label.use_sequence_id_2 = \nto embed sequence id in URL
label.ws_parameters_for = Parameters for {0}
label.switch_server = Switch server
-label.open_jabaws_web_page = Opens the JABAWS server's homepage in web browser
label.choose_jabaws_server = Choose a server for running this service
label.services_at = Services at {0}
label.rest_client_submit = {0} using {1}
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
+label.open_jabaws_web_page = Open JABAWS web page
+label.opens_the_jabaws_server_homepage = Opens the JABAWS server's homepage in web browser
+label.pdb_sequence_getcher = PDB Sequence Fetcher
+label.result = result
+label.results = results
+label.structure_chooser = Structure Chooser
+label.select = Select :
+label.invert = Invert
+label.select_pdb_file = Select PDB File
\ No newline at end of file
+++ /dev/null
-package jalview.gui;
-
-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.PDBSearchResponse.PDBResponseSummary;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
-import javax.swing.DefaultListModel;
-import javax.swing.SwingUtilities;
-
-@SuppressWarnings("serial")
-public class PDBFetchPanel extends GPDBFetchPanel
-{
- private SequenceFetcher seqFetcher;
-
- 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<PDBResponseSummary>());
- mainFrame.setTitle("PDB Sequence Fetcher");
- if (search.getText().trim().length() > 0)
- {
- long startTime = System.currentTimeMillis();
- PDBRestClient pdbRestCleint = new PDBRestClient();
- String searchTarget = ((PDBDocField) searchTargetOptions
- .getSelectedItem()).getCode();
-
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(allowEmptySequence);
- request.setResponseSize(100);
- request.setFieldToSearchBy(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()
- {
- importSelectedPDBSequencesToAlignment();
- }
-
-
- @Override
- public void backActionPerformed()
- {
- System.out.println("back! pressed!");
- }
-
- @Override
- public void cancelActionPerformed()
- {
- mainFrame.dispose();
- }
-
- private void importSelectedPDBSequencesToAlignment()
- {
- mainFrame.dispose();
- StringBuilder selectedIds = new StringBuilder();
- for (PDBResponseSummary 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();
- }
-
- public void populateSearchOptionComboBox()
- {
- 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());
- }
- });
-
- for (PDBDocField searchTarget : searchableTargets)
- {
- searchTargetOptions.addItem(searchTarget);
- }
- }
-
-}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.gui;
+
+import jalview.jbgui.GPDBSearchPanel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.DefaultListModel;
+import javax.swing.SwingUtilities;
+
+@SuppressWarnings("serial")
+public class PDBSearchPanel extends GPDBSearchPanel
+{
+ private SequenceFetcher seqFetcher;
+
+ private IProgressIndicator progressIdicator;
+
+ public PDBSearchPanel(SequenceFetcher seqFetcher)
+ {
+ this.seqFetcher = seqFetcher;
+ this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ .getProgressIndicator();
+ }
+
+ public static void main(String[] args)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ new PDBSearchPanel(null);
+ }
+ });
+ }
+
+ @Override
+ public void txt_search_ActionPerformed()
+ {
+ boolean allowEmptySequence = false;
+ lst_searchResult.setModel(new DefaultListModel<PDBResponseSummary>());
+ mainFrame.setTitle(MessageManager
+ .getString("label.pdb_sequence_getcher"));
+ if (txt_search.getText().trim().length() > 0)
+ {
+ long startTime = System.currentTimeMillis();
+ PDBRestClient pdbRestCleint = new PDBRestClient();
+ String searchTarget = ((PDBDocField) cmb_searchTarget
+ .getSelectedItem()).getCode();
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(allowEmptySequence);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy(searchTarget + ":");
+ request.setSearchTerm(txt_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);
+ // wantedFields.add(PDBDocField.RESOLUTION);
+ // wantedFields.add(PDBDocField.EXPERIMENTAL_METHOD);
+ request.setWantedFields(wantedFields);
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
+ if (resultList.getSearchSummary() != null)
+ {
+ lst_searchResult.setModel(PDBRestResponse
+ .getListModel(resultList.getSearchSummary()));
+ }
+
+ long endTime = System.currentTimeMillis();
+ int resultSetCount = resultList.getNumberOfItemsFound();
+ String result = (resultSetCount > 1) ? MessageManager
+ .getString("label.results") : MessageManager
+ .getString("label.result");
+ mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
+ + " (" + (endTime - startTime) + " milli secs)");
+ }
+ }
+
+ @Override
+ public void btn_ok_ActionPerformed()
+ {
+ loadSelectedPDBSequencesToAlignment();
+ }
+
+ @Override
+ public void btn_back_ActionPerformed()
+ {
+ mainFrame.dispose();
+ new SequenceFetcher(progressIdicator);
+ }
+
+ @Override
+ public void btn_cancel_ActionPerformed()
+ {
+ mainFrame.dispose();
+ }
+
+ public void loadSelectedPDBSequencesToAlignment()
+ {
+ mainFrame.dispose();
+ StringBuilder selectedIds = new StringBuilder();
+ for (PDBResponseSummary dataSelected : lst_searchResult
+ .getSelectedValuesList())
+ {
+ selectedIds.append(";").append(dataSelected.getPdbId());
+ }
+ String ids = selectedIds.deleteCharAt(0).toString();
+ seqFetcher.textArea.setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ }
+
+ public void populateCmbSearchTargetOptions()
+ {
+ 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());
+ }
+ });
+
+ for (PDBDocField searchTarget : searchableTargets)
+ {
+ cmb_searchTarget.addItem(searchTarget);
+ }
+ }
+
+}
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- new StructureChooser(ap, sequence);
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
}
});
return sfetch;
}
+ private IProgressIndicator progressIndicator;
public SequenceFetcher(IProgressIndicator guiIndic)
{
- final IProgressIndicator guiWindow = guiIndic;
+ this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
Thread sf = new Thread(new Runnable()
@Override
public void run()
{
- if (getSequenceFetcherSingleton(guiWindow) != null)
+ if (getSequenceFetcherSingleton(progressIndicator) != null)
{
- us.initGui(guiWindow);
+ us.initGui(progressIndicator);
}
else
{
private void pdbSourceAction()
{
databaseButt.setText(database.getSelectedItem());
- new PDBFetchPanel(this);
+ new PDBSearchPanel(this);
frame.dispose();
}
}
});
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.gui;
import jalview.datamodel.DBRefEntry;
import jalview.util.MessageManager;
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.PDBSearchResponse.PDBResponseSummary;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
-import java.awt.Component;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
+import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JOptionPane;
-import javax.swing.JTable;
import javax.swing.ListSelectionModel;
-import javax.swing.table.TableCellRenderer;
-import javax.swing.table.TableColumnModel;
+/**
+ * Provides the behaviors for the Structure chooser Panel
+ *
+ * @author tcnofoegbu
+ *
+ */
@SuppressWarnings("serial")
public class StructureChooser extends GStructureChooser
{
-
- private boolean structuresWereFound = false;
+ private boolean structuresDiscovered = false;
private SequenceI selectedSequence;
private SequenceI[] selectedSequences;
- IProgressIndicator af;
+ private IProgressIndicator progressIndicator;
+
+ private Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+
+ private PDBRestRequest pdbRequest;
- Collection<PDBResponseSummary> discoveredStructuresSet = new HashSet<PDBResponseSummary>();
+ private PDBRestClient pdbRestCleint;
- public StructureChooser(AlignmentPanel ap, final SequenceI sequence)
+
+ public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+ AlignmentPanel ap)
{
this.ap = ap;
- this.af = ap.alignFrame;
- this.selectedSequence = sequence;
- this.selectedSequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
- { sequence }
- : ap.av.getSequenceSelection());
+ this.selectedSequence = selectedSeq;
+ this.selectedSequences = selectedSeqs;
+ this.progressIndicator = (ap == null) ? null : ap.alignFrame;
init();
}
- private void init()
+ /**
+ * Initializes parameters used by the Structure Chooser Panel
+ */
+ public void init()
{
- Thread discPDBThread = new Thread(new Runnable()
+ Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
public void run()
{
long startTime = System.currentTimeMillis();
- af.setProgressBar(
- MessageManager.getString("status.fetching_db_refs"),
- startTime);
-
- fetchStructures();
- populateFilterOptions();
- af.setProgressBar(null, startTime);
+ String msg = MessageManager.getString("status.fetching_db_refs");
+ updateProgressIndicator(msg, startTime);
+ fetchStructuresMetaData();
+ populateFilterComboBox();
+ updateProgressIndicator(null, startTime);
mainFrame.setVisible(true);
updateCurrentView();
}
});
- discPDBThread.start();
+ discoverPDBStructuresThread.start();
+ }
+
+ /**
+ * Updates the progress indicator with the specified message
+ *
+ * @param message
+ * displayed message for the operation
+ * @param id
+ * unique handle for this indicator
+ */
+ public void updateProgressIndicator(String message, long id)
+ {
+ if (progressIndicator != null)
+ {
+ progressIndicator.setProgressBar(message, id);
+ }
}
- private void fetchStructures()
+ /**
+ * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
+ * selection group
+ */
+ public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
// wantedFields.add(PDBDocField.GENUS);
// wantedFields.add(PDBDocField.GENE_NAME);
wantedFields.add(PDBDocField.TITLE);
-
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(500);
- request.setFieldToSearchBy("(text:");
- request.setWantedFields(wantedFields);
-
+ pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
for (SequenceI seq : selectedSequences)
{
- request.setSearchTerm(buildQuery(seq) + ")");
- request.setAssociatedSequence(seq.getName());
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBSearchResponse resultList = pdbRestCleint.executeRequest(request);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
+ updateSequenceDbRef(seq, resultList.getSearchSummary());
}
}
int noOfStructuresFound = 0;
- if (discoveredStructuresSet != null)
+ if (discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty())
{
- jListFoundStructures.setModel(PDBSearchResponse
+ jList_FoundStructures.setModel(PDBRestResponse
.getListModel(discoveredStructuresSet));
- summaryTable.setModel(PDBSearchResponse.getTableModel(request,
+ tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
discoveredStructuresSet));
// resizeColumnWidth(summaryTable);
- structuresWereFound = true;
+ structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
}
String totalTime = (System.currentTimeMillis() - startTime)
+ " Found (" + totalTime + ")");
}
- public void resizeColumnWidth(JTable table)
- {
- // table.setAutoResizeMode(JTable.AUTO_RESIZE_LAST_COLUMN);
- final TableColumnModel columnModel = table.getColumnModel();
- for (int column = 0; column < table.getColumnCount(); column++)
- {
- int width = 50; // Min width
- for (int row = 0; row < table.getRowCount(); row++)
- {
- TableCellRenderer renderer = table.getCellRenderer(row, column);
- Component comp = table.prepareRenderer(renderer, row, column);
- width = Math.max(comp.getPreferredSize().width, width);
- }
- columnModel.getColumn(column).setPreferredWidth(width);
- }
- }
-
- protected void populateFilterOptions()
+ /**
+ * Update the DBRef entry for a given sequence with values retrieved from
+ * PDBResponseSummary
+ *
+ * @param seq
+ * the Sequence to update its DBRef entry
+ * @param responseSummaries
+ * a collection of PDBResponseSummary
+ */
+ public void updateSequenceDbRef(SequenceI seq,
+ Collection<PDBResponseSummary> responseSummaries)
{
- if (structuresWereFound)
+ for (PDBResponseSummary response : responseSummaries)
{
- filterOptionsComboBox.addItem(new FilterOptions("Best Quality",
- PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions(
- "Best UniProt Coverage", PDBDocField.UNIPROT_COVERAGE
- .getCode(), VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions("Highest Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions(
- "Highest Protein Chain", PDBDocField.PROTEIN_CHAIN_COUNT
- .getCode(), VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions(
- "Highest Bound Molecules", PDBDocField.BOUND_MOLECULE_COUNT
- .getCode(), VIEWS_FILTER));
- filterOptionsComboBox.addItem(new FilterOptions(
- "Highest Polymer Residues", PDBDocField.POLYMER_RESIDUE_COUNT
- .getCode(), VIEWS_FILTER));
+ PDBEntry newEntry = new PDBEntry();
+ newEntry.setId(response.getPdbId());
+ newEntry.setType("PDB");
+ seq.getDatasetSequence().addPDBId(newEntry);
}
- filterOptionsComboBox.addItem(new FilterOptions("Enter PDB Id", "-",
- VIEWS_ENTER_ID));
- filterOptionsComboBox.addItem(new FilterOptions("From File", "-",
- VIEWS_FROM_FILE));
}
- private String buildQuery(SequenceI seq)
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+ @SuppressWarnings("unchecked")
+ public static String buildQuery(SequenceI seq)
{
String query = seq.getName();
StringBuilder queryBuilder = new StringBuilder();
int count = 0;
+
+ if (seq.getPDBId() != null)
+ {
+ for (PDBEntry entry : (Vector<PDBEntry>) seq.getPDBId())
+ {
+ queryBuilder.append("text:").append(entry.getId()).append(" OR ");
+ }
+ }
+
if (seq.getDBRef() != null && seq.getDBRef().length != 0)
{
for (DBRefEntry dbRef : seq.getDBRef())
{
- queryBuilder.append("text:").append(dbRef.getAccessionId())
+ queryBuilder.append("text:")
+ .append(dbRef.getAccessionId().replaceAll("GO:", ""))
.append(" OR ");
++count;
if (count > 10)
int endIndex = queryBuilder.lastIndexOf(" OR ");
query = queryBuilder.toString().substring(5, endIndex);
}
+ // System.out.println("Query -----> " + query);
return query;
}
- protected void updateCurrentView()
- {
- FilterOptions currentOption = ((FilterOptions) filterOptionsComboBox
- .getSelectedItem());
- switchableViewsLayout.show(switchableViewsPanel,
- currentOption.getView());
- invertFilter.setEnabled(false);
- if (currentOption.getView() == VIEWS_FILTER)
- {
- invertFilter.setEnabled(true);
- filterResultSet(currentOption.getValue());
- }
- }
-
+ /**
+ * Filters a given list of discovered structures based on supplied argument
+ *
+ * @param fieldToFilterBy
+ * the field to filter by
+ */
public void filterResultSet(final String fieldToFilterBy)
{
Thread filterThread = new Thread(new Runnable()
{
try
{
- loadingImageLabel.setVisible(true);
- 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);
-
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(1);
- request.setFieldToSearchBy("(text:");
- request.setFieldToSortBy(fieldToFilterBy,
- !invertFilter.isSelected());
-
- request.setWantedFields(wantedFields);
-
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
- for (SequenceI seq : selectedSequences)
- {
- request.setSearchTerm(buildQuery(seq) + ")");
- request.setAssociatedSequence(seq.getName());
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBSearchResponse resultList = pdbRestCleint
- .executeRequest(request);
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
+ lbl_loading.setVisible(true);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ for (SequenceI seq : selectedSequences)
{
- filteredResponse.addAll(resultList.getSearchSummary());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint
+ .executeRequest(pdbRequest);
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
}
- }
-
- if (filteredResponse != null)
- {
- //
- // for (PDBResponseSummary s : filteredResponse)
- // {
- // System.out.println("-----------> " + s.getPdbId());
- // }
-
- int filterResponseCount = filteredResponse.size();
- List<PDBResponseSummary> list = new ArrayList<PDBResponseSummary>(
- discoveredStructuresSet);
- list.removeAll(filteredResponse);
-
- Collection<PDBResponseSummary> newSet = new ArrayList<PDBResponseSummary>();
- newSet.addAll(filteredResponse);
- newSet.addAll(list);
-
- jListFoundStructures.setModel(PDBSearchResponse
- .getListModel(newSet));
- summaryTable.setModel(PDBSearchResponse.getTableModel(request,
- newSet));
- // resizeColumnWidth(summaryTable);
- list = null;
- newSet = null;
-
- int[] filterIndice = new int[filterResponseCount];
- ListSelectionModel model = summaryTable.getSelectionModel();
- model.clearSelection();
- // int x = 0;
- for (int x = 0; x < filterResponseCount; x++)
+ if (filteredResponse != null)
{
- filterIndice[x] = x;
- model.addSelectionInterval(x, x);
+ int filterResponseCount = filteredResponse.size();
+ List<PDBResponseSummary> originalDiscoveredStructuresList = new ArrayList<PDBResponseSummary>(
+ discoveredStructuresSet);
+ originalDiscoveredStructuresList.removeAll(filteredResponse);
+
+ Collection<PDBResponseSummary> reorderedStructuresSet = new ArrayList<PDBResponseSummary>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(originalDiscoveredStructuresList);
+
+ jList_FoundStructures.setModel(PDBRestResponse
+ .getListModel(reorderedStructuresSet));
+ tbl_summary.setModel(PDBRestResponse.getTableModel(pdbRequest,
+ reorderedStructuresSet));
+
+ // int[] filterIndice = new int[filterResponseCount];
+ ListSelectionModel model = tbl_summary.getSelectionModel();
+ model.clearSelection();
+ for (int x = 0; x < filterResponseCount; x++)
+ {
+ // filterIndice[x] = x;
+ model.addSelectionInterval(x, x);
+ }
+
+ // Discard unwanted objects to make them eligible for garbage
+ // collection
+ originalDiscoveredStructuresList = null;
+ reorderedStructuresSet = null;
+
+ // jListFoundStructures.setSelectedIndices(filterIndice);
}
- jListFoundStructures.setSelectedIndices(filterIndice);
- }
- loadingImageLabel.setVisible(false);
+ lbl_loading.setVisible(false);
} catch (Exception e)
{
e.printStackTrace();
}
});
filterThread.start();
-
}
- @Override
- protected void stateChanged(ItemEvent e)
+ /**
+ * Determines the column index for the pdb id in the summary table. The pdb id
+ * serves as a unique identifier for a given row in the summary table
+ *
+ * @param wantedFeilds
+ * the available table columns in no particular order
+ * @return the pdb id field column index
+ */
+ public static int getPDBIdColumIndex(Collection<PDBDocField> wantedFeilds)
{
- if (e.getSource() instanceof JCheckBox)
+ int pdbFeildIndex = 1;
+ for (PDBDocField feild : wantedFeilds)
{
- updateCurrentView();
- }
- else
- {
- if (e.getStateChange() == ItemEvent.SELECTED)
+ if (feild.equals(PDBDocField.PDB_ID))
{
- updateCurrentView();
+ break;
}
+ ++pdbFeildIndex;
}
-
- }
-
- @Override
- public void ok_ActionPerformed()
- {
- // TODO code to load selected structures to jmol or chimera
+ return pdbFeildIndex;
}
+ /**
+ * Handles action event for btn_pdbFromFile
+ */
public void pdbFromFile_actionPerformed()
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
{ selectedSequence.getDisplayId(false) }));
int value = chooser.showOpenDialog(null);
-
if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
jalview.io.AppletFormatAdapter.FILE, selectedSequence, true,
Desktop.instance);
}
-
}
- // rpdbview.addActionListener(new ActionListener()
- // {
- //
- // @Override
- // public void actionPerformed(ActionEvent e)
- // {
- // new StructureViewer(ap.getStructureSelectionManager())
- // .viewStructures(ap, pr, ap.av.collateForPDB(pr));
- // }
- // });
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ int pdbIdCol = getPDBIdColumIndex(pdbRequest.getWantedFields());
+ int[] selectedRows = tbl_summary.getSelectedRows();
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
+ int count = 0;
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ .toString();
+ PDBEntry pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType("PDB");
+ pdbEntriesToView[count++] = pdbEntry;
+ }
+ new StructureViewer(ap.getStructureSelectionManager()).viewStructures(
+ ap, pdbEntriesToView, ap.av.collateForPDB(pdbEntriesToView));
+ }
+ /**
+ * Handles action event for manual entry of pdb ids
+ */
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
}
}
+ /**
+ * Populates the filter combo-box options dynamically depending on discovered
+ * structures
+ */
+ protected void populateFilterComboBox()
+ {
+ if (isStructuresDiscovered())
+ {
+ cmb_filterOption.addItem(new FilterOption("Best Quality",
+ PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
+ PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Resolution",
+ PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
+ PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
+ PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
+ PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ }
+ cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
+ VIEWS_ENTER_ID));
+ cmb_filterOption.addItem(new FilterOption("From File", "-",
+ VIEWS_FROM_FILE));
+ }
+
+ /**
+ * Updates the displayed view based on the selected filter option
+ */
+ protected void updateCurrentView()
+ {
+ FilterOption selectedOption = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ layout_switchableViews.show(pnl_switchableViews,
+ selectedOption.getView());
+ chk_invertFilter.setEnabled(false);
+ if (selectedOption.getView() == VIEWS_FILTER)
+ {
+ chk_invertFilter.setEnabled(true);
+ filterResultSet(selectedOption.getValue());
+ }
+ }
+
+ /**
+ * Handles the state change event for the 'filter' combo-box and 'invert'
+ * check-box
+ */
+ @Override
+ protected void stateChanged(ItemEvent e)
+ {
+ if (e.getSource() instanceof JCheckBox)
+ {
+ updateCurrentView();
+ }
+ else
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ updateCurrentView();
+ }
+ }
+
+ }
+
+
+ public boolean isStructuresDiscovered()
+ {
+ return structuresDiscovered;
+ }
+
+ public void setStructuresDiscovered(boolean structuresDiscovered)
+ {
+ this.structuresDiscovered = structuresDiscovered;
+ }
+
+ public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ {
+ return discoveredStructuresSet;
+ }
}
+++ /dev/null
-package jalview.jbgui;
-
-import jalview.gui.Desktop;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JInternalFrame;
-import javax.swing.JList;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTextField;
-import javax.swing.ListSelectionModel;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-
-@SuppressWarnings("serial")
-public abstract class GPDBFetchPanel extends JPanel
-{
- protected String frameTitle = "PDB Sequence Fetcher";
-
- protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
-
- protected JComboBox<PDBDocField> searchTargetOptions = new JComboBox<PDBDocField>();
-
- protected JButton ok = new JButton();
-
- protected JButton back = new JButton();
-
- protected JButton cancel = new JButton();
-
- protected JTextField search = new JTextField(20);
-
- protected JList<PDBResponseSummary> jListSearchResult = new JList<PDBResponseSummary>();
-
- protected JScrollPane searchResultScroller = new JScrollPane(
- jListSearchResult);
-
- private JPanel actionPanel = new JPanel();
-
- private JPanel resultPanel = new JPanel();
-
- private JPanel inputPanel = new JPanel();
-
- private BorderLayout mainLayout = new BorderLayout();
-
- public GPDBFetchPanel()
- {
- try
- {
- jbInit();
- mainFrame.invalidate();
- mainFrame.pack();
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- }
-
- private void jbInit() throws Exception
- {
- back.setFont(new java.awt.Font("Verdana", 0, 12));
- back.setText(MessageManager.getString("action.back"));
- back.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- backActionPerformed();
- }
- });
- 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)
- {
- okActionPerformed();
- }
- });
- 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)
- {
- cancelActionPerformed();
- }
- });
- actionPanel.add(back);
- actionPanel.add(ok);
- actionPanel.add(cancel);
-
- jListSearchResult
- .setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
- jListSearchResult.setLayoutOrientation(JList.VERTICAL);
- jListSearchResult.setVisibleRowCount(-1);
- searchResultScroller.setPreferredSize(new Dimension(500, 300));
- searchResultScroller
- .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- resultPanel.add(searchResultScroller);
-
- searchTargetOptions.setFont(new java.awt.Font("Verdana", 0, 12));
- searchTargetOptions.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- searchStringAction();
- }
- });
-
- populateSearchOptionComboBox();
-
- search.setFont(new java.awt.Font("Verdana", 0, 12));
- search.getDocument().addDocumentListener(new DocumentListener()
- {
- @Override
- public void insertUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
-
- @Override
- public void removeUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
-
- @Override
- public void changedUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
- });
-
- inputPanel.add(searchTargetOptions);
- inputPanel.add(search);
-
- this.setLayout(mainLayout);
- this.add(inputPanel, java.awt.BorderLayout.NORTH);
- this.add(resultPanel, java.awt.BorderLayout.CENTER);
- this.add(actionPanel, java.awt.BorderLayout.SOUTH);
- mainFrame.setVisible(true);
- mainFrame.setContentPane(this);
- mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
- }
-
- public abstract void searchStringAction();
-
- public abstract void okActionPerformed();
-
- public abstract void backActionPerformed();
-
- public abstract void cancelActionPerformed();
-
- protected abstract void populateSearchOptionComboBox();
-
-}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.jbgui;
+
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+/**
+ * GUI layout for PDB Fetch Panel
+ *
+ * @author tcnofoegbu
+ *
+ */
+@SuppressWarnings("serial")
+public abstract class GPDBSearchPanel extends JPanel
+{
+ protected String frameTitle = MessageManager
+ .getString("label.pdb_sequence_getcher");
+
+ protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+
+ protected JComboBox<PDBDocField> cmb_searchTarget = new JComboBox<PDBDocField>();
+
+ protected JButton btn_ok = new JButton();
+
+ protected JButton btn_back = new JButton();
+
+ protected JButton btn_cancel = new JButton();
+
+ protected JTextField txt_search = new JTextField(20);
+
+ protected JList<PDBResponseSummary> lst_searchResult = new JList<PDBResponseSummary>();
+
+ protected JScrollPane scrl_searchResult = new JScrollPane(
+ lst_searchResult);
+
+ private JPanel pnl_actions = new JPanel();
+
+ private JPanel pnl_results = new JPanel();
+
+ private JPanel pnl_inputs = new JPanel();
+
+ private BorderLayout mainLayout = new BorderLayout();
+
+ public GPDBSearchPanel()
+ {
+ try
+ {
+ jbInit();
+ mainFrame.invalidate();
+ mainFrame.pack();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Initializes the GUI default properties
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_back.setText(MessageManager.getString("action.back"));
+ btn_back.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ btn_back_ActionPerformed();
+ }
+ });
+ btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_ok.setText(MessageManager.getString("action.ok"));
+ btn_ok.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ btn_ok_ActionPerformed();
+ }
+ });
+ btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setText(MessageManager.getString("action.cancel"));
+ btn_cancel.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ btn_cancel_ActionPerformed();
+ }
+ });
+ pnl_actions.add(btn_back);
+ pnl_actions.add(btn_ok);
+ pnl_actions.add(btn_cancel);
+
+ lst_searchResult
+ .setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
+ lst_searchResult.setLayoutOrientation(JList.VERTICAL);
+ lst_searchResult.setVisibleRowCount(-1);
+ scrl_searchResult.setPreferredSize(new Dimension(500, 300));
+ scrl_searchResult
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ pnl_results.add(scrl_searchResult);
+
+ cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12));
+ cmb_searchTarget.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+ });
+
+ populateCmbSearchTargetOptions();
+
+ txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
+ txt_search.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+ });
+
+ pnl_inputs.add(cmb_searchTarget);
+ pnl_inputs.add(txt_search);
+
+ this.setLayout(mainLayout);
+ this.add(pnl_inputs, java.awt.BorderLayout.NORTH);
+ this.add(pnl_results, java.awt.BorderLayout.CENTER);
+ this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
+ mainFrame.setVisible(true);
+ mainFrame.setContentPane(this);
+ mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ }
+
+ public abstract void txt_search_ActionPerformed();
+
+ public abstract void btn_ok_ActionPerformed();
+
+ public abstract void btn_back_ActionPerformed();
+
+ public abstract void btn_cancel_ActionPerformed();
+
+ protected abstract void populateCmbSearchTargetOptions();
+
+}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.jbgui;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.util.MessageManager;
-import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.Dimension;
import java.awt.FlowLayout;
-import java.awt.Image;
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import javax.swing.ListSelectionModel;
@SuppressWarnings("serial")
+/**
+ * GUI layout for structure chooser
+ * @author tcnofoegbu
+ *
+ */
public abstract class GStructureChooser extends JPanel implements
ItemListener
{
- protected String frameTitle = "Structure Chooser";
+ protected String frameTitle = MessageManager
+ .getString("label.structure_chooser");
protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
-
-
- protected JComboBox<FilterOptions> filterOptionsComboBox = new JComboBox<FilterOptions>();
+ protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
protected AlignmentPanel ap;
- protected JLabel resultLabel = new JLabel("Select : ");
+ protected JLabel lbl_result = new JLabel(
+ MessageManager.getString("label.select") /* "Select : " */);
- protected JButton ok = new JButton();
+ protected JButton btn_ok = new JButton();
- protected JButton cancel = new JButton();
+ protected JButton btn_cancel = new JButton();
- protected JButton pdbFromFile = new JButton();
+ protected JButton btn_pdbFromFile = new JButton();
- protected JTextField search = new JTextField(16);
+ protected JTextField txt_search = new JTextField(18);
- protected JPanel actionPanel = new JPanel();
+ private JPanel pnl_actions = new JPanel();
- protected JPanel filterPanel = new JPanel();
+ private JPanel pnl_filter = new JPanel();
- protected JPanel idInputPanel = new JPanel();
+ private JPanel pnl_idInput = new JPanel();
- protected JPanel fileChooserPanel = new JPanel();
+ private JPanel pnl_fileChooser = new JPanel();
- protected JPanel switchableViewsPanel = new JPanel(new CardLayout());
+ protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
- protected CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
+ protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
.getLayout());
- protected BorderLayout mainLayout = new BorderLayout();
-
- protected BorderLayout idInputPanelLayout = new BorderLayout();
-
- protected BorderLayout fileChooserPanelLayout = new BorderLayout();
+ private BorderLayout mainLayout = new BorderLayout();
- protected JCheckBox rememberSettings = new JCheckBox("Don't ask me again");
+ protected JCheckBox chk_rememberSettings = new JCheckBox(
+ MessageManager.getString("label.dont_ask_me_again"));
- protected JCheckBox invertFilter = new JCheckBox("Invert");
+ protected JCheckBox chk_invertFilter = new JCheckBox(
+ MessageManager.getString("label.invert"));
protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
"/images/loading.gif"));
- protected JLabel loadingImageLabel = new JLabel(loadingImage);
+ protected JLabel lbl_loading = new JLabel(loadingImage);
protected static final String VIEWS_FILTER = "VIEWS_FILTER";
protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
- protected JList<PDBResponseSummary> jListFoundStructures = new JList<PDBResponseSummary>();
+ protected JList<PDBResponseSummary> jList_FoundStructures = new JList<PDBResponseSummary>();
- // protected JScrollPane foundStructuresScroller = new JScrollPane(
- // jListFoundStructures);
+ protected JTable tbl_summary = new JTable();
- protected JTable summaryTable = new JTable();
- protected JScrollPane foundStructuresScroller = new JScrollPane(
- summaryTable);
+ protected JScrollPane scrl_foundStructures = new JScrollPane(
+ tbl_summary);
public GStructureChooser()
{
}
}
+ /**
+ * Initializes the GUI default properties
+ *
+ * @throws Exception
+ */
private void jbInit() throws Exception
{
- ok.setFont(new java.awt.Font("Verdana", 0, 12));
- ok.setText(MessageManager.getString("action.view"));
- ok.addActionListener(new java.awt.event.ActionListener()
+ btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_ok.setText(MessageManager.getString("action.view"));
+ btn_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()
+ btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_cancel.setText(MessageManager.getString("action.cancel"));
+ btn_cancel.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
- pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
- pdbFromFile.setText(" Select PDB File ");
- pdbFromFile.addActionListener(new java.awt.event.ActionListener()
+ btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
+ String btn_title = MessageManager.getString("label.select_pdb_file");
+ btn_pdbFromFile.setText(" " + btn_title + " ");
+ btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
- jListFoundStructures
+ jList_FoundStructures
.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
- jListFoundStructures.setLayoutOrientation(JList.VERTICAL);
- jListFoundStructures.setVisibleRowCount(-1);
- foundStructuresScroller.setPreferredSize(new Dimension(500, 300));
- foundStructuresScroller
+ jList_FoundStructures.setLayoutOrientation(JList.VERTICAL);
+ jList_FoundStructures.setVisibleRowCount(-1);
+ scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
+ scrl_foundStructures
.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- filterOptionsComboBox.setFont(new java.awt.Font("Verdana", 0, 12));
- invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
- rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
+ cmb_filterOption.setFont(new java.awt.Font("Verdana", 0, 12));
+ chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
+ chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
- filterOptionsComboBox.addItemListener(this);
- invertFilter.addItemListener(this);
+ cmb_filterOption.addItemListener(this);
+ chk_invertFilter.addItemListener(this);
- actionPanel.add(rememberSettings);
- actionPanel.add(ok);
- actionPanel.add(cancel);
+ pnl_actions.add(chk_rememberSettings);
+ pnl_actions.add(btn_ok);
+ pnl_actions.add(btn_cancel);
+ pnl_filter.add(lbl_result);
+ pnl_filter.add(cmb_filterOption);
+ lbl_loading.setVisible(false);
- filterPanel.add(resultLabel);
- filterPanel.add(filterOptionsComboBox);
- loadingImageLabel.setVisible(false);
+ pnl_filter.add(lbl_loading);
- filterPanel.add(loadingImageLabel);
+ pnl_filter.add(chk_invertFilter);
- filterPanel.add(invertFilter);
+ pnl_idInput.setLayout(new FlowLayout());
+ pnl_idInput.add(txt_search);
- idInputPanel.setLayout(new FlowLayout());
- idInputPanel.add(search);
-
-
- fileChooserPanel.setLayout(new FlowLayout());
- fileChooserPanel.add(pdbFromFile);
-
- switchableViewsPanel.add(fileChooserPanel, VIEWS_FROM_FILE);
- switchableViewsPanel.add(idInputPanel, VIEWS_ENTER_ID);
- switchableViewsPanel.add(foundStructuresScroller, VIEWS_FILTER);
+ pnl_fileChooser.setLayout(new FlowLayout());
+ pnl_fileChooser.add(btn_pdbFromFile);
+ pnl_switchableViews.add(pnl_fileChooser, VIEWS_FROM_FILE);
+ pnl_switchableViews.add(pnl_idInput, VIEWS_ENTER_ID);
+ pnl_switchableViews.add(scrl_foundStructures, VIEWS_FILTER);
this.setLayout(mainLayout);
- this.add(filterPanel, java.awt.BorderLayout.NORTH);
- this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
- this.add(actionPanel, java.awt.BorderLayout.SOUTH);
+ this.add(pnl_filter, java.awt.BorderLayout.NORTH);
+ this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
+ this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
mainFrame.setVisible(true);
mainFrame.setContentPane(this);
}
- private ImageIcon scaleImageIcone(ImageIcon imageIcon, int width, int height)
- {
- Image image = imageIcon.getImage(); // transform it
-
- Image newimg = image.getScaledInstance(width, height,
- java.awt.Image.SCALE_SMOOTH); // scale it the smooth way
-
- return new ImageIcon(newimg);
- }
-
@Override
+ /**
+ * Event listener for the 'filter' combo-box and 'invert' check-box
+ */
public void itemStateChanged(ItemEvent e)
{
stateChanged(e);
}
- public class FilterOptions
+ /**
+ * This inner class provides the data model for the structure filter combo-box
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class FilterOption
{
private String name;
private String view;
- public FilterOptions(String name, String value, String view)
+ public FilterOption(String name, String value, String view)
{
this.name = name;
this.value = value;
this.view = view;
}
- // public FilterOptions(PDBDocField field, String view)
- // {
- // this.name = "Best " + field.getName();
- // this.value = field.getCode();
- // this.view = view;
- // }
-
public String getName()
{
return name;
}
}
+ public JComboBox<FilterOption> getCmbFilterOption()
+ {
+ return cmb_filterOption;
+ }
+
protected abstract void stateChanged(ItemEvent e);
protected abstract void updateCurrentView();
protected abstract void ok_ActionPerformed();
- protected abstract void populateFilterOptions();
+ protected abstract void populateFilterComboBox();
protected abstract void pdbFromFile_actionPerformed();
}
package jalview.ws.dbsources;
-import jalview.ws.uimodel.PDBSearchRequest;
-import jalview.ws.uimodel.PDBSearchResponse;
-import jalview.ws.uimodel.PDBSearchResponse.PDBResponseSummary;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.util.ArrayList;
import java.util.Iterator;
{
private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
- public static void main(String[] args)
- {
- PDBSearchRequest request = new PDBSearchRequest();
- request.setAllowEmptySeq(false);
- request.setResponseSize(100);
- request.setFieldToSearchBy("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);
- }
-
- public PDBSearchResponse executeRequest(PDBSearchRequest request)
+ /**
+ * Takes a PDBRestRequest object and returns a response upon execution
+ *
+ * @param pdbRestRequest
+ * the pdbRequest to be sent
+ * @return the pdbResponse object for the given pdbRequest
+ */
+ public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
{
ClientConfig clientConfig = new DefaultClientConfig();
clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
Boolean.TRUE);
Client client = Client.create(clientConfig);
- String query = request.getFieldToSearchBy()
- + request.getSearchTerm()
- + ((request.isAllowEmptySeq()) ? ""
+ String query = pdbRestRequest.getFieldToSearchBy()
+ + pdbRestRequest.getSearchTerm()
+ + ((pdbRestRequest.isAllowEmptySeq()) ? ""
: " AND molecule_sequence:['' TO *]");
- String wantedFields = getFieldsAsCommaDelimitedString(request
+ String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
.getWantedFields());
- String responseSize = (request.getResponseSize() == 0) ? "200" : String
- .valueOf(request.getResponseSize());
- String sortParam = (request.getFieldToSortBy() == null || request
+ String responseSize = (pdbRestRequest.getResponseSize() == 0) ? "200"
+ : String.valueOf(pdbRestRequest.getResponseSize());
+ String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
.getFieldToSortBy().trim().isEmpty()) ? ""
- : (request
- .getFieldToSortBy() + (request.isAscending() ? " asc" : " desc"));
+ : (pdbRestRequest
+ .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+ : " desc"));
WebResource webResource = client.resource(pdbSearchEndpoint)
.queryParam("wt", "json").queryParam("fl", wantedFields)
{
if (clientResponse.getStatus() == 400)
{
- throw new RuntimeException(parseException(responseString));
+ throw new RuntimeException(parseJsonExceptionString(responseString));
}
else
{
+ clientResponse.getStatus());
}
}
- // System.out.println("--------------> " + responseString);
- return parseResponse(responseString, request.getWantedFields(),
- request.getAssociatedSequence());
+ clientResponse = null;
+ client = null;
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
}
- private String parseException(String jsonResponse)
+ /**
+ * Process error response from PDB server if/when one occurs.
+ *
+ * @param jsonResponse
+ * the json string containing error message from the server
+ * @return the processed error message from the json string
+ */
+ public static String parseJsonExceptionString(String jsonErrorResponse)
{
String errorMessage = "RunTime error";
try
{
JSONParser jsonParser = new JSONParser();
- JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonResponse);
+ JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse);
JSONObject errorResponse = (JSONObject) jsonObj.get("error");
errorMessage = errorResponse.get("msg").toString();
return errorMessage;
}
+ /**
+ * Parses json response string from PDB REST API to a PDBRestResponse
+ * instance. The parsed response is dynamic and based upon some of the request
+ * parameters.
+ *
+ * @param pdbJsonResponseString
+ * the json string to be parsed
+ * @param pdbRestRequest
+ * the request object which contains parameters used to process the
+ * json string
+ * @return
+ */
@SuppressWarnings("unchecked")
- private PDBSearchResponse parseResponse(String jsonResponse,
- List<PDBDocField> wantedFields, String associatedSequence)
+ public static PDBRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString,
+ PDBRestRequest pdbRestRequest)
{
- PDBSearchResponse searchResult = new PDBSearchResponse();
+ PDBRestResponse searchResult = new PDBRestResponse();
List<PDBResponseSummary> result = null;
try
{
JSONParser jsonParser = new JSONParser();
JSONObject jsonObj = (JSONObject) jsonParser
-.parse(jsonResponse);
+ .parse(pdbJsonResponseString);
JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
JSONObject doc = docIter.next();
// if (doc.get("molecule_sequence") != null)
// {
- result.add(searchResult.new PDBResponseSummary(doc, wantedFields,
- associatedSequence));
+ result.add(searchResult.new PDBResponseSummary(doc, pdbRestRequest));
// }
}
- searchResult.setItemsFound(numFound);
+ searchResult.setNumberOfItemsFound(numFound);
searchResult.setResponseTime(queryTime);
searchResult.setSearchSummary(result);
}
return searchResult;
}
- private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
+ /**
+ * Takes a collection of PDBDocField and converts it into a comma delimited
+ * string.
+ *
+ * @param pdbDocfields
+ * @return
+ */
+ public static String getPDBDocFieldsAsCommaDelimitedString(
+ List<PDBDocField> pdbDocfields)
{
String result = "";
- if (fields != null && !fields.isEmpty())
+ if (pdbDocfields != null && !pdbDocfields.isEmpty())
{
StringBuilder returnedFields = new StringBuilder();
- for (PDBDocField field : fields)
+ for (PDBDocField field : pdbDocfields)
{
returnedFields.append(",").append(field.getCode());
}
- returnedFields.deleteCharAt(0);
+ returnedFields.deleteCharAt(0);
result = returnedFields.toString();
}
return result;
}
+ /**
+ * Represents the fields retrievable from a PDB Document response
+ *
+ */
public enum PDBDocField
{
PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
"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"), ALL("ALL", "text");
+ "Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method"), ALL("ALL",
+ "text");
private String name;
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.ws.uimodel;
import java.util.ArrayList;
import java.util.List;
-public class PDBSearchRequest
+/**
+ * Represents the PDB request to be consumed by the PDBRestClient
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestRequest
{
private String fieldToSearchBy;
private String associatedSequence;
- private boolean allowEmptySeq;
+ private boolean allowEmptySequence;
private int responseSize;
- private boolean isAscending;
+ private boolean isSortAscending;
private List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
public boolean isAllowEmptySeq()
{
- return allowEmptySeq;
+ return allowEmptySequence;
}
public void setAllowEmptySeq(boolean allowEmptySeq)
{
- this.allowEmptySeq = allowEmptySeq;
+ this.allowEmptySequence = allowEmptySeq;
}
public int getResponseSize()
return fieldToSortBy;
}
- public void setFieldToSortBy(String fieldToSortBy, boolean isAscending)
+ public void setFieldToSortBy(String fieldToSortBy, boolean isSortAscending)
{
this.fieldToSortBy = fieldToSortBy;
- this.isAscending = isAscending;
+ this.isSortAscending = isSortAscending;
}
public boolean isAscending()
{
- return isAscending;
+ return isSortAscending;
}
public String getAssociatedSequence()
this.associatedSequence = associatedSequence;
}
-
-
}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.ws.uimodel;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import org.json.simple.JSONObject;
-public class PDBSearchResponse
+/**
+ * Represents the response model produced by the PDBRestClient upon successful
+ * execution of a given request
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestResponse
{
- private int itemsFound;
+ private int numberOfItemsFound;
private String responseTime;
private Collection<PDBResponseSummary> searchSummary;
- public int getItemsFound()
+ public int getNumberOfItemsFound()
{
- return itemsFound;
+ return numberOfItemsFound;
}
- public void setItemsFound(int itemFound)
+ public void setNumberOfItemsFound(int itemFound)
{
- this.itemsFound = itemFound;
+ this.numberOfItemsFound = itemFound;
}
public String getResponseTime()
this.searchSummary = searchSummary;
}
+ /**
+ * Convenience method to obtain a List model for a given summary list
+ *
+ * @param summariesList
+ * the summary list which contains the data for generating the lists
+ * data
+ * @return the list model generated for the search summary
+ */
public static DefaultListModel<PDBResponseSummary> getListModel(
Collection<PDBResponseSummary> summariesList)
{
return defaultListModel;
}
- public static DefaultTableModel getTableModel(PDBSearchRequest request,
+ /**
+ * Convenience method to obtain a Table model for a given summary List and
+ * request
+ *
+ * @param request
+ * the PDBRestRequest object which holds useful information for
+ * creating a table model
+ * @param summariesList
+ * the summary list which contains the data for populating the
+ * table's rows
+ * @return the table model which was dynamically generated
+ */
+ public static DefaultTableModel getTableModel(PDBRestRequest request,
Collection<PDBResponseSummary> summariesList)
{
DefaultTableModel model = new DefaultTableModel();
for (PDBResponseSummary res : summariesList)
{
- model.addRow(res.getSummaryColums());
+ model.addRow(res.getSummaryData());
}
return model;
}
-
-
+ /**
+ * Model for a unique response summary
+ *
+ * @author tcnofoegbu
+ *
+ */
public class PDBResponseSummary
{
private String pdbId;
- private String summaryRow;
+ private String concatenatedSummaryData;
- private String[] summaryColums;
+ private String[] summaryData;
private String associatedSequence;
private int width = 480;
- public PDBResponseSummary(JSONObject doc,
- List<PDBDocField> diplayFields, String associatedSeq)
+ public PDBResponseSummary(JSONObject doc, PDBRestRequest request)
{
StringBuilder summaryBuilder = new StringBuilder();
-
+ List<PDBDocField> diplayFields = request.getWantedFields();
+ String associatedSeq = request.getAssociatedSequence();
int colCounter = 0;
- summaryColums = new String[(associatedSeq != null) ? diplayFields
+ summaryData = new String[(associatedSeq != null) ? diplayFields
.size() + 1 : diplayFields.size()];
if (associatedSeq != null)
{
this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq
.substring(0, 18) : associatedSeq;
- summaryColums[0] = associatedSequence;
+ summaryData[0] = associatedSequence;
colCounter = 1;
}
+ getClass().getResource("/images/sugar.png")
.toString() + "\">");
}
- summaryColums[colCounter++] = moleculeType;
+ summaryData[colCounter++] = moleculeType;
}
else if (field.equals(PDBDocField.PDB_ID)
&& doc.get(PDBDocField.PDB_ID.getCode()) != null)
{
this.pdbId = doc.get(PDBDocField.PDB_ID.getCode()).toString();
summaryBuilder.append(this.pdbId).append(" | ");
- summaryColums[colCounter++] = this.pdbId;
+ summaryData[colCounter++] = this.pdbId;
}
else if (doc.get(field.getCode()) != null)
{
summaryBuilder.append(field.getName()).append(": ")
.append(doc.get(field.getCode())).append(" | ");
- summaryColums[colCounter++] = doc.get(field.getCode()).toString();
+ summaryData[colCounter++] = doc.get(field.getCode()).toString();
}
}
int endIndex = summaryBuilder.lastIndexOf(" | ");
String fSummary = summaryBuilder.toString().substring(0, endIndex);
- this.summaryRow = fSummary.trim();
+ this.concatenatedSummaryData = fSummary.trim();
summaryBuilder = null;
}
this.pdbId = pdbId;
}
- public String getSummaryRow()
+ public String getConcatenatedSummaryData()
{
- return summaryRow;
+ return concatenatedSummaryData;
}
- public void setSummaryRow(String summary)
+ public void setConcatenatedSummaryData(String concatenatedSummaryData)
{
- this.summaryRow = summary;
+ this.concatenatedSummaryData = concatenatedSummaryData;
}
- public String[] getSummaryColums()
+ public String[] getSummaryData()
{
- return summaryColums;
+ return summaryData;
}
- public void setSummaryColums(String[] summaryColums)
+ public void setSummaryData(String[] summaryData)
{
- this.summaryColums = summaryColums;
+ this.summaryData = summaryData;
}
public String toString()
StringBuilder html = new StringBuilder();
html.append("<html><div style=\"width:" + width
+ "; word-wrap: break-word; border-bottom-style: dotted;\"> ");
- html.append(summaryRow);
+ html.append(concatenatedSummaryData);
html.append("</div></html>");
return html.toString();
}
@Override
public int hashCode()
{
- return Objects.hash(this.pdbId, this.summaryRow);
+ return Objects.hash(this.pdbId, this.concatenatedSummaryData);
}
@Override
// Custom equality check here.
