Package org.cipres.treebase.domain.tree

Examples of org.cipres.treebase.domain.tree.PhyloTreeService

111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
      }
    }
   
    LOGGER.info("doSearch old results contained " + oldRes.size() + " item(s)");
    Collection<PhyloTree> newRes;
    PhyloTreeService treeService = getSearchService().getPhyloTreeService(); 
   
    TaxonVariant[] taxonVariant = new TaxonVariant[taxon.length];
    List<String> resolutionError = new LinkedList<String> ();
    for (int i=0; i<taxon.length; i++) {
      if (taxon[i] == null) continue;
      if (taxon[i].equals(""))
        resolutionError.add("TaxonVariant name " + i + " missing");
      Set<TaxonVariant> tvSet = getTaxonLabelService().findTaxonVariantByName(taxon[i]);
      taxonVariant[i] = tvSet.isEmpty() ? null : tvSet.iterator().next(); // FIXME: This is not really the right behavior
      if (taxonVariant[i] == null)
        resolutionError.add("Couldn't resolve TaxonVariant '" + taxon[i] + "'");
      else
        LOGGER.debug("input '" + taxon[i] + "' resolved to TV " + taxonVariant[i].getId() + " ('" + taxonVariant[i].getFullName() + "')");
    }
    if (! resolutionError.isEmpty()) {
      addMessages(request, resolutionError);
      return new ModelAndView("search/treeTopSearch", Constants.RESULT_SET, oldRes);
    }
       
    switch (searchType) {
    case topology3Search:
      checkTaxa(taxonVariant, 3);
      newRes = treeService.findByTopology3(taxonVariant[0], taxonVariant[1], taxonVariant[2]);
      break;
    case topology4aSearch:
      checkTaxa(taxonVariant, 4);
      newRes = treeService.findByTopology4a(taxonVariant[0], taxonVariant[1], taxonVariant[2], taxonVariant[3]);
      break;
    case topology4sSearch:
      checkTaxa(taxonVariant, 4);
      newRes = treeService.findByTopology4s(taxonVariant[0], taxonVariant[1], taxonVariant[2], taxonVariant[3]);
      break;
    default:
      throw new Error ("Unknown search type '" + searchType + "'");
    }
   
View Full Code Here
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
      SearchType searchType,
      BindException errors,
      String searchTerm) throws InstantiationException {

    Collection<PhyloTree> matches = null;
    PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService(); 


    switch(searchType) {
    case byID:
      matches = (Collection<PhyloTree>) doSearchByIDString(request, phyloTreeService, PhyloTree.class, searchTerm);
      break;

    case byKind:
      matches = phyloTreeService
        .findSomethingByItsDescription(PhyloTree.class, "treeKind", searchTerm, true);
      break;
     
    case byQuality:
      matches = phyloTreeService
        .findSomethingByItsDescription(PhyloTree.class, "treeQuality", searchTerm, true);
      break;

    case byTitle:
      matches = phyloTreeService
        .findSomethingBySubstring(PhyloTree.class, "title", searchTerm);
      break;

    case byType:
      matches = phyloTreeService
        .findSomethingByItsDescription(PhyloTree.class, "treeType", searchTerm, true);
      break;

    case byNTAX:
      try {
          matches = phyloTreeService
          .findSomethingByRangeExpression(PhyloTree.class, "nTax", searchTerm);
        } catch (MalformedRangeExpression e) {
          addMessage(request, "Malformed range expression: " + e.getMessage());
        }
    }
View Full Code Here
45
46
47
48
49
50
51
52
53
54
55
56
57
58
      HttpServletResponse response,
      BindException errors,
      String searchTerm) throws InstantiationException {
   
    Collection<PhyloTree> matches = null;
    PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();
   
    try {
      matches = phyloTreeService.findTreesByNCBINodes(searchTerm);
    }
    catch ( NumberFormatException e ) {
      addMessage(request, "Malformed NCBI identifier '" + searchTerm );
      LOGGER.error("Couldn't parse NCBI identifier: "+e.getMessage());
    }
View Full Code Here
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
import org.cipres.treebase.domain.tree.PhyloTreeService;

public class TreeQuery extends AbstractStandalone {
  public static void main(String[] args) {
    setupContext();
    PhyloTreeService treeServ = ContextManager.getPhyloTreeService();
    TaxonLabelService tlServ = ContextManager.getTaxonLabelService();
   
    Set<TaxonVariant>[] tvSet = new Set[3];
    for (int i=0; i<3; i++) {
      tvSet[i] = tlServ.findTaxonVariantByName(args[i]);
      warn(args[i] + " yields " + tvSet[i].size() + " matches");
    }
   
    TaxonVariant[] tv = new TaxonVariant[3];
    for (int i=0; i<3; i++) {
      tv[i] = tvSet[i].iterator().next();
      tvShow(tv[i]);
    }   
   
    Set<PhyloTree> trees = treeServ.findByTopology3(tv[0], tv[1], tv[2]);
    warn("Found " + trees.size() + " trees.");
   
    for (PhyloTree t : trees) {
      System.out.println(t.getId());
    }
View Full Code Here
TOP

Related Classes of org.cipres.treebase.domain.tree.PhyloTreeService

  • org.cipres.treebase.util.TreeQuery
  • org.cipres.treebase.web.controllers.ClassificationSearchController
  • org.cipres.treebase.web.controllers.TreeSearchController
  • org.cipres.treebase.web.controllers.TreeTopSearchController
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.