JAL-2794 most method parameters/class variables made final

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
index aaf7ffb..86f0020 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxInit.java
@@ -22,21 +22,21 @@ public final class ArchaeopteryxInit
    * @param aptxTrees
    * @return
    */
-  public static MainFrame createUnboundInstance(Phylogeny aptxTree)
+  public static MainFrame createUnboundInstance(final Phylogeny aptxTree)
   {
     Phylogeny[] aptxTrees = { aptxTree };
     return createBoundAptxFrame(aptxTrees, null);
   }
 
-  public static MainFrame createInstance(Phylogeny[] aptxTrees,
+  public static MainFrame createInstance(final Phylogeny[] aptxTrees,
           AlignmentViewport jalviewAlignmentView)
   {
     return createBoundAptxFrame(aptxTrees, jalviewAlignmentView);
 
   }
 
-  public static MainFrame createInstance(Phylogeny aptxTree,
-          AlignmentViewport jalviewAlignmentView)
+  public static MainFrame createInstance(final Phylogeny aptxTree,
+          final AlignmentViewport jalviewAlignmentView)
   {
     Phylogeny[] aptxTrees = { aptxTree }; // future possibility to load in
     // several trees simultaneously
@@ -45,7 +45,7 @@ public final class ArchaeopteryxInit
   }
 
   public static MainFrame createInstance(
-          TreeBuilder calculatedTree) // very dense method, to be split up
+          final TreeBuilder calculatedTree) // very dense method, to be split up
   {
     ArchaeopteryxTreeConverter aptxTreeBuilder = new ArchaeopteryxTreeConverter(
             calculatedTree);
@@ -66,8 +66,8 @@ public final class ArchaeopteryxInit
 
 
 
-  private static MainFrame createBoundAptxFrame(Phylogeny[] aptxTrees,
-          AlignmentViewport jalviewAlignmentView)
+  private static MainFrame createBoundAptxFrame(final Phylogeny[] aptxTrees,
+          final AlignmentViewport jalviewAlignmentView)
   {
     MainFrame aptxApp = Archaeopteryx.createApplication(aptxTrees,
             "_aptx_jalview_configuration_file", null);
@@ -75,17 +75,17 @@ public final class ArchaeopteryxInit
     return aptxApp;
   }
 
-  private static void bindNodesToJalviewSequences(MainFrame aptxApp,
-          AlignmentViewport jalviewAlignViewport,
-          Map<SequenceI, PhylogenyNode> alignMappedToNodes,
-          Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+  private static void bindNodesToJalviewSequences(final MainFrame aptxApp,
+          final AlignmentViewport jalviewAlignViewport,
+          final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
+          final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
     new JalviewAptxBinding(aptxApp, jalviewAlignViewport,
             alignMappedToNodes, nodesMappedToAlign);
   }
 
 
-  private static MainFrame bindFrameToJalview(MainFrame aptxApp)
+  private static MainFrame bindFrameToJalview(final MainFrame aptxApp)
   {
     int width = 400;
     int height = 550;

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index 640c3ec..0bdd4e2 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
@@ -15,7 +15,14 @@ import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.NodeData;
 import org.forester.phylogeny.data.Sequence;
 
-public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
+/**
+ * Note that this currently demands a 1:1 relationship between nodes and
+ * sequences
+ * 
+ * @author kjvanderheide
+ *
+ */
+public class ArchaeopteryxTreeConverter
 {
   protected final SequenceI[] sequences;
 
@@ -68,7 +75,7 @@ public class ArchaeopteryxTreeConverter // implements PhylogenyFactory
     for (SequenceI sequence : sequences)
     {
       Sequence seq = ForesterConversions
-              .createForesterSequence(sequence);
+              .createForesterSequence(sequence, true);
       PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
       NodeData nodeData = sequenceNode.getNodeData();
       nodeData.setSequence(seq);

diff --git a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java b/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
index 755828d..9466924 100644 (file)
--- a/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
+++ b/src/jalview/ext/archaeopteryx/JalviewAptxBinding.java
@@ -24,16 +24,16 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
 
   AlignmentViewport parentAvport;
 
