+++ /dev/null
-package javajs.util;
-
-import java.io.BufferedReader;
-
-import java.util.Hashtable;
-
-import java.util.Map;
-
-import javajs.api.GenericCifDataParser;
-import javajs.api.GenericLineReader;
-
-
-// BH 11/21/16 -- adds support for array grouping [...] - used in 2016-format magCIF 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.
-*
-*<p>
-* regarding the treatment of single quotes vs. primes in
-* cif file, PMR wrote:
-*</p>
-*<p>
-* * There is a formal grammar for CIF
-* (see http://www.iucr.org/iucr-top/cif/index.html)
-* which confirms this. The textual explanation is
-*<p />
-*<p>
-* 14. Matching single or double quote characters (' or ") may
-* be used to bound a string representing a non-simple data value
-* provided the string does not extend over more than one line.
-*<p />
-*<p>
-* 15. Because data values are invariably separated from other
-* tokens in the file by white space, such a quote-delimited
-* character string may contain instances of the character used
-* to delimit the string provided they are not followed by white
-* space. For example, the data item
-*<code>
-* _example 'a dog's life'
-*</code>
-* is legal; the data value is a dog's life.
-*</p>
-*<p>
-* [PMR - the terminating character(s) are quote+whitespace.
-* That would mean that:
-*<code>
-* _example 'Jones' life'
-*</code>
-* would be an error
-*</p>
-*<p>
-* The CIF format was developed in that late 1980's under the aegis of the
-* International Union of Crystallography (I am a consultant to the COMCIFs
-* committee). It was ratified by the Union and there have been several
-* workshops. mmCIF is an extension of CIF which includes a relational
-* structure. The formal publications are:
-*</p>
-*<p>
-* Hall, S. R. (1991). "The STAR File: A New Format for Electronic Data
-* Transfer and Archiving", J. Chem. Inform. Comp. Sci., 31, 326-333.
-* Hall, S. R., Allen, F. H. and Brown, I. D. (1991). "The Crystallographic
-* Information File (CIF): A New Standard Archive File for Crystallography",
-* Acta Cryst., A47, 655-685.
-* Hall, S.R. & Spadaccini, N. (1994). "The STAR File: Detailed
-* Specifications," J. Chem. Info. Comp. Sci., 34, 505-508.
-*</p>
-*/
-
-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.
- *
- */
- public static final int KEY_MAX = 100;
-
- private GenericLineReader reader;
- private BufferedReader br;
-
- /**
- * 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;
- private String[] columnNames;
- private Object[] columnData = new Object[KEY_MAX];
- private boolean isLoop;
- private boolean haveData;
-
- /**
- * comments at the top of a file, including #\#CIF_2.0, for example
- */
- private SB fileHeader = new SB();
- private boolean isHeader = true;
-
-
- /**
- * Set the string value of what is returned for "." and "?"
- *
- * @param nullString null here returns "." and "?"; default is "\0"
- *
- */
- public void setNullValue(String nullString) {
- this.nullString = nullString;
- }
-
- /**
- * A global, static map that contains field information. The assumption is that
- * if we read a set of fields for, say, atom_site, once in a lifetime, then
- * that should be good forever. Those are static lists. Or should be....
- */
- private static Map<String, Integer> htFields = new Hashtable<String, Integer>();
-
- ////////////////////////////////////////////////////////////////
- // special tokenizer class
- ////////////////////////////////////////////////////////////////
-
- public CifDataParser() {
- // for reflection
- }
-
- @Override
- public Object getColumnData(int i) {
- return columnData[i];
- }
-
- @Override
- public int getColumnCount() {
- return columnCount;
- }
-
- @Override
- public String getColumnName(int i) {
- return columnNames[i];
- }
-
- /**
- * A Chemical Information File data parser.
- *
- * 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...
- *
- * @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, boolean debugging) {
- this.reader = reader;
- this.br = br;
- this.debugging = debugging;
- return this;
- }
-
-
- /**
- *
- * @return commented-out section at the start of a CIF file.
