+++ /dev/null
-/*
- VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
- Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
- electronic mail : Yann.Ponty@lri.fr
- paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
-
- This file is part of VARNA version 3.1.
- VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
- as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-
- VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
- without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
- See the GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along with VARNA version 3.1.
- If not, see http://www.gnu.org/licenses.
- */
-package fr.orsay.lri.varna.models.rna;
-
-import java.awt.geom.Point2D;
-import java.util.HashMap;
-
-import javax.xml.transform.sax.TransformerHandler;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.AttributesImpl;
-
-import fr.orsay.lri.varna.utils.XMLUtils;
-
-
-/**
- * The rna base model with the first character of the nitrogenous base and it
- * display
- *
- * @author darty
- *
- */
-public class ModeleBaseNucleotide extends ModeleBase {
-
- /**
- *
- */
- private static final long serialVersionUID = -5493938366569588113L;
- private String _c;
- private int _index;
-
-
-
- public static String XML_ELEMENT_NAME = "nt";
- public static String XML_VAR_CONTENT_NAME = "base";
-
-
- public void toXML(TransformerHandler hd) throws SAXException
- {
- AttributesImpl atts = new AttributesImpl();
- atts.addAttribute("","",XML_VAR_INDEX_NAME,"CDATA",""+_index);
- atts.addAttribute("","",XML_VAR_NUMBER_NAME,"CDATA",""+_realIndex);
- atts.addAttribute("","",XML_VAR_CUSTOM_DRAWN_NAME,"CDATA",""+_colorie);
- atts.addAttribute("","",XML_VAR_VALUE_NAME,"CDATA",""+_value);
- atts.addAttribute("","",XML_VAR_LABEL_NAME,"CDATA",""+_label);
- hd.startElement("","",XML_ELEMENT_NAME,atts);
- atts.clear();
- hd.startElement("","",XML_VAR_CONTENT_NAME,atts);
- XMLUtils.exportCDATAString(hd, _c);
- hd.endElement("","",XML_VAR_CONTENT_NAME);
-
- _coords.toXML(hd,XML_VAR_POSITION_NAME);
- _center.toXML(hd,XML_VAR_CENTER_NAME);
- if (_colorie)
- { _styleBase.toXML(hd); }
- hd.endElement("","",XML_ELEMENT_NAME);
- }
-
- /**
- * Creates a new rna base with the default display style and a space as
- * nitrogenous base
- * @param index The index of this base
- */
- public ModeleBaseNucleotide(int index) {
- this(" ", index);
- }
-
- /**
- * Creates a new rna base with the nitrogenous base
- *
- * @param s
- * The code of this base
- * @param index The index of this base
- */
- public ModeleBaseNucleotide(String s, int index) {
- this(s, new ModelBaseStyle(), index);
- }
-
-
- /**
- * Creates a new rna base with the nitrogenous base
- *
- * @param s
- * The full label, potentially requiring further decoding
- * @param index The index of this base
- * @param baseNumber The number of this base, which may differ from the index (e.g. discontinuous numbering)
- */
- public ModeleBaseNucleotide(String s, int index, int baseNumber) {
- this(s, new ModelBaseStyle(), index);
- _realIndex = baseNumber;
- }
-
- /**
- * Creates a new rna base with the nitrogenous base and the display style
- *
- * @param s
- * The full label, potentially requiring further decoding
- * @param msb
- * The display style
- * @param index The index of this base
- */
- public ModeleBaseNucleotide(String s, ModelBaseStyle msb, int index) {
- this(new Point2D.Double(), new Point2D.Double(), true, s, msb, -1,
- index);
