srcjar/fr/orsay/lri/varna/models/rna/ModeleBP.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.rna;
  19
  20 import java.awt.Color;
  21 import java.io.Serializable;
  22 import java.util.ArrayList;
  23 import java.util.Random;
  24
  25 import javax.xml.transform.sax.TransformerHandler;
  26
  27 import org.xml.sax.SAXException;
  28 import org.xml.sax.helpers.AttributesImpl;
  29
  30 import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
  31 import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
  32 import fr.orsay.lri.varna.models.VARNAConfig;
  33
  34
  35 public class ModeleBP implements Serializable, Comparable<ModeleBP> {
  36
  37         /**
  38          *
  39          */
  40         private static final long serialVersionUID = -1344722280822711931L;
  41
  42         public enum Edge {
  43                 WC, SUGAR, HOOGSTEEN;
  44         }
  45         public enum Stericity {
  46                 CIS, TRANS;
  47         }
  48
  49         private ModeleBase _partner5;
  50         private Edge _edge5;
  51         private ModeleBase _partner3;
  52         private Edge _edge3;
  53         private Stericity _stericity;
  54         private ModeleBPStyle _style;
  55
  56
  57         public static String XML_ELEMENT_NAME = "bp";
  58         public static String XML_VAR_PARTNER5_NAME = "part5";
  59         public static String XML_VAR_EDGE5_NAME = "edge5";
  60         public static String XML_VAR_PARTNER3_NAME = "part3";
  61         public static String XML_VAR_EDGE3_NAME = "edge3";
  62         public static String XML_VAR_STERICITY_NAME = "orient";
  63         public static String XML_VAR_SEC_STR_NAME = "secstr";
  64
  65         public void toXML(TransformerHandler hd, boolean inSecondaryStructure) throws SAXException
  66         {
  67                 AttributesImpl atts = new AttributesImpl();
  68                 atts.addAttribute("","",XML_VAR_PARTNER5_NAME,"CDATA",""+_partner5.getIndex());
  69                 atts.addAttribute("","",XML_VAR_PARTNER3_NAME,"CDATA",""+_partner3.getIndex());
  70                 atts.addAttribute("","",XML_VAR_EDGE5_NAME,"CDATA",""+_edge5);
  71                 atts.addAttribute("","",XML_VAR_EDGE3_NAME,"CDATA",""+_edge3);
  72                 atts.addAttribute("","",XML_VAR_STERICITY_NAME,"CDATA",""+_stericity);
  73                 atts.addAttribute("","",XML_VAR_SEC_STR_NAME,"CDATA",""+inSecondaryStructure);
  74                 hd.startElement("","",XML_ELEMENT_NAME,atts);
  75                 _style.toXML(hd);
  76                 hd.endElement("","",XML_ELEMENT_NAME);
  77         }
  78
  79         public void toXML(TransformerHandler hd) throws SAXException
  80         {
  81                 toXML(hd, false);
  82         }
  83
  84
  85
  86         public ModeleBP(ModeleBase part5, ModeleBase part3) {
  87                 this(part5, part3, Edge.WC, Edge.WC, Stericity.CIS);
  88         }
  89
  90         //private static Random rnd = new Random(System.currentTimeMillis());
  91
  92         public ModeleBP(ModeleBase part5, ModeleBase part3, Edge edge5,
  93                         Edge edge3, Stericity ster) {
  94                 _partner5 = part5;
  95                 _partner3 = part3;
  96                 _edge5 = edge5;
  97                 _edge3 = edge3;
  98                 _stericity = ster;
  99                 _style = new ModeleBPStyle();
 100         }
 101
 102         public ModeleBP(String text) throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError {
 103                 _style = new ModeleBPStyle();
 104                 assignParameters(text);
 105         }
 106
 107         public void setStericity(Stericity s) {
 108                 _stericity = s;
 109         }
 110
 111         public void setEdge5(Edge e) {
 112                 _edge5 = e;
 113         }
 114
 115         public void setEdge3(Edge e) {
 116                 _edge3 = e;
 117         }
 118
 119         public void setStyle(ModeleBPStyle e) {
 120                 _style = e;
 121         }
 122
 123         public ModeleBPStyle getStyle() {
 124                 return _style;
 125         }
 126
 127         public boolean isCanonicalGC() {
 128                 String si = _partner5.getContent();
 129                 String sj = _partner3.getContent();
 130                 if ((si.length() >= 1) && (sj.length() >= 1)) {
 131                         char ci = si.toUpperCase().charAt(0);
 132                         char cj = sj.toUpperCase().charAt(0);
 133                         if (((ci == 'G') && (cj == 'C')) || ((ci == 'C') && (cj == 'G'))) {
 134                                 return isCanonical() && (getStericity() == Stericity.CIS);
 135                         }
 136                 }
