/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.awt.*;
+import java.awt.Color;
/**
- * DOCUMENT ME!
- *
+ * Holds all annotation values for a position in an AlignmentAnnotation row
+ *
* @author $author$
* @version $Revision$
*/
public class Annotation
{
- /** DOCUMENT ME!! */
+ /** Character label - also shown below histogram */
public String displayCharacter = "";
- /** DOCUMENT ME!! */
- public String description = ""; // currently used as mouse over
+ /**
+ * Text label for position: shown in mouse over and displayed on secondary
+ * structure glyphs
+ */
+ public String description = "";
- /** DOCUMENT ME!! */
- public char secondaryStructure = ' '; // recognises H and E
+ /**
+ * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
+ * WUSS/Vienna plus extended pseudoknot symbols
+ */
+ public char secondaryStructure = ' ';
- /** DOCUMENT ME!! */
+ /** Score for the position - used in histograms, line graphs and for shading */
public float value;
- // add visual cues here
-
- /** DOCUMENT ME!! */
+ /** Colour for position */
public Color colour;
/**
* Creates a new Annotation object.
- *
- * @param displayChar DOCUMENT ME!
- * @param desc DOCUMENT ME!
- * @param ss DOCUMENT ME!
- * @param val DOCUMENT ME!
+ *
+ * @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)
{
/**
* 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!
+ *
+ * @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)
+ 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
+ * 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)
+ public Annotation(Annotation that)
+ {
+ if (that == null || this == that)
{
return;
}
- if (that.displayCharacter!=null)
+ if (that.displayCharacter != null)
displayCharacter = new String(that.displayCharacter);
- if (that.description!=null)
+ if (that.description != null)
description = new String(that.description);
secondaryStructure = that.secondaryStructure;
value = that.value;
/**
* Value only annotation.
- * @param val value at this annotation position
+ *
+ * @param val
+ * value at this annotation position
*/
public Annotation(float val)
{
this(null, null, ' ', val);
}
+
+ /**
+ * human readable representation of an annotation row element.
+ *
+ * Format is 'display Char','secondary Structure
+ * Char',"description",score,[colourstring]
+ *
+ * fields may be missing if they are null, whitespace, or equivalent to
+ * Float.NaN
+ */
+ @Override
+ public String toString()
+ {
+ StringBuffer sb = new StringBuffer();
+ if (displayCharacter != null)
+ {
+ sb.append("\'");
+ sb.append(displayCharacter);
+ sb.append("\'");
+ }
+ {
+ sb.append(",");
+ }
+ if (secondaryStructure != 0
+ && !("" + displayCharacter).equals("" + secondaryStructure))
+ {
+ sb.append("\'");
+ sb.append(secondaryStructure);
+ sb.append("\'");
+ }
+ {
+ sb.append(",");
+ }
+ if (description != null && description.length() > 0)
+ {
+ sb.append("\"");
+ sb.append(description);
+ sb.append("\"");
+ }
+ {
+ sb.append(",");
+ }
+ if (value != Float.NaN)
+ {
+ sb.append(value);
+ }
+ if (colour != null)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(",");
+ }
+ sb.append("[");
+ sb.append(colour.getRed());
+ sb.append(",");
+ sb.append(colour.getGreen());
+ sb.append(",");
+ sb.append(colour.getBlue());
+ sb.append("]");
+ }
+ return sb.toString();
+ }
}
git://source.jalview.org / jalview.git / blobdiff