/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
*
* @return Greatest sequence length within alignment.
*/
+ @Override
public int getWidth();
/**
/**
* Gets sequences as a Synchronized collection
- *
+ *
* @return All sequences in alignment.
*/
@Override
*
* @return array of AlignmentAnnotation objects
*/
+ @Override
public AlignmentAnnotation[] getAlignmentAnnotation();
/**
/**
* search for or create a specific annotation row on the alignment
- *
- * @param method - CalcId for the annotation (must match)
- * @param autoCalc - value of autocalc flag for the annotation
- * @param seqRef - null or specific sequence reference
- * @param groupRef - null or specific group reference
- * @return existing annotation matching the given attributes
+ *
+ * @param name
+ * name for annotation (must match)
+ * @param calcId
+ * calcId for the annotation (null or must match)
+ * @param autoCalc
+ * - value of autocalc flag for the annotation
+ * @param seqRef
+ * - null or specific sequence reference
+ * @param groupRef
+ * - null or specific group reference
+ * @param method
+ * - CalcId for the annotation (must match)
+ *
+ * @return existing annotation matching the given attributes
*/
- public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
- SequenceI seqRef, SequenceGroup groupRef);
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef);
/**
- * move the given group up or down in the alignment by the given number of rows.
- * Implementor assumes given group is already present on alignment - no recalculations are triggered.
+ * move the given group up or down in the alignment by the given number of
+ * rows. Implementor assumes given group is already present on alignment - no
+ * recalculations are triggered.
+ *
* @param sg
* @param map
* @param up