src/jalview/ws/uimodel/PDBSummaryListModel.java

   1 package jalview.ws.uimodel;
   2
   3 import java.util.List;
   4
   5 import javax.swing.DefaultListModel;
   6
   7 import org.json.simple.JSONObject;
   8
   9
  10 @SuppressWarnings(
  11 { "serial", "rawtypes" })
  12 public class PDBSummaryListModel extends DefaultListModel
  13 {
  14   private String pdbId;
  15
  16   private String summary;
  17
  18   private int width = 480;
  19
  20
  21   public PDBSummaryListModel(JSONObject doc, List<PDBDocField> diplayFields)
  22   {
  23     StringBuilder summaryBuilder = new StringBuilder();
  24
  25     for (PDBDocField field : diplayFields)
  26     {
  27       if (field.equals(PDBDocField.MOLECULE_TYPE)
  28               && doc.get("molecule_type") != null)
  29       {
  30         String moleculeType = doc.get("molecule_type").toString();
  31         if (moleculeType.equalsIgnoreCase("protein"))
  32         {
  33           summaryBuilder.append("<img src=\""
  34                   + getClass().getResource("/images/protein.png").toString()
  35                   + "\">");
  36         }
  37         if (moleculeType.equalsIgnoreCase("dna"))
  38         {
  39           summaryBuilder.append("<img src=\""
  40                   + getClass().getResource("/images/dna.png").toString()
  41                   + "\">");
  42         }
  43         if (moleculeType.equalsIgnoreCase("rna"))
  44         {
  45           summaryBuilder.append("<img src=\""
  46                   + getClass().getResource("/images/dna.png").toString()
  47                   + "\">");
  48         }
  49         if (moleculeType.equalsIgnoreCase("sugar"))
  50         {
  51           summaryBuilder.append("<img src=\""
  52                   + getClass().getResource("/images/sugar.png").toString()
  53                   + "\">");
  54         }
  55       }else if (doc.get(field.getCode()) != null)
  56       {
  57         summaryBuilder.append(field.getName()).append(": ")
  58                 .append(doc.get(field.getCode())).append(" | ");
  59       }
  60     }
  61     int endIndex = summaryBuilder.lastIndexOf(" | ");
  62     String fSummary = summaryBuilder.toString().substring(0, endIndex);
  63     this.summary = fSummary.trim();
  64
  65   }
  66
  67   public String getPdbId()
  68   {
  69     return pdbId;
  70   }
  71
  72   public void setPdbId(String pdbId)
  73   {
  74     this.pdbId = pdbId;
  75   }
  76
  77   public String getSummary()
  78   {
  79     return summary;
  80   }
  81
  82   public void setSummary(String summary)
  83   {
  84     this.summary = summary;
  85   }
  86
  87
  88   public String toString()
  89   {
  90     StringBuilder html = new StringBuilder();
  91     html.append("<html><div style=\"width:" + width
  92             + "; word-wrap: break-word; border-bottom-style: dotted;\"> ");
  93     html.append(summary);
  94     html.append("</div></html>");
  95     return html.toString();
  96   }
  97
  98
  99   public enum PDBDocField
 100   {
 101     PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
 102             "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
 103             "molecule_type"), MOLECULE_SEQUENCE("Sequence",
 104             "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features",
 105             "uniprot_features"), PFAM_ACCESSION("PFAM Accession",
 106             "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession",
 107             "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession",
 108             "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION(
 109             "Resolution", "resolution"), DATA_QUALITY("Data Quality",
 110             "data_quality"), OVERALL_QUALITY("Overall Quality",
 111             "overall_quality"), POLYMER_COUNT("Polymer Count",
 112             "number_of_polymers"), PROTEIN_CHAIN_COUNT(
 113             "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
 114             "Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
 115             "Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE(
 116             "UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME(
 117             "Gene Name", "gene_name");
 118
 119     private String name;
 120
 121     private String code;
 122
 123     PDBDocField(String name, String code)
 124     {
 125       this.name = name;
 126       this.code = code;
 127     }
 128
 129     public String getName()
 130     {
 131       return name;
 132     }
 133
 134     public String getCode()
 135     {
 136       return code;
 137     }
 138
 139     public String toString()
 140     {
 141       return name;
 142     }
 143   }
 144 }