int end = -1;\r
String sid = acc;\r
/*\r
- * Retrieve hash of annotations for this accession\r
- * Associate Annotation with accession\r
+ * Retrieve hash of annotations for this accession Associate\r
+ * Annotation with accession\r
*/\r
Hashtable accAnnotations = null;\r
\r
if (seqAnn != null && seqAnn.containsKey(acc))\r
{\r
accAnnotations = (Hashtable) seqAnn.remove(acc);\r
- //TODO: add structures to sequence\r
+ // TODO: add structures to sequence\r
}\r
\r
// Split accession in id and from/to\r
jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
// seqO.addDBRef(dbref);\r
}\r
- } \r
+ }\r
if (accAnnotations != null && accAnnotations.containsKey("SS"))\r
{\r
- Vector v = (Vector) accAnnotations.get("SS");\r
- \r
- for (int i = 0; i < v.size(); i++)\r
- {\r
- AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
- seqO.addAlignmentAnnotation(an);\r
- //annotations.add(an);\r
- }\r
+ Vector v = (Vector) accAnnotations.get("SS");\r
+\r
+ for (int i = 0; i < v.size(); i++)\r
+ {\r
+ AlignmentAnnotation an = (AlignmentAnnotation) v.elementAt(i);\r
+ seqO.addAlignmentAnnotation(an);\r
+ // annotations.add(an);\r
+ }\r
}\r
- \r
+\r
Hashtable features = null;\r
// We need to adjust the positions of all features to account for gaps\r
try\r
ann = new Hashtable();\r
seqAnn.put(acc, ann);\r
}\r
- //TODO test structure, call parseAnnotationRow with vector from hashtable for specific sequence\r
+ // TODO test structure, call parseAnnotationRow with vector from\r
+ // hashtable for specific sequence\r
Hashtable features;\r
// Get an object with all the content for an annotation\r
if (ann.containsKey("features"))\r
}\r
ns += seq;\r
content.put(description, ns);\r
-
- if(type.equals("SS")){\r
- Hashtable strucAnn;\r
- if (seqAnn.containsKey(acc))\r
- {\r
- strucAnn = (Hashtable) seqAnn.get(acc);\r
- }\r
- else\r
- {\r
- strucAnn = new Hashtable();\r
- }\r
- \r
- Vector newStruc=new Vector();\r
- parseAnnotationRow(newStruc, type,ns);\r
- \r
- strucAnn.put(type, newStruc);\r
- seqAnn.put(acc, strucAnn);\r
- }\r
+\r
+ if (type.equals("SS"))\r
+ {\r
+ Hashtable strucAnn;\r
+ if (seqAnn.containsKey(acc))\r
+ {\r
+ strucAnn = (Hashtable) seqAnn.get(acc);\r
+ }\r
+ else\r
+ {\r
+ strucAnn = new Hashtable();\r
+ }\r
+\r
+ Vector newStruc = new Vector();\r
+ parseAnnotationRow(newStruc, type, ns);\r
+\r
+ strucAnn.put(type, newStruc);\r
+ seqAnn.put(acc, strucAnn);\r
+ }\r
}\r
else\r
{\r
}\r
}\r
\r
- private AlignmentAnnotation parseAnnotationRow(Vector annotation,\r
- String label, String annots)\r
+ protected static AlignmentAnnotation parseAnnotationRow(\r
+ Vector annotation, String label, String annots)\r
{\r
String convert1, convert2 = null;\r
\r
annot.annotations.length);\r
System.arraycopy(els, 0, anns, annot.annotations.length, els.length);\r
annot.annotations = anns;\r
- //System.out.println("else: ");\r
+ // System.out.println("else: ");\r
}\r
return annot;\r
}\r
}\r
}\r
\r
- private String id2type(String id)\r
+ protected static String id2type(String id)\r
{\r
if (typeIds.containsKey(id))\r
{\r