Jalview 2.6 source licence

[jalview.git] / src / jalview / datamodel / Annotation.java

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 18e4ee7..762a62c 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,80 +1,120 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package jalview.datamodel;\r
-\r
-import java.awt.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Annotation\r
-{\r
-    /** DOCUMENT ME!! */\r
-    public String displayCharacter = "";\r
-\r
-    /** DOCUMENT ME!! */\r
-    public String description = ""; // currently used as mouse over\r
-\r
-    /** DOCUMENT ME!! */\r
-    public char secondaryStructure = ' '; // recognises H and E\r
-\r
-    /** DOCUMENT ME!! */\r
-    public float value;\r
-\r
-    // add visual cues here\r
-\r
-    /** DOCUMENT ME!! */\r
-    public Color colour = Color.black;\r
-\r
-    /**\r
-     * Creates a new Annotation object.\r
-     *\r
-     * @param displayChar DOCUMENT ME!\r
-     * @param desc DOCUMENT ME!\r
-     * @param ss DOCUMENT ME!\r
-     * @param val DOCUMENT ME!\r
-     */\r
-    public Annotation(String displayChar, String desc, char ss, float val)\r
-    {\r
-        displayCharacter = displayChar;\r
-        description = desc;\r
-        secondaryStructure = ss;\r
-        value = val;\r
-    }\r
-\r
-    /**\r
-     * Creates a new Annotation object.\r
-     *\r
-     * @param displayChar DOCUMENT ME!\r
-     * @param desc DOCUMENT ME!\r
-     * @param ss DOCUMENT ME!\r
-     * @param val DOCUMENT ME!\r
-     * @param colour DOCUMENT ME!\r
-     */\r
-    public Annotation(String displayChar, String desc, char ss, float val,\r
-        Color colour)\r
-    {\r
-        this(displayChar, desc, ss, val);\r
-        this.colour = colour;\r
-    }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Annotation
+{
+  /** DOCUMENT ME!! */
+  public String displayCharacter = "";
+
+  /** DOCUMENT ME!! */
+  public String description = ""; // currently used as mouse over
+
+  /** DOCUMENT ME!! */
+  public char secondaryStructure = ' '; // recognises H and E
+
+  /** DOCUMENT ME!! */
+  public float value;
+
+  // add visual cues here
+
+  /** 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;
+  }
+
+  /**
+   * 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);
+  }
+}