From: kiramt Date: Wed, 11 Oct 2017 07:20:21 +0000 (+0100) Subject: JAL-2742 removed unused getViewAsCigars X-Git-Tag: Release_2_10_3b1~111^2~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=142304c420500eb47ea9af5b9be156caf4afaafd;p=jalview.git JAL-2742 removed unused getViewAsCigars --- diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 9e6d1c0..3cb06c1 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -24,7 +24,6 @@ import jalview.analysis.Conservation; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; -import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.ProfilesI; import jalview.datamodel.SearchResultsI; @@ -243,16 +242,6 @@ public interface AlignViewportI extends ViewStyleI void clearSequenceColours(); /** - * This method returns the visible alignment as text, as seen on the GUI, ie - * if columns are hidden they will not be returned in the result. Use this for - * calculating trees, PCA, redundancy etc on views which contain hidden - * columns. - * - * @return String[] - */ - CigarArray getViewAsCigars(boolean selectedRegionOnly); - - /** * return a compact representation of the current alignment selection to pass * to an analysis function * @@ -486,6 +475,7 @@ public interface AlignViewportI extends ViewStyleI * * @return */ + @Override boolean isProteinFontAsCdna(); /** @@ -493,5 +483,6 @@ public interface AlignViewportI extends ViewStyleI * * @return */ + @Override void setProteinFontAsCdna(boolean b); } diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 3702cd0..b260cab 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -33,7 +33,6 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; -import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; @@ -1673,13 +1672,6 @@ public abstract class AlignmentViewport } @Override - public CigarArray getViewAsCigars(boolean selectedRegionOnly) - { - return new CigarArray(alignment, alignment.getHiddenColumns(), - (selectedRegionOnly ? selectionGroup : null)); - } - - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) {