From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 15 Nov 2018 14:04:08 +0000 (+0000)
Subject: JAL-3063 remove commented code, suppress debug output
X-Git-Tag: Release_2_11_4_0~45^2~18^2~398
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9f35269974743dfcc0d80aed3f86bb434f111896;p=jalview.git

JAL-3063 remove commented code, suppress debug output
---

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 47a07a0..fae9e8c 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2549,14 +2549,14 @@ public class Jalview2XML
 				@Override
 				public JarInputStream getJarInputStream() throws IOException {
 					if (bytes != null) {
-						System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
+//						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);
+//						System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
 						return new JarInputStream(_url.openStream());
 					} else {
-						System.out.println("Jalview2XML: opening file jarInputStream for " + file);
+//						System.out.println("Jalview2XML: opening file jarInputStream for " + file);
 						return new JarInputStream(new FileInputStream(file));
 					}
 				}
@@ -2608,14 +2608,10 @@ public class Jalview2XML
         for (int i = 0; i < entryCount; i++)
         {
           jarentry = jin.getNextJarEntry();
-          System.out.println("Jalview2XML#loadJalviewAlign: jarentry=" + (jarentry == null ? null : jarentry.getName()));
         }
 
         if (jarentry != null && jarentry.getName().endsWith(".xml"))
         {
-          InputStreamReader in = new InputStreamReader(jin, UTF_8);
-          // JalviewModel object = new JalviewModel();
-
           JAXBContext jc = JAXBContext
                   .newInstance("jalview.xml.binding.jalview");
           XMLStreamReader streamReader = XMLInputFactory.newInstance()
@@ -2624,12 +2620,7 @@ public class Jalview2XML
           JAXBElement<JalviewModel> jbe = um
                   .unmarshal(streamReader, JalviewModel.class);
           JalviewModel object = jbe.getValue();
-          System.out.println("processing JalviewModel object=" + object);
-          /*
-          Unmarshaller unmar = new Unmarshaller(object);
-          unmar.setValidation(false);
-          object = (JalviewModel) unmar.unmarshal(in);
-          */
+
           if (true) // !skipViewport(object))
           {
             _af = loadFromObject(object, file, true, jprovider);
@@ -2971,7 +2962,6 @@ public class Jalview2XML
       do
       {
         entry = jin.getNextJarEntry();
-      	System.out.println("Jalview2XML#copyJarEntry: jarentry=" + (entry == null ? null : entry.getName()));
       } while (entry != null && !entry.getName().equals(jarEntryName));
       if (entry != null)
       {
@@ -5809,7 +5799,6 @@ public class Jalview2XML
       do
       {
         entry = jin.getNextJarEntry();
-      	System.out.println("Jalview2XML#readJarEntry: jarentry=" + (entry == null ? null : entry.getName()));
       } while (entry != null && !entry.getName().equals(jarEntryName));
 
       if (entry != null)