/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
package jalview.datamodel;
+
import java.awt.*;
+import java.util.ArrayList;
+
+import fr.orsay.lri.varna.models.rna.RNA;
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
public class Annotation
{
- public String displayCharacter="";
- public String description=""; // currently used as mouse over
- public char secondaryStructure=' '; // recognises H and E
+ /** DOCUMENT ME!! */
+ public String displayCharacter = "";
+
+ /** DOCUMENT ME!! */
+ public String description = ""; // currently used as mouse over
+
+ /** DOCUMENT ME!! */
+ public char secondaryStructure = ' '; // recognises H, E and S(?)
+
+ /** DOCUMENT ME!! */
public float value;
+
+
// add visual cues here
- public Color colour = Color.black;
+ /** DOCUMENT ME!! */
+ public Color colour;
+
+ /**
+ * Creates a new Annotation object.
+ *
+ * @param displayChar
+ * DOCUMENT ME!
+ * @param desc
+ * DOCUMENT ME!
+ * @param ss
+ * DOCUMENT ME!
+ * @param val
+ * DOCUMENT ME!
+ */
public Annotation(String displayChar, String desc, char ss, float val)
{
displayCharacter = displayChar;
description = desc;
secondaryStructure = ss;
value = val;
+
}
- public Annotation(String displayChar, String desc, char ss, float val, Color colour) {
+
+ /**
+ * Creates a new Annotation object.
+ *
+ * @param displayChar
+ * DOCUMENT ME!
+ * @param desc
+ * DOCUMENT ME!
+ * @param ss
+ * DOCUMENT ME!
+ * @param val
+ * DOCUMENT ME!
+ * @param colour
+ * DOCUMENT ME!
+ */
+ public Annotation(String displayChar, String desc, char ss, float val,
+ Color colour)
+ {
this(displayChar, desc, ss, val);
this.colour = colour;
}
+
+ /**
+ * Copy constructor New annotation takes on the same (or duplicated)
+ * attributes as the given template
+ *
+ * @param that
+ * template annotation
+ */
+ public Annotation(Annotation that)
+ {
+ if (that == null || this == that)
+ {
+ return;
+ }
+ if (that.displayCharacter != null)
+ displayCharacter = new String(that.displayCharacter);
+ if (that.description != null)
+ description = new String(that.description);
+ secondaryStructure = that.secondaryStructure;
+ value = that.value;
+ colour = that.colour;
+
+ }
+
+ /**
+ * Value only annotation.
+ *
+ * @param val
+ * value at this annotation position
+ */
+ public Annotation(float val)
+ {
+ this(null, null, ' ', val,null);
+ }
+
+
+
+
}