--- /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;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+
+import javax.xml.transform.sax.TransformerHandler;
+
+import org.xml.sax.Attributes;
+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;
+import fr.orsay.lri.varna.models.rna.ModeleBP;
+import fr.orsay.lri.varna.models.rna.ModeleBPStyle;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.ModeleColorMap;
+import fr.orsay.lri.varna.utils.XMLUtils;
+
+public class VARNAConfig implements Serializable, Cloneable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 2853916694420964233L;
+ /**
+ *
+ */
+ public static final int MAJOR_VERSION = 3;
+ public static final int MINOR_VERSION = 9;
+
+ public static String getFullName()
+ {
+ return "VARNA "+MAJOR_VERSION+"."+MINOR_VERSION;
+ }
+
+ /**
+ * Enum types and internal classes
+ */
+
+ public enum BP_STYLE implements Serializable {
+ NONE, SIMPLE, RNAVIZ, LW, LW_ALT;
+ public String toString()
+ {
+ switch(this)
+ {
+ case LW: return "Leontis/Westhof (Centered)";
+ case SIMPLE: return "Line";
+ case RNAVIZ: return "Circles";
+ case NONE: return "None";
+ case LW_ALT: return "Leontis/Westhof (End)";
+ }
+ return "Unspecified";
+ }
+ public String getOpt()
+ {
+ switch(this)
+ {
+ case NONE: return "none";
+ case SIMPLE: return "simple";
+ case LW: return "lw";
+ case RNAVIZ: return "rnaviz";
+ case LW_ALT: return "lwalt";
+ }
+ return "x";
+ }
+ public static BP_STYLE getStyle(String opt)
+ {
+ for(BP_STYLE b: BP_STYLE.values())
+ {
+ if (opt.toLowerCase().equals(b.getOpt().toLowerCase()))
+ return b;
+ }
+ return null;
+ }
+ };
+
+ /**
+ * Default values for config options
+ */
+
+ public static final double MAX_ZOOM = 60;
+ public static final double MIN_ZOOM = 0.5;
+ public static final double DEFAULT_ZOOM = 1;
+ public static final double MAX_AMOUNT = 2;
+ public static final double MIN_AMOUNT = 1.01;
+ public static final double DEFAULT_AMOUNT = 1.2;
+ public static final double DEFAULT_BP_THICKNESS = 1.0;
+ public static final double DEFAULT_DIST_NUMBERS = 3.0;
+
+ public static final int DEFAULT_PERIOD = 10;
+
+ public static final Color DEFAULT_TITLE_COLOR = Color.black;
+ public static final Color DEFAULT_BACKBONE_COLOR = Color.DARK_GRAY.brighter();
+ public static final Color DEFAULT_BOND_COLOR = Color.blue;
+ public static final Color DEFAULT_SPECIAL_BASE_COLOR = Color.green.brighter();
+ public static final Color DEFAULT_DASH_BASE_COLOR = Color.yellow.brighter();
+ public static final double DEFAULT_BASE_OUTLINE_THICKNESS = 1.5;
+ public static final Color BASE_OUTLINE_COLOR_DEFAULT = Color.DARK_GRAY.brighter();
+ public static final Color BASE_INNER_COLOR_DEFAULT = new Color(242, 242,242);
+ public static final Color BASE_NUMBER_COLOR_DEFAULT = Color.DARK_GRAY;
+ public static final Color BASE_NAME_COLOR_DEFAULT = Color.black;
+
+ public static final Color DEFAULT_HOVER_COLOR = new Color(230, 230,230);
+
+ public static final Color DEFAULT_BACKGROUND_COLOR = Color.WHITE;
+ public static final Font DEFAULT_TITLE_FONT = new Font("SansSerif", Font.BOLD,18);
+ public static final Font DEFAULT_BASE_FONT = new Font("SansSerif", Font.PLAIN, 18);
+ public static final Font DEFAULT_NUMBERS_FONT = new Font("SansSerif",
+ Font.BOLD, 18);
+ public static final Font DEFAULT_MESSAGE_FONT = Font.decode("dialog-PLAIN-25");
+ public static final Color DEFAULT_MESSAGE_COLOR = new Color(230, 230,230);
+
+
+ public static final BP_STYLE DEFAULT_BP_STYLE = BP_STYLE.LW;
+
+ public static final ModeleColorMap DEFAULT_COLOR_MAP = ModeleColorMap.defaultColorMap();
+ public static final Color DEFAULT_COLOR_MAP_OUTLINE = Color.gray;
+ public static final double DEFAULT_BP_INCREMENT = 0.65;
+
+ public static double DEFAULT_COLOR_MAP_WIDTH = 120;
+ public static double DEFAULT_COLOR_MAP_HEIGHT = 30;
+ public static double DEFAULT_COLOR_MAP_X_OFFSET = 40;
+ public static double DEFAULT_COLOR_MAP_Y_OFFSET = 0;
+ public static int DEFAULT_COLOR_MAP_STRIPE_WIDTH = 2;
+ public static int DEFAULT_COLOR_MAP_FONT_SIZE = 20;
+ public static Color DEFAULT_COLOR_MAP_FONT_COLOR = Color.gray.darker();
+
+ public static double DEFAULT_SPACE_BETWEEN_BASES = 1.0;
+
+ /**
+ * Various options.
