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JAL-4265 Added saveState and restoreState to interface with no-op methods in abstract...
[jalview.git]
/
src
/
jalview
/
ws
/
rest
/
params
/
SeqGroupIndexVector.java
diff --git
a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index
af96fea
..
9210414
100644
(file)
--- a/
src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/
src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-48,8
+48,8
@@
import org.apache.http.entity.mime.content.StringBody;
* @author JimP
*
*/
* @author JimP
*
*/
-public class SeqGroupIndexVector extends InputType implements
- AlignmentProcessor
+public class SeqGroupIndexVector extends InputType
+ implements AlignmentProcessor
{
public SeqGroupIndexVector()
{
{
public SeqGroupIndexVector()
{
@@
-75,6
+75,7
@@
public class SeqGroupIndexVector extends InputType implements
* - alignment to be processed
* @return al or a new alignment with appropriate attributes/order for input
*/
* - alignment to be processed
* @return al or a new alignment with appropriate attributes/order for input
*/
+ @Override
public AlignmentI prepareAlignment(AlignmentI al)
{
jalview.analysis.AlignmentSorter.sortByGroup(al);
public AlignmentI prepareAlignment(AlignmentI al)
{
jalview.analysis.AlignmentSorter.sortByGroup(al);
@@
-90,21
+91,19
@@
public class SeqGroupIndexVector extends InputType implements
AlignmentI al = rj.getAlignmentForInput(token, type);
// assume that alignment is properly ordered so groups form consecutive
// blocks
AlignmentI al = rj.getAlignmentForInput(token, type);
// assume that alignment is properly ordered so groups form consecutive
// blocks
- ArrayList<int[]> gl = new ArrayList<int[]>();
+ ArrayList<int[]> gl = new ArrayList<>();
int p = 0, lowest = al.getHeight(), highest = 0;
int p = 0, lowest = al.getHeight(), highest = 0;
- List<SequenceGroup> sgs;
- synchronized (sgs = al.getGroups())
+ List<SequenceGroup> sgs = al.getGroups();
+ synchronized (sgs)
{
for (SequenceGroup sg : sgs)
{
if (sg.getSize() < minsize)
{
{
for (SequenceGroup sg : sgs)
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException(
- MessageManager
- .formatMessage(
- "exception.notvaliddata_group_contains_less_than_min_seqs",
- new String[] { Integer.valueOf(minsize)
- .toString() }));
+ throw new NoValidInputDataException(MessageManager.formatMessage(
+ "exception.notvaliddata_group_contains_less_than_min_seqs",
+ new String[]
+ { Integer.valueOf(minsize).toString() }));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
@@
-127,9
+126,13
@@
public class SeqGroupIndexVector extends InputType implements
else
{
if (p < se[0])
else
{
if (p < se[0])
+ {
se[0] = p;
se[0] = p;
+ }
if (p > se[1])
if (p > se[1])
+ {
se[1] = p;
se[1] = p;
+ }
}
}
if (se != null)
}
}
if (se != null)
@@
-170,7
+173,9
@@
public class SeqGroupIndexVector extends InputType implements
int[][] vals = gl.toArray(new int[gl.size()][]);
int[] srt = new int[gl.size()];
for (int i = 0; i < vals.length; i++)
int[][] vals = gl.toArray(new int[gl.size()][]);
int[] srt = new int[gl.size()];
for (int i = 0; i < vals.length; i++)
+ {
srt[i] = vals[i][0];
srt[i] = vals[i][0];
+ }
jalview.util.QuickSort.sort(srt, vals);
list = false;
int last = vals[0][0] - 1;
jalview.util.QuickSort.sort(srt, vals);
list = false;
int last = vals[0][0] - 1;
@@
-212,7
+217,7
@@
public class SeqGroupIndexVector extends InputType implements
@Override
public List<String> getURLEncodedParameter()
{
@Override
public List<String> getURLEncodedParameter()
{
- ArrayList<String> prms = new ArrayList<String>();
+ ArrayList<String> prms = new ArrayList<>();
super.addBaseParams(prms);
prms.add("minsize='" + minsize + "'");
prms.add("sep='" + sep + "'");
super.addBaseParams(prms);
prms.add("minsize='" + minsize + "'");
prms.add("sep='" + sep + "'");
@@
-245,7
+250,9
@@
public class SeqGroupIndexVector extends InputType implements
{
minsize = Integer.valueOf(val);
if (minsize >= 0)
{
minsize = Integer.valueOf(val);
if (minsize >= 0)
+ {
return true;
return true;
+ }
} catch (Exception x)
{
} catch (Exception x)
{
@@
-261,8
+268,8
@@
public class SeqGroupIndexVector extends InputType implements
return true;
} catch (Exception x)
{
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);
for (molType v : molType.values())
{
warnings.append(" " + v);
@@
-279,8
+286,8
@@
public class SeqGroupIndexVector extends InputType implements
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
List<OptionI> lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
- null));
+ sep, Arrays.asList(new String[]
+ { " ", ",", ";", "\t", "|" }), null));
lst.add(new IntegerParameter("minsize",
"Minimum size of partition allowed by service", true, 1,
minsize, 1, 0));
lst.add(new IntegerParameter("minsize",
"Minimum size of partition allowed by service", true, 1,
minsize, 1, 0));