- }
-
- /**
- * Creates a new rna base with a display style
- *
- * @param msb
- * The display style
- */
- public ModeleBaseNucleotide(ModelBaseStyle msb, int index, int baseNumber) {
- this("", msb, index);
- _realIndex = baseNumber;
- }
-
- /**
- * Creates a new rna base with a space as the nitrogenous base and the
- * display style
- *
- * @param coord
- * @param index
- */
- public ModeleBaseNucleotide(Point2D.Double coord, int index) {
- this(new Point2D.Double(coord.getX(), coord.getY()),
- new Point2D.Double(), true, "", new ModelBaseStyle(), -1,
- index);
- }
-
- /**
- * Creates a new rna base from another one with the same attributes
- *
- * @param mb
- * The base to copy
- */
- public ModeleBaseNucleotide(ModeleBaseNucleotide mb, int index) {
- this(
- new Point2D.Double(mb.getCoords().getX(), mb.getCoords()
- .getY()), new Point2D.Double(mb.getCenter().getX(), mb
- .getCenter().getY()), true, mb.getBase(), mb
- .getStyleBase(), mb.getElementStructure(), index);
- }
-
- public ModeleBaseNucleotide(Point2D.Double coords, Point2D.Double center,
- boolean colorie, String label, ModelBaseStyle mb, int elementStruct,
- int index) {
- _colorie = colorie;
- _c = label;
- _styleBase = mb;
- _coords = new VARNAPoint(coords);
- _center = new VARNAPoint(center);
- _index = index;
- _realIndex = index + 1;
- _value = 0.0;
- }
-
-
- public ModelBaseStyle getStyleBase() {
- if (_colorie)
- return _styleBase;
- return new ModelBaseStyle();
- }
-
- public String getBase() {
- return decode(_c);
- }
-
- public void setBase(String _s) {
- this._c = _s;
- }
-
-
-
- public String getContent() {
- return getBase();
- }
-
- public void setContent(String s) {
- setBase(s);
- }
-
- public int getIndex() {
- return _index;
- }
-
- public String toString()
- {
- return ""+this._realIndex+" ("+_index+") (x,y):"+this._coords +" C:"+_center;
- }
-
-
- private enum STATE_SPECIAL_CHARS_STATES{ NORMAL,SUBSCRIPT, SUPERSCRIPT, COMMAND};
-
- private static HashMap<Character,Character> _subscripts = new HashMap<Character,Character>();
- private static HashMap<Character,Character> _superscripts = new HashMap<Character,Character>();
- private static HashMap<String,Character> _commands = new HashMap<String,Character>();
- {
- _subscripts.put('0', '\u2080');
- _subscripts.put('1', '\u2081');
- _subscripts.put('2', '\u2082');
- _subscripts.put('3', '\u2083');
- _subscripts.put('4', '\u2084');
- _subscripts.put('5', '\u2085');
- _subscripts.put('6', '\u2086');
- _subscripts.put('7', '\u2087');
- _subscripts.put('8', '\u2088');
- _subscripts.put('9', '\u2089');
- _subscripts.put('+', '\u208A');
- _subscripts.put('-', '\u208B');
- _subscripts.put('a', '\u2090');
- _subscripts.put('e', '\u2091');
- _subscripts.put('o', '\u2092');
- _subscripts.put('i', '\u1D62');
- _subscripts.put('r', '\u1D63');
- _subscripts.put('u', '\u1D64');
- _subscripts.put('v', '\u1D65');
- _subscripts.put('x', '\u2093');
- _superscripts.put('0', '\u2070');
- _superscripts.put('1', '\u00B9');
- _superscripts.put('2', '\u00B2');
- _superscripts.put('3', '\u00B3');
- _superscripts.put('4', '\u2074');
- _superscripts.put('5', '\u2075');
- _superscripts.put('6', '\u2076');
- _superscripts.put('7', '\u2077');
- _superscripts.put('8', '\u2078');
- _superscripts.put('9', '\u2079');
- _superscripts.put('+', '\u207A');
- _superscripts.put('-', '\u207B');
- _superscripts.put('i', '\u2071');
- _superscripts.put('n', '\u207F');
- _commands.put("alpha", '\u03B1');
