From 93d63f3c608771bb48b5ac18f761194a1ea28554 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 17 Jun 2015 21:50:15 +0100
Subject: [PATCH] JAL-1784 refactor parse method to directly parse FileParser
 input reader stream.

---
 src/jalview/io/HtmlFile.java |    5 ++---
 src/jalview/io/JSONFile.java |   35 +++++++++++++++--------------------
 2 files changed, 17 insertions(+), 23 deletions(-)

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 73aa5d2..e847c58 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -22,6 +22,7 @@
 package jalview.io;
 
 import java.io.IOException;
+import java.io.StringReader;
 
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
@@ -75,9 +76,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
       Document doc = Jsoup.parse(htmlData.toString());
       Element content = doc.getElementById("seqData");
-      String alignmentJsonString = content.val();
-
-      JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
+      JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
       this.seqs = jsonFile.getSeqs();
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index f977b04..bbbc122 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -21,18 +21,6 @@
 
 package jalview.io;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
-
 import jalview.api.AlignViewportI;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
@@ -55,6 +43,19 @@ import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+
 public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private ColourSchemeI colourScheme;
@@ -105,13 +106,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @Override
   public void parse() throws IOException
   {
-    StringBuilder jsonStringBuilder = new StringBuilder();
-    String currentLine;
-    while ((currentLine = nextLine()) != null)
-    {
-      jsonStringBuilder.append(currentLine);
-    }
-    parse(jsonStringBuilder.toString());
+    parse(getReader());
 
   }
 
@@ -354,7 +349,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   @SuppressWarnings("unchecked")
-  public JSONFile parse(String jsonAlignmentString)
+  public JSONFile parse(Reader jsonAlignmentString)
   {
     try
     {
-- 
1.7.10.2