X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAnnotation.java;h=609158dd74eb34c9bbe01e2ba53784f0fa66e83c;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=e0c49c8ab5ab8df48a5745309f6f1fa61fc42ea6;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index e0c49c8..609158d 100755
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,79 +1,120 @@
-/*
- * 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
- */
-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 = Color.black;
-
-  /**
-   * 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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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);
+  }
+}