--- /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.awt.geom.Point2D;
+
+import javax.xml.transform.sax.TransformerHandler;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.AttributesImpl;
+
+import fr.orsay.lri.varna.utils.XMLUtils;
+
+
+/**
+ * <b>The RNA base comparison model</b>. In each bases we'll place <b>two
+ * characters</b> representing nitrogenous bases of both RNA that have to be
+ * compared. So, in each base in the comparison model, we'll have a <b>couple of
+ * bases</b>, with the same coordinates on the final drawing.
+ *
+ * @author Masson
+ *
+ */
+public class ModeleBasesComparison extends ModeleBase {
+
+ /*
+ * LOCAL FIELDS
+ */
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = -2733063250714562463L;
+
+ /**
+ * The base of the first RNA associated with the base of the second RNA.
+ */
+ private Character _base1;
+
+ /**
+ * The base of the second RNA associated with the base of the first RNA.
+ */
+ private Character _base2;
+
+ /**
+ * This ModeleBasesComparison owning statement. It's value will be 0 if this
+ * base is common for both RNA that had been compared, 1 if this base is
+ * related to the first RNA, 2 if related to the second. Default is -1.
+ */
+ private int _appartenance = -1;
+
+ /**
+ * This base's offset in the sequence
+ */
+ private int _index;
+
+ public static String XML_ELEMENT_NAME = "NTPair";
+ public static String XML_VAR_FIRST_CONTENT_NAME = "base1";
+ public static String XML_VAR_SECOND_CONTENT_NAME = "base2";
+ public static String XML_VAR_MEMBERSHIP_NAME = "type";
+
+
+
+ public void toXML(TransformerHandler hd) throws SAXException
+ {
+ AttributesImpl atts = new AttributesImpl();
+ atts.addAttribute("","",XML_VAR_INDEX_NAME,"CDATA",""+_index);
+ atts.addAttribute("","",XML_VAR_NUMBER_NAME,"CDATA",""+_realIndex);
+ atts.addAttribute("","",XML_VAR_CUSTOM_DRAWN_NAME,"CDATA",""+_colorie);
+ atts.addAttribute("","",XML_VAR_LABEL_NAME,"CDATA",""+_label);
+ atts.addAttribute("","",XML_VAR_MEMBERSHIP_NAME,"CDATA",""+_appartenance);
+ atts.addAttribute("","","VALUE","CDATA",""+_value);
+ hd.startElement("","",XML_ELEMENT_NAME,atts);
+ atts.clear();
+ hd.startElement("","",XML_VAR_FIRST_CONTENT_NAME,atts);
+ XMLUtils.exportCDATAString(hd, ""+_base1);
+ hd.endElement("","",XML_VAR_FIRST_CONTENT_NAME);
+ atts.clear();
+ hd.startElement("","",XML_VAR_SECOND_CONTENT_NAME,atts);
+ XMLUtils.exportCDATAString(hd, ""+_base2);
+ hd.endElement("","",XML_VAR_SECOND_CONTENT_NAME);
+
+ _coords.toXML(hd,XML_VAR_POSITION_NAME);
+ _center.toXML(hd,XML_VAR_CENTER_NAME);
+ if (_colorie)
+ { _styleBase.toXML(hd); }
+ hd.endElement("","",XML_ELEMENT_NAME);
+
+ }
+
+
+ /*
+ * -> END LOCAL FIELDS <--
+ */
+
+ public static Color FIRST_RNA_COLOR = Color.decode("#FFDD99");
+ public static Color SECOND_RNA_COLOR = Color.decode("#99DDFF");
+ public static Color BOTH_RNA_COLOR = Color.decode("#99DD99");
+ public static Color DEFAULT_RNA_COLOR = Color.white;
+
+ /*
+ * CONSTRUCTORS
+ */
+
+ /**
+ * Creates a new comparison base with the default display style and no
+ * nitrogenous bases.
+ */
+ public ModeleBasesComparison(int index) {
+ this(' ', ' ', index);
+ }
+
+ /**
+ * Creates a new comparison base at the specified coordinates, with the
+ * default display style and no nitrogenous bases.
+ *
+ * @param coords
+ * - The coordinates in which the comparison base has to be
+ * placed.
+ */
+ public ModeleBasesComparison(Point2D coords, int index) {
+ this(' ', ' ', new Point2D.Double(coords.getX(), coords.getY()), index);
+ }
+
+ /**
+ * Creates a new comparison base with the specified nitrogenous bases.
+ *
+ * @param base1
+ * - The first RNA' nitrogenous base
+ * @param base2
+ * - The second RNA' nitrogenous base
+ */
+ public ModeleBasesComparison(char base1, char base2, int index) {
+ this(base1, base2, -1, index);
+ }
+
+ /**
+ * Creates a new comparison base with the specified nitrogenous bases, at
+ * the specified coordinates.
+ *
+ * @param base1
+ * - The first RNA' nitrogenous base
+ * @param base2
+ * - The second RNA' nitrogenous base
+ * @param coords
+ * - The coordinates in which the comparison base has to be
+ * placed.
+ */
+ public ModeleBasesComparison(char base1, char base2, Point2D coords,
+ int index) {
+ this(new Point2D.Double(coords.getX(), coords.getY()), base1, base2,
+ true, new ModelBaseStyle(), -1, index);
+ }
+
+ /**
+ * Creates a new comparison base with the specified nitrogenous bases.
+ *
+ * @param base1
+ * - The first RNA' nitrogenous base
+ * @param base2
+ * - The second RNA' nitrogenous base
+ */
+ public ModeleBasesComparison(char base1, char base2, int elementStructure,
+ int index) {
+ this(new Point2D.Double(), base1, base2, true, new ModelBaseStyle(),
+ elementStructure, index);
+ }
+
+ /**
+ * Creates a new comparison base with the specified nitrogenous bases.
+ *
+ * @param coords
+ * - This base's XY coordinates
+ * @param base1
+ * - The first RNA' nitrogenous base
+ * @param base2
+ * - The second RNA' nitrogenous base
+ * @param colorie
+ * - Whether or not this base will be drawn
+ * @param mb
+ * - The drawing style for this base
+ * @param elementStructure
+ * - The index of a bp partner in the secondary structure
+ * @param index
+ * - Index of this base in its initial sequence
+ */
+ public ModeleBasesComparison(Point2D coords, char base1, char base2,
+ boolean colorie, ModelBaseStyle mb, int elementStructure, int index) {
+ _colorie = colorie;
+ _base1 = base1;
+ _base2 = base2;
+ _styleBase = mb;
+ _coords = new VARNAPoint(coords.getX(), coords.getY());
+ _index = index;
+ }
+
+ /*
+ * -> END CONSTRUCTORS <--
+ */
+
+ /*
+ * GETTERS & SETTERS
+ */
+
+ /**
+ * Return the display style associated to this comparison base.
+ *
+ * @return The display style associated to this comparison base.
+ */
+ public ModelBaseStyle getStyleBase() {
+ if (_colorie)
+ return _styleBase;
+ return new ModelBaseStyle();
+ }
+
+ /**
+ * Allows to know if this comparison base is colored.
+ *
+ * @return TRUE if this comparison base is colored, else FALSE.
+ */
+ public Boolean getColored() {
+ return _colorie;
+ }
+
+ /**
+ * Sets the coloration authorization of this comparison base.
+ *
+ * @param colored
+ * - TRUE if this comparison base has to be colored, else FALSE.
+ */
+ public void set_colored(Boolean colored) {
+ this._colorie = colored;
+ }
+
+
+ /**
+ * Return the base of the first RNA in this comparison base.
+ *
+ * @return The base of the first RNA in this comparison base.
+ */
+ public Character getBase1() {
+ return _base1;
+ }
+
+ /**
+ * Sets the base of the first RNA in this comparison base.
+ *
+ * @param _base1
+ * - The base of the first RNA in this comparison base.
+ */
+ public void setBase1(Character _base1) {
+ this._base1 = _base1;
+ }
+
+ /**
+ * Return the base of the second RNA in this comparison base.
+ *
+ * @return The base of the second RNA in this comparison base.
+ */
+ public Character getBase2() {
+ return _base2;
+ }
+
+ /**
+ * Sets the base of the second RNA in this comparison base.
+ *
+ * @param _base2
+ * - The base of the second RNA in this comparison base.
+ */
+ public void setBase2(Character _base2) {
+ this._base2 = _base2;
+ }
+
+ /*
+ * --> END GETTERS & SETTERS <--
+ */
+
+ /**
+ * Gets the string representation of the two bases in this
+ * ModeleBasesComparison.
+ *
+ * @return the string representation of the two bases in this
+ * ModeleBasesComparison.
+ */
+ public String getBases() {
+ return String.valueOf(_base1) + String.valueOf(_base2);
+ }
+
+ public String getContent() {
+ return getBases();
+ }
+
+
+ /**
+ * Gets this base's related RNA.
+ *
+ * @return 0 if this base is common for both RNA<br>
+ * 1 if this base is related to the first RNA<br>
+ * 2 if this base is related to the second RNA
+ */
+ public int get_appartenance() {
+ return _appartenance;
+ }
+
+ /**
+ * Sets this base's related RNA.
+ *
+ * @param _appartenance
+ * : 0 if this base is common for both RNA<br>
+ * 1 if this base is related to the first RNA<br>
+ * 2 if this base is related to the second RNA.
+ */
+ public void set_appartenance(int _appartenance) {
+ if (_appartenance == 0) {
+ this.getStyleBase().setBaseInnerColor(BOTH_RNA_COLOR);
+ } else if (_appartenance == 1) {
+ this.getStyleBase().setBaseInnerColor(FIRST_RNA_COLOR);
+ } else if (_appartenance == 2) {
+ this.getStyleBase().setBaseInnerColor(SECOND_RNA_COLOR);
+ } else {
+ this.getStyleBase().setBaseInnerColor(DEFAULT_RNA_COLOR);
+ }
+ this._appartenance = _appartenance;
+ }
+
+
+
+ public int getIndex() {
+ return _index;
+ }
+
+ @Override
+ public void setContent(String s) {
+ this.setBase1(s.charAt(0));
+ this.setBase2(s.charAt(1));
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff