JAL-3032 upgrade to Jmol 14.29.17; clearing of src2 directory
[jalview.git] / src2 / fr / orsay / lri / varna / models / rna / ModeleBP.java
diff --git a/src2/fr/orsay/lri/varna/models/rna/ModeleBP.java b/src2/fr/orsay/lri/varna/models/rna/ModeleBP.java
deleted file mode 100644 (file)
index 138edb0..0000000
+++ /dev/null
@@ -1,331 +0,0 @@
-/*
- 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.Color;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Random;
-
-import javax.xml.transform.sax.TransformerHandler;
-
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.AttributesImpl;
-
-import fr.orsay.lri.varna.exceptions.ExceptionModeleStyleBaseSyntaxError;
-import fr.orsay.lri.varna.exceptions.ExceptionParameterError;
-import fr.orsay.lri.varna.models.VARNAConfig;
-
-
-public class ModeleBP implements Serializable, Comparable<ModeleBP> {
-
-       /**
-        * 
-        */
-       private static final long serialVersionUID = -1344722280822711931L;
-
-       public enum Edge {
-               WC, SUGAR, HOOGSTEEN;
-       }
-       public enum Stericity {
-               CIS, TRANS;
-       }
-
-       private ModeleBase _partner5;
-       private Edge _edge5;
-       private ModeleBase _partner3;
-       private Edge _edge3;
-       private Stericity _stericity;
-       private ModeleBPStyle _style;
-
-       
-       public static String XML_ELEMENT_NAME = "bp";
-       public static String XML_VAR_PARTNER5_NAME = "part5";
-       public static String XML_VAR_EDGE5_NAME = "edge5";
-       public static String XML_VAR_PARTNER3_NAME = "part3";
-       public static String XML_VAR_EDGE3_NAME = "edge3";
-       public static String XML_VAR_STERICITY_NAME = "orient";
-       public static String XML_VAR_SEC_STR_NAME = "secstr";
-
-       public void toXML(TransformerHandler hd, boolean inSecondaryStructure) throws SAXException
-       {
-               AttributesImpl atts = new AttributesImpl();
-               atts.addAttribute("","",XML_VAR_PARTNER5_NAME,"CDATA",""+_partner5.getIndex());
-               atts.addAttribute("","",XML_VAR_PARTNER3_NAME,"CDATA",""+_partner3.getIndex());
-               atts.addAttribute("","",XML_VAR_EDGE5_NAME,"CDATA",""+_edge5);
-               atts.addAttribute("","",XML_VAR_EDGE3_NAME,"CDATA",""+_edge3);
-               atts.addAttribute("","",XML_VAR_STERICITY_NAME,"CDATA",""+_stericity);
-               atts.addAttribute("","",XML_VAR_SEC_STR_NAME,"CDATA",""+inSecondaryStructure);
-               hd.startElement("","",XML_ELEMENT_NAME,atts);
-               _style.toXML(hd);
-               hd.endElement("","",XML_ELEMENT_NAME);
-       }
-       
-       public void toXML(TransformerHandler hd) throws SAXException
-       {
-               toXML(hd, false);
-       }
-       
-
-       
-       public ModeleBP(ModeleBase part5, ModeleBase part3) {
-               this(part5, part3, Edge.WC, Edge.WC, Stericity.CIS);
-       }
-
-       //private static Random rnd = new Random(System.currentTimeMillis());
-
-       public ModeleBP(ModeleBase part5, ModeleBase part3, Edge edge5,
-                       Edge edge3, Stericity ster) {
-               _partner5 = part5;
-               _partner3 = part3;
-               _edge5 = edge5;
-               _edge3 = edge3;
-               _stericity = ster;
-               _style = new ModeleBPStyle();
-       }
-
-       public ModeleBP(String text) throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError {
-               _style = new ModeleBPStyle();
-               assignParameters(text);         
-       }
-       
-       public void setStericity(Stericity s) {
-               _stericity = s;
-       }
-
-       public void setEdge5(Edge e) {
-               _edge5 = e;
-       }
-
-       public void setEdge3(Edge e) {
-               _edge3 = e;
-       }
-
-       public void setStyle(ModeleBPStyle e) {
-               _style = e;
-       }
-       
-       public ModeleBPStyle getStyle() {
-               return _style;
-       }
-               
-       public boolean isCanonicalGC() {
-               String si = _partner5.getContent();
-               String sj = _partner3.getContent();
-               if ((si.length() >= 1) && (sj.length() >= 1)) {
-                       char ci = si.toUpperCase().charAt(0);
-                       char cj = sj.toUpperCase().charAt(0);
-                       if (((ci == 'G') && (cj == 'C')) || ((ci == 'C') && (cj == 'G'))) {
