+++ /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