JAL-1953 moved now-generic methods outside of Aptx package

[jalview.git] / src / jalview / ext / archaeopteryx / AptxInit.java

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index 5752e51..d0ec425 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -1,28 +1,23 @@
 package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
-import jalview.datamodel.SequenceI;
 import jalview.ext.forester.UtilityMethods;
 import jalview.ext.treeviewer.LoadedTreeAssociationI;
+import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
 import jalview.ext.treeviewer.TreeBuilderI;
 import jalview.ext.treeviewer.TreeFrameI;
 import jalview.ext.treeviewer.TreeI;
-import jalview.ext.treeviewer.TreeNodeI;
-import jalview.ext.treeviewer.TreeViewerBindingI;
-import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
+import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.Dimension;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
-import java.util.HashMap;
-import java.util.Map;
 
 import org.forester.archaeopteryx.AptxUtil;
 import org.forester.archaeopteryx.Configuration;
@@ -74,7 +69,7 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
-  private static Map<TreeFrameI, TreeViewerBindingI> activeAptx = new HashMap<>();
+
 
 
 
@@ -495,10 +490,10 @@ public final class AptxInit
             jalviewTree);
     bindAptxNodes.associateLeavesToSequences();
 
-    bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
+    TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
             bindAptxNodes.getAlignmentWithNodes(),
             bindAptxNodes.getNodesWithAlignment());
-    bindTreeViewFrameToJalview(aptxApp);
+    TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
 
     // adaptAptxGui(aptxApp); //moved to AptxFrame
     return aptxApp;
@@ -518,52 +513,16 @@ public final class AptxInit
             jalviewTree);
     bindAptxNodes.associateLeavesToSequences();
 
-    bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
+    TreeViewerUtils.associateNodesWithJalviewSequences(aptxApp, jalviewAlignport,
             bindAptxNodes.getAlignmentWithNodes(),
             bindAptxNodes.getNodesWithAlignment());
-    bindTreeViewFrameToJalview(aptxApp);
+    TreeViewerUtils.addTreeViewFrameToJalview(aptxApp);
 
     // adaptAptxGui(aptxApp); //moved to AptxFrame
     return aptxApp;
   }
 
 
-  protected static TreeViewerBindingI bindNodesToJalviewSequences(
-          final TreeFrameI aptxApp,
-          final AlignmentViewport jalviewAlignViewport,
-          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
-          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
-  {
-    TreeViewerBindingI treeBinding = new JalviewBinding(aptxApp,
-            jalviewAlignViewport,
-            alignMappedToNodes, nodesMappedToAlign);
-    activeAptx.put(aptxApp, treeBinding);
-    return treeBinding;
-  }
-
-
-  protected static TreeFrameI bindTreeViewFrameToJalview(
-          final TreeFrameI aptxApp)
-  {
-    int width = 400;
-    int height = 550;
-    aptxApp.setMinimumSize(new Dimension(width, height));
-    // aptxApp.setFont(Desktop.instance.getFont());
-    // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
-    String frameTitle = MessageManager.getString("label.aptx_title");
-    File treeFile = aptxApp.getTreePanel().getTreeFile();
-    if (treeFile != null)
-    {
-      frameTitle += MessageManager.formatMessage("label.aptx_title_append",
-              new String[]
-              { treeFile.getAbsolutePath() });
-    }
-    aptxApp.addFrameToJalview(frameTitle, true, width, height, true,
-            true);
-    return aptxApp;
-
-  }
-
   private static boolean validateConfig(Configuration aptxConfig)
   {
     if (aptxConfig == null || aptxConfig.isCouldReadConfigFile() == false)
@@ -587,11 +546,4 @@ public final class AptxInit
   }
 
 
-
-  public static Map<TreeFrameI, TreeViewerBindingI> getAllAptxFrames()
-  {
-    return activeAptx;
-  }
-
-
 }