X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=06e93d7a4322aea1f8b8feb2267d0a071e4f2c22;hb=54904100ca490c7ca4484a88bf40963e48a35eec;hp=e14c1e96db8aa9edcb1dff11d617de9967b5ca88;hpb=c1ffd6dd15b79a56ec0a37eebbe4df05341ca57c;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index e14c1e9..06e93d7 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -111,17 +111,8 @@ public interface AlignmentI * @param start Start index of columns to delete. * @param end End index to columns to delete. */ - public void deleteColumns(int start, int end); + public void deleteColumns(SequenceI seqs [], int start, int end); - /** - * Deletes all residues in every sequence of alignment within given columns. - * - * @param seq1 Index of first sequence to delete columns from. - * @param seq2 Index of last sequence to delete columns from. - * @param start Start index of columns to delete. - * @param end End index of columns to delete. - */ - public void deleteColumns(int seq1, int seq2, int start, int end); /** * Finds sequence in alignment using sequence name as query. @@ -161,25 +152,7 @@ public interface AlignmentI */ public void removeGaps(); - /** - * Removes redundant sequences from alignment. - * - * @param threshold Remove all sequences above the given threshold. - * @param sel Set of sequences which will have redundant sequences removed from. - * - * @return All sequences below redundancy threshold. - */ - public Vector removeRedundancy(float threshold, Vector sel); - /** - * Finds group that sequence at index i in alignment is part of. - * - * @param i Index in alignment. - * - * @return First group found for sequence at position i. WARNING : - * Sequences may be members of several groups. This method is incomplete. - */ - public SequenceGroup findGroup(int i); /** * Finds group that given sequence is part of. @@ -297,5 +270,9 @@ public interface AlignmentI public void adjustSequenceAnnotations(); public HiddenSequences getHiddenSequences(); - + /** + * Compact representation of alignment + * @return CigarArray + */ + public CigarArray getCompactAlignment(); }