Package org.patika.mada.util

Examples of org.patika.mada.util.XRef

95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
          if (id.length() < 1) continue;
         
          String dbtext = Character.isDigit(id.charAt(0)) ?
            XRef.ENTREZ_GENE : XRef.UNIPROT;

          refs.add(new XRef(dbtext + ":" + id));
        }
      }
    }

    if (!refs.isEmpty())
    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");

        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler();
        Map<String, String> pathToID = new HashMap<String, String>();
        List<String> resultPathways = new ArrayList<String>();

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
View Full Code Here
75
76
77
78
79
80
81
82
   */
  private void extractReferences()
  {
    for (xref xr : cmp.getXREF())
    {
      this.addReference(new XRef(xr));
    }
  }
View Full Code Here
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
          if (id.length() < 1) continue;

          String dbtext = Character.isDigit(id.charAt(0)) ?
            XRef.ENTREZ_GENE : XRef.UNIPROT;

          refs.add(new XRef(dbtext + ":" + id));
        }
      }
    }

    if (!refs.isEmpty())
    {
      try
      {
        main.lockWithMessage("Querying Pathway Commons Database ...");
        PathwayCommonsIOHandler ioHandler = new PathwayCommonsIOHandler(new SimpleIOHandler());

        // Names of new pathways for the neighborhood
        Map<XRef, String> ref2pname = new HashMap<XRef, String>();

        // Query for only one xref

        XRef xr = XRef.getFirstRef(refs,
          new String[]{XRef.CPATH, XRef.ENTREZ_GENE, XRef.UNIPROT});

        refs.clear();
        if (xr != null)
        {
View Full Code Here
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
  {
    String names = "";

    if (ent.getStandardName() != null && ent.getStandardName().length() > 0)
    {
      this.addReference(new XRef(NAME_REF, ent.getStandardName()));
      names = ent.getStandardName();
    }

    for (String nm : ent.getName())
    {
      this.addReference(new XRef(NAME_REF, nm));
      names += (names.length() == 0 ? "" : "\n") + nm;
    }

//    for (xref xr : new ClassFilterSet<unificationXref>(ent.getXREF(), unificationXref.class))
    for (Xref xr : ent.getXref())
    {
      if (xr != null)
      {
        this.addReference(new XRef(xr));
      }
    }

    return names;
  }
View Full Code Here
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
  {
    Set<String> nameSet = new HashSet<String>();

    if (ent.getSHORT_NAME() != null && ent.getSHORT_NAME().length() > 0)
    {
      this.addReference(new XRef(NAME_REF, ent.getSHORT_NAME()));
      if(ent.getSHORT_NAME() != null) nameSet.add(ent.getSHORT_NAME());
    }

    if (ent.getNAME() != null && ent.getNAME().length() > 0)
    {
      this.addReference(new XRef(NAME_REF, ent.getNAME()));
      nameSet.add(ent.getNAME());
    }

    for (String syn : ent.getSYNONYMS())
    {
      if (syn != null)
      {
        XRef ref = new XRef(NAME_REF, syn);

        if (!this.getReferences().contains(ref))
        {
          this.addReference(ref);
          nameSet.add(syn);
        }
      }
    }

//    for (xref xr : new ClassFilterSet<unificationXref>(ent.getXREF(), unificationXref.class))
    for (xref xr : ent.getXREF())
    {
      if (xr != null)
      {
        this.addReference(new XRef(xr));
      }
    }
    String names = "";

    Iterator<String> iter = nameSet.iterator();
View Full Code Here
309
310
311
312
313
314
315
316
317
318
319
      String d = "";

      for (Object ref : row.getRef())
      {
        d += new XRef((Reference) ref).toString() + " ";
      }

      d = d.trim();
      d = d.toLowerCase();
View Full Code Here
TOP

Related Classes of org.patika.mada.util.XRef

  • org.gvt.action.GOIofSIFAction
  • org.gvt.action.QueryNeighborsAction
  • org.gvt.action.QueryPathwaysAction
  • org.gvt.model.biopaxl2.BioPAXNode
  • org.gvt.model.biopaxl2.Complex
  • org.gvt.model.biopaxl3.BioPAXNode
  • org.gvt.model.biopaxl3.ChbComplex
  • org.gvt.util.SIFReader
  • org.patika.mada.gui.ExperimentDataVisualizationDialog
  • org.patika.mada.gui.ExperimentValuesTableModel
    • 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.