src2/fr/orsay/lri/varna/models/VARNAConfig.java

   1 /*
   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
   6
   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.
  10
  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.
  14
  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.
  17  */
  18 package fr.orsay.lri.varna.models;
  19
  20 import java.awt.Color;
  21 import java.awt.Font;
  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;
  27
  28 import javax.xml.transform.sax.TransformerHandler;
  29
  30 import org.xml.sax.Attributes;
  31 import org.xml.sax.SAXException;
  32 import org.xml.sax.helpers.AttributesImpl;
  33
  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;
  41
  42 public class VARNAConfig implements Serializable, Cloneable {
  43
  44         /**
  45          *
  46          */
  47         private static final long serialVersionUID = 2853916694420964233L;
  48         /**
  49          *
  50          */
  51         public static final int MAJOR_VERSION = 3;
  52         public static final int MINOR_VERSION = 9;
  53
  54         public static String getFullName()
  55         {
  56                 return "VARNA "+MAJOR_VERSION+"."+MINOR_VERSION;
  57         }
  58
  59         /**
  60          * Enum types and internal classes
  61          */
  62
  63         public enum BP_STYLE implements Serializable {
  64                 NONE, SIMPLE, RNAVIZ, LW, LW_ALT;
  65                 public String toString()
  66                 {
  67                         switch(this)
  68                         {
  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)";
  74                         }
  75                         return "Unspecified";
  76                 }
  77                 public String getOpt()
  78                 {
  79                         switch(this)
  80                         {
  81                                 case NONE: return "none";
  82                                 case SIMPLE: return "simple";
  83                                 case LW: return "lw";
  84                                 case RNAVIZ: return "rnaviz";
  85                                 case LW_ALT: return "lwalt";
  86                         }
  87                         return "x";
  88                 }
  89                 public static BP_STYLE getStyle(String opt)
  90                 {
  91                         for(BP_STYLE b: BP_STYLE.values())
  92                         {
  93                                 if (opt.toLowerCase().equals(b.getOpt().toLowerCase()))
  94                                         return b;
  95                         }
  96                         return null;
  97                 }
  98         };
  99
 100         /**
 101          * Default values for config options
 102          */
 103
 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;
 112
 113         public static final int DEFAULT_PERIOD = 10;
 114
 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;
 125
 126         public static final Color DEFAULT_HOVER_COLOR  =  new Color(230, 230,230);
 127
 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",
 132                         Font.BOLD, 18);
 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);
 135
 136
 137         public static final BP_STYLE DEFAULT_BP_STYLE = BP_STYLE.LW;
 138
 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;
 142
 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();
 150
 151         public static double DEFAULT_SPACE_BETWEEN_BASES = 1.0;
 152
 153         /**
 154          * Various options.
 155          */
 156
 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";
 174
 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";
 184
 185         public static String XML_VAR_NUM_PERIOD = "numperiod";
 186
 187         public static String XML_VAR_MAIN_BP_STYLE = "bpstyle";
 188
 189         public static String XML_VAR_CM = "cm";
 190
 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";
 199
 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";
 203
 204         public static String XML_VAR_CM_CAPTION = "cmcaption";
 205         public static String XML_VAR_TITLE = "title";
 206
 207
 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;
 225
 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;
 236
 237         public int _numPeriod = DEFAULT_PERIOD;
 238         public BP_STYLE _mainBPStyle = DEFAULT_BP_STYLE;
 239
 240         public ModeleColorMap _cm = DEFAULT_COLOR_MAP;
 241
 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;
 249
 250         public Font _titleFont           = DEFAULT_TITLE_FONT;
 251         public Font _numbersFont         = DEFAULT_NUMBERS_FONT;
 252         public Font _fontBasesGeneral    = DEFAULT_BASE_FONT;
 253
 254         public String _colorMapCaption = "";
 255         //public String _title = "";
 256
 257
 258         public static String XML_ELEMENT_NAME = "config";
 259
 260         public void toXML(TransformerHandler hd) throws SAXException
 261         {
 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);
 280
 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);
 291
 292
 293                 atts.addAttribute("","",XML_VAR_NUM_PERIOD,"CDATA",     ""+_numPeriod);
 294
 295                 atts.addAttribute("","",XML_VAR_MAIN_BP_STYLE,"CDATA",  ""+_mainBPStyle.getOpt());
 296
 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));
 304
 305                 atts.addAttribute("","",XML_VAR_CM,"CDATA",                             _cm.getParamEncoding());
 306
 307
 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);
 312
 313                 XMLUtils.exportCDATAElem(hd,XML_VAR_CM_CAPTION, _colorMapCaption);
 314                 hd.endElement("","",XML_ELEMENT_NAME);
 315         }
 316
 317
 318
 319
 320         public void loadFromXMLAttributes(Attributes attributes)
 321         {
 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));
 339
 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);
 350
 351                 _numPeriod            = Integer.parseInt(attributes.getValue(XML_VAR_NUM_PERIOD));
 352
 353                 _mainBPStyle          = BP_STYLE.getStyle(attributes.getValue(XML_VAR_MAIN_BP_STYLE));
 354
 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));
 362
 363                 _cm                   = ModeleColorMap.parseColorMap(attributes.getValue(XML_VAR_CM));
 364         }
 365
 366
 367
 368     public VARNAConfig clone ()
 369     {
 370
 371       /**
 372        * @j2sNative
 373        *
 374        * return this;
 375        *
 376        */
 377         try
 378         {
 379             ByteArrayOutputStream out = new ByteArrayOutputStream ();
 380             ObjectOutputStream oout = new ObjectOutputStream (out);
 381             oout.writeObject (this);
 382
 383             ObjectInputStream in = new ObjectInputStream (
 384                 new ByteArrayInputStream (out.toByteArray ()));
 385             return (VARNAConfig)in.readObject ();
 386         }
 387         catch (Exception e)
 388         {
 389             throw new RuntimeException ("cannot clone class [" +
 390                 this.getClass ().getName () + "] via serialization: " +
 391                 e.toString ());
 392         }
 393     }
 394
 395 }