X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FModeleBP.java;fp=srcjar%2Ffr%2Forsay%2Flri%2Fvarna%2Fmodels%2Frna%2FModeleBP.java;h=138edb0bb62e34c60a051329c62ac9a14a79b6cd;hb=4898f0ae429e0c61ddba72ca46be89b34bb4df8b;hp=0000000000000000000000000000000000000000;hpb=5a6ac5b535856903629234ad43a71319a91ebee5;p=jalview.git diff --git a/srcjar/fr/orsay/lri/varna/models/rna/ModeleBP.java b/srcjar/fr/orsay/lri/varna/models/rna/ModeleBP.java new file mode 100644 index 0000000..138edb0 --- /dev/null +++ b/srcjar/fr/orsay/lri/varna/models/rna/ModeleBP.java @@ -0,0 +1,331 @@ +/* + 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 { + + /** + * + */ + 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 namesArray = new ArrayList(); + ArrayList valuesArray = new ArrayList(); + 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(); + + } + + + +}