label.description = Description
label.include_description= Include Description
action.back = Back
+label.hide_insertions = Hide Insertions
+label.mark_as_representative = Mark as representative
+label.open_jabaws_web_page = Open JABAWS web page
\ No newline at end of file
+++ /dev/null
-package jalview.gui;
-
-import jalview.jbgui.GEBIFetchPanel;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.uimodel.PDBSearchOptionListModel;
-import jalview.ws.uimodel.PDBSearchResultPojo;
-import jalview.ws.uimodel.PDBSummaryListModel;
-
-import javax.swing.DefaultListModel;
-import javax.swing.SwingUtilities;
-
-@SuppressWarnings("serial")
-public class EBIFetchPanel extends GEBIFetchPanel
-{
- private SequenceFetcher seqFetcher;
-
- public EBIFetchPanel()
- {
- }
-
- public EBIFetchPanel(SequenceFetcher seqFetcher)
- {
- this();
- this.seqFetcher = seqFetcher;
- }
-
- public static void main(String[] args)
- {
- SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- new EBIFetchPanel();
- }
- });
- }
-
- @Override
- public void searchStringAction()
- {
-
- jListSearchResult.setModel(new DefaultListModel<PDBSummaryListModel>());
- mainFrame.setTitle("PDB Sequence Fetcher");
- if (search.getText().trim().length() > 0)
- {
- long startTime = System.currentTimeMillis();
-
- PDBSearchResultPojo resultList = new PDBRestClient().searchResult(
- ((PDBSearchOptionListModel) searchFeild.getSelectedItem()).getCode(),
- search.getText());
- if (resultList.getSearchSummary() != null)
- {
- jListSearchResult.setModel(resultList.getSearchSummary());
- }
- long endTime = System.currentTimeMillis();
- mainFrame.setTitle("PDB Sequence Fetcher - "
- + resultList.getItemFound() + " results ("
- + (endTime - startTime) + " milli secs)");
- }
-
- }
-
- @Override
- public void okActionPerformed()
- {
- processPDBResponseData();
- }
-
-
- @Override
- public void backActionPerformed()
- {
- System.out.println("back! pressed!");
- }
-
- @Override
- public void cancelActionPerformed()
- {
- mainFrame.dispose();
- }
-
- private void processPDBResponseData()
- {
- mainFrame.dispose();
- StringBuilder selectedIds = new StringBuilder();
- for (PDBSummaryListModel dataSelected : jListSearchResult
- .getSelectedValuesList())
- {
- selectedIds.append(";").append(dataSelected.getPdbId());
- }
- String ids = selectedIds.deleteCharAt(0).toString();
- seqFetcher.textArea.setText(ids);
- Thread worker = new Thread(seqFetcher);
-
- // Thread worker = new Thread(this);
- worker.start();
- }
-
- // @Override
- // public void run()
- // {
- // for (PDBSummaryListModel sum : jListSearchResult
- // .getSelectedValuesList())
- // {
- // System.out.println("you selected ------------> " + sum.getPdbId());
- // }
- // seqFetcher.guiWindow.setProgressBar(MessageManager
- // .getString("status.processing"), Thread.currentThread()
- // .hashCode());
- // try
- // {
- // Thread.sleep(1000 * 2);
- // } catch (InterruptedException e)
- // {
- // e.printStackTrace();
- // }
- // seqFetcher.guiWindow.setProgressBar(null, Thread.currentThread()
- // .hashCode());
- // }
-
-}
--- /dev/null
+package jalview.gui;
+
+import jalview.jbgui.GPDBFetchPanel;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.uimodel.PDBSearchRequest;
+import jalview.ws.uimodel.PDBSearchResponse;
+import jalview.ws.uimodel.PDBSummaryListModel;
+import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.DefaultListModel;
+import javax.swing.SwingUtilities;
+
+@SuppressWarnings("serial")
+public class PDBFetchPanel extends GPDBFetchPanel
+{
+ private SequenceFetcher seqFetcher;
+
+ public enum FieldType
+ {
+ INT, STRING, BOOLEAN;
+ }
+
+ public PDBFetchPanel()
+ {
+ }
+
+ public PDBFetchPanel(SequenceFetcher seqFetcher)
+ {
+ this();
+ this.seqFetcher = seqFetcher;
+ }
+
+ public static void main(String[] args)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ new PDBFetchPanel();
+ }
+ });
+ }
+
+ @Override
+ public void searchStringAction()
+ {
+ boolean allowEmptySequence = false;
+ jListSearchResult.setModel(new DefaultListModel<PDBSummaryListModel>());
+ mainFrame.setTitle("PDB Sequence Fetcher");
+ if (search.getText().trim().length() > 0)
+ {
+ long startTime = System.currentTimeMillis();
+ PDBRestClient pdbRestCleint = new PDBRestClient();
+ String searchTarget = ((PDBSearchOptionList) searchTargetOptions