-                               return isCanonical() && (getStericity() == Stericity.CIS);
-                       }
-               }
-               return false;
-       }
-
-       public boolean isCanonicalAU() {
-               String si = _partner5.getContent();
-               String sj = _partner3.getContent();
-               if ((si.length() >= 1) && (sj.length() >= 1)) {
-                       char ci = si.toUpperCase().charAt(0);
-                       char cj = sj.toUpperCase().charAt(0);
-                       if (((ci == 'A') && (cj == 'U')) 
-                                       || ((ci == 'U') && (cj == 'A'))
-                                       || ((ci == 'U') && (cj == 'T'))
-                                       || ((ci == 'T') && (cj == 'U'))) {
-                               return isCanonical();
-                       }
-               }
-               return false;
-       }
-
-       public boolean isWobbleUG() {
-               String si = _partner5.getContent();
-               String sj = _partner3.getContent();
-               if ((si.length() >= 1) && (sj.length() >= 1)) {
-                       char ci = si.toUpperCase().charAt(0);
-                       char cj = sj.toUpperCase().charAt(0);
-                       if (((ci == 'G') && (cj == 'U')) || ((ci == 'U') && (cj == 'G'))) {
-                               return (isCanonical());
-                       }
-               }
-               return false;
-       }
-
-       public boolean isCanonical() {
-               return (_edge5 == Edge.WC) && (_edge3 == Edge.WC)
-                               && (_stericity == Stericity.CIS);
-       }
-
-       public Stericity getStericity() {
-               return _stericity;
-       }
-
-       public boolean isCIS() {
-               return (_stericity == Stericity.CIS);
-       }
-
-       public boolean isTRANS() {
-               return (_stericity == Stericity.TRANS);
-       }
-
-       public Edge getEdgePartner5() {
-               return _edge5;
-       }
-
-       public Edge getEdgePartner3() {
-               return _edge3;
-       }
-       
-       public ModeleBase getPartner(ModeleBase mb) {
-               if (mb == _partner3)
-                       return _partner5;
-               else
-                       return _partner3;
-       }
-
-       public ModeleBase getPartner5() {
-               return _partner5;
-       }
-
-       public ModeleBase getPartner3() {
-               return _partner3;
-       }
-
-       public int getIndex5() {
-               return _partner5.getIndex();
-       }
-
-       public int getIndex3() {
-               return _partner3.getIndex();
-       }
-
-       public void setPartner5(ModeleBase mb) {
-               _partner5 = mb;
-       }
-
-       public void setPartner3(ModeleBase mb) {
-               _partner3 = mb;
-       }
-
-
-
-       public static final String PARAM_COLOR = "color";
-       public static final String PARAM_THICKNESS = "thickness";
-       public static final String PARAM_EDGE5 = "edge5";
-       public static final String PARAM_EDGE3 = "edge3";
-       public static final String PARAM_STERICITY = "stericity";
-
-       public static final String VALUE_WATSON_CRICK = "wc";
-       public static final String VALUE_HOOGSTEEN = "h";
-       public static final String VALUE_SUGAR = "s";
-       public static final String VALUE_CIS = "cis";
-       public static final String VALUE_TRANS = "trans";
-
-       public void assignParameters(String parametersValue)
-                       throws ExceptionModeleStyleBaseSyntaxError, ExceptionParameterError {
-               if (parametersValue.equals(""))
-                       return;
-
-               String[] parametersL = parametersValue.split(",");
-
-               ArrayList<String> namesArray = new ArrayList<String>();
-               ArrayList<String> valuesArray = new ArrayList<String>();
-               String[] param;
-               for (int i = 0; i < parametersL.length; i++) {
-                       param = parametersL[i].split("=");
-                       if (param.length != 2)
-                               throw new ExceptionModeleStyleBaseSyntaxError(
-                                               "Bad parameter: '" + param[0] + "' ...");
-                       namesArray.add(param[0].replace(" ", ""));
-                       valuesArray.add(param[1].replace(" ", ""));
