1 /*******************************************************************************
2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 *******************************************************************************/
18 package jalview.ws.rest.params;
20 import jalview.datamodel.AlignmentI;
21 import jalview.datamodel.SequenceGroup;
22 import jalview.datamodel.SequenceI;
23 import jalview.ws.params.OptionI;
24 import jalview.ws.params.simple.IntegerParameter;
25 import jalview.ws.params.simple.Option;
26 import jalview.ws.rest.AlignmentProcessor;
27 import jalview.ws.rest.InputType;
28 import jalview.ws.rest.NoValidInputDataException;
29 import jalview.ws.rest.RestJob;
30 import jalview.ws.rest.RestServiceDescription;
31 import jalview.ws.rest.InputType.molType;
33 import java.io.UnsupportedEncodingException;
34 import java.util.ArrayList;
35 import java.util.Arrays;
36 import java.util.List;
37 import java.util.Vector;
39 import org.apache.http.entity.mime.content.ContentBody;
40 import org.apache.http.entity.mime.content.StringBody;
43 * Represents the partitions defined on the alignment as indices e.g. for a
44 * partition (A,B,C),(D,E),(F) The indices would be 3,2,1. Note, the alignment
45 * must be ordered so groups are contiguous before this input type can be used.
50 public class SeqGroupIndexVector extends InputType implements
53 public SeqGroupIndexVector()
56 { AlignmentI.class });
60 * separator for list of sequence Indices - default is ','
62 public String sep = ",";
65 * min size of each partition
67 public int minsize = 1;
72 * prepare the context alignment for this input
75 * - alignment to be processed
76 * @return al or a new alignment with appropriate attributes/order for input
78 public AlignmentI prepareAlignment(AlignmentI al)
80 jalview.analysis.AlignmentSorter.sortByGroup(al);
85 public ContentBody formatForInput(RestJob rj)
86 throws UnsupportedEncodingException, NoValidInputDataException
88 StringBuffer idvector = new StringBuffer();
90 AlignmentI al = rj.getAlignmentForInput(token, type);
91 // assume that alignment is properly ordered so groups form consecutive
93 ArrayList<int[]> gl = new ArrayList<int[]>();
95 List<SequenceGroup> sgs;
96 synchronized (sgs=al.getGroups())
98 for (SequenceGroup sg : sgs)
100 if (sg.getSize() < minsize)
102 throw new NoValidInputDataException("Group contains less than "
103 + minsize + " sequences.");
105 // TODO: refactor to sequenceGroup for efficiency -
106 // getAlignmentRowInterval(AlignmentI al)
108 for (SequenceI sq : sg.getSequencesInOrder(al))
110 p = al.findIndex(sq);
130 // are there any more sequences ungrouped that should be added as a single
131 // remaining group ? - these might be at the start or the end
134 int[] tail = gl.get(0);
137 if (1 + tail[0] > minsize)
144 // lets be intelligent here - if the remaining sequences aren't enough
145 // to make a final group, then don't make one.
147 // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
152 tail = gl.get(gl.size() - 1);
153 if (1 + tail[1] < al.getHeight())
155 if (al.getHeight() - (1 + tail[1]) > minsize)
158 { tail[1] + 1, al.getHeight() - 1 });
162 // lets be intelligent here - if the remaining sequences aren't
163 // enough to make a final group, then don't make one.
165 // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
173 { 0, al.getHeight() - 1 });
175 if (min >= 0 && gl.size() < min)
177 throw new NoValidInputDataException(
178 "Not enough sequence groups for input. Need at least " + min
179 + " groups (including ungrouped regions).");
181 if (max > 0 && gl.size() > max)
183 throw new NoValidInputDataException(
184 "Too many sequence groups for input. Need at most " + max
185 + " groups (including ungrouped regions).");
187 int[][] vals = gl.toArray(new int[gl.size()][]);
188 int[] srt = new int[gl.size()];
189 for (int i = 0; i < vals.length; i++)
191 jalview.util.QuickSort.sort(srt, vals);
193 int last = vals[0][0] - 1;
194 for (int[] range : vals)
200 idvector.append(sep);
202 idvector.append(range[1] - last);
207 return new StringBody(idvector.toString());
211 * set minimum number of sequences allowed in a partition. Default is 1
215 * (number greater than 1)
217 public void setMinsize(int i)
230 public List<String> getURLEncodedParameter()
232 ArrayList<String> prms = new ArrayList<String>();
233 super.addBaseParams(prms);
234 prms.add("minsize='" + minsize + "'");
235 prms.add("sep='" + sep + "'");
238 prms.add("type='" + type + "'");
244 public String getURLtokenPrefix()
250 public boolean configureProperty(String tok, String val,
251 StringBuffer warnings)
254 if (tok.startsWith("sep"))
259 if (tok.startsWith("minsize"))
263 minsize = Integer.valueOf(val);
266 } catch (Exception x)
270 warnings.append("Invalid minsize value '" + val
271 + "'. Must be a positive integer.\n");
273 if (tok.startsWith("type"))
277 type = molType.valueOf(val);
279 } catch (Exception x)
281 warnings.append("Invalid molecule type '" + val
282 + "'. Must be one of (");
283 for (molType v : molType.values())
285 warnings.append(" " + v);
287 warnings.append(")\n");
294 public List<OptionI> getOptions()
296 List<OptionI> lst = getBaseOptions();
297 lst.add(new Option("sep",
298 "Separator character between elements of vector", true, ",",
299 sep, Arrays.asList(new String[]
300 { " ", ",", ";", "\t", "|" }), null));
301 lst.add(new IntegerParameter("minsize", "Minimum size of partition allowed by service", true, 1, minsize, 1,0));
302 lst.add(createMolTypeOption("type", "Sequence type", false, type, molType.MIX));