X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=f6919cd36058cbfdacf9503e3aee84ac2bf516de;hb=375a7d14a156804a7b2771e7bd813e17f2f8397e;hp=16ede508eeb13439a9c2b605d3e31c23b08dd754;hpb=59a81cfb8e64c68d882182601663d82016f1a866;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 16ede50..f6919cd 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,25 +1,220 @@
+/*
+ * 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.
+ *  
+ * 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;
+
+/**
+ * Holds all annotation values for a position in an AlignmentAnnotation row
+ * 
+ * @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
+  /**
+   * 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 = "";
+
+  /**
+   * Text label for position: shown in mouse over and displayed on secondary
+   * structure glyphs
+   */
+  public String description = "";
+
+  /**
+   * Secondary structure symbol: Protein symbols are H, E and S(?), RNA are
+   * WUSS/Vienna plus extended pseudoknot symbols
+   */
+  public char secondaryStructure = ' ';
+
+  /**
+   * Score for the position - used in histograms, line graphs and for shading
+   */
   public float value;
 
-  // add visual cues here
-  public Color colour = Color.black;
+  /** 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!
+   */
   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);
+  }
+
+  /**
+   * 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)
+                    || (displayCharacter.equals(" ."))) // RNA Stockholm blank
+                                                        // displayCharacter can
+                                                        // end up like this
+            && (secondaryStructure == '\0' || (secondaryStructure == ' '))
+            && colour == null);
+  }
 }