 137                 return false;
 138         }
 139
 140         public boolean isCanonicalAU() {
 141                 String si = _partner5.getContent();
 142                 String sj = _partner3.getContent();
 143                 if ((si.length() >= 1) && (sj.length() >= 1)) {
 144                         char ci = si.toUpperCase().charAt(0);
 145                         char cj = sj.toUpperCase().charAt(0);
 146                         if (((ci == 'A') && (cj == 'U'))
 147                                         || ((ci == 'U') && (cj == 'A'))
 148                                         || ((ci == 'U') && (cj == 'T'))
 149                                         || ((ci == 'T') && (cj == 'U'))) {
 150                                 return isCanonical();
 151                         }
 152                 }
 153                 return false;
 154         }
 155
 156         public boolean isWobbleUG() {
 157                 String si = _partner5.getContent();
 158                 String sj = _partner3.getContent();
 159                 if ((si.length() >= 1) && (sj.length() >= 1)) {
 160                         char ci = si.toUpperCase().charAt(0);
 161                         char cj = sj.toUpperCase().charAt(0);
 162                         if (((ci == 'G') && (cj == 'U')) || ((ci == 'U') && (cj == 'G'))) {
 163                                 return (isCanonical());
 164                         }
 165                 }
 166                 return false;
 167         }
 168
 169         public boolean isCanonical() {
 170                 return (_edge5 == Edge.WC) && (_edge3 == Edge.WC)
 171                                 && (_stericity == Stericity.CIS);
 172         }
 173
 174         public Stericity getStericity() {
 175                 return _stericity;
 176         }
 177
 178         public boolean isCIS() {
 179                 return (_stericity == Stericity.CIS);
 180         }
 181
 182         public boolean isTRANS() {
 183                 return (_stericity == Stericity.TRANS);
 184         }
 185
 186         public Edge getEdgePartner5() {
 187                 return _edge5;
 188         }
 189
 190         public Edge getEdgePartner3() {
 191                 return _edge3;
 192         }
 193
 194         public ModeleBase getPartner(ModeleBase mb) {
 195                 if (mb == _partner3)
 196                         return _partner5;
 197                 else
 198                         return _partner3;
 199         }
 200
 201         public ModeleBase getPartner5() {
 202                 return _partner5;
 203         }
 204
 205         public ModeleBase getPartner3() {
 206                 return _partner3;
 207         }
 208
 209         public int getIndex5() {
 210                 return _partner5.getIndex();
 211         }
 212
 213         public int getIndex3() {
 214                 return _partner3.getIndex();
 215         }
 216
 217         public void setPartner5(ModeleBase mb) {
 218                 _partner5 = mb;
 219         }
 220
 221         public void setPartner3(ModeleBase mb) {
 222                 _partner3 = mb;
 223         }
 224
 225
 226
 227         public static final String PARAM_COLOR = "color";
 228         public static final String PARAM_THICKNESS = "thickness";
 229         public static final String PARAM_EDGE5 = "edge5";
 230         public static final String PARAM_EDGE3 = "edge3";
 231         public static final String PARAM_STERICITY = "stericity";
 232
 233         public static final String VALUE_WATSON_CRICK = "wc";
 234         public static final String VALUE_HOOGSTEEN = "h";
 235         public static final String VALUE_SUGAR = "s";
 236         public static final String VALUE_CIS = "cis";
 237         public static final String VALUE_TRANS = "trans";
 238
 239         public void assignParameters(String parametersValue)
 240                         throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError {
 241                 if (parametersValue.equals(""))
 242                         return;
 243
 244                 String[] parametersL = parametersValue.split(",");
 245
 246                 ArrayList<String> namesArray = new ArrayList<String>();
 247                 ArrayList<String> valuesArray = new ArrayList<String>();
 248                 String[] param;
 249                 for (int i = 0; i < parametersL.length; i++) {
 250                         param = parametersL[i].split("=");
 251                         if (param.length != 2)
 252                                 throw new ExceptionModeleStyleBaseSyntaxError(
 253                                                 "Bad parameter: '" + param[0] + "' ...");
 254                         namesArray.add(param[0].replace(" ", ""));