- *
- */
- @Override
- public String getFileHeader() {
- return fileHeader.toString();
- }
-
-
- /**
- * Parses all CIF data for a reader defined in the constructor
- * into a standard Map structure and close the BufferedReader if
- * it exists.
- *
- * @return Hashtable of models Vector of Hashtable data
- */
- @Override
- public Map<String, Object> getAllCifData() {
- line = "";
- String key;
- 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(data0 = data = new Hashtable<String, Object>());
- data.put("name", key);
- continue;
- }
- if (key.startsWith("loop_")) {
- getAllCifLoopData(data);
- continue;
- }
- if (key.startsWith("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 {
- Object value = (asObject ? getNextTokenObject() : getNextToken());
- if (value == null) {
- System.out.println("CIF ERROR ? end of file; data missing: " + key);
- } else {
- data.put(fixKey(key), value);
- }
- }
- }
- } catch (Exception e) {
- // ?
- }
- asObject = false;
- try {
- if (br != null)
- br.close();
- } catch (Exception e) {
- // ?
- }
- nullString = "\0";
- return allData;
- }
-
- /**
- * create our own list of keywords and for each one create a list
- * of data associated with that keyword. For example, a list of all
- * x coordinates, then a list of all y coordinates, etc.
- *
- * @param data
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- private void getAllCifLoopData(Map<String, Object> data) throws Exception {
- String key;
- Lst<String> keyWords = new Lst<String>();
- 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;
- isLoop = true;
- while (getData())
- for (int i = 0; i < columnCount; i++)
- ((Lst<Object>)data.get(keyWords.get(i))).addLast(columnData[i]);
- isLoop = false;
- }
-
- @Override
- public String readLine() {
- try {
- line = (reader == null ? br.readLine() : reader.readNextLine());
- if (line == null)
- return null;
- if (isHeader) {
- if (line.startsWith("#"))
- fileHeader.append(line).appendC('\n');
- else
- isHeader = false;
- }
- return line;
- } catch (Exception e) {
- return null;
- }
- }
-
- /**
- * The work horse; a general reader for loop data. Fills colunnData with
- * fieldCount fields.
- *
- * @return false if EOF
- * @throws Exception
- */
- @Override
- public boolean getData() throws Exception {
- // line is already present, and we leave with the next line to parse
- if (isLoop) {
- for (int i = 0; i < columnCount; ++i)
- if ((columnData[i] = getNextDataToken()) == null)
- return false;
- } else if (haveData) {
- haveData = false;
- } else {
- return false;
- }
- return (columnCount > 0);
- }
-
- /**
- *
- * Skips all associated loop data. (Skips to next control word.)
- *
- * @throws Exception
- */
- @Override
- public String skipLoop(boolean doReport) throws Exception {
- String str;
- SB ret = (doReport ? new SB() : null);
- int n = 0;
- while ((str = (String) peekToken()) != null && str.charAt(0) == '_') {
- if (ret != null)
- ret.append(str).append("\n");
- getTokenPeeked();
- n++;
- }
- if (n == 0)
- n = columnCount; // end-of-label-section skip
- int m = 0;
- while ((str = (String) getNextDataToken()) != null) {
- if (ret == null)
- continue;
- ret.append(str).append(" ");
- if ((++m % n) == 0)
- ret.append("\n");
- }
- return (ret == null ? null : ret.toString());
- }
-
- /**
- * Get a token as a String value (for the reader)
- *
- * @return the next token of any kind, or null
- * @throws Exception
- */
- @Override
- public String getNextToken() throws Exception {
- wasUnquoted = true;
- return (String) getNextTokenProtected();
- }
-
- /**
- * Get the token as a Java Object
- *
- * @return the next token of any kind, or null
- * @throws Exception
- */
- public Object getNextTokenObject() throws Exception {
- wasUnquoted = true;
- return getNextTokenProtected();
- }
-
- /**
- * Just makes sure
- * @return String from buffer.
