git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3063 remove commented code, suppress debug output
[jalview.git]
/
src
/
jalview
/
project
/
Jalview2XML.java
diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
47a07a0
..
fae9e8c
100644
(file)
--- 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) {
@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) {
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 {
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));
}
}
return new JarInputStream(new FileInputStream(file));
}
}
@@
-2608,14
+2608,10
@@
public class Jalview2XML
for (int i = 0; i < entryCount; i++)
{
jarentry = jin.getNextJarEntry();
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"))
{
}
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()
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();
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);
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
@@
-2971,7
+2962,6
@@
public class Jalview2XML
do
{
entry = jin.getNextJarEntry();
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)
{
} while (entry != null && !entry.getName().equals(jarEntryName));
if (entry != null)
{
@@
-5809,7
+5799,6
@@
public class Jalview2XML
do
{
entry = jin.getNextJarEntry();
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)
} while (entry != null && !entry.getName().equals(jarEntryName));
if (entry != null)