+ .getSelectedItem()).getCode();
+
+ PDBSearchRequest request = new PDBSearchRequest();
+ request.setAllowEmptySeq(allowEmptySequence);
+ request.setResponseSize(100);
+ request.setSearchTarget(searchTarget + ":");
+ request.setSearchTerm(search.getText());
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ request.setWantedFields(wantedFields);
+
+ PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
+
+ if (resultList.getSearchSummary() != null)
+ {
+ jListSearchResult.setModel(PDBSearchResponse
+ .getListModel(resultList.getSearchSummary()));
+ }
+ long endTime = System.currentTimeMillis();
+ mainFrame.setTitle("PDB Sequence Fetcher - "
+ + resultList.getItemsFound() + " results ("
+ + (endTime - startTime) + " milli secs)");
+ }
+
+ }
+
+ @Override
+ public void okActionPerformed()
+ {
+ processPDBResponseData();
+ }
+
+
+ @Override
+ public void backActionPerformed()
+ {
+ System.out.println("back! pressed!");
+ }
+
+ @Override
+ public void cancelActionPerformed()
+ {
+ mainFrame.dispose();
+ }
+
+ private void processPDBResponseData()
+ {
+ mainFrame.dispose();
+ StringBuilder selectedIds = new StringBuilder();
+ for (PDBSummaryListModel dataSelected : jListSearchResult
+ .getSelectedValuesList())
+ {
+ selectedIds.append(";").append(dataSelected.getPdbId());
+ }
+ String ids = selectedIds.deleteCharAt(0).toString();
+ seqFetcher.textArea.setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ }
+
+ @SuppressWarnings("unchecked")
+ public void populateSearchOptionCombo()
+
+ {
+ 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()
+ {
+
+ }
+
+ @Override
+ public int compareTo(Object o)
+ {
+ return this.name.compareTo(((PDBSearchOptionList) o).getName());
+ }
+
+ }
+}
JMenu jMenu1 = new JMenu();
- JMenu structureMenu = new JMenu();
+ JMenuItem structureMenu = new JMenuItem();
JMenu viewStructureMenu = new JMenu();
new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
new PDBEntry[reppdb.size()]);
final JMenuItem gpdbview, rpdbview;
- if (pdbe.size() == 1)
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_structure_for", new String[]
- { sqass.getDisplayId(false) })));
- }
- else
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_all_structures", new String[]
- { new Integer(pdbe.size()).toString() })));
- }
- gpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
- gpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pe, ap.av.collateForPDB(pe));
- }
- });
- if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
- {
- structureMenu.add(rpdbview = new JMenuItem(MessageManager
- .formatMessage(
- "label.view_all_representative_structures",
- new String[]
- { new Integer(reppdb.size()).toString() })));
- rpdbview.setToolTipText(MessageManager
- .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
- rpdbview.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- new StructureViewer(ap.getStructureSelectionManager())
- .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- }
- });
- }
+ // if (pdbe.size() == 1)
+ // {
+ // structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ // .formatMessage("label.view_structure_for", new String[]
+ // { sqass.getDisplayId(false) })));
+ // }
+ // else
+ // {
+ // structureMenu.add(gpdbview = new JMenuItem(MessageManager
+ // .formatMessage("label.view_all_structures", new String[]
+ // { new Integer(pdbe.size()).toString() })));
+ // }
+ // gpdbview.setToolTipText(MessageManager
+ // .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
+ // gpdbview.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // new StructureViewer(ap.getStructureSelectionManager())
+ // .viewStructures(ap, pe, ap.av.collateForPDB(pe));
+ // }
+ // });
+ // if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
+ // {
+ // structureMenu.add(rpdbview = new JMenuItem(MessageManager
+ // .formatMessage(
+ // "label.view_all_representative_structures",
+ // new String[]
+ // { new Integer(reppdb.size()).toString() })));
+ // rpdbview.setToolTipText(MessageManager
+ // .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
+ // rpdbview.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // new StructureViewer(ap.getStructureSelectionManager())
+ // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ // }
+ // });
+ // }
}
}
else
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
