/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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();
// 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++)
{