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JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS
[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
..
d40446d
100644
(file)
--- a/
src/jalview/io/packed/ParsePackedSet.java
+++ b/
src/jalview/io/packed/ParsePackedSet.java
@@
-52,7
+52,7
@@
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
+151,14
@@
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
+223,19
@@
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());
if (jtype != null)
{
final FileParse fp;
if (jtype != null)
{
final FileParse fp;
@@
-271,8
+273,8
@@
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
+298,8
@@
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.");
}
}
}
}
}
}