+ // structureMenu.setText(MessageManager.getString("label.structure"));
+ structureMenu.setText(MessageManager.getString("label.view_structure"));
+ structureMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ new StructureChooser(ap, sequence);
+ }
+ });
+
viewStructureMenu.setText(MessageManager
.getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
+ // structureMenu.add(pdbMenu);
+ // structureMenu.add(viewStructureMenu);
// structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
private void pdbSourceAction()
{
databaseButt.setText(database.getSelectedItem());
- new EBIFetchPanel(this);
+ new PDBFetchPanel(this);
frame.dispose();
}
--- /dev/null
+package jalview.gui;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.uimodel.PDBSearchRequest;
+import jalview.ws.uimodel.PDBSearchResponse;
+import jalview.ws.uimodel.PDBSummaryListModel;
+import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+@SuppressWarnings("serial")
+public class StructureChooser extends GStructureChooser
+{
+
+
+ private SequenceI sequence;
+
+
+ public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
+ {
+ this.ap = ap;
+ this.sequence = sequence;
+ fetchStructures();
+ }
+
+ @Override
+ public void ok_ActionPerformed()
+ {
+ jListFoundStructures.setSelectedValue("op1x", true);
+ }
+
+ public void pdbFromFile_actionPerformed()
+ {
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle(MessageManager.formatMessage(
+ "label.select_pdb_file_for", new String[]
+ { sequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { sequence.getDisplayId(false) }));
+
+ int value = chooser.showOpenDialog(null);
+
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
+ jalview.io.AppletFormatAdapter.FILE, sequence, true,
+ Desktop.instance);
+ }
+
+ }
+
+ public void discoverPDB_actionPerformed()
+ {
+
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.getSequenceSelection());
+ Thread discpdb = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+
+ new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+ .fetchDBRefs(false);
+ }
+
+ });
+ discpdb.start();
+ }
+
+ // rpdbview.addActionListener(new ActionListener()
+ // {
+ //
+ // @Override
+ // public void actionPerformed(ActionEvent e)
+ // {
+ // new StructureViewer(ap.getStructureSelectionManager())
+ // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
+ // }
+ // });
+
+ public void enterPDB_actionPerformed()
+ {
+ String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+ MessageManager.getString("label.enter_pdb_id"),
+ MessageManager.getString("label.enter_pdb_id"),
+ JOptionPane.QUESTION_MESSAGE);
+ if (id != null && id.length() > 0)
+ {
+ PDBEntry entry = new PDBEntry();
+ entry.setId(id.toUpperCase());
+ sequence.getDatasetSequence().addPDBId(entry);
+ }
+ }
+
+ public static void main(String[] args)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ new StructureChooser(null, null);
+ }
+ });
+ }
+
+ @SuppressWarnings("unchecked")
+ protected void populateFilterOptions()
+ {
+ filterOptions.addItem(new FilterOptions("- Filter Criteria -", "",
+ VIEWS_AUTO));
+ filterOptions.addItem(new FilterOptions("All", "all", VIEWS_AUTO));
+ filterOptions
+ .addItem(new FilterOptions("Best Coverage", "", VIEWS_AUTO));
+ filterOptions.addItem(new FilterOptions("Best Resolution", "",
+ VIEWS_AUTO));
+ filterOptions
+ .addItem(new FilterOptions("Best Quality", "", VIEWS_AUTO));
+ filterOptions.addItem(new FilterOptions("Enter PDB Id", "", VIEWS_ID));
+ filterOptions.addItem(new FilterOptions("From File", "", VIEWS_FILE));
+ }
+
+ protected void updateCurrentView()
+ {
+ String currentView = ((FilterOptions) filterOptions.getSelectedItem())
+ .getView();
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
+ }
+
+ private void fetchStructures()
+ {
+ long startTime = System.currentTimeMillis();
+ final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
+ { sequence }
+ : ap.av.getSequenceSelection());
+ int foundStructures = 0;
+ PDBSearchRequest request = new PDBSearchRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(500);
+ request.setSearchTarget("(text:");
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ request.setWantedFields(wantedFields);
+
+ Collection<PDBSummaryListModel> searchSummaries = new HashSet<PDBSummaryListModel>();
+ // searchSummaries.
