src/jalview/ws/uimodel/PDBSearchResponse.java

   1 package jalview.ws.uimodel;
   2
   3 import jalview.ws.dbsources.PDBRestClient.PDBDocField;
   4
   5 import java.util.Collection;
   6 import java.util.List;
   7 import java.util.Objects;
   8
   9 import javax.swing.DefaultListModel;
  10 import javax.swing.table.DefaultTableModel;
  11
  12 import org.json.simple.JSONObject;
  13
  14 public class PDBSearchResponse
  15 {
  16   private int itemsFound;
  17
  18   private String responseTime;
  19
  20   private Collection<PDBResponseSummary> searchSummary;
  21
  22   public int getItemsFound()
  23   {
  24     return itemsFound;
  25   }
  26
  27   public void setItemsFound(int itemFound)
  28   {
  29     this.itemsFound = itemFound;
  30   }
  31
  32   public String getResponseTime()
  33   {
  34     return responseTime;
  35   }
  36
  37   public void setResponseTime(String responseTime)
  38   {
  39     this.responseTime = responseTime;
  40   }
  41
  42   public Collection<PDBResponseSummary> getSearchSummary()
  43   {
  44     return searchSummary;
  45   }
  46
  47   public void setSearchSummary(Collection<PDBResponseSummary> searchSummary)
  48   {
  49     this.searchSummary = searchSummary;
  50   }
  51
  52   public static DefaultListModel<PDBResponseSummary> getListModel(
  53           Collection<PDBResponseSummary> summariesList)
  54   {
  55     DefaultListModel<PDBResponseSummary> defaultListModel = new DefaultListModel<PDBResponseSummary>();
  56     for (PDBResponseSummary summaryList : summariesList)
  57     {
  58       defaultListModel.addElement(summaryList);
  59     }
  60     return defaultListModel;
  61   }
  62
  63   public static DefaultTableModel getTableModel(PDBSearchRequest request,
  64           Collection<PDBResponseSummary> summariesList)
  65   {
  66     DefaultTableModel model = new DefaultTableModel();
  67
  68     if (request.getAssociatedSequence() != null)
  69     {
  70       model.addColumn("Sequence");
  71     }
  72     for (PDBDocField field : request.getWantedFields())
  73     {
  74       model.addColumn(field.getName());
  75     }
  76
  77     for (PDBResponseSummary res : summariesList)
  78     {
  79       model.addRow(res.getSummaryColums());
  80     }
  81     return model;
  82   }
  83
  84
  85
  86   public class PDBResponseSummary
  87   {
  88     private String pdbId;
  89
  90     private String summaryRow;
  91
  92     private String[] summaryColums;
  93
  94     private String associatedSequence;
  95
  96     private int width = 480;
  97
  98     public PDBResponseSummary(JSONObject doc,
  99             List<PDBDocField> diplayFields, String associatedSeq)
 100     {
 101       StringBuilder summaryBuilder = new StringBuilder();
 102
 103       int colCounter = 0;
 104       summaryColums = new String[(associatedSeq != null) ? diplayFields
 105               .size() + 1 : diplayFields.size()];
 106       if (associatedSeq != null)
 107       {
 108         this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq
 109                 .substring(0, 18) : associatedSeq;
 110         summaryColums[0] = associatedSequence;
 111         colCounter = 1;
 112       }
 113
 114       for (PDBDocField field : diplayFields)
 115       {
 116         if (field.equals(PDBDocField.MOLECULE_TYPE)
 117                 && doc.get(PDBDocField.MOLECULE_TYPE.getCode()) != null)
 118         {
 119           String moleculeType = doc
 120                   .get(PDBDocField.MOLECULE_TYPE.getCode()).toString();
 121           if (moleculeType.equalsIgnoreCase("protein"))
 122           {
 123             summaryBuilder.append("<img src=\""
 124                     + getClass().getResource("/images/protein.png")
 125                             .toString() + "\">");
 126           }
 127           if (moleculeType.equalsIgnoreCase("dna"))
 128           {
 129             summaryBuilder.append("<img src=\""
 130                     + getClass().getResource("/images/dna.png").toString()
 131                     + "\">");
 132           }
 133           if (moleculeType.equalsIgnoreCase("rna"))
 134           {
 135             summaryBuilder.append("<img src=\""
 136                     + getClass().getResource("/images/dna.png").toString()
 137                     + "\">");
 138           }
 139           if (moleculeType.equalsIgnoreCase("sugar"))
 140           {
 141             summaryBuilder.append("<img src=\""
 142                     + getClass().getResource("/images/sugar.png")
 143                             .toString() + "\">");
 144           }
 145           summaryColums[colCounter++] = moleculeType;
 146         }
 147         else if (field.equals(PDBDocField.PDB_ID)
 148                 && doc.get(PDBDocField.PDB_ID.getCode()) != null)
 149         {
 150           this.pdbId = doc.get(PDBDocField.PDB_ID.getCode()).toString();
 151           summaryBuilder.append(this.pdbId).append(" | ");
 152           summaryColums[colCounter++] = this.pdbId;
 153         }
 154         else if (doc.get(field.getCode()) != null)
 155         {
 156           summaryBuilder.append(field.getName()).append(": ")
 157                   .append(doc.get(field.getCode())).append(" | ");
 158           summaryColums[colCounter++] = doc.get(field.getCode()).toString();
 159         }
 160       }
 161       int endIndex = summaryBuilder.lastIndexOf(" | ");
 162       String fSummary = summaryBuilder.toString().substring(0, endIndex);
 163       this.summaryRow = fSummary.trim();
 164       summaryBuilder = null;
 165     }
 166
 167     public String getPdbId()
 168     {
 169       return pdbId;
 170     }
 171
 172     public void setPdbId(String pdbId)
 173     {
 174       this.pdbId = pdbId;
 175     }
 176
 177     public String getSummaryRow()
 178     {
 179       return summaryRow;
 180     }
 181
 182     public void setSummaryRow(String summary)
 183     {
 184       this.summaryRow = summary;
 185     }
 186
 187     public String[] getSummaryColums()
 188     {
 189       return summaryColums;
 190     }
 191
 192     public void setSummaryColums(String[] summaryColums)
 193     {
 194       this.summaryColums = summaryColums;
 195     }
 196
 197     public String toString()
 198     {
 199       StringBuilder html = new StringBuilder();
 200       html.append("<html><div style=\"width:" + width
 201               + "; word-wrap: break-word; border-bottom-style: dotted;\"> ");
 202       html.append(summaryRow);
 203       html.append("</div></html>");
 204       return html.toString();
 205     }
 206
 207     @Override
 208     public int hashCode()
 209     {
 210       return Objects.hash(this.pdbId, this.summaryRow);
 211     }
 212
 213     @Override
 214     public boolean equals(Object other)
 215     {
 216       if (!(other instanceof PDBResponseSummary))
 217       {
 218         return false;
 219       }
 220
 221       PDBResponseSummary that = (PDBResponseSummary) other;
 222
 223       // Custom equality check here.
 224       return this.pdbId.equals(that.pdbId)
 225               && this.summaryRow.equals(that.summaryRow);
 226     }
 227
 228   }
 229
 230 }
 231