From 6ca3c1f776640accdca0526bc3c426e77c49b2cd Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Tue, 14 Nov 2017 16:00:29 +0000 Subject: [PATCH] JAL-2805 finished up interface comments --- src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java | 5 ++++- src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java | 3 +++ src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java | 4 +++- src/jalview/ext/forester/io/ExternalTreeParserI.java | 5 ++++- 4 files changed, 14 insertions(+), 3 deletions(-) diff --git a/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java b/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java index 08a0cdc..5e820b7 100644 --- a/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java +++ b/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java @@ -3,7 +3,10 @@ package jalview.ext.archaeopteryx; import jalview.datamodel.SequenceI; /** - * Note that this will take anything as a Tree object. + * Interface for associating the leaves of a loaded in (not calculated) tree to + * the alignment sequences in Jalview. Note that this will take anything as a + * Tree object as no assumptions can be made about the inheritance structure of + * Tree (besides being an Object). * * @author kjvanderheide * diff --git a/src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java b/src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java index 8f10e73..17ae7f8 100644 --- a/src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java +++ b/src/jalview/ext/archaeopteryx/ExternalTreeBuilderI.java @@ -5,6 +5,9 @@ import jalview.datamodel.SequenceI; import java.util.Map; /** + * Note that this will take anything as a Tree or TreeNode object as no + * assumptions can be made about the inheritance structure of Tree or TreeNode + * (besides being Objects). * * @author kjvanderheide * diff --git a/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java b/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java index 2a807a3..8acbbf0 100644 --- a/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java +++ b/src/jalview/ext/archaeopteryx/ExternalTreeViewerBindingI.java @@ -31,7 +31,9 @@ import java.awt.event.MouseListener; /** * * Interface for binding a tree viewer to Jalview alignments. Assumes a tree - * viewer will both want to receive and send selection events. + * viewer will both want to receive and send selection events. Note that this + * will take anything as a TreeNode object as no assumptions can be made about + * the inheritance structure of the TreeNode (besides being an Object). * * @author kjvanderheide * diff --git a/src/jalview/ext/forester/io/ExternalTreeParserI.java b/src/jalview/ext/forester/io/ExternalTreeParserI.java index 2c26623..2d912a1 100644 --- a/src/jalview/ext/forester/io/ExternalTreeParserI.java +++ b/src/jalview/ext/forester/io/ExternalTreeParserI.java @@ -1,8 +1,11 @@ package jalview.ext.forester.io; +import jalview.viewmodel.AlignmentViewport; + import javax.swing.JInternalFrame; /** + * Interface for loading in existing trees to an external tree viewer. * * @author kjvanderheide * @@ -11,5 +14,5 @@ import javax.swing.JInternalFrame; */ public interface ExternalTreeParserI { - public F loadTree(); + public F loadTree(AlignmentViewport viewport); } -- 1.7.10.2