 255                         valuesArray.add(param[1].replace(" ", ""));
 256
 257                 }
 258                 for (int i = 0; i < namesArray.size(); i++) {
 259                         if (namesArray.get(i).toLowerCase().equals(PARAM_COLOR)) {
 260                                 try {
 261                                         _style.setCustomColor(ModelBaseStyle
 262                                                         .getSafeColor(valuesArray.get(i)));
 263                                 } catch (NumberFormatException e) {
 264                                         throw new ExceptionParameterError(e.getMessage(),
 265                                                         "Bad inner color Syntax:" + valuesArray.get(i));
 266                                 }
 267                         } else if (namesArray.get(i).toLowerCase().equals(PARAM_THICKNESS)) {
 268                                 try {
 269                                         _style.setThickness(Double.parseDouble(valuesArray.get(i)));
 270                                 } catch (NumberFormatException e) {
 271                                         throw new ExceptionParameterError(e.getMessage(),
 272                                                         "Bad value for bp thickness:" + valuesArray.get(i));
 273                                 }
 274                         } else if (namesArray.get(i).toLowerCase().equals(PARAM_EDGE5)) {
 275                                 String s = valuesArray.get(i);
 276                                 if (s.toLowerCase().equals(VALUE_WATSON_CRICK)) {
 277                                         setEdge5(Edge.WC);
 278                                 } else if (s.toLowerCase().equals(VALUE_HOOGSTEEN)) {
 279                                         setEdge5(Edge.HOOGSTEEN);
 280                                 } else if (s.toLowerCase().equals(VALUE_SUGAR)) {
 281                                         setEdge5(Edge.SUGAR);
 282                                 } else
 283                                         throw new ExceptionParameterError("Bad value for edge:"
 284                                                         + valuesArray.get(i));
 285                         } else if (namesArray.get(i).toLowerCase().equals(PARAM_EDGE3)) {
 286                                 String s = valuesArray.get(i);
 287                                 if (s.toLowerCase().equals(VALUE_WATSON_CRICK)) {
 288                                         setEdge3(Edge.WC);
 289                                 } else if (s.toLowerCase().equals(VALUE_HOOGSTEEN)) {
 290                                         setEdge3(Edge.HOOGSTEEN);
 291                                 } else if (s.toLowerCase().equals(VALUE_SUGAR)) {
 292                                         setEdge3(Edge.SUGAR);
 293                                 } else
 294                                         throw new ExceptionParameterError("Bad value for edge:"
 295                                                         + valuesArray.get(i));
 296                         } else if (namesArray.get(i).toLowerCase().equals(PARAM_STERICITY)) {
 297                                 String s = valuesArray.get(i);
 298                                 if (s.toLowerCase().equals(VALUE_CIS)) {
 299                                         setStericity(Stericity.CIS);
 300                                 } else if (s.toLowerCase().equals(VALUE_TRANS)) {
 301                                         setStericity(Stericity.TRANS);
 302                                 } else
 303                                         throw new ExceptionParameterError(
 304                                                         "Bad value for stericity:" + valuesArray.get(i));
 305                         } else
 306                                 throw new ExceptionModeleStyleBaseSyntaxError(
 307                                                 "Unknown parameter:" + namesArray.get(i));
 308                 }
 309         }
 310
 311         public String toString() {
 312                 String result = "";
 313                 result += "(" + _partner5.getIndex() + "," + _partner3.getIndex() + ")";
 314                 //result += " [" + _partner5.getElementStructure() + ","
 315                 //              + _partner3.getElementStructure() + "]\n";
 316                 //result += "  5':" + _partner5 + "\n";
 317                 //result += "  3':" + _partner3;
 318                 return result;
 319         }
 320
 321
 322         public int compareTo(ModeleBP mb) {
 323                 if (getIndex5()!=mb.getIndex5())
 324                 {  return getIndex5()-mb.getIndex5();  }
 325                 return getIndex3()-mb.getIndex3();
 326
 327         }
 328
 329
 330
 331 }