--- /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;
+ }
+
+
+}
git://source.jalview.org / jalview.git / blobdiff