AddAnnotation with start index

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

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index e4d64fa..fcf9844 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -27,6 +27,8 @@ package jalview.datamodel;
  */\r
 public class AlignmentAnnotation\r
 {\r
+    public SequenceI refSequence;\r
+\r
     /** DOCUMENT ME!! */\r
     public String label;\r
 \r
@@ -43,6 +45,7 @@ public class AlignmentAnnotation
     /** DOCUMENT ME!! */\r
     public float graphMax;\r
 \r
+    public java.util.Vector graphLines;\r
 \r
     // Graphical hints and tips\r
 \r
@@ -58,16 +61,30 @@ public class AlignmentAnnotation
     /** 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 static int NO_GRAPH = 0;\r
+    public int graphHeight = 40;\r
 \r
-    public static int BAR_GRAPH = 1;\r
+    public static final int NO_GRAPH = 0;\r
 \r
-    public static int LINE_GRAPH = 2;\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
@@ -123,6 +140,7 @@ public class AlignmentAnnotation
 \r
         if (min == max)\r
         {\r
+            min = 999999999;\r
             for (int i = 0; i < annotations.length; i++)\r
             {\r
                 if (annotations[i] == null)\r
@@ -208,5 +226,24 @@ public class AlignmentAnnotation
         }\r
 \r
         return buffer.toString();\r
-    }\r
+      }\r
+\r
+      public void addGraphLine(GraphLine line)\r
+      {\r
+        if(graphLines==null)\r
+          graphLines = new java.util.Vector();\r
+\r
+        graphLines.add(line);\r
+      }\r
+\r
+      public GraphLine getGraphLine(int index)\r
+      {\r
+        if(graphLines!=null && index<graphLines.size())\r
+          return (GraphLine)graphLines.elementAt(index);\r
+\r
+        else\r
+          return null;\r
+      }\r
 }\r
+\r
+\r