* @param properties\r
* @return feature file as a string.\r
*/\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
* @param properties\r
* @return feature file as a string.\r
*/\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
- return printAnnotations(annotations, groups, properties, null);\r
+ return printAnnotations(annotations, list, properties, null);\r
* @param properties\r
* @param views\r
* @return annotation file\r
*/\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
* @param properties\r
* @param views\r
* @return annotation file\r
*/\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
{\r
// TODO: resolve views issue : annotationFile could contain visible region,\r
// or full data + hidden region specifications for a view.\r
{\r
// TODO: resolve views issue : annotationFile could contain visible region,\r
// or full data + hidden region specifications for a view.\r
}\r
// Finally, resolve the groupRefs\r
Enumeration en = groupRefRows.keys();\r
}\r
// Finally, resolve the groupRefs\r
Enumeration en = groupRefRows.keys();\r
while (en.hasMoreElements())\r
{\r
groupRef = (String) en.nextElement();\r
boolean matched = false;\r
// Resolve group: TODO: add a getGroupByName method to alignments\r
while (en.hasMoreElements())\r
{\r
groupRef = (String) en.nextElement();\r
boolean matched = false;\r
// Resolve group: TODO: add a getGroupByName method to alignments\r