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Merge branch 'develop' into features/JAL-1793VCF
[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
1f568d6
..
dcb7fab
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 2.8.2)
- * Copyright (C) 2014 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.
*
@@
-23,6
+23,7
@@
package jalview.ws.rest.params;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
@@
-47,13
+48,12
@@
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()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
}
/**
@@
-91,7
+91,7
@@
public class SeqGroupIndexVector extends InputType implements
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
- 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;
synchronized (sgs = al.getGroups())
{
@@
-99,8
+99,10
@@
public class SeqGroupIndexVector extends InputType implements
{
if (sg.getSize() < minsize)
{
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException("Group contains less than "
- + minsize + " sequences.");
+ 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)
@@
-108,18
+110,17
@@
public class SeqGroupIndexVector extends InputType implements
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
- if (lowest>p)
+ if (lowest > p)
{
{
- lowest=p;
+ lowest = p;
}
}
- if (highest<p)
+ if (highest < p)
{
{
- highest=p;
+ highest = p;
}
if (se == null)
{
}
if (se == null)
{
- se = new int[]
- { p, p };
+ se = new int[] { p, p };
}
else
{
}
else
{
@@
-139,20
+140,18
@@
public class SeqGroupIndexVector extends InputType implements
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
- if (lowest-1>minsize)
+ if (lowest - 1 > minsize)
{
{
- gl.add(0, new int[]
- { 0, lowest-2});
+ gl.add(0, new int[] { 0, lowest - 2 });
}
}
- if ((al.getHeight()-1-highest)>minsize)
+ if ((al.getHeight() - 1 - highest) > minsize)
{
{
- gl.add(new int[] { highest+1, al.getHeight()-1});
+ gl.add(new int[] { highest + 1, al.getHeight() - 1 });
}
}
else
{
}
}
else
{
- gl.add(new int[]
- { 0, al.getHeight() - 1 });
+ gl.add(new int[] { 0, al.getHeight() - 1 });
}
if (min >= 0 && gl.size() < min)
{
}
if (min >= 0 && gl.size() < min)
{
@@
-260,8
+259,8
@@
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);