+ for (SequenceI seq : sequences)
+ {
+ // System.out.println("Selected : " + seq.getName());
+ request.setSearchTerm(buildQuery(seq) + ")");
+
+ PDBRestClient pdbRestCleint = new PDBRestClient();
+
+ PDBSearchResponse resultList = pdbRestCleint
+ .executeRequest(request);
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ searchSummaries.addAll(resultList.getSearchSummary());
+ }
+ }
+
+ foundStructures = searchSummaries.size();
+ if (searchSummaries != null)
+ {
+ jListFoundStructures.setModel(PDBSearchResponse
+ .getListModel(searchSummaries));
+ }
+
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - " + foundStructures
+ + " Found (" + totalTime + ")");
+ }
+
+ private String buildQuery(SequenceI seq)
+ {
+ String query = seq.getName();
+ StringBuilder queryBuilder = new StringBuilder();
+ int count = 0;
+ if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+ {
+ for (DBRefEntry dbRef : seq.getDBRef())
+ {
+ System.out.println("dbref : " + dbRef.getAccessionId());
+ queryBuilder.append("text:").append(dbRef.getAccessionId())
+ .append(" OR ");
+ ++count;
+ if (count > 10)
+ {
+ break;
+ }
+ }
+ // int beginIndex = queryBuilder. firstIndexOf("text");
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ query = queryBuilder.toString().substring(5, endIndex);
+ }
+ System.out.println("------------> " + query);
+ return query;
+ }
+
+ public class FilterOptions
+ {
+ private String name;
+
+ private String value;
+
+ private String view;
+
+ public FilterOptions(String name, String value, String view)
+ {
+ this.name = name;
+ this.value = value;
+ this.view = view;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ public String getView()
+ {
+ return view;
+ }
+
+ public void setView(String view)
+ {
+ this.view = view;
+ }
+
+ public String toString()
+ {
+ return this.name;
+ }
+ }
+}
package jalview.jbgui;
import jalview.gui.Desktop;
+import jalview.gui.PDBFetchPanel.PDBSearchOptionList;
import jalview.util.MessageManager;
-import jalview.ws.uimodel.PDBSearchOptionListModel;
import jalview.ws.uimodel.PDBSummaryListModel;
import java.awt.BorderLayout;
import javax.swing.event.DocumentListener;
@SuppressWarnings("serial")
-public abstract class GEBIFetchPanel extends JPanel
+public abstract class GPDBFetchPanel extends JPanel
{
protected String frameTitle = "PDB Sequence Fetcher";
protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
- protected JComboBox<PDBSearchOptionListModel> searchFeild = new JComboBox<PDBSearchOptionListModel>();
+ protected JComboBox<PDBSearchOptionList> searchTargetOptions = new JComboBox<PDBSearchOptionList>();
protected JButton ok = new JButton();
- public GEBIFetchPanel()
+ public GPDBFetchPanel()
{
try
{
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
resultPanel.add(searchResultScroller);
- searchFeild.setFont(new java.awt.Font("Verdana", 0, 12));
- searchFeild.addActionListener(new ActionListener()
+ searchTargetOptions.setFont(new java.awt.Font("Verdana", 0, 12));
+ searchTargetOptions.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
- PDBSearchOptionListModel.populateCombo(searchFeild);
+ populateSearchOptionCombo();
search.setFont(new java.awt.Font("Verdana", 0, 12));
search.getDocument().addDocumentListener(new DocumentListener()
}
});
- inputPanel.add(searchFeild);
+ inputPanel.add(searchTargetOptions);
inputPanel.add(search);
public abstract void cancelActionPerformed();
+ protected abstract void populateSearchOptionCombo();
+
}
--- /dev/null
+package jalview.jbgui;
+
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.CardLayout;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+
+@SuppressWarnings("serial")
+public abstract class GStructureChooser extends JPanel implements
+ ItemListener
+{
+ protected String frameTitle = "Structure Chooser";
+
+ protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+