+ */
+
+ public static String XML_VAR_DRAW_OUTLINE = "drawoutline";
+ public static String XML_VAR_FILL_BASE = "fillbase";
+ public static String XML_VAR_AUTO_FIT = "autofit";
+ public static String XML_VAR_AUTO_CENTER = "autocenter";
+ public static String XML_VAR_MODIFIABLE = "modifiable";
+ public static String XML_VAR_ERRORS = "errors";
+ public static String XML_VAR_SPECIAL_BASES = "specialbases";
+ public static String XML_VAR_DASH_BASES = "dashbases";
+ public static String XML_VAR_USE_BASE_BPS = "usebasebps";
+ public static String XML_VAR_DRAW_NC = "drawnc";
+ public static String XML_VAR_DRAW_NON_PLANAR = "drawnonplanar";
+ public static String XML_VAR_SHOW_WARNINGS = "warnings";
+ public static String XML_VAR_COMPARISON_MODE = "comparison";
+ public static String XML_VAR_FLAT = "flat";
+ public static String XML_VAR_DRAW_BACKGROUND = "drawbackground";
+ public static String XML_VAR_COLOR_MAP = "drawcm";
+ public static String XML_VAR_DRAW_BACKBONE = "drawbackbone";
+
+ public static String XML_VAR_CM_HEIGHT = "cmh";
+ public static String XML_VAR_CM_WIDTH = "cmw";
+ public static String XML_VAR_CM_X_OFFSET = "cmx";
+ public static String XML_VAR_CM_Y_OFFSET = "cmy";
+ public static String XML_VAR_DEFAULT_ZOOM = "defaultzoom";
+ public static String XML_VAR_ZOOM_AMOUNT = "zoominc";
+ public static String XML_VAR_BP_THICKNESS = "bpthick";
+ public static String XML_VAR_BASE_THICKNESS = "basethick";
+ public static String XML_VAR_DIST_NUMBERS = "distnumbers";
+
+ public static String XML_VAR_NUM_PERIOD = "numperiod";
+
+ public static String XML_VAR_MAIN_BP_STYLE = "bpstyle";
+
+ public static String XML_VAR_CM = "cm";
+
+ public static String XML_VAR_BACKBONE_COLOR = "backbonecol";
+ public static String XML_VAR_HOVER_COLOR = "hovercol";
+ public static String XML_VAR_BACKGROUND_COLOR = "backgroundcol";
+ public static String XML_VAR_BOND_COLOR = "bondcol";
+ public static String XML_VAR_TITLE_COLOR = "titlecol";
+ public static String XML_VAR_SPECIAL_BASES_COLOR = "specialco";
+ public static String XML_VAR_DASH_BASES_COLOR = "dashcol";
+ public static String XML_VAR_SPACE_BETWEEN_BASES = "spacebetweenbases";
+
+ public static String XML_VAR_TITLE_FONT = "titlefont";
+ public static String XML_VAR_NUMBERS_FONT = "numbersfont";
+ public static String XML_VAR_FONT_BASES = "basefont";
+
+ public static String XML_VAR_CM_CAPTION = "cmcaption";
+ public static String XML_VAR_TITLE = "title";
+
+
+ public boolean _drawOutlineBases = true;
+ public boolean _fillBases = true;
+ public boolean _autoFit = true;
+ public boolean _autoCenter = true;
+ public boolean _modifiable = true;
+ public boolean _errorsOn = false;
+ public boolean _colorSpecialBases = false;
+ public boolean _colorDashBases = false;
+ public boolean _useBaseColorsForBPs = false;
+ public boolean _drawnNonCanonicalBP = true;
+ public boolean _drawnNonPlanarBP = true;