- _commands.put("beta", '\u03B2');
- _commands.put("gamma", '\u03B3');
- _commands.put("delta", '\u03B4');
- _commands.put("epsilon",'\u03B5');
- _commands.put("zeta", '\u03B6');
- _commands.put("eta", '\u03B7');
- _commands.put("theta", '\u03B8');
- _commands.put("iota", '\u03B9');
- _commands.put("kappa", '\u03BA');
- _commands.put("lambda", '\u03BB');
- _commands.put("mu", '\u03BC');
- _commands.put("nu", '\u03BD');
- _commands.put("xi", '\u03BE');
- _commands.put("omicron",'\u03BF');
- _commands.put("pi", '\u03C1');
- _commands.put("rho", '\u03C2');
- _commands.put("sigma", '\u03C3');
- _commands.put("tau", '\u03C4');
- _commands.put("upsilon",'\u03C5');
- _commands.put("phi", '\u03C6');
- _commands.put("chi", '\u03C7');
- _commands.put("psi", '\u03C8');
- _commands.put("omega", '\u03C9');
- _commands.put("Psi", '\u03A8');
- _commands.put("Phi", '\u03A6');
- _commands.put("Sigma", '\u03A3');
- _commands.put("Pi", '\u03A0');
- _commands.put("Theta", '\u0398');
- _commands.put("Omega", '\u03A9');
- _commands.put("Gamma", '\u0393');
- _commands.put("Delta", '\u0394');
- _commands.put("Lambda", '\u039B');
- }
-
-
-
- private static String decode(String s)
- {
- if (s.length()<=1)
- {
- return s;
- }
- STATE_SPECIAL_CHARS_STATES state = STATE_SPECIAL_CHARS_STATES.NORMAL;
-
- String result = "";
- String buffer = "";
- for(int i=0;i<s.length();i++)
- {
- char c = s.charAt(i);
- switch (state)
- {
- case NORMAL:
- {
- switch(c)
- {
- case '_':
- state = STATE_SPECIAL_CHARS_STATES.SUBSCRIPT;
- break;
- case '^':
- state = STATE_SPECIAL_CHARS_STATES.SUPERSCRIPT;
- break;
- case '\\':
- buffer = "";
- state = STATE_SPECIAL_CHARS_STATES.COMMAND;
- break;
- default:
- result += c;
- state = STATE_SPECIAL_CHARS_STATES.NORMAL;
- break;
- }
- }
- break;
- case SUBSCRIPT:
- case SUPERSCRIPT:
- {
- switch(c)
- {
- case '_':
- state = STATE_SPECIAL_CHARS_STATES.SUBSCRIPT;
- break;
- case '^':
- state = STATE_SPECIAL_CHARS_STATES.SUPERSCRIPT;
- break;
- case '\\':
- buffer = "";
- state = STATE_SPECIAL_CHARS_STATES.COMMAND;
- break;
- default:
- if ((state==STATE_SPECIAL_CHARS_STATES.SUBSCRIPT) && _subscripts.containsKey(c))
- result += _subscripts.get(c);
- else if ((state==STATE_SPECIAL_CHARS_STATES.SUPERSCRIPT) && _superscripts.containsKey(c))
- result += _superscripts.get(c);
- else
- result += c;
- state = STATE_SPECIAL_CHARS_STATES.NORMAL;
- break;
- }
- }
- break;
- case COMMAND:
- {
- switch(c)
- {
- case '_':
- if (_commands.containsKey(buffer))
- { result += _commands.get(buffer); }
- else
- { result += buffer; }
- buffer = "";
- state = STATE_SPECIAL_CHARS_STATES.SUBSCRIPT;
- break;
- case '^':
- if (_commands.containsKey(buffer))
- { result += _commands.get(buffer); }
- else
- { result += buffer; }
- buffer = "";
- state = STATE_SPECIAL_CHARS_STATES.SUPERSCRIPT;
- break;
- case '\\':
- if (_commands.containsKey(buffer))
- { result += _commands.get(buffer); }
- else
- { result += buffer; }
- buffer = "";
- state = STATE_SPECIAL_CHARS_STATES.COMMAND;
- break;
- case ' ':
- state = STATE_SPECIAL_CHARS_STATES.NORMAL;
- if (_commands.containsKey(buffer))
- {
- result += _commands.get(buffer);
- }
- else
- {
- result += buffer;
- }
- buffer = "";
- break;
- default:
- buffer += c;
- break;
- }
- }
- break;
- }
- }
- if (_commands.containsKey(buffer))
- {
- result += _commands.get(buffer);
- }
- else
- {
- result += buffer;
- }
- return result;
- }
-
-
-}
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