- * @throws Exception
- */
- protected Object getNextTokenProtected() throws Exception {
- return (getNextLine() ? nextStrToken() : null);
- }
-
- /**
- *
- * first checks to see if the next token is an unquoted
- * control code, and if so, returns null
- *
- * @return next data token or null
- * @throws Exception
- */
- @Override
- public Object getNextDataToken() throws Exception {
- Object o = peekToken();
- if (o == null)
- return null;
- 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();
- }
-
- /**
- * Just look at the next token. Saves it for retrieval
- * using getTokenPeeked()
- *
- * @return next token or null if EOF
- * @throws Exception
- */
- @Override
- public Object peekToken() throws Exception {
- if (!getNextLine())
- return null;
- int ich = this.ich;
- strPeeked = nextStrToken();
- ichPeeked= this.ich;
- this.ich = ich;
- 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)
- return false;
- return true;
- }
-
- /**
- *
- * @return the token last acquired; may be null
- */
- @Override
- public Object getTokenPeeked() {
- ich = ichPeeked;
- return strPeeked;
- }
-
- /**
- * Used especially for data that might be multi-line data that
- * might have unwanted white space at start or end.
- *
- * @param str
- * @return str without any leading/trailing white space, and no '\n'
- */
- @Override
- public String fullTrim(String str) {
- int pt0 = -1;
- int pt1 = str.length();
- while (++pt0 < pt1 && PT.isWhitespace(str.charAt(pt0))) {
- }
- while (--pt1 > pt0 && PT.isWhitespace(str.charAt(pt1))) {
- }
- return str.substring(pt0, pt1 + 1);
- }
-
- private final static String grABC =
- "ABX\u0394E\u03A6\u0393H" // ABCDEFGH
- + "I_K\u039BMNO\u03A0" // I_KLMNOP
- + "\u0398P\u03A3TY_\u03A9\u039E\u03A5Z"; // QRSTU_WXYZ
- private final static String grabc =
- "\u03B1\u03B2\u03C7\u03A4\u03A5\u03C6\u03B3\u03B7" // abcdefgh
- + "\u03B9_\u03BA\u03BB\u03BC\u03BD\u03BF\u03C0" // i_klmnop
- + "\u03B8\u03C1\u03C3\u03C4\u03C5_\u03C9\u03BE\u03C5\u03B6"; // qrstu_wxyz
-
- /**
- * Only translating the basic Greek set here, not all the other stuff. See
- * http://www.iucr.org/resources/cif/spec/version1.1/semantics#markup
- *
- * @param data
- * @return cleaned string
- */
- @Override
- public String toUnicode(String data) {
- int pt;
- try {
- while ((pt = data.indexOf('\\')) >= 0) {
- int c = data.charAt(pt + 1);
- String ch = (c >= 65 && c <= 90 ? grABC.substring(c - 65, c - 64)
- : c >= 97 && c <= 122 ? grabc.substring(c - 97, c - 96) : "_");
- data = data.substring(0, pt) + ch + data.substring(pt + 2);
- }
- } catch (Exception e) {
- // ignore
- }
-
- return data;
- }
-
- /**
- * Process a data block, with or without a loop_.
- *
- * Passed an array of field names, this method fills two int[] arrays. The
- * first, key2col, maps desired key values to actual order of appearance
- * (column number) in the file; the second, col2key, is a reverse loop-up for
- * that, mapping column numbers to desired field indices.
- *
- * When called within a loop_ context, this.columnData will be created but not filled.
- *
- * Alternatively, if fields is null, then this.fieldNames is
- * filled, in order, with key data, and both key2col and col2key will be
- * simply 0,1,2,... This array is used in cases such as matrices for which
- * there are simply too many possibilities to list, and the key name itself
- * contains information that we need.
- *
- * When not a loop_ context, keys are expected to be in the mmCIF form
- * category.subkey and will be unique within a data block (see
- * http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html).
- * Keys and data will be read for all data in the same category, filling this.columnData.
- *
- *
- * In this way, the calling class does not need to enumerate all possible
- * category names, but instead can focus on just those of interest.
