X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=6ec31ef9886fdfe3827e1c470725960940a498a0;hb=8647c805617f33b905c4f72ebe30aab3c21b56f4;hp=fe49488f18fce3d4cfec2b491cf33b60b630e23b;hpb=4663ab6ec8142df859d031bff618d78809e22082;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index fe49488..6ec31ef 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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. * @@ -40,7 +40,7 @@ import java.util.Map; * @author jimp * */ -public interface AlignViewportI +public interface AlignViewportI extends ViewStyleI { int getCharWidth(); @@ -77,8 +77,6 @@ public interface AlignViewportI Hashtable[] getRnaStructureConsensusHash(); - - boolean getCentreColumnLabels(); boolean isIgnoreGapsConsensus(); boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation); @@ -320,10 +318,9 @@ public interface AlignViewportI * first column (inclusive, from 0) * @param max * last column (exclusive) - * @return int[][] range of {start,end} visible positions TODO: change to list - * of int ranges + * @return int[][] range of {start,end} visible positions */ - int[][] getVisibleRegionBoundaries(int min, int max); + List getVisibleRegionBoundaries(int min, int max); /** * This method returns an array of new SequenceI objects derived from the @@ -366,4 +363,33 @@ public interface AlignViewportI * @param settingsForView */ public void setViewStyle(ViewStyleI settingsForView); + + /** + * Returns a viewport which holds the cDna for this (protein), or vice versa, + * or null if none is set. + * + * @return + */ + AlignViewportI getCodingComplement(); + + /** + * Sets the viewport which holds the cDna for this (protein), or vice versa. + * Implementation should guarantee that the reciprocal relationship is always + * set, i.e. each viewport is the complement of the other. + */ + void setCodingComplement(AlignViewportI sl); + + /** + * Answers true if viewport hosts DNA/RNA, else false. + * + * @return + */ + boolean isNucleotide(); + + /** + * Returns an id guaranteed to be unique for this viewport. + * + * @return + */ + String getViewId(); }