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Merge branch 'patch/JAL-4345_pae_epas1_doubleclick' into develop
[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
1635682
..
ef231e5
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-20,6
+20,8
@@
*/
package jalview.io.packed;
*/
package jalview.io.packed;
+import java.util.Locale;
+
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
@@
-52,7
+54,7
@@
public class ParsePackedSet
public Object[] getAlignment(JalviewDataset context,
Iterable<DataProvider> files) throws Exception
{
public Object[] getAlignment(JalviewDataset context,
Iterable<DataProvider> files) throws Exception
{
- List<Object> rslt = new ArrayList<Object>();
+ List<Object> rslt = new ArrayList<>();
if (context == null)
{
context = new JalviewDataset();
if (context == null)
{
context = new JalviewDataset();
@@
-151,7
+153,7
@@
public class ParsePackedSet
// if not, create one.
if (context.featureColours == null)
{
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new HashMap<String, FeatureColourI>();
+ context.featureColours = new HashMap<>();
}
try
{
}
try
{
@@
-223,18
+225,19
@@
public class ParsePackedSet
* would be created.
*
* @param args
* would be created.
*
* @param args
+ * @j2sIgnore
*/
public static void main(String args[])
{
// make data providers from the set of keys/files
int i = 0;
*/
public static void main(String args[])
{
// make data providers from the set of keys/files
int i = 0;
- List<DataProvider> dp = new ArrayList<DataProvider>();
+ List<DataProvider> dp = new ArrayList<>();
while ((i + 1) < args.length)
{
String type = args[i++];
final String file = args[i++];
final JvDataType jtype = DataProvider.JvDataType
while ((i + 1) < args.length)
{
String type = args[i++];
final String file = args[i++];
final JvDataType jtype = DataProvider.JvDataType
- .valueOf(type.toUpperCase());
+ .valueOf(type.toUpperCase(Locale.ROOT));
if (jtype != null)
{
final FileParse fp;
if (jtype != null)
{
final FileParse fp;
@@
-243,8
+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;
}
@@
-252,8
+256,8
@@
public class ParsePackedSet
}
else
{
}
else
{
- System.out.println("Couldn't parse source type token '"
- + type.toUpperCase() + "'");
+ jalview.bin.Console.outPrintln("Couldn't parse source type token '"
+ + type.toUpperCase(Locale.ROOT) + "'");
}
}
if (i < args.length)
}
}
if (i < args.length)
@@
-266,7
+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;
@@
-276,7
+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;
}
@@
-284,7
+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
@@
-297,7
+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.");
}
}