- *
- *
- * @param fields
- * list of normalized field names, such as
- * "_pdbx_struct_assembly_gen_assembly_id" (with "_" instead of ".")
- * @param key
- * null to indicate a loop_ construct, otherwise the initial category.subkey
- * found
- * @param data
- * when not loop_ the initial data read, otherwise ignored
- * @param key2col
- * map of desired keys to actual columns
- * @param col2key
- * map of actual columns to desired keys
- * @throws Exception
- */
- @Override
- 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
- columnNames = new String[KEY_MAX];
- } else {
- if (!htFields.containsKey(fields[0]))
- for (int i = fields.length; --i >= 0;)
- htFields.put(fields[i], Integer.valueOf(i));
- for (int i = fields.length; --i >= 0;)
- key2col[i] = NONE;
- }
- columnCount = 0;
- int pt, i;
- if (isLoop) {
- while (true) {
- 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 (!(o instanceof String) || ((String) o).charAt(0) != '_')
- break;
-
- pt = columnCount++;
- s = fixKey((String) getTokenPeeked());
- if (fields == null) {
- // just make a linear model, saving the list
- columnNames[col2key[pt] = key2col[pt] = pt] = s;
- continue;
- }
- Integer iField = htFields.get(s);
- i = (iField == null ? NONE : iField.intValue());
- if ((col2key[pt] = i) != NONE)
- key2col[i] = pt;
- }
- } else {
- pt = key.indexOf(".");
- String str0 = (pt < 0 ? key : key.substring(0, pt + 1));
- while (true) {
- // end of the loop is a new token not starting with underscore
- pt = columnCount++;
- if (key == null) {
- 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 ((o = peekToken()) == null || !(o instanceof String) || !((String) o).startsWith(str0))
- break;
- key = null;
- }
- haveData = (columnCount > 0);
- }
- }
-
- @Override
- public String fixKey(String key) {
- // PRELIMINARY -- BilBao _magnetic
- // PRELIMINARY -- Jana2006
- return (
- key.startsWith("_magnetic") ? key.substring(9)
- : key.startsWith("_jana") ? key.substring(5)
- : key).replace('.', '_').toLowerCase();
- }
-
- //////////////////// private methods ////////////////////
-
-
- /**
- * sets global str and line to be parsed from the beginning
- *
- * \1 .... \1 indicates an embedded fully escaped data object
- *
- * @param str new data string
- * @return str
- */
- protected String setString(String str) {
- this.str = line = str;
- cch = (str == null ? 0 : str.length());
- ich = 0;
- return str;
- }
-
- /*
- * http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax
- *
- * 17. The special sequence of end-of-line followed
- * immediately by a semicolon in column one (denoted "<eol>;")
- * may also be used as a delimiter at the beginning and end
- * of a character string comprising a data value. The complete
- * bounded string is called a text field, and may be used to
- * convey multi-line values. The end-of-line associated with
- * the closing semicolon does not form part of the data value.
- * Within a multi-line text field, leading white space within
- * text lines must be retained as part of the data value; trailing
- * white space on a line may however be elided.
- *
- * 18. A text field delimited by the <eol>; digraph may not
- * include a semicolon at the start of a line of text as
- * part of its value.
- *
- * 20. For example, the data value foo may be expressed
- * equivalently as an unquoted string foo, as a quoted
- * string 'foo' or as a text field
- *
- *;foo
- *;
- *
- * By contrast the value of the text field
- *
- *; foo
- * bar
- *;
- *
- * is foo<eol> bar (where <eol> represents an end-of-line);
- * the embedded space characters are significant.
- *
- *
- * I (BH) note, however, that we sometimes have:
- *
- * _some_name
- * ;
- * the name here
- * ;
- *
- * so this should actually be
- *
- * ;the name here
- * ;
- *
- * for this, we use fullTrim();
- *
- */
-
- /**
- *
- * sets the string for parsing to be from the next line
- * when the token buffer is empty, and if ';' is at the
- * beginning of that line, extends the string to include
- * that full multiline string. Uses \1 to indicate that
- * this is a special quotation.
