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 for (SequenceGroup sg : (Vector<SequenceGroup>) al.getGroups())
97 if (sg.getSize() < minsize)
99 throw new NoValidInputDataException("Group contains less than "
100 + minsize + " sequences.");
102 // TODO: refactor to sequenceGroup for efficiency -
103 // getAlignmentRowInterval(AlignmentI al)
105 for (SequenceI sq : sg.getSequencesInOrder(al))
107 p = al.findIndex(sq);
126 // are there any more sequences ungrouped that should be added as a single
127 // remaining group ? - these might be at the start or the end
130 int[] tail = gl.get(0);
133 if (1 + tail[0] > minsize)
140 // lets be intelligent here - if the remaining sequences aren't enough
141 // to make a final group, then don't make one.
143 // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
148 tail = gl.get(gl.size() - 1);
149 if (1 + tail[1] < al.getHeight())
151 if (al.getHeight() - (1 + tail[1]) > minsize)
154 { tail[1] + 1, al.getHeight() - 1 });
158 // lets be intelligent here - if the remaining sequences aren't
159 // enough to make a final group, then don't make one.
161 // NoValidInputDataException("Group from remaining ungrouped sequences in input contains less than "+minsize+" sequences.");
169 { 0, al.getHeight() - 1 });
171 if (min >= 0 && gl.size() < min)
173 throw new NoValidInputDataException(
174 "Not enough sequence groups for input. Need at least " + min
175 + " groups (including ungrouped regions).");
177 if (max > 0 && gl.size() > max)
179 throw new NoValidInputDataException(
180 "Too many sequence groups for input. Need at most " + max
181 + " groups (including ungrouped regions).");
183 int[][] vals = gl.toArray(new int[gl.size()][]);
184 int[] srt = new int[gl.size()];
185 for (int i = 0; i < vals.length; i++)
187 jalview.util.QuickSort.sort(srt, vals);
189 int last = vals[0][0] - 1;
190 for (int[] range : vals)
196 idvector.append(sep);
198 idvector.append(range[1] - last);
203 return new StringBody(idvector.toString());
207 * set minimum number of sequences allowed in a partition. Default is 1
211 * (number greater than 1)
213 public void setMinsize(int i)
226 public List<String> getURLEncodedParameter()
228 ArrayList<String> prms = new ArrayList<String>();
229 super.addBaseParams(prms);
230 prms.add("minsize='" + minsize + "'");
231 prms.add("sep='" + sep + "'");
234 prms.add("type='" + type + "'");
240 public String getURLtokenPrefix()
246 public boolean configureProperty(String tok, String val,
247 StringBuffer warnings)
250 if (tok.startsWith("sep"))
255 if (tok.startsWith("minsize"))
259 minsize = Integer.valueOf(val);
262 } catch (Exception x)
266 warnings.append("Invalid minsize value '" + val
267 + "'. Must be a positive integer.\n");
269 if (tok.startsWith("type"))
273 type = molType.valueOf(val);
275 } catch (Exception x)
277 warnings.append("Invalid molecule type '" + val
278 + "'. Must be one of (");
279 for (molType v : molType.values())
281 warnings.append(" " + v);
283 warnings.append(")\n");
290 public List<OptionI> getOptions()
292 List<OptionI> lst = getBaseOptions();
293 lst.add(new Option("sep",
294 "Separator character between elements of vector", true, ",",
295 sep, Arrays.asList(new String[]
296 { " ", ",", ";", "\t", "|" }), null));
297 lst.add(new IntegerParameter("minsize", "Minimum size of partition allowed by service", true, 1, minsize, 1,0));
298 lst.add(createMolTypeOption("type", "Sequence type", false, type, molType.MIX));