indexOf("'''") == ich)
tripleChar = "'''";
- else if (line.indexOf("\"\"\"") == 0)
+ else if (this.str.indexOf("\"\"\"") == ich)
tripleChar = "\"\"\"";
int nchar = (tripleChar == null ? 1 : 3);
- int pt = nchar;
+ int pt = ich + nchar;
int pt1 = 0;
- str = "";
- while (line != null
- && (pt1 = (tripleChar == null ? line.indexOf(quoteChar, pt) : line
- .indexOf(tripleChar, pt))) < 0) {
- str += "\n" + line.substring(pt);
- readLine();
- pt = 0;
+ while ((pt1 = (tripleChar == null ? this.str.indexOf(quoteChar, pt) :
+ this.str.indexOf(tripleChar, pt))) < 0) {
+ if (readLine() == null)
+ break;
+ this.str += line;
}
- str += (line == null ? "" : line.substring(pt, pt1));
- setString(line.substring(pt1 + nchar));
+ ich = pt1 + nchar;
+ cch = this.str.length();
+ str = this.str.substring(pt, pt1);
if (cterm != '\0')
- str = PT.esc(str);
+ return (asObject ? str : PT.esc(str));
break;
}
} catch (Exception e) {
@@ -281,53 +299,66 @@
return fixLineFolding(str);
}
- public String readListAsJSON(int ichStart) throws Exception {
+ public Object readList(int ichStart) throws Exception {
String str = "";
- ich = ichStart;
+ ich = ichStart;
int n = 0;
char cterm0 = cterm;
cterm = ']';
+ Lst<Object> lst = (asObject ? new Lst<Object>() : null);
+ String ns = nullString;
nullString = null;
while (true) {
- String s = getNextToken();
+ Object s = (asObject ? getNextTokenObject() : getNextToken());
if (s == null || s.equals("]"))
break;
+ if (asObject) {
+ lst.addLast(s);
+ continue;
+ }
if (n++ > 0)
str += ",";
str += s;
}
cterm = cterm0;
str = "[" + str + "]";
-// if (cterm == '\0')
-// System.out.println("CIF2 list: " + str);
- nullString = "\0";
- return str;
+ if (cterm == '\0' && debugging)
+ Logger.debug("CIF2 list: " + str);
+ nullString = ns;
+ return (asObject ? lst : str);
}
- public String readTableAsJSON(int ichStart) throws Exception {
+ public Object readTable(int ichStart) throws Exception {
String str = "";
int n = 0;
ich = ichStart;
char cterm0 = cterm;
cterm = '}';
+ String ns = nullString;
nullString = null;
+ Map<String, Object> map = (asObject ? new Hashtable<String, Object>()
+ : null);
while (true) {
String key = getNextToken();
- if (key == null || key.equals("}"))
+ if (key == null || key.equals("}"))
break;
while (isSpaceOrColon(ich))
ich++;
- String value = getNextToken();
- if (n++ > 0)
- str += ",";
- str += key + ":" + value;
+ if (asObject) {
+ map.put(key, getNextTokenObject());
+ } else {
+ String value = getNextToken();
+ if (n++ > 0)
+ str += ",";
+ str += key + ":" + value;
+ }
}
cterm = cterm0;
str = "{" + str + "}";
- nullString = "\0";
-// if (cterm == '\0')
-// System.out.println("CIF2 table: " + str);
- return str;
+ nullString = ns;
+ if (cterm == '\0' && debugging)
+ Logger.debug("CIF2 table: " + str);
+ return (asObject ? map : str);
}
@@ -344,8 +375,8 @@
}
@Override
- protected String unquoted(String s) {
- if (cterm == '\0')
+ protected Object unquoted(String s) {
+ if (cterm == '\0' && !asObject)
return s;
int n = s.length();
if (n > 0) {
@@ -358,18 +389,22 @@
s = s.substring(0, pt);
try {
if (isFloat) {
- s = "" + Float.parseFloat(s);
+ float f = Float.parseFloat(s);
+ if (asObject)
+ return Float.valueOf(f);
+ s = "" + f;
if (s.indexOf(".") < 0 && s.indexOf("E") < 0)
s += ".0";
return s;
}
- return "" + Integer.parseInt(s);
+ int i = Integer.parseInt(s);
+ return (asObject ? Integer.valueOf(i) : "" + i);
} catch (Throwable e) {
// ignore
}
}
}
- return PT.esc(s);
+ return (asObject ? s : PT.esc(s));
}
@@ -403,7 +438,8 @@
if (pt < eol)
str = str.substring(0, pt) + str.substring(eol + 1);
}
- //System.out.println("fixed: >>" + str + "<<");
+ if (debugging)
+ Logger.debug("CIF2 folded: " + str.replace("\1", "~~"));
return str;
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2Reader.java 2016-12-01
15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/Cif2Reader.java 2016-12-01
23:10:35 UTC (rev 21293)
@@ -40,7 +40,7 @@
@Override
protected GenericCifDataParser getCifDataParser() {
- return new Cif2DataParser().set(this, null);
+ return new Cif2DataParser().set(this, null, debugging);
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-12-01
15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-12-01
23:10:35 UTC (rev 21293)
@@ -170,13 +170,13 @@
*/
parser = getCifDataParser();
line = "";
- while ((key = parser.peekToken()) != null)
+ while ((key = (String) parser.peekToken()) != null)
if (!readAllData())
break;
if (appendedData != null) {
parser = ((GenericCifDataParser)
getInterface("javajs.util.CifDataParser"))
- .set(null, Rdr.getBR(appendedData));
- while ((key = parser.peekToken()) != null)
+ .set(null, Rdr.getBR(appendedData), debugging);
+ while ((key = (String) parser.peekToken()) != null)
if (!readAllData())
break;
}
@@ -184,13 +184,13 @@
protected GenericCifDataParser getCifDataParser() {
// overridden in Cif2Reader
- return new CifDataParser().set(this, null);
+ return new CifDataParser().set(this, null, debugging);
}
private boolean readAllData() throws Exception {
if (key.startsWith("data_")) {
isLigand = false;
- if (asc.atomSetCount == 0)
+ if (asc.atomSetCount == 0)
iHaveDesiredModel = false;
if (iHaveDesiredModel)
return false;
@@ -731,10 +731,10 @@
* @throws Exception
*/
private boolean getData() throws Exception {
- key = parser.getTokenPeeked();
+ key = (String) parser.getTokenPeeked();
data = parser.getNextToken();
- //if (debugging && data != null && data.charAt(0) != '\0')
- Logger.debug(">> " + key + " " + data);
+ if (debugging && data != null && data.length() > 0 && data.charAt(0) !=
'\0')
+ Logger.debug(">> " + key + " " + data);
if (data == null) {
Logger.warn("CIF ERROR ? end of file; data missing: " + key);
return false;
@@ -753,7 +753,7 @@
*/
protected void processLoopBlock() throws Exception {
parser.getTokenPeeked(); //loop_
- key = parser.peekToken();
+ key = (String) parser.peekToken();
if (key == null)
return;
key = parser.fixKey(key0 = key);
@@ -822,13 +822,13 @@
String str;
int n = 0;
try {
- while ((str = parser.peekToken()) != null && str.charAt(0) == '_') {
+ while ((str = (String) parser.peekToken()) != null && str.charAt(0) ==
'_') {
parser.getTokenPeeked();
n++;
}
int m = 0;
String s = "";
- while ((str = parser.getNextDataToken()) != null) {
+ while ((str = (String) parser.getNextDataToken()) != null) {
s += str + (m % n == 0 ? "=" : " ");
if (++m % n == 0) {
appendUunitCellInfo(s.trim());
@@ -840,7 +840,7 @@
}
protected int fieldProperty(int i) {
- return (i >= 0 && (field = parser.getColumnData(i)).length() > 0
+ return (i >= 0 && (field = (String) parser.getColumnData(i)).length() > 0
&& (firstChar = field.charAt(0)) != '\0' ? col2key[i] : NONE);
}
@@ -1251,7 +1251,7 @@
if (field.equalsIgnoreCase("Uiso")) {
int j = key2col[U_ISO_OR_EQUIV];
if (j != NONE)
- asc.setU(atom, 7, parseFloatStr(parser.getColumnData(j)));
+ asc.setU(atom, 7, parseFloatStr((String)
parser.getColumnData(j)));
}
break;
case ANISO_U11:
@@ -1964,7 +1964,7 @@
protected String getField(byte type) {
int i = key2col[type];
- return (i == NONE ? "\0" : parser.getColumnData(i));
+ return (i == NONE ? "\0" : (String) parser.getColumnData(i));
}
protected boolean isNull(String key) {
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java 2016-12-01
15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MSCifRdr.java 2016-12-01
23:10:35 UTC (rev 21293)
@@ -603,7 +603,7 @@
}
private int fieldProperty(CifReader cr, int i) {
- return ((field = cr.parser.getColumnData(i)).length() > 0
+ return ((field = (String) cr.parser.getColumnData(i)).length() > 0
&& field.charAt(0) != '\0' ?
cr.col2key[i] : NONE);
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2016-12-01 15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2016-12-01 23:10:35 UTC (rev 21293)
@@ -131,8 +131,8 @@
int n = 0;
readerList = new Lst<AtomSetCollectionReader>();
for (int i = 0; i < array.length; i++)
- if (array[i].ac > 0 || array[i].reader != null
- && array[i].reader.mustFinalizeModelSet)
+ if (array[i] != null && (array[i].ac > 0 || array[i].reader != null
+ && array[i].reader.mustFinalizeModelSet))
appendAtomSetCollection(n++, array[i]);
if (n > 1)
setInfo("isMultiFile", Boolean.TRUE);
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
2016-12-01 15:04:17 UTC (rev 21292)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
2016-12-01 23:10:35 UTC (rev 21293)
@@ -194,8 +194,6 @@
//FilesOpenThread
Viewer vwr = (Viewer) htParams.get("vwr"); // don't pass this on to user
int size = names.length;
- AtomSetCollectionReader[] readers = (getReadersOnly ? new
AtomSetCollectionReader[size]
- : null);
Object reader = null;
if (htParams.containsKey("concatenate")) {
String s = "";
@@ -231,6 +229,8 @@
size = 1;
reader = Rdr.getBR(s);
}
+ AtomSetCollectionReader[] readers = (getReadersOnly ? new
AtomSetCollectionReader[size]
+ : null);
AtomSetCollection[] atomsets = (getReadersOnly ? null
: new AtomSetCollection[size]);
AtomSetCollectionReader r = null;
@@ -299,6 +299,7 @@
: (AtomSetCollection[]) atomsets);
if (atomsets == null) {
for (int i = 0; i < readers.length; i++) {
+ if (readers[i] != null)
try {
Object ret = readers[i].readData();
if (!(ret instanceof AtomSetCollection))
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-12-01 15:04:17 UTC
(rev 21292)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-12-01 23:10:35 UTC
(rev 21293)
@@ -51,8 +51,12 @@
new feature: fully implemented CIF 2.0 reader
-new feature: CIF reader allows for [ .... ] array notation
- -- returned as an unaltered string for CIF 1.x
+new feature: x = getProperty("cifInfo", "c:/temp/test.cif")
+ -- reads CIF file data in structured format
+ -- automatically uses CIF 1.0 or CIF 2.0, as needed.
+
+new feature: CIF reader allows for nonstandard [ .... ] array notation in CIF
1.0 files
+ -- returned as an unaltered string for CIF 1.x; JSON string in CIF 2.x
JmolVersion="14.7.4_2016.11.28"
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2016-12-01 15:04:17 UTC
(rev 21292)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2016-12-01 23:10:35 UTC
(rev 21293)
@@ -174,6 +174,7 @@
"domainInfo" , atomExpression, "{visible}",
"validationInfo" , atomExpression, "{visible}",
"service" , "<hashTable>", "",
+ "CIFInfo" , "<filename>", "_modelFile",
};
@@ -228,7 +229,8 @@
private final static int PROP_DOM_INFO = 42;
private final static int PROP_VAL_INFO = 43;
private final static int PROP_SERVICE = 44;
- private final static int PROP_COUNT = 45;
+ private final static int PROP_CIF_INFO = 45;
+ private final static int PROP_COUNT = 46;
//// static methods used by Eval and Viewer ////
@@ -766,6 +768,8 @@
return vwr.getModelExtract(myParam, true, false, "MOL");
case PROP_FILE_INFO:
return getFileInfo(vwr.getFileData(), myParam.toString());
+ case PROP_CIF_INFO:
+ return vwr.readCifData(myParam.toString(), null);
case PROP_FILENAME:
return vwr.fm.getFullPathName(false);
case PROP_FILEHEADER:
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-12-01 15:04:17 UTC (rev
21292)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2016-12-01 23:10:35 UTC (rev
21293)
@@ -2108,9 +2108,8 @@
Map<String, Object> htParams,
boolean isAppend) {
// loadInline, openStringInline
-
- BufferedReader br = Rdr.getBR(strModel);
- String type = getModelAdapter().getFileTypeName(br);
+
+ String type = getModelAdapter().getFileTypeName(Rdr.getBR(strModel));
if (type == null)
return "unknown file type";
if (type.equals("spt")) {
@@ -2860,10 +2859,20 @@
}
public Map<String, Object> getCifData(int modelIndex) {
- String data = getFileAsString3(ms.getModelFileName(modelIndex), false,
null);
- return (data == null ? null : Rdr.readCifData(
+ return readCifData(ms.getModelFileName(modelIndex),
ms.getModelFileType(modelIndex));
+ }
+
+ public Map<String, Object> readCifData(String fileName, String type) {
+ String data = getFileAsString3(
+ (fileName == null || fileName.length() == 0 ?
getCurrentFileAsString("script"): fileName), false, null);
+ if (data == null)
+ return null;
+ BufferedReader rdr = Rdr.getBR(data);
+ if (type == null)
+ type = getModelAdapter().getFileTypeName(rdr);
+ return (type == null ? null : Rdr.readCifData(
(GenericCifDataParser) Interface.getInterface(
- "javajs.util.CifDataParser", this, "script"), Rdr.getBR(data)));
+ ("cif2".equals(type.toLowerCase()) ?
"org.jmol.adapter.readers.cif.Cif2DataParser" : "javajs.util.CifDataParser"),
this, "script"), rdr));
}
JmolStateCreator jsc;
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