- *
- *
- *
- * @return the next line or null if EOF
- * @throws Exception
- */
- protected String prepareNextLine() throws Exception {
- setString(readLine());
- if (line == null || line.length() == 0)
- return line;
- if (line.charAt(0) == ';')
- return preprocessString();
- if (str.startsWith("###non-st#"))
- ich = 10;
- return line;
- }
-
- /**
- * 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());
- }
-
- /**
- * Encapsulate a multi-line ; .... ; string with \1 ... \1
- *
- * CIF 1.0 and CIF 2.0
- *
- * @return ecapsulated string
- * @throws Exception
- */
- protected String preprocessSemiString() throws Exception {
- ich = 1;
- String str = '\1' + line.substring(1) + '\n';
- while (readLine() != null) {
- if (line.startsWith(";")) {
- // remove trailing <eol> only, and attach rest of next line
- str = str.substring(0, str.length() - 1)
- + '\1' + line.substring(1);
- break;
- }
- str += line + '\n';
- }
- return str;
- }
-
- /**
- * @return TRUE if there are more tokens in the line buffer
- *
- */
- private boolean strHasMoreTokens() {
- if (str == null)
- return false;
- char ch = '#';
- while (ich < cch && ((ch = str.charAt(ich)) == ' ' || ch == '\t'))
- ++ich;
- return (ich < cch && ch != '#');
- }
-
- /**
- * assume that hasMoreTokens() has been called and that ich is pointing at a
- * non-white character. Also sets boolean wasUnQuoted, because we need to know
- * if we should be checking for a control keyword. 'loop_' is different from
- * just loop_ without the quotes.
- *
- * @return null if no more tokens, "\0" if '.' or '?', or next token
- */
- private Object nextStrToken() {
- if (ich == cch)
- return null;
- char ch = str.charAt(ich);
- if (isQuote(ch)) {
- wasUnquoted = false;
- return getQuotedStringOrObject(ch);
- }
- int ichStart = ich;
- wasUnquoted = true;
- while (ich < cch && !isTerminator(ch = str.charAt(ich)))
- ++ich;
- if (ich == ichStart + 1)
- if (nullString != null
- && (str.charAt(ichStart) == '.' || str.charAt(ichStart) == '?'))
- return nullString;
- String s = str.substring(ichStart, ich);
- return unquoted(s);
- }
-
- /**
- * In CIF 2.0, this method turns a String into an Integer or Float
- * In CIF 1.0 (here) just return the unchanged value.
- * @param s unquoted string
- * @return unchanged value
- */
- protected Object unquoted(String s) {
- return s;
- }
-
- /**
- * The token terminator is space or tab in CIF 1.0,
- * but it can be quoted strings in CIF 2.0.
- *
- * @param c
- * @return true if this character is a terminator
- */
- protected boolean isTerminator(char c) {
- return c == ' ' || c == '\t' || c == cterm ;
- }
-
- /**
- * CIF 1.0 only; we handle various quote types here
- * @param ch
- * @return true if this character is a (starting) quote
- */
- protected boolean isQuote(char ch) {
- switch (ch) {
- case '\'':
- case '\"':
- case '\1':
- return true;
- }
- return false;
- }
-
- /**
- * CIF 1.0 only.
- *
- *
- * @param ch current character being pointed to
- * @return a String data object
- */
- protected Object getQuotedStringOrObject(char ch) {
- int ichStart = ich;
- char chClosingQuote = ch;
- 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 or EOL
- if (wasQuote && (ch == ' ' || ch == '\t'))
- break;
- wasQuote = (ch == chClosingQuote);
- }
- int pt1 = ichStart + 1;
- int pt2 = ich - 1;
- if (ich == cch && !wasQuote) {
- // reached the end of the string without finding closing '
- // so take the whole thing. Probably a bad CIF file.
- pt1--;
- pt2++;
- } else {
- // throw away the last white character
- ++ich;
- }
- return str.substring(pt1, pt2);
- }
-
-
-}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff