X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=5df38d600d8efbb01db37592e92522741035a88d;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=8482f6b2a9441f80e1198c8adf6b53e7b76acf6c;hpb=882adcab8cf6f9c72a7e946223f817878c5ee444;p=jalview.git diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 8482f6b..5df38d6 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -20,11 +20,6 @@ */ package jalview.api; -import java.awt.Color; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; - import jalview.analysis.Conservation; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -36,6 +31,11 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; +import java.awt.Color; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; + /** * @author jimp * @@ -178,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI */ void updateGroupAnnotationSettings(boolean applyGlobalSettings, boolean preserveNewGroupSettings); - + void setSequenceColour(SequenceI seq, Color col); Color getSequenceColour(SequenceI seq); @@ -251,8 +251,11 @@ public interface AlignViewportI extends ViewStyleI /** * get a copy of the currently visible alignment annotation - * @param selectedOnly if true - trim to selected regions on the alignment - * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only + * + * @param selectedOnly + * if true - trim to selected regions on the alignment + * @return an empty list or new alignment annotation objects shown only + * visible columns trimmed to selected region only */ List getVisibleAlignmentAnnotation( boolean selectedOnly);