+
+
+ protected JComboBox filterOptions = new JComboBox();
+
+ protected AlignmentPanel ap;
+
+ protected JLabel resultLabel = new JLabel("View : ");
+
+ protected JButton ok = new JButton();
+
+ protected JButton cancel = new JButton();
+
+ protected JButton selectFile = new JButton();
+
+ protected JTextField search = new JTextField(16);
+
+ protected JPanel actionPanel = new JPanel();
+
+ protected JPanel filterPanel = new JPanel();
+
+ protected JPanel idInputPanel = new JPanel();
+
+ protected JPanel fileChooserPanel = new JPanel();
+
+ protected JPanel switchableViewsPanel = new JPanel(new CardLayout());
+
+ protected CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
+ .getLayout());
+
+ protected BorderLayout mainLayout = new BorderLayout();
+
+ protected BorderLayout idInputPanelLayout = new BorderLayout();
+
+ protected BorderLayout fileChooserPanelLayout = new BorderLayout();
+
+ protected JCheckBox rememberSettings = new JCheckBox("Don't ask me again");
+
+
+ protected static final String VIEWS_AUTO = "auto_view";
+
+ protected static final String VIEWS_FILE = "file_view";
+
+ protected static final String VIEWS_ID = "id_view";
+
+ protected JList jListFoundStructures = new JList();
+
+ protected JScrollPane foundStructuresScroller = new JScrollPane(
+ jListFoundStructures);
+
+ public GStructureChooser()
+ {
+ try
+ {
+ jbInit();
+ mainFrame.invalidate();
+ mainFrame.pack();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+
+ ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_ActionPerformed();
+ }
+ });
+ cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ mainFrame.dispose();
+ }
+ });
+
+ jListFoundStructures
+ .setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+ jListFoundStructures.setLayoutOrientation(JList.VERTICAL);
+ jListFoundStructures.setVisibleRowCount(-1);
+ foundStructuresScroller.setPreferredSize(new Dimension(500, 300));
+ foundStructuresScroller
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ actionPanel.add(rememberSettings);
+ actionPanel.add(ok);
+ actionPanel.add(cancel);
+
+ filterOptions.addItemListener(this);
+
+ filterPanel.add(resultLabel);
+ filterPanel.add(filterOptions);
+
+ idInputPanel.setLayout(new FlowLayout());
+ idInputPanel.add(search);
+
+
+ selectFile.setText(" Select File ");
+ fileChooserPanel.setLayout(new FlowLayout());
+ fileChooserPanel.add(selectFile);
+
+ switchableViewsPanel.add(fileChooserPanel, VIEWS_FILE);
+ switchableViewsPanel.add(idInputPanel, VIEWS_ID);
+ switchableViewsPanel.add(foundStructuresScroller, VIEWS_AUTO);
+
+
+ this.setLayout(mainLayout);
+ this.add(filterPanel, java.awt.BorderLayout.NORTH);
+ this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
+ this.add(actionPanel, java.awt.BorderLayout.SOUTH);
+ populateFilterOptions();
+ updateCurrentView();
+ mainFrame.setVisible(true);
+ mainFrame.setContentPane(this);
+ mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ updateCurrentView();
+ }
+
+ protected abstract void updateCurrentView();
+
+ protected abstract void ok_ActionPerformed();
+
+ protected abstract void populateFilterOptions();
+}
package jalview.ws.dbsources;
-import jalview.ws.uimodel.PDBSearchResultPojo;
+import jalview.ws.uimodel.PDBSearchRequest;
+import jalview.ws.uimodel.PDBSearchResponse;
import jalview.ws.uimodel.PDBSummaryListModel;
+import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+import java.util.ArrayList;
import java.util.Iterator;
+import java.util.List;
-import javax.swing.DefaultListModel;
import javax.ws.rs.core.MediaType;
import org.json.simple.JSONArray;
{
private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
-
public static void main(String[] args)
{
- new PDBRestClient().searchResult("pfam_name", "Lipoc*");
+ PDBSearchRequest request = new PDBSearchRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setSearchTarget("pfam_name");
