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Merge JAL-2136_phyre2_integration to develop
[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
87a1d9a
..
8306873
100644
(file)
--- a/
src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/
src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@
-1,19
+1,21
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.rest.params;
@@
-21,6
+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;
@@
-50,8
+53,7
@@
public class SeqGroupIndexVector extends InputType implements
{
public SeqGroupIndexVector()
{
{
public SeqGroupIndexVector()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
}
/**
@@
-89,7
+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())
{
@@
-97,8
+99,12
@@
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)
@@
-106,18
+112,17
@@
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
{
@@
-137,20
+142,18
@@
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)
{
@@
-276,8
+279,8
@@
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));