2 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.
3 Copyright (C) 2008 Kevin Darty, Alain Denise and Yann Ponty.
4 electronic mail : Yann.Ponty@lri.fr
5 paper mail : LRI, bat 490 Université Paris-Sud 91405 Orsay Cedex France
7 This file is part of VARNA version 3.1.
8 VARNA version 3.1 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License
9 as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 VARNA version 3.1 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
12 without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
13 See the GNU General Public License for more details.
15 You should have received a copy of the GNU General Public License along with VARNA version 3.1.
16 If not, see http://www.gnu.org/licenses.
18 package fr.orsay.lri.varna.models;
20 import java.awt.Color;
22 import java.io.ByteArrayInputStream;
23 import java.io.ByteArrayOutputStream;
24 import java.io.ObjectInputStream;
25 import java.io.ObjectOutputStream;
26 import java.io.Serializable;
28 import javax.xml.transform.sax.TransformerHandler;
30 import org.xml.sax.Attributes;
31 import org.xml.sax.SAXException;
32 import org.xml.sax.helpers.AttributesImpl;
34 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
35 import fr.orsay.lri.varna.models.annotations.TextAnnotation;
36 import fr.orsay.lri.varna.models.rna.ModeleBP;
37 import fr.orsay.lri.varna.models.rna.ModeleBPStyle;
38 import fr.orsay.lri.varna.models.rna.ModeleBase;
39 import fr.orsay.lri.varna.models.rna.ModeleColorMap;
40 import fr.orsay.lri.varna.utils.XMLUtils;
42 public class VARNAConfig implements Serializable, Cloneable {
47 private static final long serialVersionUID = 2853916694420964233L;
51 public static final int MAJOR_VERSION = 3;
52 public static final int MINOR_VERSION = 9;
54 public static String getFullName()
56 return "VARNA "+MAJOR_VERSION+"."+MINOR_VERSION;
60 * Enum types and internal classes
63 public enum BP_STYLE implements Serializable {
64 NONE, SIMPLE, RNAVIZ, LW, LW_ALT;
65 public String toString()
69 case LW: return "Leontis/Westhof (Centered)";
70 case SIMPLE: return "Line";
71 case RNAVIZ: return "Circles";
72 case NONE: return "None";
73 case LW_ALT: return "Leontis/Westhof (End)";
77 public String getOpt()
81 case NONE: return "none";
82 case SIMPLE: return "simple";
84 case RNAVIZ: return "rnaviz";
85 case LW_ALT: return "lwalt";
89 public static BP_STYLE getStyle(String opt)
91 for(BP_STYLE b: BP_STYLE.values())
93 if (opt.toLowerCase().equals(b.getOpt().toLowerCase()))
101 * Default values for config options
104 public static final double MAX_ZOOM = 60;
105 public static final double MIN_ZOOM = 0.5;
106 public static final double DEFAULT_ZOOM = 1;
107 public static final double MAX_AMOUNT = 2;
108 public static final double MIN_AMOUNT = 1.01;
109 public static final double DEFAULT_AMOUNT = 1.2;
110 public static final double DEFAULT_BP_THICKNESS = 1.0;
111 public static final double DEFAULT_DIST_NUMBERS = 3.0;
113 public static final int DEFAULT_PERIOD = 10;
115 public static final Color DEFAULT_TITLE_COLOR = Color.black;
116 public static final Color DEFAULT_BACKBONE_COLOR = Color.DARK_GRAY.brighter();
117 public static final Color DEFAULT_BOND_COLOR = Color.blue;
118 public static final Color DEFAULT_SPECIAL_BASE_COLOR = Color.green.brighter();
119 public static final Color DEFAULT_DASH_BASE_COLOR = Color.yellow.brighter();