+ request.setSearchTerm("Lipoc*");
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ request.setWantedFields(wantedFields);
+ new PDBRestClient().executeRequest(request);
}
- private String executeRestSearch(String qParam,
- String searchTerm)
+ public PDBSearchResponse executeRequest(PDBSearchRequest request)
{
ClientConfig clientConfig = new DefaultClientConfig();
clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
Boolean.TRUE);
Client client = Client.create(clientConfig);
+
+ String query = request.getSearchTarget()
+ + request.getSearchTerm()
+ + ((request.isAllowEmptySeq()) ? ""
+ : " AND molecule_sequence:['' TO *]");
+
+ String wantedFields = getFieldsAsCommaDelimitedString(request
+ .getWantedFields());
+
+ String responseSize = (request.getResponseSize() == 0) ? "200" : String
+ .valueOf(request.getResponseSize());
WebResource webResource = client.resource(pdbSearchEndpoint)
- .queryParam("wt", "json")
-.queryParam("rows", "100")
- .queryParam("q", qParam + ":" + searchTerm);
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", responseSize)
+ .queryParam("q", query);
ClientResponse clientResponse = webResource.accept(
MediaType.APPLICATION_JSON).get(ClientResponse.class);
throw new RuntimeException("Failed : HTTP error code : "
+ clientResponse.getStatus());
}
- return responseString;
+ // System.out.println("--------------> " + responseString);
+ return parseResponse(responseString, request.getWantedFields());
}
- public PDBSearchResultPojo searchResult(String qParam,
- String searchTerm)
+ private PDBSearchResponse parseResponse(String jsonResponse,
+ List<PDBDocField> wantedFields)
{
- String jsonResponseString = executeRestSearch(qParam, searchTerm);
- PDBSearchResultPojo searchResult = new PDBSearchResultPojo();
- DefaultListModel<PDBSummaryListModel> result = null;
+ PDBSearchResponse searchResult = new PDBSearchResponse();
+ List<PDBSummaryListModel> result = null;
try
{
JSONParser jsonParser = new JSONParser();
JSONObject jsonObj = (JSONObject) jsonParser
- .parse(jsonResponseString);
+.parse(jsonResponse);
JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
.valueOf(pdbResponse.get("numFound").toString());
if (numFound > 0)
{
- result = new DefaultListModel<PDBSummaryListModel>();
+ result = new ArrayList<PDBSummaryListModel>();
JSONArray docs = (JSONArray) pdbResponse.get("docs");
for (Iterator<JSONObject> docIter = docs.iterator(); docIter
.hasNext();)
{
JSONObject doc = docIter.next();
- if (doc.get("molecule_sequence") != null)
- {
- result.addElement(new PDBSummaryListModel(doc));
- }
+ // if (doc.get("molecule_sequence") != null)
+ // {
+ result.add(new PDBSummaryListModel(doc, wantedFields));
+ // }
}
- searchResult.setItemFound(numFound);
+ searchResult.setItemsFound(numFound);
searchResult.setResponseTime(queryTime);
searchResult.setSearchSummary(result);
}
return searchResult;
}
+ private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
+ {
+ String result = "";
+ if (fields != null && !fields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (PDBDocField field : fields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+
}
+++ /dev/null
-package jalview.ws.uimodel;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.DefaultListModel;
-import javax.swing.JComboBox;
-
-@SuppressWarnings(
-{ "unchecked", "serial", "rawtypes" })
-public class PDBSearchOptionListModel extends DefaultListModel implements Comparable
-{
- private String name;
-
- private String code;
-
- private boolean showInSummary;
-
- private boolean searchFilter;
-
- private FieldType type;
-
- public enum FieldType
- {
- INT, STRING, BOOLEAN;
- };
-
- public PDBSearchOptionListModel(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 PDBSearchOptionListModel()
- {
-
- }
-
