datasetSequence derive method and some checks

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

diff --git a/src/jalview/datamodel/Annotation.java b/src/jalview/datamodel/Annotation.java
index 7858e3f..18e4ee7 100755 (executable)
--- a/src/jalview/datamodel/Annotation.java
+++ b/src/jalview/datamodel/Annotation.java
@@ -1,44 +1,79 @@
-/*
-* 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
+* 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
-public class Annotation {\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
-    public Annotation(String displayChar, String desc, char ss, float val) {\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
+        Color colour)\r
+    {\r
         this(displayChar, desc, ss, val);\r
         this.colour = colour;\r
     }\r