--- /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 Universit� 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.geom.Point2D;
+import java.io.Serializable;
+
+import javax.xml.transform.sax.TransformerHandler;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.AttributesImpl;
+
+import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
+import fr.orsay.lri.varna.models.annotations.TextAnnotation;
+
+
+/**
+ * The abstract rna base model
+ *
+ * @author darty
+ *
+ */
+public abstract class ModeleBase implements Serializable, java.lang.Comparable<ModeleBase> {
+
+ private ModeleBP _BP;
+ /**
+ * The base style.
+ */
+ protected ModelBaseStyle _styleBase = new ModelBaseStyle();
+ /**
+ * TRUE if this InterfaceBase has to be colored, else FALSE.
+ */
+ protected Boolean _colorie = new Boolean(true);
+ /**
+ * The coordinate representation of this InterfaceBase on the final graphic.
+ */
+ protected VARNAPoint _coords = new VARNAPoint();
+ /**
+ * The nearest loop center of this InterfaceBase.
+ */
+ protected VARNAPoint _center = new VARNAPoint();
+
+ /**
+ * The label of this base.
+ */
+ protected String _label = "";
+
+ protected double _value;
+ protected int _realIndex = -1;
+
+ public abstract void toXML(TransformerHandler hd) throws SAXException;
+
+
+
+ /**
+ * The internal index for this Base
+ */
+ public abstract int getIndex();
+
+ public abstract String getContent();
+ public abstract void setContent(String s);
+
+ /**
+ * Gets this InterfaceBase style.
+ *
+ * @return this InterfaceBase style.
+ */
+ public ModelBaseStyle getStyleBase() {
+ return _styleBase;
+ }
+
+ public double getValue()
+ {
+ return _value;
+ }
+
+ public void setValue(double d)
+ {
+ _value = d;
+ }
+
+
+ /**
+ * Sets this InterfaceBase style.
+ *
+ * @param base
+ * - This InterfaceBase new style.
+ */
+ public void setStyleBase(ModelBaseStyle base) {
+ _styleBase = new ModelBaseStyle(base);
+ }
+
+ /**
+ * Gets this InterfaceBase color statement.
+ *
+ * @return TRUE if this InterfaceBase has to be colored, else FALSE.
+ */
+ public final Boolean getColorie() {
+ return _colorie;
+ }
+
+ /**
+ * Sets this InterfaceBase color statement.
+ *
+ * @param _colorie
+ * - TRUE if you want this InterfaceBase to be colored, else
+ * FALSE
+ */
+ public final void setColorie(Boolean _colorie) {
+ this._colorie = _colorie;
+ }
+
+
+ /**
+ * Gets this InterfaceBase associated structure element.
+ *
+ * @return this InterfaceBase associated structure element.
+ */
+ public int getElementStructure() {
+ if (_BP==null)
+ return -1;
+ else
+ {
+ if (_BP.getPartner5()==this)
+ return _BP.getPartner3().getIndex();
+ else
+ return _BP.getPartner5().getIndex();
+ }
+ }
+
+
+ /**
+ * Sets this InterfaceBase assiocated structure element.
+ *
+ * @param structure
+ * - This new assiocated structure element.
+
+ public void setElementStructure(int structure) {
+ setElementStructure(structure, new ModeleBP());
+ } */
+
+ /**
+ * Sets this InterfaceBase associated structure element.
+ *
+ * @param structure
+ * - This new associated structure element.
+ * @param type
+ * - The type of this base pair.
+ */
+ public void setElementStructure(int structure, ModeleBP type) {
+// _elementStructure = structure;
+ _BP = type;
+
+ }
+
+ public void removeElementStructure() {
+// _elementStructure = -1;
+ _BP = null;
+ }
+
+
+ /**
+ * Gets the base pair type for this element.
+ *
+ * @return the base pair type for this element.
+ */
+ public ModeleBP getStyleBP() {
+ return _BP;
+ }
+
+ /**
+ * Sets the base pair type for this element.
+ *
+ * @param type
+ * - The new base pair type for this element.
+ */
+ public void setStyleBP(ModeleBP type) {
+ _BP = type;
+ }
+
+ public int getBaseNumber() {
+ return _realIndex;
+ }
+
+ public void setBaseNumber(int bn) {
+ _realIndex = bn;
+ }
+
+ public Point2D.Double getCoords() {
+ return new Point2D.Double(_coords.x,_coords.y);
+ }
+
+ public void setCoords(Point2D.Double coords) {
+ this._coords.x = coords.x;
+ this._coords.y = coords.y;
+ }
+
+ public Point2D.Double getCenter() {
+ return new Point2D.Double(_center.x,_center.y);
+ }
+
+ public void setCenter(Point2D.Double center) {
+ this._center.x = center.x;
+ this._center.y = center.y;
+ }
+
+ public String getLabel() {
+ if (_label==null || _label.equals(""))
+ {
+ return ""+this.getBaseNumber();
+ }
+ else
+ {
+ return _label;
+ }
+
+ }
+
+ public void setLabel(String s) {
+ _label= s;
+ }
+
+ public void setLabel(Point2D.Double center) {
+ this._center.x = center.x;
+ this._center.y = center.y;
+ }
+
+
+ public int compareTo(ModeleBase other) {
+ int nombre1 = ((ModeleBase) other).getIndex();
+ int nombre2 = this.getIndex();
+ if (nombre1 > nombre2) return -1;
+ else if(nombre1 == nombre2) return 0;
+ else return 1;
+ }
+
+ public static String XML_VAR_TYPE_NAME = "type";
+ public static String XML_VAR_INDEX_NAME = "index";
+ public static String XML_VAR_LABEL_NAME = "label";
+ public static String XML_VAR_VALUE_NAME = "val";
+ public static String XML_VAR_POSITION_NAME = "pos";
+ public static String XML_VAR_CENTER_NAME = "center";
+ public static String XML_VAR_NUMBER_NAME = "num";
+ public static String XML_VAR_CUSTOM_DRAWN_NAME = "custom";
+
+
+}
git://source.jalview.org / jalview.git / blobdiff