Package org.biopax.paxtools.model.level2

Examples of org.biopax.paxtools.model.level2.physicalEntity

118
119
120
121
122
123
124
125
126
127
128
      for (GraphObject go : content)
      {
        if (go instanceof Conversion)
        {
          Conversion conv = (Conversion) go;
          conversion cnv = conv.getConversion();
          convSet.add(cnv);
        }
      }

      Set<pathwayComponent> components = l2p.getPATHWAY_COMPONENTS();
View Full Code Here
129
130
131
132
133
134
135
136
137
138
139
      for (GraphObject go : withContent)
      {
        if (go instanceof Conversion)
        {
          Conversion conv = (Conversion) go;
          conversion cnv = conv.getConversion();
          convSet.add(cnv);
        }
      }

      Set<pathwayComponent> components = p.getPATHWAY_COMPONENTS();
View Full Code Here
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
    {
      BioPAXGraph graph = (BioPAXGraph) root;

      if (graph.isMechanistic() && graph.getPathway() == null)
      {
        pathway p = createNewPathway();
        if (graph.getName() != null)
        {
          p.setNAME(adviceTabName(graph.getName()));
        }
        else
        {
          p.setNAME(adviceTabName(null));
        }
        graph.setName(p.getNAME());

        graph.setName(p.getNAME());
        graph.setPathway(p);
        graph.registerContentsToPathway();
        allPathwayNames.add(p.getNAME());
      }
      else
      {
        graph.setName(graph.getPathway() != null ? graph.getPathway().getNAME() :
          adviceTabName(graph.getName()));
View Full Code Here
345
346
347
348
349
350
351
352
353
354
    return name;
  }

  private pathway createNewPathway()
  {
    pathway p = ((Level2Factory) BioPAXLevel.L2.getDefaultFactory()).createPathway();
    p.setRDFId("http://www.chisio.org/user#" + System.currentTimeMillis());
    this.getOwlModel().add(p);
    return p;
  }
View Full Code Here
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
    Object compmod = tabToViewerMap.get(tab).getContents().getModel();
    if (compmod instanceof BioPAXGraph)
    {
      BioPAXGraph graph = (BioPAXGraph) compmod;
      pathway p = graph.getPathway();

      if (p != null)
      {
        p.setNAME(newName);
      }
      graph.setName(newName);
    }
    tab.setText(newName);
View Full Code Here
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
    {
      BioPAXGraph graph = (BioPAXGraph) root;

      if (graph.isMechanistic() && graph.getPathway() == null)
      {
        pathway p = createNewPathway();
        if (graph.getName() != null)
        {
          p.setNAME(adviceTabName(graph.getName()));
        }
        else
        {
          p.setNAME(adviceTabName(null));
        }
        graph.setName(p.getNAME());

        graph.setName(p.getNAME());
        graph.setPathway(p);
        graph.registerContentsToPathway();
        allPathwayNames.add(p.getNAME());
      }
      else
      {
        graph.setName(graph.getPathway() != null ? graph.getPathway().getNAME() :
          adviceTabName(graph.getName()));
View Full Code Here
341
342
343
344
345
346
347
348
349
350
    return name;
  }

  private pathway createNewPathway()
  {
    pathway p = ((Level2Factory) BioPAXLevel.L2.getDefaultFactory()).createPathway();
    p.setRDFId("http://www.chisio.org/user#" + System.currentTimeMillis());
    this.getOwlModel().add(p);
    return p;
  }
View Full Code Here
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
    Object compmod = tabToViewerMap.get(tab).getContents().getModel();
    if (compmod instanceof BioPAXGraph)
    {
      BioPAXGraph graph = (BioPAXGraph) compmod;
      pathway p = graph.getPathway();

      if (p != null)
      {
        p.setNAME(newName);
      }
      graph.setName(newName);
    }
    tab.setText(newName);
View Full Code Here
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
        return;
      }

      original.recordLayout();
      pathway p = original.getPathway();
      BioPAXGraph graph = main.getRootGraph().excise(p);
      graph.setPathway(null);

      String name = p.getNAME();

      // If the name contains a copy number at the end (like "pathway name (2)"), remove it

      if (name.indexOf(" ") > 0)
      {
        String last = name.substring(name.lastIndexOf(" ") + 1);
        if (last.indexOf("(") == 0 && last.indexOf(")") == last.length() - 1)
        {
          boolean isdigit = true;
          for (int i = 1; isdigit && i < last.length() - 1; i++)
          {
            isdigit = Character.isDigit(last.charAt(i));
          }

          if (isdigit) name = name.substring(0, name.lastIndexOf(" "));
        }
      }

      graph.setName(name);
      main.createNewTab(graph);
      graph.fetchLayout(p.getRDFId());
    }
  }
View Full Code Here
100
101
102
103
104
105
106
107
108
109
110
111
      if (graph.isMechanistic())
      {
        graph.forgetLayout();
        Model model = graph.getBiopaxModel();
        pathway p = graph.getPathway();
        model.remove(p);

        main.getAllPathwayNames().remove(p.getNAME());
      }
    }
  }
View Full Code Here
TOP

Related Classes of org.biopax.paxtools.model.level2.physicalEntity

  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.DuplicatePathwayAction
  • org.gvt.action.LocalCommonStreamQueryAction
  • org.gvt.action.SearchCausativePathsAction
  • org.gvt.action.UpdatePathwayAction
  • org.gvt.ChisioMain
  • org.gvt.inspector.CommonStreamQueryParamWithEntitiesDialog
  • org.gvt.inspector.GoIQueryParamWithEntitiesDialog
  • org.gvt.inspector.NeighborhoodQueryParamWithEntitiesDialog
  • org.gvt.inspector.PoIQueryParamWithEntitiesDialog
    • 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.