import jalview.jbgui.GPDBFetchPanel;
import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.uimodel.PDBSearchRequest;
import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSummaryListModel;
-import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import javax.swing.DefaultListModel;
public void searchStringAction()
{
boolean allowEmptySequence = false;
- jListSearchResult.setModel(new DefaultListModel<PDBSummaryListModel>());
+ jListSearchResult.setModel(new DefaultListModel<PDBResponseSummary>());
mainFrame.setTitle("PDB Sequence Fetcher");
if (search.getText().trim().length() > 0)
{
long startTime = System.currentTimeMillis();
PDBRestClient pdbRestCleint = new PDBRestClient();
- String searchTarget = ((PDBSearchOptionList) searchTargetOptions
+ String searchTarget = ((PDBDocField) searchTargetOptions
.getSelectedItem()).getCode();
PDBSearchRequest request = new PDBSearchRequest();
@Override
public void okActionPerformed()
{
- processPDBResponseData();
+ importSelectedPDBSequencesToAlignment();
}
mainFrame.dispose();
}
- private void processPDBResponseData()
+ private void importSelectedPDBSequencesToAlignment()
{
mainFrame.dispose();
StringBuilder selectedIds = new StringBuilder();
- for (PDBSummaryListModel dataSelected : jListSearchResult
+ for (PDBResponseSummary dataSelected : jListSearchResult
.getSelectedValuesList())
{
selectedIds.append(";").append(dataSelected.getPdbId());
worker.start();
}
- @SuppressWarnings("unchecked")
- public void populateSearchOptionCombo()
-
+ public void populateSearchOptionComboBox()
{
- List<PDBSearchOptionList> searchOptions = new ArrayList<PDBSearchOptionList>();
- searchOptions.add(new PDBSearchOptionList("PDB ID", "pdb_id",
- FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("PFAM Name", "pfam_name",
- FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("ALL", "text",
- FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("Molecule Type",
- "molecule_type", FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("Title", "title",
- FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("Molecule Name",
- "molecule_name", FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("Tax ID", "tax_id",
- FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("UniProt Accession",
- "uniprot_accession", FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("Gene Name", "gene_name",
- FieldType.STRING));
- searchOptions.add(new PDBSearchOptionList("Genus", "genus",
- FieldType.STRING));
-
- java.util.Collections.sort(searchOptions);
-
- for (PDBSearchOptionList pdbSO : searchOptions)
- {
- searchTargetOptions.addItem(pdbSO);
- }
- }
-
- @SuppressWarnings("rawtypes")
- public class PDBSearchOptionList implements Comparable
- {
- private String name;
-
- private String code;
-
- private boolean showInSummary;
-
- private boolean searchFilter;
-
- private FieldType type;
-
- public PDBSearchOptionList(String name, String code, FieldType type)
- {
- this.name = name;
- this.code = code;
- this.type = type;
- }
-
- public String getName()
- {
- return name;
- }
-
- public void setName(String name)
- {
- this.name = name;
- }
-
- public String getCode()
- {
- return code;
- }
-
- public void setCode(String code)
- {
- this.code = code;
- }
-
- public boolean isShowInSummary()
- {
- return showInSummary;
- }
-
- public void setShowInSummary(boolean showInSummary)
- {
- this.showInSummary = showInSummary;
- }
-
- public boolean isSearchFilter()
- {
- return searchFilter;
- }
-
- public void setSearchFilter(boolean searchFilter)
- {
- this.searchFilter = searchFilter;
- }
-
- public FieldType getFieldType()
- {
- return type;
- }
-
- public void setFieldType(FieldType type)
- {
- this.type = type;
- }
-
- public String toString()
- {
- return name;
- }
-
- public PDBSearchOptionList()
- {
-
- }
+ List<PDBDocField> searchableTargets = new ArrayList<PDBDocField>();
+ searchableTargets.add(PDBDocField.PDB_ID);
+ searchableTargets.add(PDBDocField.PFAM_ACCESSION);
+ searchableTargets.add(PDBDocField.MOLECULE_TYPE);
+ searchableTargets.add(PDBDocField.MOLECULE_NAME);
+ searchableTargets.add(PDBDocField.UNIPROT_ACCESSION);
+ searchableTargets.add(PDBDocField.GENE_NAME);
+ searchableTargets.add(PDBDocField.GENUS);
+ searchableTargets.add(PDBDocField.ALL);
+
+ Collections.sort(searchableTargets, new Comparator<PDBDocField>()
+ {
+ @Override
+ public int compare(PDBDocField o1, PDBDocField o2)
+ {
+ return o1.getName().compareTo(o2.getName());
+ }
+ });
- @Override
- public int compareTo(Object o)
+ for (PDBDocField searchTarget : searchableTargets)
{
- return this.name.compareTo(((PDBSearchOptionList) o).getName());
+ searchTargetOptions.addItem(searchTarget);
}
-
}
+
}