--- /dev/null
+/*
+ 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();
+
+ }
+
+
+
+}
git://source.jalview.org / jalview.git / blobdiff