remove seqref annotations

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

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 7858e3f..adb9bc5 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,45 +1,106 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/\r
-package jalview.datamodel;\r
-\r
-import java.awt.*;\r
-\r
-\r
-public class Annotation {\r
-    public String displayCharacter = "";\r
-    public String description = ""; // currently used as mouse over\r
-    public char secondaryStructure = ' '; // recognises H and E\r
-    public float value;\r
-\r
-    // add visual cues here\r
-    public Color colour = Color.black;\r
-\r
-    public Annotation(String displayChar, String desc, char ss, float val) {\r
-        displayCharacter = displayChar;\r
-        description = desc;\r
-        secondaryStructure = ss;\r
-        value = val;\r
-    }\r
-\r
-    public Annotation(String displayChar, String desc, char ss, float val,\r
-        Color colour) {\r
-        this(displayChar, desc, ss, val);\r
-        this.colour = colour;\r
-    }\r
-}\r
+ * 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;
+  }
+  /**
+   * 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, '\0', val);
+  }
+}