120 public static final double DEFAULT_BASE_OUTLINE_THICKNESS = 1.5;
121 public static final Color BASE_OUTLINE_COLOR_DEFAULT = Color.DARK_GRAY.brighter();
122 public static final Color BASE_INNER_COLOR_DEFAULT = new Color(242, 242,242);
123 public static final Color BASE_NUMBER_COLOR_DEFAULT = Color.DARK_GRAY;
124 public static final Color BASE_NAME_COLOR_DEFAULT = Color.black;
126 public static final Color DEFAULT_HOVER_COLOR = new Color(230, 230,230);
128 public static final Color DEFAULT_BACKGROUND_COLOR = Color.WHITE;
129 public static final Font DEFAULT_TITLE_FONT = new Font("SansSerif", Font.BOLD,18);
130 public static final Font DEFAULT_BASE_FONT = new Font("SansSerif", Font.PLAIN, 18);
131 public static final Font DEFAULT_NUMBERS_FONT = new Font("SansSerif",
133 public static final Font DEFAULT_MESSAGE_FONT = Font.decode("dialog-PLAIN-25");
134 public static final Color DEFAULT_MESSAGE_COLOR = new Color(230, 230,230);
137 public static final BP_STYLE DEFAULT_BP_STYLE = BP_STYLE.LW;
139 public static final ModeleColorMap DEFAULT_COLOR_MAP = ModeleColorMap.defaultColorMap();
140 public static final Color DEFAULT_COLOR_MAP_OUTLINE = Color.gray;
141 public static final double DEFAULT_BP_INCREMENT = 0.65;
143 public static double DEFAULT_COLOR_MAP_WIDTH = 120;
144 public static double DEFAULT_COLOR_MAP_HEIGHT = 30;
145 public static double DEFAULT_COLOR_MAP_X_OFFSET = 40;
146 public static double DEFAULT_COLOR_MAP_Y_OFFSET = 0;
147 public static int DEFAULT_COLOR_MAP_STRIPE_WIDTH = 2;
148 public static int DEFAULT_COLOR_MAP_FONT_SIZE = 20;
149 public static Color DEFAULT_COLOR_MAP_FONT_COLOR = Color.gray.darker();
151 public static double DEFAULT_SPACE_BETWEEN_BASES = 1.0;
157 public static String XML_VAR_DRAW_OUTLINE = "drawoutline";
158 public static String XML_VAR_FILL_BASE = "fillbase";
159 public static String XML_VAR_AUTO_FIT = "autofit";
160 public static String XML_VAR_AUTO_CENTER = "autocenter";
161 public static String XML_VAR_MODIFIABLE = "modifiable";
162 public static String XML_VAR_ERRORS = "errors";
163 public static String XML_VAR_SPECIAL_BASES = "specialbases";
164 public static String XML_VAR_DASH_BASES = "dashbases";
165 public static String XML_VAR_USE_BASE_BPS = "usebasebps";
166 public static String XML_VAR_DRAW_NC = "drawnc";
167 public static String XML_VAR_DRAW_NON_PLANAR = "drawnonplanar";
168 public static String XML_VAR_SHOW_WARNINGS = "warnings";
169 public static String XML_VAR_COMPARISON_MODE = "comparison";
170 public static String XML_VAR_FLAT = "flat";
171 public static String XML_VAR_DRAW_BACKGROUND = "drawbackground";
172 public static String XML_VAR_COLOR_MAP = "drawcm";
173 public static String XML_VAR_DRAW_BACKBONE = "drawbackbone";
175 public static String XML_VAR_CM_HEIGHT = "cmh";
176 public static String XML_VAR_CM_WIDTH = "cmw";
177 public static String XML_VAR_CM_X_OFFSET = "cmx";
178 public static String XML_VAR_CM_Y_OFFSET = "cmy";
179 public static String XML_VAR_DEFAULT_ZOOM = "defaultzoom";
180 public static String XML_VAR_ZOOM_AMOUNT = "zoominc";
181 public static String XML_VAR_BP_THICKNESS = "bpthick";
182 public static String XML_VAR_BASE_THICKNESS = "basethick";
183 public static String XML_VAR_DIST_NUMBERS = "distnumbers";
185 public static String XML_VAR_NUM_PERIOD = "numperiod";