return this.pdbId.equals(that.pdbId)
- && this.summaryRow.equals(that.summaryRow);
+ && this.concatenatedSummaryData
+ .equals(that.concatenatedSummaryData);
}
}
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBSearchPanelTest
+{
+
+ @Before
+ public void setUp() throws Exception
+ {
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test
+ public void test()
+ {
+ fail("Not yet implemented");
+ }
+
+}
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class StructureChooserTest
+{
+ Sequence seq;
+
+ @Before
+ public void setUp() throws Exception
+ {
+ seq = new Sequence("Test_Seq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1, 26);
+ seq.setDatasetSequence(seq);
+ for (int x = 1; x < 5; x++)
+ {
+ DBRefEntry dbRef = new DBRefEntry();
+ dbRef.setAccessionId("XYZ_" + x);
+ seq.addDBRef(dbRef);
+ }
+
+ PDBEntry dbRef = new PDBEntry();
+ dbRef.setId("1tim");
+
+ Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+ pdbIds.add(dbRef);
+
+ seq.setPDBId(pdbIds);
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ seq = null;
+ }
+
+ @Test
+ public void getPDBIdColumIndexTest()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ assertEquals(5, StructureChooser.getPDBIdColumIndex(wantedFields));
+ }
+
+ @Test
+ public void buildQueryTest()
+ {
+ assertEquals(
+ "1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+ StructureChooser.buildQuery(seq));
+ }
+
+ @Test
+ public void populateFilterComboBoxTest()
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { seq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq,
+ null);
+ sc.populateFilterComboBox();
+ int optionsSize = sc.getCmbFilterOption().getItemCount();
+ assertEquals(2, optionsSize); // if structures are not discovered then don't
+ // populate filter options
+
+ sc.setStructuresDiscovered(true);
+ sc.populateFilterComboBox();
+ optionsSize = sc.getCmbFilterOption().getItemCount();
+ assertTrue(optionsSize > 2); // if structures are found, filter options
+ // should be populated
+ }
+
+ @Test
+ public void fetchStructuresInfoTest()
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { seq };
+ StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+ sc.fetchStructuresMetaData();
+ assertTrue(sc.getDiscoveredStructuresSet() != null);
+ assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+
+ }
+}
--- /dev/null
+{
+ "responseHeader": {
+ "status": 400,
+ "QTime": 0,
+ "params": {
+ "sort": "",
+ "fl": "pdb_id",
+ "q": "text:abc OR text:go:abc AND molecule_sequence:['' TO *]",
+ "wt": "json",
+ "rows": "100"
+ }
+ },
+ "error": {
+ "msg": "org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.",
+ "code": 400
+ }
+}
\ No newline at end of file
--- /dev/null
+{
+ "responseHeader": {
+ "status": 0,
+ "QTime": 0,
+ "params": {
+ "sort": "",
+ "fl": "molecule_type,pdb_id,genus,gene_name,title",
+ "q": "text:abc AND molecule_sequence:['' TO *]",
+ "wt": "json",
+ "rows": "100"
+ }
+ },
+ "response": {
+ "numFound": 931,
+ "start": 0,
+ "docs": [
+ {
+ "pdb_id": "3qf4",
+ "title": "Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "THEMA_03290",
+ "Tmari_0285",
+ "TM_0287"
+ ]
+ },
+ {
+ "pdb_id": "4wbs",
+ "title": "Crystal structure of an ABC transporter related protein from Burkholderia phymatum",
+ "genus": [
+ "Burkholderia"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "Bphy_0327"
+ ]
+ },
+ {
+ "pdb_id": "1hn0",
+ "title": "CRYSTAL STRUCTURE OF CHONDROITIN ABC LYASE I FROM PROTEUS VULGARIS AT 1.9 ANGSTROMS RESOLUTION",
+ "genus": [
+ "Proteus"
+ ],
+ "molecule_type": "Protein"
+ },
+ {
+ "pdb_id": "4a82",
+ "title": "Fitted model of staphylococcus aureus sav1866 model ABC transporter in the human cystic fibrosis transmembrane conductance regulator volume map EMD-1966.",
+ "genus": [
+ "Homo"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "SAV1866"
+ ]
+ },
+ {
+ "pdb_id": "3nh6",
+ "title": "Nucleotide Binding Domain of human ABCB6 (apo structure)",
+ "genus": [
+ "Homo"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "ABCB6",
+ "UMAT",
+ "MTABC3",
+ "PRP"
+ ]
+ },
+ {
+ "pdb_id": "2nq2",
+ "title": "An inward-facing conformation of a putative metal-chelate type ABC transporter.",
+ "genus": [
+ "Haemophilus"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "HI_1471"
+ ]
+ },
+ {
+ "pdb_id": "3s4u",
+ "title": "Crystal structure of open, unliganded E. coli PhnD H157A",
+ "genus": [
+ "Escherichia"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "phnD",
+ "UTI89_C4699"
+ ]
+ },
+ {
+ "pdb_id": "4q4a",
+ "title": "Improved model of AMP-PNP bound TM287/288",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "1oxs",
+ "title": "Crystal structure of GlcV, the ABC-ATPase of the glucose ABC transporter from Sulfolobus solfataricus",
+ "genus": [
+ "Sulfolobus"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "SSO2850"
+ ]
+ },
+ {
+ "pdb_id": "4q4j",
+ "title": "Structure of crosslinked TM287/288_S498C_S520C mutant",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "1oxt",
+ "title": "Crystal structure of GlcV, the ABC-ATPase of the glucose ABC transporter from Sulfolobus solfataricus",
+ "genus": [
+ "Sulfolobus"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "SSO2850"
+ ]
+ },
+ {
+ "pdb_id": "4q4h",
+ "title": "TM287/288 in its apo state",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "3qf4",
+ "title": "Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation",
+ "genus": [
+ "Thermotoga"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "TM_0288"
+ ]
+ },
+ {
+ "pdb_id": "2fgk",
+ "title": "Crystal structure of the ABC-cassette E631Q mutant of HlyB with bound ATP",
+ "genus": [
+ "Escherichia"
+ ],
+ "molecule_type": "Protein",
+ "gene_name": [
+ "hlyB"
+ ]
+ }
+ ]
+ }
+}
\ No newline at end of file
--- /dev/null
+package jalview.ws.dbsources;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class PDBRestClientTest
+{
+
+ @Before
+ public void setUp() throws Exception
+ {
+ }
+
+ @After
+ public void tearDown() throws Exception
+ {
+ }
+
+ @Test
+ public void executeRequestTest()
+ {
+ 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);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("text:");
+ request.setSearchTerm("abc");
+ request.setWantedFields(wantedFields);
+
+ PDBRestResponse response = new PDBRestClient().executeRequest(request);
+ assertTrue(response.getNumberOfItemsFound() > 99);
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getSearchSummary().size() > 99);
+ }
+
+ @Test
+ public void getPDBDocFieldsAsCommaDelimitedStringTest()
+ {
+ 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);
+ assertEquals("molecule_type,pdb_id,genus,gene_name,title",
+ PDBRestClient
+ .getPDBDocFieldsAsCommaDelimitedString(wantedFields));
+ }
+
+ @Test
+ public void parsePDBJsonExceptionStringTest()
+ {
+ 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);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy("text:");
+ request.setSearchTerm("abc");
+ request.setWantedFields(wantedFields);
+
+ String jsonErrorResponse = "";
+ try
+ {
+ jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+
+ String parsedErrorResponse = PDBRestClient
+ .parseJsonExceptionString(jsonErrorResponse);
+ String expectedErrorMsg = "org.apache.solr.search.SyntaxError: Cannot parse 'text:abc OR text:go:abc AND molecule_sequence:['' TO *]': Encountered \" \":\" \": \"\" at line 1, column 19.{\"q\":\"text:abc OR text:go:abc AND molecule_sequence:['' TO *]\",\"fl\":\"pdb_id\",\"sort\":\"\",\"rows\":\"100\",\"wt\":\"json\"}";
+
+ assertEquals(expectedErrorMsg, parsedErrorResponse);
+ }
+
+ @Test(expected = RuntimeException.class)
+ public void testForExpectedRuntimeException()
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setFieldToSearchBy("text:");
+ request.setSearchTerm("abc OR text:go:abc");
+ request.setWantedFields(wantedFields);
+ new PDBRestClient().executeRequest(request);
+ }
+
+ @Test
+ public void parsePDBJsonResponseTest()
+ {
+ 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);
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(false);
+ request.setWantedFields(wantedFields);
+
+ String jsonString = "";
+ try
+ {
+ jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ PDBRestResponse response = PDBRestClient.parsePDBJsonResponse(
+ jsonString, request);
+ assertTrue(response.getSearchSummary() != null);
+ assertTrue(response.getNumberOfItemsFound() == 931);
+ assertTrue(response.getSearchSummary().size() == 14);
+ }
+
+ public String readJsonStringFromFile(String filePath) throws IOException
+ {
+ String fileContent;
+ BufferedReader br = new BufferedReader(new FileReader(filePath));
+ try
+ {
+ StringBuilder sb = new StringBuilder();
+ String line = br.readLine();
+
+ while (line != null)
+ {
+ sb.append(line);
+ sb.append(System.lineSeparator());
+ line = br.readLine();
+ }
+ fileContent = sb.toString();
+ } finally
+ {
+ br.close();
+ }
+ return fileContent;
+ }
+
+
+}
git://source.jalview.org / jalview.git / commitdiff