X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=ae2941786fd442b26ddfe6ee854775e08a5ec4a6;hb=a990c2c6facfd04d61d316dcafba31d03747d162;hp=b0464dd1bbeb009ad42ee6bb805f68c6231d788f;hpb=722f0bee96b96ceeb8ef69b3ccd1aeff13786b2b;p=jalview.git
diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index b0464dd..ae29417 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,47 +1,62 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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!! */
+ /**
+ * the empty annotation - proxy for null entries in annotation row
+ */
+ public static final Annotation EMPTY_ANNOTATION = new Annotation("", "",
+ ' ', 0f);
+
+ /** 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, E and S(?)
+ /**
+ * 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;
/**
@@ -62,6 +77,7 @@ public class Annotation
description = desc;
secondaryStructure = ss;
value = val;
+
}
/**
@@ -99,12 +115,17 @@ public class Annotation
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;
+
}
/**
@@ -115,6 +136,82 @@ public class Annotation
*/
public Annotation(float val)
{
- this(null, null, ' ', val);
+ this(null, null, ' ', val, null);
+ }
+
+ /**
+ * 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 (!Float.isNaN(value))
+ {
+ 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();
+ }
+
+ /**
+ * @return true if annot is 'whitespace' annotation (zero score, whitespace or
+ * zero length display character, label, description
+ */
+ public boolean isWhitespace()
+ {
+ return ((value == 0f)
+ && ((description == null) || (description.trim().length() == 0))
+ && ((displayCharacter == null)
+ || (displayCharacter.trim().length() == 0))
+ && (secondaryStructure == '\0' || (secondaryStructure == ' '))
+ && colour == null);
}
}