-  StructureSelectionManager ssm;
+  final StructureSelectionManager ssm;
 
   Map<SequenceI, PhylogenyNode> sequencesBoundToNodes;
 
   Map<PhylogenyNode, SequenceI> nodesBoundToSequences;
 
-  public JalviewAptxBinding(MainFrame archaeopteryx,
-          AlignmentViewport jalviewAlignmentViewport,
-          Map<SequenceI, PhylogenyNode> alignMappedToNodes,
-          Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
+  public JalviewAptxBinding(final MainFrame archaeopteryx,
+          final AlignmentViewport jalviewAlignmentViewport,
+          final Map<SequenceI, PhylogenyNode> alignMappedToNodes,
+          final Map<PhylogenyNode, SequenceI> nodesMappedToAlign)
   {
     parentAvport = jalviewAlignmentViewport;
     sequencesBoundToNodes = alignMappedToNodes;
@@ -56,7 +56,7 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
   }
 
   @Override
-  public void mousePressed(MouseEvent e)
+  public void mousePressed(final MouseEvent e)
   {
     showNodeSelectionOnAlign(e);
   }
@@ -76,12 +76,14 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
   {
   }
 
+
   @Override
-  public void selection(SequenceGroup seqsel, ColumnSelection colsel,
-          HiddenColumns hidden, SelectionSource source)
+  public void selection(final SequenceGroup seqsel,
+          final ColumnSelection colsel, final HiddenColumns hidden,
+          final SelectionSource source)
   {
     if (source == parentAvport) // check if source is alignment from where the
-                                // tree originates
+    // tree originates
     {
       treeView.setFoundNodes0(
               new HashSet<Long>(seqsel.getSequences().size()));
@@ -103,10 +105,11 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
   }
 
   /**
-   * Note that this currently only checks external nodes
+   * If a node is selected in the tree panel this method highlights the
+   * corresponding sequence in the Jalview alignment view.
    */
   @Override
-  public void showNodeSelectionOnAlign(MouseEvent e)
+  public void showNodeSelectionOnAlign(final MouseEvent e)
   {
     final PhylogenyNode node = treeView.findNode(e.getX(), e.getY());
     if (node != null)
@@ -131,11 +134,13 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
 
         treeSelectionChanged(matchingSequence);
         parentAvport.sendSelection(); // not actually needed?
-
         PaintRefresher.Refresh(treeView, parentAvport.getSequenceSetId());
+
+
       }
     }
 
+
   }
 
   /**
@@ -143,7 +148,7 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
    * 
    * @param sequence
    */
-  public void treeSelectionChanged(SequenceI sequence)
+  public void treeSelectionChanged(final SequenceI sequence)
   {
     SequenceGroup selected = parentAvport.getSelectionGroup();
 
@@ -163,7 +168,7 @@ public class JalviewAptxBinding implements JalviewTreeViewerBindingI
     return parentAvport;
   }
 
-  public void setParentAvport(AlignmentViewport parentAvport)
+  public void setParentAvport(final AlignmentViewport parentAvport)
   {
     this.parentAvport = parentAvport;
   }

diff --git a/src/jalview/ext/forester/ForesterConversions.java b/src/jalview/ext/forester/ForesterConversions.java
index e35132c..5a66974 100644 (file)
--- a/src/jalview/ext/forester/ForesterConversions.java
+++ b/src/jalview/ext/forester/ForesterConversions.java
@@ -9,14 +9,17 @@ import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 public final class ForesterConversions
 {
   public static org.forester.phylogeny.data.Sequence createForesterSequence(
-          SequenceI jalviewSequence)
+          final SequenceI jalviewSequence, final boolean sequenceIsAligned)
   {
     org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
+
     if (jalviewSequence.getDescription() != null)
     {
       foresterSeq.setName(jalviewSequence.getDescription());
     }
-    foresterSeq.setMolecularSequenceAligned(true); // all tree sequences should
+    foresterSeq.setMolecularSequenceAligned(sequenceIsAligned); // all tree
+                                                              // sequences
+                                                              // should
                                                    // be aligned already
     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
     if (jalviewSequence.isProtein()) // add checks for DNA or RNA (infer from