- public static void populateCombo(JComboBox searchItems)
- {
- List<PDBSearchOptionListModel> searchOptions = new ArrayList<PDBSearchOptionListModel>();
- searchOptions.add(new PDBSearchOptionListModel("PDB ID", "pdb_id",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("PFAM Name", "pfam_name",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("ALL", "text",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("Molecule Type", "molecule_type",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("Title", "title",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("Molecule Name", "molecule_name",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("Tax ID", "tax_id",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("UniProt Accession",
- "uniprot_accession", PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("Gene Name", "gene_name",
- PDBSearchOptionListModel.FieldType.STRING));
- searchOptions.add(new PDBSearchOptionListModel("Genus", "genus",
- PDBSearchOptionListModel.FieldType.STRING));
-
- java.util.Collections.sort(searchOptions);
-
- for (PDBSearchOptionListModel pdbSO : searchOptions)
- {
- searchItems.addItem(pdbSO);
- }
- }
-
- @Override
- public int compareTo(Object o)
- {
- return this.name.compareTo(((PDBSearchOptionListModel) o).getName());
- }
-
-}
--- /dev/null
+package jalview.ws.uimodel;
+
+import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class PDBSearchRequest
+{
+ private String searchTarget;
+
+ private String searchTerm;
+
+ private boolean allowEmptySeq;
+
+ private int responseSize;
+
+ private List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+
+ public String getSearchTarget()
+ {
+ return searchTarget;
+ }
+
+ public void setSearchTarget(String searchTarget)
+ {
+ this.searchTarget = searchTarget;
+ }
+
+ public String getSearchTerm()
+ {
+ return searchTerm;
+ }
+
+ public void setSearchTerm(String searchTerm)
+ {
+ this.searchTerm = searchTerm;
+ }
+
+ public boolean isAllowEmptySeq()
+ {
+ return allowEmptySeq;
+ }
+
+ public void setAllowEmptySeq(boolean allowEmptySeq)
+ {
+ this.allowEmptySeq = allowEmptySeq;
+ }
+
+ public int getResponseSize()
+ {
+ return responseSize;
+ }
+
+ public void setResponseSize(int responseSize)
+ {
+ this.responseSize = responseSize;
+ }
+
+ public List<PDBDocField> getWantedFields()
+ {
+ return wantedFields;
+ }
+
+ public void setWantedFields(List<PDBDocField> wantedFields)
+ {
+ this.wantedFields = wantedFields;
+ }
+}
--- /dev/null
+package jalview.ws.uimodel;
+
+import java.util.Collection;
+
+import javax.swing.DefaultListModel;
+
+public class PDBSearchResponse
+{
+ private int itemsFound;
+
+ private String responseTime;
+
+ private Collection<PDBSummaryListModel> searchSummary;
+
+ public int getItemsFound()
+ {
+ return itemsFound;
+ }
+
+ public void setItemsFound(int itemFound)
+ {
+ this.itemsFound = itemFound;
+ }
+
+ public String getResponseTime()
+ {
+ return responseTime;
+ }
+
+ public void setResponseTime(String responseTime)
+ {
+ this.responseTime = responseTime;
+ }
+
+ public Collection<PDBSummaryListModel> getSearchSummary()
+ {
+ return searchSummary;
+ }
+
+ public void setSearchSummary(Collection<PDBSummaryListModel> searchSummary)
+ {
+ this.searchSummary = searchSummary;
+ }
+
+ public static DefaultListModel<PDBSummaryListModel> getListModel(
+ Collection<PDBSummaryListModel> summariesList)
+ {
+ DefaultListModel<PDBSummaryListModel> defaultListModel = new DefaultListModel<PDBSummaryListModel>();
+ for (PDBSummaryListModel summaryList : summariesList)
+ {
+ defaultListModel.addElement(summaryList);
+ }
+ return defaultListModel;
+ }
+}
+
+++ /dev/null
-package jalview.ws.uimodel;
-
-import javax.swing.DefaultListModel;
-
-public class PDBSearchResultPojo
-{
- private int itemFound;
-
- private String responseTime;
-
