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Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentI.java
diff --git
a/src/jalview/datamodel/AlignmentI.java
b/src/jalview/datamodel/AlignmentI.java
index
2209f87
..
752235b
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentI.java
+++ b/
src/jalview/datamodel/AlignmentI.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
*
* This file is part of Jalview.
*
@@
-156,15
+156,16
@@
public interface AlignmentI extends AnnotatedCollectionI
int findIndex(SequenceI s);
/**
int findIndex(SequenceI s);
/**
- * Finds group that given sequence is part of.
+ * Returns the first group (in the order in which groups were added) that
+ * includes the given sequence and aligned position (base 0), or null if none
+ * found
*
*
- * @param s
- * Sequence in alignment.
+ * @param seq
+ * @param position
*
*
- * @return First group found for sequence. WARNING : Sequences may be members
- * of several groups. This method is incomplete.
+ * @return
*/
*/
- SequenceGroup findGroup(SequenceI s);
+ SequenceGroup findGroup(SequenceI seq, int position);
/**
* Finds all groups that a given sequence is part of.
/**
* Finds all groups that a given sequence is part of.
@@
-284,13
+285,6
@@
public interface AlignmentI extends AnnotatedCollectionI
char getGapCharacter();
/**
char getGapCharacter();
/**
- * Test for all nucleotide alignment
- *
- * @return true if alignment is nucleotide sequence
- */
- boolean isNucleotide();
-
- /**
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
* Test if alignment contains RNA structure
*
* @return true if RNA structure AligmnentAnnotation was added to alignment
@@
-298,12
+292,6
@@
public interface AlignmentI extends AnnotatedCollectionI
boolean hasRNAStructure();
/**
boolean hasRNAStructure();
/**
- * Set alignment to be a nucleotide sequence
- *
- */
- void setNucleotide(boolean b);
-
- /**
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
* Get the associated dataset for the alignment.
*
* @return Alignment containing dataset sequences or null of this is a
@@
-426,7
+414,7
@@
public interface AlignmentI extends AnnotatedCollectionI
* @param results
* @return -1 or index of sequence in alignment
*/
* @param results
* @return -1 or index of sequence in alignment
*/
- int findIndex(SearchResults results);
+ int findIndex(SearchResultsI results);
/**
* append sequences and annotation from another alignment object to this one.
/**
* append sequences and annotation from another alignment object to this one.