package jalview.ws.uimodel; import java.util.List; import javax.swing.DefaultListModel; import org.json.simple.JSONObject; @SuppressWarnings( { "serial", "rawtypes" }) public class PDBSummaryListModel extends DefaultListModel { private String pdbId; private String summary; private int width = 480; public PDBSummaryListModel(JSONObject doc, List diplayFields) { StringBuilder summaryBuilder = new StringBuilder(); for (PDBDocField field : diplayFields) { if (field.equals(PDBDocField.MOLECULE_TYPE) && doc.get("molecule_type") != null) { String moleculeType = doc.get("molecule_type").toString(); if (moleculeType.equalsIgnoreCase("protein")) { summaryBuilder.append("

"); } if (moleculeType.equalsIgnoreCase("dna")) { summaryBuilder.append("

"); } if (moleculeType.equalsIgnoreCase("rna")) { summaryBuilder.append("

"); } if (moleculeType.equalsIgnoreCase("sugar")) { summaryBuilder.append("

"); } }else if (doc.get(field.getCode()) != null) { summaryBuilder.append(field.getName()).append(": ") .append(doc.get(field.getCode())).append(" | "); } } int endIndex = summaryBuilder.lastIndexOf(" | "); String fSummary = summaryBuilder.toString().substring(0, endIndex); this.summary = fSummary.trim(); } public String getPdbId() { return pdbId; } public void setPdbId(String pdbId) { this.pdbId = pdbId; } public String getSummary() { return summary; } public void setSummary(String summary) { this.summary = summary; } public String toString() { StringBuilder html = new StringBuilder(); html.append("

"); html.append(summary); html.append("

"); return html.toString(); } public enum PDBDocField { PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME( "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type", "molecule_type"), MOLECULE_SEQUENCE("Sequence", "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features", "uniprot_features"), PFAM_ACCESSION("PFAM Accession", "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession", "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession", "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION( "Resolution", "resolution"), DATA_QUALITY("Data Quality", "data_quality"), OVERALL_QUALITY("Overall Quality", "overall_quality"), POLYMER_COUNT("Polymer Count", "number_of_polymers"), PROTEIN_CHAIN_COUNT( "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT( "Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT( "Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE( "UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME( "Gene Name", "gene_name"); private String name; private String code; PDBDocField(String name, String code) { this.name = name; this.code = code; } public String getName() { return name; } public String getCode() { return code; } public String toString() { return name; } } }