- private DefaultListModel<PDBSummaryListModel> searchSummary;
-
- public int getItemFound()
- {
- return itemFound;
- }
-
- public void setItemFound(int itemFound)
- {
- this.itemFound = itemFound;
- }
-
- public String getResponseTime()
- {
- return responseTime;
- }
-
- public void setResponseTime(String responseTime)
- {
- this.responseTime = responseTime;
- }
-
- public DefaultListModel<PDBSummaryListModel> getSearchSummary()
- {
- return searchSummary;
- }
-
- public void setSearchSummary(
- DefaultListModel<PDBSummaryListModel> searchSummary)
- {
- this.searchSummary = searchSummary;
- }
-}
package jalview.ws.uimodel;
+import java.util.List;
+
import javax.swing.DefaultListModel;
import org.json.simple.JSONObject;
private String summary;
- private JSONObject rawJson;
-
private int width = 480;
- public PDBSummaryListModel(JSONObject doc)
+ public PDBSummaryListModel(JSONObject doc, List<PDBDocField> diplayFields)
{
- this.rawJson = doc;
- StringBuilder summary = new StringBuilder();
- if (doc.get("molecule_type") != null)
+ StringBuilder summaryBuilder = new StringBuilder();
+
+ for (PDBDocField field : diplayFields)
{
- String moleculeType = doc.get("molecule_type").toString();
- if (moleculeType.equalsIgnoreCase("protein"))
- {
- summary.append("<img src=\""
- + getClass().getResource("/images/protein.png").toString()
- + "\">");
- }
- if (moleculeType.equalsIgnoreCase("dna"))
+ if (field.equals(PDBDocField.MOLECULE_TYPE)
+ && doc.get("molecule_type") != null)
{
- summary.append("<img src=\""
- + getClass().getResource("/images/dna.png").toString()
- + "\">");
- }
- if (moleculeType.equalsIgnoreCase("rna"))
- {
- summary.append("<img src=\""
- + getClass().getResource("/images/dna.png").toString()
- + "\">");
- }
- if (moleculeType.equalsIgnoreCase("sugar"))
+ String moleculeType = doc.get("molecule_type").toString();
+ if (moleculeType.equalsIgnoreCase("protein"))
+ {
+ summaryBuilder.append("<img src=\""
+ + getClass().getResource("/images/protein.png").toString()
+ + "\">");
+ }
+ if (moleculeType.equalsIgnoreCase("dna"))
+ {
+ summaryBuilder.append("<img src=\""
+ + getClass().getResource("/images/dna.png").toString()
+ + "\">");
+ }
+ if (moleculeType.equalsIgnoreCase("rna"))
+ {
+ summaryBuilder.append("<img src=\""
+ + getClass().getResource("/images/dna.png").toString()
+ + "\">");
+ }
+ if (moleculeType.equalsIgnoreCase("sugar"))
+ {
+ summaryBuilder.append("<img src=\""
+ + getClass().getResource("/images/sugar.png").toString()
+ + "\">");
+ }
+ }else if (doc.get(field.getCode()) != null)
{
- summary.append("<img src=\""
- + getClass().getResource("/images/sugar.png").toString()
- + "\">");
+ summaryBuilder.append(field.getName()).append(": ")
+ .append(doc.get(field.getCode())).append(" | ");
}
}
- this.pdbId = doc.get("pdb_id").toString();
- summary.append("PDB ID: ").append(pdbId);
+ int endIndex = summaryBuilder.lastIndexOf(" | ");
+ String fSummary = summaryBuilder.toString().substring(0, endIndex);
+ this.summary = fSummary.trim();
-
- if (doc.get("molecule_name") != null)
- {
- summary.append(" | Molecule Name: ").append(doc.get("molecule_name"));
- }
- if (doc.get("gene_name") != null)
- {
- summary.append(" | Gene Name: ").append(doc.get("gene_name"));
- }
- if (doc.get("genus") != null)
- {
- summary.append(" | Genus: ").append(doc.get("genus"));
- }
- if (doc.get("title") != null)
- {
- summary.append(" | Title: ").append(doc.get("title"));
- }
- this.summary = summary.toString();
}
public String getPdbId()
this.summary = summary;
}
- public JSONObject getRawJson()
- {
- return rawJson;
- }
-
- public void setRawJson(JSONObject rawJson)
- {
- this.rawJson = rawJson;
- }
public String toString()
{
html.append("</div></html>");
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;
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff