X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=e99563b9586694800c734989812d3b84c655f9b1;hb=HEAD;hp=084b80e4212dc2f22fa8324b452e472c9bd44977;hpb=842f1ce11feca83cb655ca764c9b3f3541d2034c;p=jalview.git diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 084b80e..e99563b 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -48,15 +48,29 @@ public interface AlignmentI extends AnnotatedCollectionI /** * - * Calculates the maximum width of the alignment, including gaps. + * Answers the width of the alignment, including gaps, that is, the length of + * the longest sequence, or -1 if there are no sequences. Avoid calling this + * method repeatedly where possible, as it has to perform a calculation. Note + * that this width includes any hidden columns. * - * @return Greatest sequence length within alignment, or -1 if no sequences - * present + * @return + * @see AlignmentI#getVisibleWidth() */ @Override int getWidth(); /** + * + * Answers the visible width of the alignment, including gaps, that is, the + * length of the longest sequence, excluding any hidden columns. Answers -1 if + * there are no sequences. Avoid calling this method repeatedly where + * possible, as it has to perform a calculation. + * + * @return + */ + int getVisibleWidth(); + + /** * Calculates if this set of sequences (visible and invisible) are all the * same length * @@ -580,6 +594,33 @@ public interface AlignmentI extends AnnotatedCollectionI */ AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo); - public void setHiddenColumns(HiddenColumns cols); + /** + * Set the hidden columns collection on the alignment. Answers true if the + * hidden column selection changed, else false. + * + * @param cols + * @return + */ + public boolean setHiddenColumns(HiddenColumns cols); + + /** + * Set the first sequence as representative and hide its insertions. Typically + * used when loading JPred files. + */ + public void setupJPredAlignment(); + /** + * Add gaps into the sequences aligned to profileseq under the given + * AlignmentView + * + * @param profileseq + * sequence in al which sequences are aligned to + * @param input + * alignment view where sequence corresponding to profileseq is first + * entry + * @return new HiddenColumns for new alignment view, with insertions into + * profileseq marked as hidden. + */ + public HiddenColumns propagateInsertions(SequenceI profileseq, + AlignmentView input); }