- public String label;\r
- public String description;\r
- public Annotation [] annotations;\r
- public boolean isGraph = false;\r
- public float graphMin, graphMax;\r
- public int windowLength;\r
-\r
- // Graphical hints and tips\r
- public boolean editable = false;\r
- public boolean hasIcons; //\r
- public boolean hasText;\r
- public boolean visible = true;\r
- public int height=0;\r
-\r
- public AlignmentAnnotation(String label, String description, Annotation [] annotations)\r
- {\r
- // always editable?\r
- editable = true;\r
- this.label = label;\r
- this.description = description;\r
- this.annotations = annotations;\r
- for(int i=0; i<annotations.length; i++)\r
+ public SequenceI sequenceRef;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String label;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String description;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public Annotation[] annotations;\r
+\r
+ public java.util.Hashtable sequenceMapping;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public float graphMin;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public float graphMax;\r
+\r
+ public GraphLine threshold;\r
+\r
+ // Graphical hints and tips\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean editable = false;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean hasIcons; //\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean hasText;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean visible = true;\r
+\r
+ public int graphGroup = -1;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public int height = 0;\r
+\r
+ public int graph = 0;\r
+\r
+ public int graphHeight = 40;\r
+\r
+ public static final int NO_GRAPH = 0;\r
+\r
+ public static final int BAR_GRAPH = 1;\r
+\r
+ public static final int LINE_GRAPH = 2;\r
+\r
+ public static int getGraphValueFromString(String string)\r
+ {\r
+ if(string.equalsIgnoreCase("BAR_GRAPH"))\r
+ return BAR_GRAPH;\r
+ else if(string.equalsIgnoreCase("LINE_GRAPH"))\r
+ return LINE_GRAPH;\r
+ else\r
+ return NO_GRAPH;\r
+ }\r
+\r
+ /**\r
+ * Creates a new AlignmentAnnotation object.\r
+ *\r
+ * @param label DOCUMENT ME!\r
+ * @param description DOCUMENT ME!\r
+ * @param annotations DOCUMENT ME!\r
+ */\r
+ public AlignmentAnnotation(String label, String description,\r
+ Annotation[] annotations)\r