-
-               }
-               for (int i = 0; i < namesArray.size(); i++) {
-                       if (namesArray.get(i).toLowerCase().equals(PARAM_COLOR)) {
-                               try {
-                                       _style.setCustomColor(ModelBaseStyle
-                                                       .getSafeColor(valuesArray.get(i)));
-                               } catch (NumberFormatException e) {
-                                       throw new ExceptionParameterError(e.getMessage(),
-                                                       "Bad inner color Syntax:" + valuesArray.get(i));
-                               }
-                       } else if (namesArray.get(i).toLowerCase().equals(PARAM_THICKNESS)) {
-                               try {
-                                       _style.setThickness(Double.parseDouble(valuesArray.get(i)));
-                               } catch (NumberFormatException e) {
-                                       throw new ExceptionParameterError(e.getMessage(),
-                                                       "Bad value for bp thickness:" + valuesArray.get(i));
-                               }
-                       } else if (namesArray.get(i).toLowerCase().equals(PARAM_EDGE5)) {
-                               String s = valuesArray.get(i);
-                               if (s.toLowerCase().equals(VALUE_WATSON_CRICK)) {
-                                       setEdge5(Edge.WC);
-                               } else if (s.toLowerCase().equals(VALUE_HOOGSTEEN)) {
-                                       setEdge5(Edge.HOOGSTEEN);
-                               } else if (s.toLowerCase().equals(VALUE_SUGAR)) {
-                                       setEdge5(Edge.SUGAR);
-                               } else
-                                       throw new ExceptionParameterError("Bad value for edge:"
-                                                       + valuesArray.get(i));
-                       } else if (namesArray.get(i).toLowerCase().equals(PARAM_EDGE3)) {
-                               String s = valuesArray.get(i);
-                               if (s.toLowerCase().equals(VALUE_WATSON_CRICK)) {
-                                       setEdge3(Edge.WC);
-                               } else if (s.toLowerCase().equals(VALUE_HOOGSTEEN)) {
-                                       setEdge3(Edge.HOOGSTEEN);
-                               } else if (s.toLowerCase().equals(VALUE_SUGAR)) {
-                                       setEdge3(Edge.SUGAR);
-                               } else
-                                       throw new ExceptionParameterError("Bad value for edge:"
-                                                       + valuesArray.get(i));
-                       } else if (namesArray.get(i).toLowerCase().equals(PARAM_STERICITY)) {
-                               String s = valuesArray.get(i);
-                               if (s.toLowerCase().equals(VALUE_CIS)) {
-                                       setStericity(Stericity.CIS);
-                               } else if (s.toLowerCase().equals(VALUE_TRANS)) {
-                                       setStericity(Stericity.TRANS);
-                               } else
-                                       throw new ExceptionParameterError(
-                                                       "Bad value for stericity:" + valuesArray.get(i));
-                       } else
-                               throw new ExceptionModeleStyleBaseSyntaxError(
-                                               "Unknown parameter:" + namesArray.get(i));
-               }
-       }
-       
-       public String toString() {
-               String result = "";
-               result += "(" + _partner5.getIndex() + "," + _partner3.getIndex() + ")";
-               //result += " [" + _partner5.getElementStructure() + ","
-               //              + _partner3.getElementStructure() + "]\n";
-               //result += "  5':" + _partner5 + "\n";
-               //result += "  3':" + _partner3;
-               return result;
-       }
-
-
-       public int compareTo(ModeleBP mb) {
-               if (getIndex5()!=mb.getIndex5())
-               {  return getIndex5()-mb.getIndex5();  }
-               return getIndex3()-mb.getIndex3(); 
-               
-       }
-       
-       
-
-}