JAL-2805 finished up interface comments

diff --git a/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java b/src/jalview/ext/archaeopteryx/ExternalLoadedTreeAssociationI.java
index 08a0cdc..5e820b7 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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<F extends JInternalFrame>
 {
-  public F loadTree();
+  public F loadTree(AlignmentViewport viewport);
 }