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Merge branch 'develop' (JAL-4102 2.11.2.6 patch release) into features/r2_11_2_alphaf...
[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
138fef7
..
37dd66b
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();
@@
-151,13
+153,14
@@
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
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
context.updateSetModified(ff.parse(context.getLastAlignment(),
}
try
{
jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
context.updateSetModified(ff.parse(context.getLastAlignment(),
- context.featureColours, false, context.relaxedIdMatching));
+ context.featureColours, false,
+ context.relaxedIdMatching));
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
} catch (Exception e)
{
errmsg = ("Failed to parse the Features file associated with the alignment.");
@@
-222,18
+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++];
while ((i + 1) < args.length)
{
String type = args[i++];
final String file = args[i++];
- final JvDataType jtype = DataProvider.JvDataType.valueOf(type
- .toUpperCase());
+ final JvDataType jtype = DataProvider.JvDataType
+ .valueOf(type.toUpperCase(Locale.ROOT));
if (jtype != null)
{
final FileParse fp;
if (jtype != null)
{
final FileParse fp;
@@
-252,7
+256,7
@@
public class ParsePackedSet
else
{
System.out.println("Couldn't parse source type token '"
else
{
System.out.println("Couldn't parse source type token '"
- + type.toUpperCase() + "'");
+ + type.toUpperCase(Locale.ROOT) + "'");
}
}
if (i < args.length)
}
}
if (i < args.length)
@@
-271,8
+275,8
@@
public class ParsePackedSet
ParsePackedSet pps;
try
{
ParsePackedSet pps;
try
{
- newdm = (pps = new ParsePackedSet()).getAlignment(
- context = new JalviewDataset(), dp);
+ newdm = (pps = new ParsePackedSet())
+ .getAlignment(context = new JalviewDataset(), dp);
} catch (Exception e)
{
System.out.println("Test failed for these arguments.\n");
} catch (Exception e)
{
System.out.println("Test failed for these arguments.\n");
@@
-296,8
+300,8
@@
public class ParsePackedSet
{
if (context.getLastAlignmentSet().isModified())
{
{
if (context.getLastAlignmentSet().isModified())
{
- System.err
- .println("Initial alignment set was modified and any associated views should be updated.");
+ System.err.println(
+ "Initial alignment set was modified and any associated views should be updated.");
}
}
}
}
}
}