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JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance...
[jalview.git]
/
src
/
jalview
/
io
/
packed
/
ParsePackedSet.java
diff --git
a/src/jalview/io/packed/ParsePackedSet.java
b/src/jalview/io/packed/ParsePackedSet.java
index
37dd66b
..
ef231e5
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-246,8
+246,9
@@
public class ParsePackedSet
fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
} catch (Exception e)
{
fp = new FileParse(file, AppletFormatAdapter.checkProtocol(file));
} catch (Exception e)
{
- System.err.println("Couldn't handle datasource of type " + jtype
- + " using URI " + file);
+ jalview.bin.Console
+ .errPrintln("Couldn't handle datasource of type " + jtype
+ + " using URI " + file);
e.printStackTrace();
return;
}
e.printStackTrace();
return;
}
@@
-255,7
+256,7
@@
public class ParsePackedSet
}
else
{
}
else
{
- System.out.println("Couldn't parse source type token '"
+ jalview.bin.Console.outPrintln("Couldn't parse source type token '"
+ type.toUpperCase(Locale.ROOT) + "'");
}
}
+ type.toUpperCase(Locale.ROOT) + "'");
}
}
@@
-269,7
+270,7
@@
public class ParsePackedSet
System.out.print("\n");
}
System.out.print("\n");
}
- System.out.println("Now trying to parse set:");
+ jalview.bin.Console.outPrintln("Now trying to parse set:");
JalviewDataset context;
Object[] newdm;
ParsePackedSet pps;
JalviewDataset context;
Object[] newdm;
ParsePackedSet pps;
@@
-279,7
+280,7
@@
public class ParsePackedSet
.getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
.getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
- System.out.println("Test failed for these arguments.\n");
+ jalview.bin.Console.outPrintln("Test failed for these arguments.\n");
e.printStackTrace(System.out);
return;
}
e.printStackTrace(System.out);
return;
}
@@
-287,7
+288,8
@@
public class ParsePackedSet
{
for (Object o : newdm)
{
{
for (Object o : newdm)
{
- System.out.println("Will need to create an " + o.getClass());
+ jalview.bin.Console
+ .outPrintln("Will need to create an " + o.getClass());
}
// now test uniquify/deuniquify stuff
}
// now test uniquify/deuniquify stuff
@@
-300,7
+302,7
@@
public class ParsePackedSet
{
if (context.getLastAlignmentSet().isModified())
{
{
if (context.getLastAlignmentSet().isModified())
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Initial alignment set was modified and any associated views should be updated.");
}
}
"Initial alignment set was modified and any associated views should be updated.");
}
}