protected Vector groups = new Vector();\r
protected ArrayList superGroup = new ArrayList();\r
protected char gapCharacter = '-';\r
+ public AlignmentAnnotation [] annotations;\r
+ public Conservation conservation;\r
+\r
public boolean featuresAdded = false;\r
\r
/** Make an alignment from an array of Sequences.\r
return false;\r
\r
return true;\r
+ }\r
+\r
+ public void deleteAnnotation(AlignmentAnnotation aa)\r
+ {\r
+ int aSize = 1;\r
+ if(annotations!=null)\r
+ aSize = annotations.length;\r
+\r
+ AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];\r
+\r
+ int tIndex = 0;\r
+ for (int i = 0; i < aSize; i++)\r
+ {\r
+ if(annotations[i]==aa)\r
+ continue;\r
+\r
+\r
+ temp[tIndex] = annotations[i];\r
+ tIndex++;\r
+ }\r
+\r
+ annotations = temp;\r
\r
+ }\r
+\r
+ public void addAnnotation(AlignmentAnnotation aa)\r
+ {\r
+ int aSize = 1;\r
+ if(annotations!=null)\r
+ aSize = annotations.length+1;\r
+\r
+ AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];\r
+ int i=0;\r
+ if (aSize > 1)\r
+ for (i = 0; i < aSize-1; i++)\r
+ temp[i] = annotations[i];\r
+\r
+ temp[i] = aa;\r
+\r
+ annotations = temp;\r
}\r
+ public AlignmentAnnotation[] getAlignmentAnnotation()\r
+ {\r
+ return annotations;\r
+ }\r
+\r
}\r
\r
\r