From 9c2e22bf15e9679ff71cc1e6d0d490c26b4df5ad Mon Sep 17 00:00:00 2001 From: kjvdheide Date: Mon, 13 Nov 2017 20:07:06 +0000 Subject: [PATCH] JAL-2805 some more name changes --- .../{AptxAssociation.java => AptxNodeAssociation.java} | 4 ++-- src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java | 4 ++-- .../{ForesterConversions.java => ForesterDataConversions.java} | 2 +- src/jalview/ext/forester/ForesterMatrix.java | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) rename src/jalview/ext/archaeopteryx/{AptxAssociation.java => AptxNodeAssociation.java} (96%) rename src/jalview/ext/forester/{ForesterConversions.java => ForesterDataConversions.java} (98%) diff --git a/src/jalview/ext/archaeopteryx/AptxAssociation.java b/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java similarity index 96% rename from src/jalview/ext/archaeopteryx/AptxAssociation.java rename to src/jalview/ext/archaeopteryx/AptxNodeAssociation.java index 0dfccdf..ec7ca27 100644 --- a/src/jalview/ext/archaeopteryx/AptxAssociation.java +++ b/src/jalview/ext/archaeopteryx/AptxNodeAssociation.java @@ -9,14 +9,14 @@ import java.util.List; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyNode; -public class AptxAssociation +public class AptxNodeAssociation implements ExternalLoadedTreeAssociationI { SequenceI[] alignSequences; Phylogeny tree; - public AptxAssociation(SequenceI[] alignmentSequences, + public AptxNodeAssociation(SequenceI[] alignmentSequences, Phylogeny aptxTree) { alignSequences = alignmentSequences; diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java index 02ecdf0..af270c2 100644 --- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java +++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java @@ -2,7 +2,7 @@ package jalview.ext.archaeopteryx; import jalview.analysis.TreeBuilder; import jalview.datamodel.SequenceI; -import jalview.ext.forester.ForesterConversions; +import jalview.ext.forester.ForesterDataConversions; import jalview.ext.forester.ForesterMatrix; import jalview.util.MessageManager; @@ -80,7 +80,7 @@ public class ArchaeopteryxTreeBuilder for (SequenceI sequence : sequences) { - Sequence seq = ForesterConversions + Sequence seq = ForesterDataConversions .createForesterSequence(sequence, true); PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName()); NodeData nodeData = sequenceNode.getNodeData(); diff --git a/src/jalview/ext/forester/ForesterConversions.java b/src/jalview/ext/forester/ForesterDataConversions.java similarity index 98% rename from src/jalview/ext/forester/ForesterConversions.java rename to src/jalview/ext/forester/ForesterDataConversions.java index 5a66974..6168820 100644 --- a/src/jalview/ext/forester/ForesterConversions.java +++ b/src/jalview/ext/forester/ForesterDataConversions.java @@ -6,7 +6,7 @@ import jalview.math.MatrixI; import org.forester.evoinference.matrix.distance.DistanceMatrix; import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException; -public final class ForesterConversions +public final class ForesterDataConversions { public static org.forester.phylogeny.data.Sequence createForesterSequence( final SequenceI jalviewSequence, final boolean sequenceIsAligned) diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java index 7d3d295..6c60622 100644 --- a/src/jalview/ext/forester/ForesterMatrix.java +++ b/src/jalview/ext/forester/ForesterMatrix.java @@ -166,7 +166,7 @@ public class ForesterMatrix implements DistanceMatrix final MatrixI jalviewInputMatrix, final SequenceI[] matrixSequences) { - return ForesterConversions.createForesterDistanceMatrix( + return ForesterDataConversions.createForesterDistanceMatrix( jalviewInputMatrix, matrixSequences); } @@ -175,7 +175,7 @@ public class ForesterMatrix implements DistanceMatrix final MatrixI jalviewInputMatrix, final String[] matrixIdentifiers) { - return ForesterConversions.createForesterDistanceMatrix( + return ForesterDataConversions.createForesterDistanceMatrix( jalviewInputMatrix, matrixIdentifiers); } -- 1.7.10.2