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JAL-1620 version bump and release notes
[jalview.git]
/
src
/
jalview
/
datamodel
/
SequenceI.java
diff --git
a/src/jalview/datamodel/SequenceI.java
b/src/jalview/datamodel/SequenceI.java
index
7722f44
..
64a57ba
100755
(executable)
--- a/
src/jalview/datamodel/SequenceI.java
+++ b/
src/jalview/datamodel/SequenceI.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
@@
-20,7
+20,7
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
-
+import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
@@
-137,10
+137,12
@@
public interface SequenceI
* create a new sequence object from start to end of this sequence
*
* @param start
* create a new sequence object from start to end of this sequence
*
* @param start
- * int
+ * int index for start position
* @param end
* @param end
- * int
+ * int index for end position
+ *
* @return SequenceI
* @return SequenceI
+ * @note implementations may use getSequence to get the sequence data
*/
public SequenceI getSubSequence(int start, int end);
*/
public SequenceI getSubSequence(int start, int end);
@@
-189,7
+191,7
@@
public interface SequenceI
* Returns the sequence position for an alignment position
*
* @param i
* Returns the sequence position for an alignment position
*
* @param i
- * column index in alignment (from 1)
+ * column index in alignment (from 0..<length)
*
* @return residue number for residue (left of and) nearest ith column
*/
*
* @return residue number for residue (left of and) nearest ith column
*/
@@
-315,6
+317,8
@@
public interface SequenceI
public AlignmentAnnotation[] getAnnotation();
public AlignmentAnnotation[] getAnnotation();
+ public boolean hasAnnotation(AlignmentAnnotation ann);
+
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
public void addAlignmentAnnotation(AlignmentAnnotation annotation);
public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
@@
-343,9
+347,22
@@
public interface SequenceI
public AlignmentAnnotation[] getAnnotation(String label);
/**
public AlignmentAnnotation[] getAnnotation(String label);
/**
+ * Return a list of any annotations which match the given calcId (source) and
+ * label (type). Null values do not match.
+ *
+ * @param calcId
+ * @param label
+ * @return
+ */
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label);
+
+ /**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
- * references on the sequence onto the dataset.
+ * references on the sequence onto the dataset. It will also make a duplicate
+ * of existing annotation rows for the dataset sequence, rather than relocate
+ * them in order to preserve external references (since 2.8.2).
*
* @return dataset sequence for this sequence
*/
*
* @return dataset sequence for this sequence
*/
@@
-353,7
+370,9
@@
public interface SequenceI
/**
* Transfer any database references or annotation from entry under a sequence
/**
* Transfer any database references or annotation from entry under a sequence
- * mapping.
+ * mapping. <br/>
+ * <strong>Note: DOES NOT transfer sequence associated alignment
+ * annotation </strong><br/>
*
* @param entry
* @param mp
*
* @param entry
* @param mp
@@
-371,17
+390,17
@@
public interface SequenceI
* @return The index of the sequence in the alignment
*/
public int getIndex();
* @return The index of the sequence in the alignment
*/
public int getIndex();
-
+
/**
* @return The RNA of the sequence in the alignment
*/
/**
* @return The RNA of the sequence in the alignment
*/
-
+
public RNA getRNA();
public RNA getRNA();
-
+
/**
/**
- * @param rna The RNA.
+ * @param rna
+ * The RNA.
*/
public void setRNA(RNA rna);
*/
public void setRNA(RNA rna);
-
}
}