187 public static String XML_VAR_MAIN_BP_STYLE = "bpstyle";
189 public static String XML_VAR_CM = "cm";
191 public static String XML_VAR_BACKBONE_COLOR = "backbonecol";
192 public static String XML_VAR_HOVER_COLOR = "hovercol";
193 public static String XML_VAR_BACKGROUND_COLOR = "backgroundcol";
194 public static String XML_VAR_BOND_COLOR = "bondcol";
195 public static String XML_VAR_TITLE_COLOR = "titlecol";
196 public static String XML_VAR_SPECIAL_BASES_COLOR = "specialco";
197 public static String XML_VAR_DASH_BASES_COLOR = "dashcol";
198 public static String XML_VAR_SPACE_BETWEEN_BASES = "spacebetweenbases";
200 public static String XML_VAR_TITLE_FONT = "titlefont";
201 public static String XML_VAR_NUMBERS_FONT = "numbersfont";
202 public static String XML_VAR_FONT_BASES = "basefont";
204 public static String XML_VAR_CM_CAPTION = "cmcaption";
205 public static String XML_VAR_TITLE = "title";
208 public boolean _drawOutlineBases = true;
209 public boolean _fillBases = true;
210 public boolean _autoFit = true;
211 public boolean _autoCenter = true;
212 public boolean _modifiable = true;
213 public boolean _errorsOn = false;
214 public boolean _colorSpecialBases = false;
215 public boolean _colorDashBases = false;
216 public boolean _useBaseColorsForBPs = false;
217 public boolean _drawnNonCanonicalBP = true;
218 public boolean _drawnNonPlanarBP = true;
219 public boolean _showWarnings = false;
220 public boolean _comparisonMode = false;
221 public boolean _flatExteriorLoop = true;
222 public boolean _drawBackground = false;
223 public boolean _drawColorMap = false;
224 public boolean _drawBackbone = true;
226 public double _colorMapHeight = DEFAULT_COLOR_MAP_HEIGHT;
227 public double _colorMapWidth = DEFAULT_COLOR_MAP_WIDTH;
228 public double _colorMapXOffset = DEFAULT_COLOR_MAP_X_OFFSET;
229 public double _colorMapYOffset = DEFAULT_COLOR_MAP_Y_OFFSET;
230 public double _zoom = DEFAULT_ZOOM;
231 public double _zoomAmount = DEFAULT_AMOUNT;
232 public double _bpThickness = 1.0;
233 public double _baseThickness = DEFAULT_BASE_OUTLINE_THICKNESS;
234 public double _distNumbers = DEFAULT_DIST_NUMBERS;
235 public double _spaceBetweenBases = DEFAULT_SPACE_BETWEEN_BASES;
237 public int _numPeriod = DEFAULT_PERIOD;
238 public BP_STYLE _mainBPStyle = DEFAULT_BP_STYLE;
240 public ModeleColorMap _cm = DEFAULT_COLOR_MAP;
242 public Color _backboneColor = DEFAULT_BACKBONE_COLOR;
243 public Color _hoverColor = DEFAULT_HOVER_COLOR;
244 public Color _backgroundColor = DEFAULT_BACKGROUND_COLOR;
245 public Color _bondColor = DEFAULT_BOND_COLOR;
246 public Color _titleColor = DEFAULT_TITLE_COLOR;
247 public Color _specialBasesColor = DEFAULT_SPECIAL_BASE_COLOR;
248 public Color _dashBasesColor = DEFAULT_DASH_BASE_COLOR;
250 public Font _titleFont = DEFAULT_TITLE_FONT;
251 public Font _numbersFont = DEFAULT_NUMBERS_FONT;
252 public Font _fontBasesGeneral = DEFAULT_BASE_FONT;
254 public String _colorMapCaption = "";
255 //public String _title = "";
258 public static String XML_ELEMENT_NAME = "config";
260 public void toXML(TransformerHandler hd) throws SAXException
262 AttributesImpl atts = new AttributesImpl();
263 atts.addAttribute("","",XML_VAR_DRAW_OUTLINE,"CDATA", ""+_drawOutlineBases);
264 atts.addAttribute("","",XML_VAR_FILL_BASE,"CDATA", ""+_fillBases);
265 atts.addAttribute("","",XML_VAR_AUTO_FIT,"CDATA", ""+_autoFit);
