-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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
* 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.
- *
+ *
* 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;
import jalview.datamodel.AlignmentI;
import jalview.ws.rest.InputType;
import jalview.ws.rest.NoValidInputDataException;
import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
-import java.util.Vector;
import org.apache.http.entity.mime.content.ContentBody;
import org.apache.http.entity.mime.content.StringBody;
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
- int p = 0;
- for (SequenceGroup sg : (Vector<SequenceGroup>) al.getGroups())
+ int p = 0,lowest=al.getHeight(), highest=0;
+ List<SequenceGroup> sgs;
+ synchronized (sgs = al.getGroups())
{
- if (sg.getSize() < minsize)
+ for (SequenceGroup sg : sgs)
{
- throw new NoValidInputDataException("Group contains less than "
- + minsize + " sequences.");
- }
- // TODO: refactor to sequenceGroup for efficiency -
- // getAlignmentRowInterval(AlignmentI al)
- int[] se = null;
- for (SequenceI sq : sg.getSequencesInOrder(al))
- {
- p = al.findIndex(sq);
- if (se == null)
+ if (sg.getSize() < minsize)
+ {
+ throw new NoValidInputDataException("Group contains less than "
+ + minsize + " sequences.");
+ }
+ // TODO: refactor to sequenceGroup for efficiency -
+ // getAlignmentRowInterval(AlignmentI al)
+ int[] se = null;
+ for (SequenceI sq : sg.getSequencesInOrder(al))
{
- se = new int[]
- { p, p };
+ p = al.findIndex(sq);
+ if (lowest>p)
+ {
+ lowest=p;
+ }
+ if (highest<p)
+ {
+ highest=p;
+ }
+ if (se == null)
+ {
+ se = new int[]
+ { p, p };
+ }
+ else
+ {
+ if (p < se[0])
+ se[0] = p;
+ if (p > se[1])
+ se[1] = p;
+ }
}
- else
+ if (se != null)
{
- if (p < se[0])
- se[0] = p;
- if (p > se[1])
- se[1] = p;
+ gl.add(se);
}
}
- if (se != null)
- {
- gl.add(se);
- }
}
// are there any more sequences ungrouped that should be added as a single
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
- int[] tail = gl.get(0);
- if (tail[0] > 0)
+ if (lowest-1>minsize)
{
- if (1 + tail[0] > minsize)
- {
- gl.add(0, new int[]
- { 0, tail[0] - 1 });
- }
- else
- {
- // lets be intelligent here - if the remaining sequences aren't enough
- // to make a final group, then don't make one.
- // throw new
- // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
- }
+ gl.add(0, new int[]
+ { 0, lowest-2});
}
- else
+ if ((al.getHeight()-1-highest)>minsize)
{
- tail = gl.get(gl.size() - 1);
- if (1 + tail[1] < al.getHeight())
- {
- if (al.getHeight() - (1 + tail[1]) > minsize)
- {
- gl.add(new int[]
- { tail[1] + 1, al.getHeight() - 1 });
- }
- else
- {
- // lets be intelligent here - if the remaining sequences aren't
- // enough to make a final group, then don't make one.
- // throw new
- // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
- }
- }
+ gl.add(new int[] { highest+1, al.getHeight()-1});
}
}
else
"Separator character between elements of vector", true, ",",
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(createMolTypeOption("type", "Sequence type", false, type, molType.MIX));
+ lst.add(new IntegerParameter("minsize",
+ "Minimum size of partition allowed by service", true, 1,
+ minsize, 1, 0));
+ lst.add(createMolTypeOption("type", "Sequence type", false, type,
+ molType.MIX));
return lst;
}
git://source.jalview.org / jalview.git / blobdiff