From 19262eceac6a9d7a77c5a4220ab07042bd545e98 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 9 Jan 2018 11:51:02 +0000
Subject: [PATCH] JAL-2805 added Aptx factory method reading directly from a
 File

---
 src/jalview/ext/archaeopteryx/AptxInit.java |  126 ++++++++++++++-------------
 1 file changed, 66 insertions(+), 60 deletions(-)

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index f8347bd..ba34213 100644
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -88,84 +88,90 @@ public final class AptxInit
     return aptxApp;
   }
 
-
-  /**
-   * Refactored from Archaeopteryx.main
-   * 
-   * @param filePath
-   * @param viewport
-   * @return
-   * @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;
+  }
+
+  /**
+   * Refactored from Archaeopteryx.main
+   * 
+   * @param filePath
+   * @param viewport
+   * @return
+   * @throws IOException
+   * @throws FileNotFoundException
+   */
+  public static TreeFrameI[] createInstancesFromFile(
+          String filePath,
+          AlignmentViewport viewport)
+          throws FileNotFoundException, IOException
+  {
+    File treeFile = new File(filePath);
+    return createInstancesFromFile(treeFile, viewport);
+
     }
 
 
-- 
1.7.10.2