266 atts.addAttribute("","",XML_VAR_AUTO_CENTER,"CDATA", ""+_autoCenter);
267 atts.addAttribute("","",XML_VAR_MODIFIABLE,"CDATA", ""+_modifiable);
268 atts.addAttribute("","",XML_VAR_ERRORS,"CDATA", ""+_errorsOn);
269 atts.addAttribute("","",XML_VAR_SPECIAL_BASES,"CDATA", ""+_colorSpecialBases);
270 atts.addAttribute("","",XML_VAR_DASH_BASES,"CDATA", ""+_colorDashBases);
271 atts.addAttribute("","",XML_VAR_USE_BASE_BPS,"CDATA", ""+_useBaseColorsForBPs);
272 atts.addAttribute("","",XML_VAR_DRAW_NC,"CDATA", ""+_drawnNonCanonicalBP);
273 atts.addAttribute("","",XML_VAR_DRAW_NON_PLANAR,"CDATA",""+_drawnNonPlanarBP);
274 atts.addAttribute("","",XML_VAR_SHOW_WARNINGS,"CDATA", ""+_showWarnings);
275 atts.addAttribute("","",XML_VAR_COMPARISON_MODE,"CDATA",""+_comparisonMode);
276 atts.addAttribute("","",XML_VAR_FLAT,"CDATA", ""+_flatExteriorLoop);
277 atts.addAttribute("","",XML_VAR_DRAW_BACKGROUND,"CDATA",""+_drawBackground);
278 atts.addAttribute("","",XML_VAR_COLOR_MAP,"CDATA", ""+_drawColorMap);
279 atts.addAttribute("","",XML_VAR_DRAW_BACKBONE,"CDATA", ""+_drawBackbone);
281 atts.addAttribute("","",XML_VAR_CM_HEIGHT,"CDATA", ""+_colorMapHeight);
282 atts.addAttribute("","",XML_VAR_CM_WIDTH,"CDATA", ""+_colorMapWidth);
283 atts.addAttribute("","",XML_VAR_CM_X_OFFSET,"CDATA", ""+_colorMapXOffset);
284 atts.addAttribute("","",XML_VAR_CM_Y_OFFSET,"CDATA", ""+_colorMapYOffset);
285 atts.addAttribute("","",XML_VAR_DEFAULT_ZOOM,"CDATA", ""+_zoom);
286 atts.addAttribute("","",XML_VAR_ZOOM_AMOUNT,"CDATA", ""+_zoomAmount);
287 atts.addAttribute("","",XML_VAR_BP_THICKNESS,"CDATA", ""+_bpThickness);
288 atts.addAttribute("","",XML_VAR_BASE_THICKNESS,"CDATA", ""+_baseThickness);
289 atts.addAttribute("","",XML_VAR_DIST_NUMBERS,"CDATA", ""+_distNumbers);
290 atts.addAttribute("","",XML_VAR_SPACE_BETWEEN_BASES,"CDATA", ""+_spaceBetweenBases);
293 atts.addAttribute("","",XML_VAR_NUM_PERIOD,"CDATA", ""+_numPeriod);
295 atts.addAttribute("","",XML_VAR_MAIN_BP_STYLE,"CDATA", ""+_mainBPStyle.getOpt());
297 atts.addAttribute("","",XML_VAR_BACKBONE_COLOR,"CDATA", XMLUtils.toHTMLNotation(_backboneColor));
298 atts.addAttribute("","",XML_VAR_HOVER_COLOR,"CDATA", XMLUtils.toHTMLNotation(_hoverColor));
299 atts.addAttribute("","",XML_VAR_BACKGROUND_COLOR,"CDATA", XMLUtils.toHTMLNotation(_backgroundColor));
300 atts.addAttribute("","",XML_VAR_BOND_COLOR,"CDATA", XMLUtils.toHTMLNotation(_bondColor));
301 atts.addAttribute("","",XML_VAR_TITLE_COLOR,"CDATA", XMLUtils.toHTMLNotation(_titleColor));
302 atts.addAttribute("","",XML_VAR_SPECIAL_BASES_COLOR,"CDATA",XMLUtils.toHTMLNotation(_specialBasesColor));
303 atts.addAttribute("","",XML_VAR_DASH_BASES_COLOR,"CDATA", XMLUtils.toHTMLNotation(_dashBasesColor));
305 atts.addAttribute("","",XML_VAR_CM,"CDATA", _cm.getParamEncoding());
308 hd.startElement("","",XML_ELEMENT_NAME,atts);
309 XMLUtils.toXML(hd, _titleFont,XML_VAR_TITLE_FONT);
310 XMLUtils.toXML(hd, _numbersFont,XML_VAR_NUMBERS_FONT);
311 XMLUtils.toXML(hd, _fontBasesGeneral,XML_VAR_FONT_BASES);
313 XMLUtils.exportCDATAElem(hd,XML_VAR_CM_CAPTION, _colorMapCaption);
314 hd.endElement("","",XML_ELEMENT_NAME);
320 public void loadFromXMLAttributes(Attributes attributes)
322 _drawOutlineBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_OUTLINE));
323 _fillBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_FILL_BASE));
