package jalview.ws.uimodel;
+import jalview.datamodel.SequenceI;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField.Group;
import java.util.Collection;
import java.util.Objects;
+import javax.swing.JTable;
import javax.swing.table.DefaultTableModel;
import org.json.simple.JSONObject;
this.searchSummary = searchSummary;
}
-
/**
- * Convenience method to obtain a Table model for a given summary List and
- * request
+ * Convenience method to obtain a Table model for a given summary List based
+ * on the request parameters
*
* @param request
* the PDBRestRequest object which holds useful information for
public static DefaultTableModel getTableModel(PDBRestRequest request,
Collection<PDBResponseSummary> summariesList)
{
- DefaultTableModel tableModel = new DefaultTableModel();
+ final PDBDocField[] cols = request.getWantedFields().toArray(
+ new PDBDocField[0]);
+ final int colOffset = request.getAssociatedSequence() == null ? 0 : 1;
+ DefaultTableModel tableModel = new DefaultTableModel()
+ {
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex)
+ {
+ if (colOffset == 1 && columnIndex == 0)
+ {
+ return String.class;
+ }
+ if (cols[columnIndex - colOffset].getGroup().getName()
+ .equalsIgnoreCase(Group.QUALITY_MEASURES.getName()))
+ {
+ return Double.class;
+ }
+ return String.class;
+ }
+ };
if (request.getAssociatedSequence() != null)
{
- tableModel.addColumn("Sequence"); // Create sequence column header if
- // exists in the request
+ tableModel.addColumn("Ref Sequence"); // Create sequence column header if
+ // exists in the request
}
for (PDBDocField field : request.getWantedFields())
{
tableModel.addRow(res.getSummaryData()); // Populate table rows with
// summary list
}
+
return tableModel;
}
/**
* Model for a unique response summary
*
- * @author tcnofoegbu
- *
*/
public class PDBResponseSummary
{
private String pdbId;
- private String[] summaryRowData;
+ private Object[] summaryRowData;
- private String associatedSequence;
+ private SequenceI associatedSequence;
- public PDBResponseSummary(JSONObject doc, PDBRestRequest request)
+ public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
{
Collection<PDBDocField> diplayFields = request.getWantedFields();
- String associatedSeq = request.getAssociatedSequence();
+ SequenceI associatedSeq = request.getAssociatedSequence();
int colCounter = 0;
- summaryRowData = new String[(associatedSeq != null) ? diplayFields
+ summaryRowData = new Object[(associatedSeq != null) ? diplayFields
.size() + 1 : diplayFields.size()];
if (associatedSeq != null)
{
- this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq
- .substring(0, 18) : associatedSeq;
+ this.associatedSequence = associatedSeq;
summaryRowData[0] = associatedSequence;
colCounter = 1;
}
for (PDBDocField field : diplayFields)
{
- String fieldData = (doc.get(field.getCode()) == null) ? "" : doc
- .get(field.getCode()).toString();
- if (field.equals(PDBDocField.PDB_ID)
- && doc.get(PDBDocField.PDB_ID.getCode()) != null)
+ String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
+ : pdbJsonDoc.get(field.getCode()).toString();
+ if (field.equals(PDBDocField.PDB_ID))
{
this.pdbId = fieldData;
summaryRowData[colCounter++] = this.pdbId;
}
else
{
- summaryRowData[colCounter++] = fieldData;
+ if (field.getGroup().getName()
+ .equals(Group.QUALITY_MEASURES.getName()))
+ {
+ try
+ {
+ if (fieldData == null || fieldData.isEmpty())
+ {
+ summaryRowData[colCounter++] = null;
+ }
+ else
+ {
+ Double value = Double.valueOf(fieldData);
+ summaryRowData[colCounter++] = value;
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ System.out.println("offending value:" + fieldData);
+ summaryRowData[colCounter++] = 0.0;
+ }
+ }else{
+ summaryRowData[colCounter++] = (fieldData == null || fieldData
+ .isEmpty()) ? null : fieldData;
+ }
}
}
}
- public String getPdbId()
+ public Object getPdbId()
{
return pdbId;
}
this.pdbId = pdbId;
}
- public String[] getSummaryData()
+ public Object[] getSummaryData()
{
return summaryRowData;
}
- public void setSummaryData(String[] summaryData)
+ public void setSummaryData(Object[] summaryData)
{
this.summaryRowData = summaryData;
}
+ /**
+ * Returns a string representation of this object;
+ */
@Override
public String toString()
{
StringBuilder summaryFieldValues = new StringBuilder();
- for (String summaryField : summaryRowData)
+ for (Object summaryField : summaryRowData)
{
- summaryFieldValues.append(summaryField).append("\t");
+ summaryFieldValues.append(
+ summaryField == null ? " " : summaryField.toString())
+ .append("\t");
}
return summaryFieldValues.toString();
}
+ /**
+ * Returns hash code value for this object
+ */
@Override
public int hashCode()
{
return Objects.hash(this.pdbId, this.toString());
}
+ /**
+ * Indicates whether some object is equal to this one
+ */
@Override
public boolean equals(Object that)
{
}
+ public static void configureTableColumn(JTable tbl_summary,
+ Collection<PDBDocField> wantedFields)
+ {
+ try
+ {
+ // wait for table model initialisation to complete
+ Thread.sleep(1200);
+ } catch (InterruptedException e1)
+ {
+ e1.printStackTrace();
+ }
+ for (PDBDocField wantedField : wantedFields)
+ {
+ try
+ {
+ if (wantedField.equals(PDBDocField.PDB_ID))
+ {
+ tbl_summary.getColumn(wantedField.getName()).setMinWidth(40);
+ tbl_summary.getColumn(wantedField.getName()).setMaxWidth(60);
+ tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(45);
+ }
+ else if (wantedField.equals(PDBDocField.TITLE))
+ {
+ tbl_summary.getColumn(wantedField.getName()).setMinWidth(300);
+ tbl_summary.getColumn(wantedField.getName()).setMaxWidth(1000);
+ tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(400);
+ }
+ else if (wantedField.getGroup() == Group.QUALITY_MEASURES)
+ {
+ tbl_summary.getColumn(wantedField.getName()).setMinWidth(50);
+ tbl_summary.getColumn(wantedField.getName()).setMaxWidth(150);
+ tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(85);
+ }
+ else
+ {
+ tbl_summary.getColumn(wantedField.getName()).setMinWidth(50);
+ tbl_summary.getColumn(wantedField.getName()).setMaxWidth(400);
+ tbl_summary.getColumn(wantedField.getName()).setPreferredWidth(95);
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
}
-
git://source.jalview.org / jalview.git / blobdiff