From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 17 Oct 2019 13:02:21 +0000 (+0100)
Subject: JAL-3436 move/rename/private fields refactoring only
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e7921fdc9d6ab87ef91bb7781dd7d9316e671e3f;p=jalview.git

JAL-3436 move/rename/private fields refactoring only
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0c25262..2ef31a2 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -194,9 +194,9 @@ public class AlignFrame extends GAlignFrame
   /**
    * Current filename for this alignment
    */
-  String fileName = null;
+  private String fileName = null;
 
-  File fileObject;
+  private File fileObject;
 
   /**
    * Creates a new AlignFrame object with specific width and height.
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ccfe460..9507a87 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -161,6 +161,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
@@ -266,6 +267,25 @@ public class Jalview2XML
   private Map<RnaModel, String> rnaSessions = new HashMap<>();
 
   /**
+   * contains last error message (if any) encountered by XML loader.
+   */
+  String errorMessage = null;
+
+  /**
+   * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+   * exceptions are raised during project XML parsing
+   */
+  public boolean attemptversion1parse = false;
+
+  /*
+   * JalviewJS only -- to allow read file bytes to be saved in the
+   * created AlignFrame, allowing File | Reload of a project file to work
+   * 
+   * BH 2019 JAL-3436
+   */
+  private File jarFile;
+
+  /**
    * A helper method for safely using the value of an optional attribute that
    * may be null if not present in the XML. Answers the boolean value, or false
    * if null.
@@ -2731,24 +2751,6 @@ public class Jalview2XML
   }
 
   /**
-   * contains last error message (if any) encountered by XML loader.
-   */
-  String errorMessage = null;
-
-  /**
-   * flag to control whether the Jalview2XML_V1 parser should be deferred to if
-   * exceptions are raised during project XML parsing
-   */
-  public boolean attemptversion1parse = false;
-
-  /**
-   * JalviewJS only -- to preserve bytes in AlignFrame
-   * 
-   * BH 2019 JAL-3436
-   */
-  private File file;
-
-  /**
    * Load a jalview project archive from a jar file
    * 
    * @param file
@@ -2800,55 +2802,50 @@ public class Jalview2XML
   }
 
 	@SuppressWarnings("unused")
-	private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
-
-		// BH 2018 allow for bytes already attached to File object
-		try {
-			String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+  private jarInputStreamProvider createjarInputStreamProvider(
+          final Object ofile) throws MalformedURLException
+  {
+    try
+    {
+      String file = (ofile instanceof File
+              ? ((File) ofile).getCanonicalPath()
+              : ofile.toString());
       byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
               : null;
       if (bytes != null)
       {
-        this.file = (File) ofile;
-      }
-			URL url = null;
-			errorMessage = null;
-			uniqueSetSuffix = null;
-			seqRefIds = null;
-			viewportsAdded.clear();
-			frefedSequence = null;
-
-			if (file.startsWith("http://")) {
-				url = new URL(file);
-			}
-			final URL _url = url;
-			return new jarInputStreamProvider() {
-
-				@Override
-				public JarInputStream getJarInputStream() throws IOException {
-					if (bytes != null) {
-//						System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
-						return new JarInputStream(new ByteArrayInputStream(bytes));
-					}
-					if (_url != null) {
-//						System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
-						return new JarInputStream(_url.openStream());
-					} else {
-//						System.out.println("Jalview2XML: opening file jarInputStream for " + file);
-						return new JarInputStream(new FileInputStream(file));
-					}
-				}
-
-				@Override
-				public String getFilename() {
-					return file;
-				}
-			};
-		} catch (IOException e) {
-			e.printStackTrace();
-			return null;
-		}
-	}
+        this.jarFile = (File) ofile;
+      }
+      errorMessage = null;
+      uniqueSetSuffix = null;
+      seqRefIds = null;
+      viewportsAdded.clear();
+      frefedSequence = null;
+
+      URL url = file.startsWith("http://") ? new URL(file) : null;
+      return new jarInputStreamProvider()
+      {
+        @Override
+        public JarInputStream getJarInputStream() throws IOException
+        {
+          InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
+                  : (url != null ? url.openStream()
+                          : new FileInputStream(file));
+          return new JarInputStream(is);
+        }
+
+        @Override
+        public String getFilename()
+        {
+          return file;
+        }
+      };
+    } catch (IOException e)
+    {
+      e.printStackTrace();
+      return null;
+    }
+  }
 
   /**
    * Recover jalview session from a jalview project archive. Caller may
@@ -5029,7 +5026,7 @@ public class Jalview2XML
     ;
     af.alignPanel.setHoldRepaint(true);
     af.setFileName(fileName, FileFormat.Jalview);
-    af.setFileObject(file); // BH 2019 JAL-3436
+    af.setFileObject(jarFile); // BH 2019 JAL-3436
 
     final AlignViewport viewport = af.getViewport();
     for (int i = 0; i < JSEQ.size(); i++)