324 _autoFit = Boolean.parseBoolean(attributes.getValue(XML_VAR_AUTO_FIT));
325 _autoCenter = Boolean.parseBoolean(attributes.getValue(XML_VAR_AUTO_CENTER));
326 _modifiable = Boolean.parseBoolean(attributes.getValue(XML_VAR_MODIFIABLE));
327 _errorsOn = Boolean.parseBoolean(attributes.getValue(XML_VAR_ERRORS));
328 _colorSpecialBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_SPECIAL_BASES));
329 _colorDashBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_DASH_BASES));
330 _useBaseColorsForBPs = Boolean.parseBoolean(attributes.getValue(XML_VAR_USE_BASE_BPS));
331 _drawnNonCanonicalBP = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_NC));
332 _drawnNonPlanarBP = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_NON_PLANAR));
333 _showWarnings = Boolean.parseBoolean(attributes.getValue(XML_VAR_SHOW_WARNINGS));
334 _comparisonMode = Boolean.parseBoolean(attributes.getValue(XML_VAR_COMPARISON_MODE));
335 _flatExteriorLoop = Boolean.parseBoolean(attributes.getValue(XML_VAR_FLAT));
336 _drawBackground = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_BACKGROUND));
337 _drawColorMap = Boolean.parseBoolean(attributes.getValue(XML_VAR_COLOR_MAP));
338 _drawBackbone = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_BACKBONE));
340 _colorMapHeight = Double.parseDouble(attributes.getValue(XML_VAR_CM_HEIGHT));
341 _colorMapWidth = Double.parseDouble(attributes.getValue(XML_VAR_CM_WIDTH));
342 _colorMapXOffset = Double.parseDouble(attributes.getValue(XML_VAR_CM_X_OFFSET));
343 _colorMapYOffset = Double.parseDouble(attributes.getValue(XML_VAR_CM_Y_OFFSET));
344 _zoom = Double.parseDouble(attributes.getValue(XML_VAR_DEFAULT_ZOOM));
345 _zoomAmount = Double.parseDouble(attributes.getValue(XML_VAR_ZOOM_AMOUNT));
346 _bpThickness = Double.parseDouble(attributes.getValue(XML_VAR_BP_THICKNESS));
347 _baseThickness = Double.parseDouble(attributes.getValue(XML_VAR_BASE_THICKNESS));
348 _distNumbers = Double.parseDouble(attributes.getValue(XML_VAR_DIST_NUMBERS));
349 _spaceBetweenBases = XMLUtils.getDouble(attributes, XML_VAR_SPACE_BETWEEN_BASES, DEFAULT_SPACE_BETWEEN_BASES);
351 _numPeriod = Integer.parseInt(attributes.getValue(XML_VAR_NUM_PERIOD));
353 _mainBPStyle = BP_STYLE.getStyle(attributes.getValue(XML_VAR_MAIN_BP_STYLE));
355 _backboneColor = Color.decode(attributes.getValue(XML_VAR_BACKBONE_COLOR));
356 _hoverColor = Color.decode(attributes.getValue(XML_VAR_HOVER_COLOR));
357 _backgroundColor = Color.decode(attributes.getValue(XML_VAR_BACKGROUND_COLOR));
358 _bondColor = Color.decode(attributes.getValue(XML_VAR_BOND_COLOR));
359 _titleColor = Color.decode(attributes.getValue(XML_VAR_TITLE_COLOR));
360 _specialBasesColor = Color.decode(attributes.getValue(XML_VAR_SPECIAL_BASES_COLOR));
361 _dashBasesColor = Color.decode(attributes.getValue(XML_VAR_DASH_BASES_COLOR));
363 _cm = ModeleColorMap.parseColorMap(attributes.getValue(XML_VAR_CM));
368 public VARNAConfig clone ()
379 ByteArrayOutputStream out = new ByteArrayOutputStream ();
380 ObjectOutputStream oout = new ObjectOutputStream (out);
381 oout.writeObject (this);
383 ObjectInputStream in = new ObjectInputStream (
384 new ByteArrayInputStream (out.toByteArray ()));
385 return (VARNAConfig)in.readObject ();
389 throw new RuntimeException ("cannot clone class [" +
390 this.getClass ().getName () + "] via serialization: " +