+ public boolean _showWarnings = false;
+ public boolean _comparisonMode = false;
+ public boolean _flatExteriorLoop = true;
+ public boolean _drawBackground = false;
+ public boolean _drawColorMap = false;
+ public boolean _drawBackbone = true;
+
+ public double _colorMapHeight = DEFAULT_COLOR_MAP_HEIGHT;
+ public double _colorMapWidth = DEFAULT_COLOR_MAP_WIDTH;
+ public double _colorMapXOffset = DEFAULT_COLOR_MAP_X_OFFSET;
+ public double _colorMapYOffset = DEFAULT_COLOR_MAP_Y_OFFSET;
+ public double _zoom = DEFAULT_ZOOM;
+ public double _zoomAmount = DEFAULT_AMOUNT;
+ public double _bpThickness = 1.0;
+ public double _baseThickness = DEFAULT_BASE_OUTLINE_THICKNESS;
+ public double _distNumbers = DEFAULT_DIST_NUMBERS;
+ public double _spaceBetweenBases = DEFAULT_SPACE_BETWEEN_BASES;
+
+ public int _numPeriod = DEFAULT_PERIOD;
+ public BP_STYLE _mainBPStyle = DEFAULT_BP_STYLE;
+
+ public ModeleColorMap _cm = DEFAULT_COLOR_MAP;
+
+ public Color _backboneColor = DEFAULT_BACKBONE_COLOR;
+ public Color _hoverColor = DEFAULT_HOVER_COLOR;
+ public Color _backgroundColor = DEFAULT_BACKGROUND_COLOR;
+ public Color _bondColor = DEFAULT_BOND_COLOR;
+ public Color _titleColor = DEFAULT_TITLE_COLOR;
+ public Color _specialBasesColor = DEFAULT_SPECIAL_BASE_COLOR;
+ public Color _dashBasesColor = DEFAULT_DASH_BASE_COLOR;
+
+ public Font _titleFont = DEFAULT_TITLE_FONT;
+ public Font _numbersFont = DEFAULT_NUMBERS_FONT;
+ public Font _fontBasesGeneral = DEFAULT_BASE_FONT;
+
+ public String _colorMapCaption = "";
+ //public String _title = "";
+
+
+ public static String XML_ELEMENT_NAME = "config";
+
+ public void toXML(TransformerHandler hd) throws SAXException
+ {
+ AttributesImpl atts = new AttributesImpl();
+ atts.addAttribute("","",XML_VAR_DRAW_OUTLINE,"CDATA", ""+_drawOutlineBases);
+ atts.addAttribute("","",XML_VAR_FILL_BASE,"CDATA", ""+_fillBases);
+ atts.addAttribute("","",XML_VAR_AUTO_FIT,"CDATA", ""+_autoFit);
+ atts.addAttribute("","",XML_VAR_AUTO_CENTER,"CDATA", ""+_autoCenter);
+ atts.addAttribute("","",XML_VAR_MODIFIABLE,"CDATA", ""+_modifiable);
+ atts.addAttribute("","",XML_VAR_ERRORS,"CDATA", ""+_errorsOn);
+ atts.addAttribute("","",XML_VAR_SPECIAL_BASES,"CDATA", ""+_colorSpecialBases);
+ atts.addAttribute("","",XML_VAR_DASH_BASES,"CDATA", ""+_colorDashBases);
+ atts.addAttribute("","",XML_VAR_USE_BASE_BPS,"CDATA", ""+_useBaseColorsForBPs);
+ atts.addAttribute("","",XML_VAR_DRAW_NC,"CDATA", ""+_drawnNonCanonicalBP);
+ atts.addAttribute("","",XML_VAR_DRAW_NON_PLANAR,"CDATA",""+_drawnNonPlanarBP);
+ atts.addAttribute("","",XML_VAR_SHOW_WARNINGS,"CDATA", ""+_showWarnings);
+ atts.addAttribute("","",XML_VAR_COMPARISON_MODE,"CDATA",""+_comparisonMode);
+ atts.addAttribute("","",XML_VAR_FLAT,"CDATA", ""+_flatExteriorLoop);
+ atts.addAttribute("","",XML_VAR_DRAW_BACKGROUND,"CDATA",""+_drawBackground);
+ atts.addAttribute("","",XML_VAR_COLOR_MAP,"CDATA", ""+_drawColorMap);
+ atts.addAttribute("","",XML_VAR_DRAW_BACKBONE,"CDATA", ""+_drawBackbone);
+
+ atts.addAttribute("","",XML_VAR_CM_HEIGHT,"CDATA", ""+_colorMapHeight);
+ atts.addAttribute("","",XML_VAR_CM_WIDTH,"CDATA", ""+_colorMapWidth);
+ atts.addAttribute("","",XML_VAR_CM_X_OFFSET,"CDATA", ""+_colorMapXOffset);
+ atts.addAttribute("","",XML_VAR_CM_Y_OFFSET,"CDATA", ""+_colorMapYOffset);
+ atts.addAttribute("","",XML_VAR_DEFAULT_ZOOM,"CDATA", ""+_zoom);
+ atts.addAttribute("","",XML_VAR_ZOOM_AMOUNT,"CDATA", ""+_zoomAmount);
+ atts.addAttribute("","",XML_VAR_BP_THICKNESS,"CDATA", ""+_bpThickness);
+ atts.addAttribute("","",XML_VAR_BASE_THICKNESS,"CDATA", ""+_baseThickness);
+ atts.addAttribute("","",XML_VAR_DIST_NUMBERS,"CDATA", ""+_distNumbers);
+ atts.addAttribute("","",XML_VAR_SPACE_BETWEEN_BASES,"CDATA", ""+_spaceBetweenBases);
+
+
+ atts.addAttribute("","",XML_VAR_NUM_PERIOD,"CDATA", ""+_numPeriod);
+
+ atts.addAttribute("","",XML_VAR_MAIN_BP_STYLE,"CDATA", ""+_mainBPStyle.getOpt());
+
+ atts.addAttribute("","",XML_VAR_BACKBONE_COLOR,"CDATA", XMLUtils.toHTMLNotation(_backboneColor));
+ atts.addAttribute("","",XML_VAR_HOVER_COLOR,"CDATA", XMLUtils.toHTMLNotation(_hoverColor));
+ atts.addAttribute("","",XML_VAR_BACKGROUND_COLOR,"CDATA", XMLUtils.toHTMLNotation(_backgroundColor));
+ atts.addAttribute("","",XML_VAR_BOND_COLOR,"CDATA", XMLUtils.toHTMLNotation(_bondColor));
+ atts.addAttribute("","",XML_VAR_TITLE_COLOR,"CDATA", XMLUtils.toHTMLNotation(_titleColor));
+ atts.addAttribute("","",XML_VAR_SPECIAL_BASES_COLOR,"CDATA",XMLUtils.toHTMLNotation(_specialBasesColor));
+ atts.addAttribute("","",XML_VAR_DASH_BASES_COLOR,"CDATA", XMLUtils.toHTMLNotation(_dashBasesColor));
+
+ atts.addAttribute("","",XML_VAR_CM,"CDATA", _cm.getParamEncoding());
+
+
+ hd.startElement("","",XML_ELEMENT_NAME,atts);
+ XMLUtils.toXML(hd, _titleFont,XML_VAR_TITLE_FONT);
+ XMLUtils.toXML(hd, _numbersFont,XML_VAR_NUMBERS_FONT);
+ XMLUtils.toXML(hd, _fontBasesGeneral,XML_VAR_FONT_BASES);
+
+ XMLUtils.exportCDATAElem(hd,XML_VAR_CM_CAPTION, _colorMapCaption);
+ hd.endElement("","",XML_ELEMENT_NAME);
+ }
+
+
+
+
+ public void loadFromXMLAttributes(Attributes attributes)
+ {
+ _drawOutlineBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_OUTLINE));
+ _fillBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_FILL_BASE));
+ _autoFit = Boolean.parseBoolean(attributes.getValue(XML_VAR_AUTO_FIT));
+ _autoCenter = Boolean.parseBoolean(attributes.getValue(XML_VAR_AUTO_CENTER));
+ _modifiable = Boolean.parseBoolean(attributes.getValue(XML_VAR_MODIFIABLE));
+ _errorsOn = Boolean.parseBoolean(attributes.getValue(XML_VAR_ERRORS));
+ _colorSpecialBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_SPECIAL_BASES));
+ _colorDashBases = Boolean.parseBoolean(attributes.getValue(XML_VAR_DASH_BASES));
+ _useBaseColorsForBPs = Boolean.parseBoolean(attributes.getValue(XML_VAR_USE_BASE_BPS));
+ _drawnNonCanonicalBP = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_NC));
+ _drawnNonPlanarBP = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_NON_PLANAR));
+ _showWarnings = Boolean.parseBoolean(attributes.getValue(XML_VAR_SHOW_WARNINGS));
+ _comparisonMode = Boolean.parseBoolean(attributes.getValue(XML_VAR_COMPARISON_MODE));
+ _flatExteriorLoop = Boolean.parseBoolean(attributes.getValue(XML_VAR_FLAT));
+ _drawBackground = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_BACKGROUND));
+ _drawColorMap = Boolean.parseBoolean(attributes.getValue(XML_VAR_COLOR_MAP));
+ _drawBackbone = Boolean.parseBoolean(attributes.getValue(XML_VAR_DRAW_BACKBONE));
+
+ _colorMapHeight = Double.parseDouble(attributes.getValue(XML_VAR_CM_HEIGHT));
+ _colorMapWidth = Double.parseDouble(attributes.getValue(XML_VAR_CM_WIDTH));
+ _colorMapXOffset = Double.parseDouble(attributes.getValue(XML_VAR_CM_X_OFFSET));
+ _colorMapYOffset = Double.parseDouble(attributes.getValue(XML_VAR_CM_Y_OFFSET));
+ _zoom = Double.parseDouble(attributes.getValue(XML_VAR_DEFAULT_ZOOM));
+ _zoomAmount = Double.parseDouble(attributes.getValue(XML_VAR_ZOOM_AMOUNT));
+ _bpThickness = Double.parseDouble(attributes.getValue(XML_VAR_BP_THICKNESS));
+ _baseThickness = Double.parseDouble(attributes.getValue(XML_VAR_BASE_THICKNESS));
+ _distNumbers = Double.parseDouble(attributes.getValue(XML_VAR_DIST_NUMBERS));
+ _spaceBetweenBases = XMLUtils.getDouble(attributes, XML_VAR_SPACE_BETWEEN_BASES, DEFAULT_SPACE_BETWEEN_BASES);
+
+ _numPeriod = Integer.parseInt(attributes.getValue(XML_VAR_NUM_PERIOD));
+
+ _mainBPStyle = BP_STYLE.getStyle(attributes.getValue(XML_VAR_MAIN_BP_STYLE));
+
+ _backboneColor = Color.decode(attributes.getValue(XML_VAR_BACKBONE_COLOR));
+ _hoverColor = Color.decode(attributes.getValue(XML_VAR_HOVER_COLOR));
+ _backgroundColor = Color.decode(attributes.getValue(XML_VAR_BACKGROUND_COLOR));
+ _bondColor = Color.decode(attributes.getValue(XML_VAR_BOND_COLOR));
+ _titleColor = Color.decode(attributes.getValue(XML_VAR_TITLE_COLOR));
+ _specialBasesColor = Color.decode(attributes.getValue(XML_VAR_SPECIAL_BASES_COLOR));
+ _dashBasesColor = Color.decode(attributes.getValue(XML_VAR_DASH_BASES_COLOR));
+
+ _cm = ModeleColorMap.parseColorMap(attributes.getValue(XML_VAR_CM));
+ }
+
+
+
+ public VARNAConfig clone ()
+ {
+
+ /**
+ * @j2sNative
+ *
+ * return this;
+ *
+ */
+ try
+ {
+ ByteArrayOutputStream out = new ByteArrayOutputStream ();
+ ObjectOutputStream oout = new ObjectOutputStream (out);
+ oout.writeObject (this);
+
+ ObjectInputStream in = new ObjectInputStream (
+ new ByteArrayInputStream (out.toByteArray ()));
+ return (VARNAConfig)in.readObject ();
+ }
+ catch (Exception e)
+ {
+ throw new RuntimeException ("cannot clone class [" +
+ this.getClass ().getName () + "] via serialization: " +
+ e.toString ());
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff