*/
package jalview.io;
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
public class ModellerDescription
{
* single line, and sequence start/end and other properties. See PIRFile IO
* for its use.
*/
- final String[] seqTypes =
- { "sequence", "structure", "structureX", "structureN" };
+ final String[] seqTypes = { "sequence", "structure", "structureX",
+ "structureN" };
- final String[] Fields =
- { "objectType", "objectId", "startField", "startCode", "endField",
- "endCode", "description1", "description2", "resolutionField",
- "tailField" };
+ final String[] Fields = { "objectType", "objectId", "startField",
+ "startCode", "endField", "endCode", "description1", "description2",
+ "resolutionField", "tailField" };
final int TYPE = 0;
/**
* 0 is free text or empty 1 is something that parses to an integer, or \@
*/
- final int Types[] =
- { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
+ final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
- final char Padding[] =
- { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.' };
+ final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
+ '.' };
java.util.Hashtable fields = new java.util.Hashtable();
resCode(int v)
{
- val = new Integer(v);
+ val = Integer.valueOf(v);
field = val.toString();
}
};
{
// Set start and end before we update the type (in the case of a
// synthesized field set)
- if (getStartCode() == null
- || (getStartNum() != seq.getStart() && getStartCode().val != null))
+ if (getStartCode() == null || (getStartNum() != seq.getStart()
+ && getStartCode().val != null))
{
// unset or user updated sequence start position
setStartCode(seq.getStart());
}
- if (getEndCode() == null
- || (getEndNum() != seq.getEnd() && getStartCode() != null && getStartCode().val != null))
+ if (getEndCode() == null || (getEndNum() != seq.getEnd()
+ && getStartCode() != null && getStartCode().val != null))
{
setEndCode(seq.getEnd());
}
// sets the local reference field
int t = 0; // sequence
if (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getDBRef() != null)
+ && seq.getDatasetSequence().getDBRefs() != null)
{
jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
- .getDBRef();
+ .getDBRefs();
int i, j;
for (i = 0, j = dbr.length; i < j; i++)
{