X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=d35d3f7efb64126b22c71e36c726800a58e0898d;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=71467f72ea57d71a14b8a0b9d97534e8eb0accee;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 71467f7..d35d3f7 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -1,18 +1,18 @@
/*
* 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
- *
+ *
* 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
+ * 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
+ *
+ * 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
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.datamodel;
@@ -36,6 +36,7 @@ public interface AlignmentI extends AnnotatedCollectionI
*
* @return Greatest sequence length within alignment.
*/
+ @Override
public int getWidth();
/**
@@ -56,11 +57,12 @@ public interface AlignmentI extends AnnotatedCollectionI
public boolean isAligned(boolean includeHidden);
/**
- * Gets sequences as a Vector
+ * Gets sequences as a Synchronized collection
*
* @return All sequences in alignment.
*/
- public Vector getSequences();
+ @Override
+ public List getSequences();
/**
* Gets sequences as a SequenceI[]
@@ -236,6 +238,7 @@ public interface AlignmentI extends AnnotatedCollectionI
*
* @return array of AlignmentAnnotation objects
*/
+ @Override
public AlignmentAnnotation[] getAlignmentAnnotation();
/**
@@ -434,13 +437,36 @@ public interface AlignmentI extends AnnotatedCollectionI
/**
* 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
- */
- public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
- SequenceI seqRef, SequenceGroup groupRef);
+ *
+ * @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,
+ 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.
+ *
+ * @param sg
+ * @param map
+ * @param up
+ * @param i
+ */
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map map, boolean up);
}