From 492b8dc7cde0b6f527d78d2b67a4d4ddc693e006 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 27 Jul 2016 11:55:51 +0100
Subject: [PATCH] JAL-2156 refactor saveState & saveAlignment to common method

---
 src/jalview/gui/Jalview2XML.java |   40 ++++++++++++++++++--------------------
 1 file changed, 19 insertions(+), 21 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 0694525..9861697 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -108,6 +108,7 @@ import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -492,7 +493,20 @@ public class Jalview2XML
     {
       return;
     }
+    saveAllFrames(Arrays.asList(frames), jout);
+  }
 
+  /**
+   * core method for storing state for a set of AlignFrames.
+   * 
+   * @param frames
+   *          - frames involving all data to be exported (including containing
+   *          splitframes)
+   * @param jout
+   *          - project output stream
+   */
+  private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+  {
     Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
 
     /*
@@ -512,9 +526,9 @@ public class Jalview2XML
       List<String> viewIds = new ArrayList<String>();
 
       // REVERSE ORDER
-      for (int i = frames.length - 1; i > -1; i--)
+      for (int i = frames.size() - 1; i > -1; i--)
       {
-        AlignFrame af = frames[i];
+        AlignFrame af = frames.get(i);
         // skip ?
         if (skipList != null
                 && skipList
@@ -617,30 +631,14 @@ public class Jalview2XML
   {
     try
     {
-      int ap = 0;
-      int apSize = af.alignPanels.size();
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
-      Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
-      List<String> viewIds = new ArrayList<String>();
+      List<AlignFrame> frames = new ArrayList<AlignFrame>();
 
-      for (AlignmentPanel apanel : af.alignPanels)
       {
-        String jfileName = apSize == 1 ? fileName : fileName + ap;
-        ap++;
-        if (!jfileName.endsWith(".xml"))
-        {
-          jfileName = jfileName + ".xml";
-        }
-        saveState(apanel, jfileName, jout, viewIds);
-        String dssid = getDatasetIdRef(af.getViewport().getAlignment()
-                .getDataset());
-        if (!dsses.containsKey(dssid))
-        {
-          dsses.put(dssid, af);
-        }
       }
-      writeDatasetFor(dsses, fileName, jout);
+        frames.add(af);
+      saveAllFrames(frames, jout);
       try
       {
         jout.flush();
-- 
1.7.10.2