JAL-2805 removed unused Aptx instance creation code

[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 0337829..9b89cea 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -1,10 +1,8 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.analysis.TreeBuilder;
 import jalview.ext.forester.io.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.TreeViewerUtils;
@@ -75,25 +73,31 @@ public final class AptxInit
           .getTaxonomyExtraction();
 
 
+  public static TreeFrameI createInstanceFromNhx(String treeTitle,
+          String nhxString, AlignmentViewport viewport)
+          throws IOException
+  {
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.startLoading(treeTitle);
+    }
 
+    Phylogeny aptxPhylogeny = Phylogeny
+            .createInstanceFromNhxString(nhxString);
+    aptxPhylogeny.setName(treeTitle);
 
+    TreeFrameI aptxFrame = createAptxFrame(aptxPhylogeny, viewport,
+            treeTitle);
 
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
 
-  public static TreeFrameI createInstanceFromCalculation(
-          final TreeBuilder calculatedTree)
-  {
-    TreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
-            calculatedTree);
-
-    TreeI aptxTree = aptxTreeBuilder.buildTree();
+    return aptxFrame;
 
-    TreeFrameI aptxApp = createAptxFrame(aptxTree,
-            calculatedTree.getAvport(), null);
-            
-    return aptxApp;
   }
 
-
   /**
    * Refactored from Archaeopteryx.main
    * 
@@ -103,77 +107,84 @@ public final class AptxInit
    * @throws IOException
    * @throws FileNotFoundException
    */
-  public static TreeFrameI[] createInstancesFromFile(
-          String filePath,
+  public static TreeFrameI[] createInstancesFromFile(File treeFile,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException
   {
-    File treeFile = new File(filePath);
     TreeFrameI[] aptxFrames = null;
     if (UtilityMethods.canForesterReadFile(treeFile))
     {
 
-    if (Desktop.instance != null)
-    {
-      Desktop.instance.startLoading(filePath);
-    }
-    boolean nhx_or_nexus = false;
-    final PhylogenyParser parser = ParserUtils
-            .createParserDependingOnFileType(
-            treeFile, VALIDATE_PHYLOXML_XSD);
-    if (parser instanceof NHXParser)
-    {
-      nhx_or_nexus = true;
-      final NHXParser nhx = (NHXParser) parser;
-      nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
-      nhx.setIgnoreQuotes(false);
-      nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
-    }
-    else if (parser instanceof NexusPhylogeniesParser)
-    {
-      nhx_or_nexus = true;
-      final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
-      nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
-      nex.setIgnoreQuotes(false);
-    }
-    else if (parser instanceof PhyloXmlParser)
-    {
-      if (VALIDATE_PHYLOXML_XSD == false)
+      if (Desktop.instance != null)
       {
-        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                MessageManager.getString("error.phyloxml_validation"),
-                MessageManager.getString("label.file_open_error"),
-                                       JvOptionPane.WARNING_MESSAGE );
+        Desktop.instance.startLoading(treeFile.getCanonicalPath());
       }
-    }
-    Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser,
-            treeFile);
+      boolean nhx_or_nexus = false;
+      final PhylogenyParser parser = ParserUtils
+              .createParserDependingOnFileType(treeFile,
+                      VALIDATE_PHYLOXML_XSD);
+      if (parser instanceof NHXParser)
+      {
+        nhx_or_nexus = true;
+        final NHXParser nhx = (NHXParser) parser;
+        nhx.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+        nhx.setIgnoreQuotes(false);
+        nhx.setTaxonomyExtraction(TAXONOMY_EXTRACTION);
+      }
+      else if (parser instanceof NexusPhylogeniesParser)
+      {
+        nhx_or_nexus = true;
+        final NexusPhylogeniesParser nex = (NexusPhylogeniesParser) parser;
+        nex.setReplaceUnderscores(REPLACE_NHX_UNDERSCORES);
+        nex.setIgnoreQuotes(false);
+      }
+      else if (parser instanceof PhyloXmlParser)
+      {
+        if (VALIDATE_PHYLOXML_XSD == false)
+        {
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  MessageManager.getString("error.phyloxml_validation"),
+                  MessageManager.getString("label.file_open_error"),
+                  JvOptionPane.WARNING_MESSAGE);
+        }
+      }
+      Phylogeny[] trees = PhylogenyMethods.readPhylogenies(parser,
+              treeFile);
       aptxFrames = new TreeFrameI[trees.length];
 
-
-    for (int i = 0; i < trees.length; i++)
+      for (int i = 0; i < trees.length; i++)
       {
-      Phylogeny aptxPhylogeny = trees[i];
+        Phylogeny aptxPhylogeny = trees[i];
 
-      if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
-      {
-        PhylogenyMethods.transferInternalNodeNamesToConfidence(aptxPhylogeny,
-                "");
-      }
-      String treeTitle = treeFile.getName() + "[" + i + "]";
-      aptxPhylogeny.setName(treeTitle);
+        if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+        {
+          PhylogenyMethods
+                  .transferInternalNodeNamesToConfidence(aptxPhylogeny, "");
+        }
+        String treeTitle = treeFile.getName() + "[" + i + "]";
+        aptxPhylogeny.setName(treeTitle);
         aptxFrames[i] = createAptxFrame(aptxPhylogeny, viewport, treeTitle);
 
-    }
-    if (Desktop.instance != null)
-    {
-      Desktop.instance.stopLoading();
+      }
+      if (Desktop.instance != null)
+      {
+        Desktop.instance.stopLoading();
       }
     }
     return aptxFrames;
-    }
+  }
 
 
+  public static TreeFrameI[] createInstancesFromFile(
+          String filePath,
+          AlignmentViewport viewport)
+          throws FileNotFoundException, IOException
+  {
+    File treeFile = new File(filePath);
+    return createInstancesFromFile(treeFile, viewport);
+
+    }
+
   public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException, RuntimeException
@@ -465,12 +476,9 @@ public final class AptxInit
         {
           // Not important if this fails, do nothing.
         }
-        // _main_frame.getContentPane().repaint();
       }
     }
 
-    System.gc();
-
 
     if (Desktop.instance != null)
     {