<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
+ <classpathentry kind="lib" path="lib/jersey-client-1.19.jar"/>
+ <classpathentry kind="lib" path="lib/jersey-core-1.19.jar"/>
+ <classpathentry kind="lib" path="lib/jersey-json-1.19.jar"/>
+ <classpathentry kind="lib" path="lib/jsr311-api-1.1.1.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin.jar"/>
<classpathentry kind="output" path="classes"/>
</classpath>
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}
label.display_name = Display Label
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
+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
+info.select_filter_option = Select Filter Option/Manual Entry
+info.associate_wit_sequence = Associate with Sequence
+label.search_result = Search Result
+label.found_structures_summary = Found Structures Summary
+label.configure_displayed_columns = Configure Displayed Columns
label.start_jalview = Start Jalview
label.biojs_html_export = BioJS
--- /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.jbgui.PDBDocFieldPreferences;
+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 java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import javax.swing.table.DefaultTableModel;
+
+@SuppressWarnings("serial")
+public class PDBSearchPanel extends GPDBSearchPanel
+{
+ private SequenceFetcher seqFetcher;
+
+ private IProgressIndicator progressIdicator;
+
+ private Collection<PDBDocField> wantedFields;
+
+ public PDBSearchPanel(SequenceFetcher seqFetcher)
+ {
+ this.seqFetcher = seqFetcher;
+ this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
+ .getProgressIndicator();
+ }
+
+
+ /**
+ * Action performed when an input is detected on txt_search field.
+ */
+ @Override
+ public void txt_search_ActionPerformed()
+ {
+ boolean allowEmptySequence = false;
+ mainFrame.setTitle(MessageManager
+ .getString("label.pdb_sequence_getcher"));
+ tbl_summary.setModel(new DefaultTableModel());
+ if (txt_search.getText().trim().length() > 0)
+ {
+ long startTime = System.currentTimeMillis();
+
+ String searchTarget = ((PDBDocField) cmb_searchTarget
+ .getSelectedItem()).getCode();
+
+ wantedFields = PDBDocFieldPreferences
+ .getSearchSummaryFields();
+
+ PDBRestRequest request = new PDBRestRequest();
+ request.setAllowEmptySeq(allowEmptySequence);
+ request.setResponseSize(100);
+ request.setFieldToSearchBy(searchTarget + ":");
+ request.setSearchTerm(txt_search.getText());
+ request.setWantedFields(wantedFields);
+
+ PDBRestClient pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
+ if (resultList.getSearchSummary() != null)
+ {
+ tbl_summary.setModel(PDBRestResponse.getTableModel(request,
+ 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();
+ }
+
+ /**
+ * Add the discovered/selected sequences to a target alignment window
+ */
+ public void loadSelectedPDBSequencesToAlignment()
+ {
+ mainFrame.dispose();
+ StringBuilder selectedIds = new StringBuilder();
+ int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
+ int[] selectedRows = tbl_summary.getSelectedRows();
+ for (int summaryRow : selectedRows)
+ {
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ .toString();
+ selectedIds.append(";").append(pdbIdStr);
+ }
+
+ String ids = selectedIds.deleteCharAt(0).toString();
+ seqFetcher.textArea.setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ }
+
+ /**
+ * Populates search target combo-box options
+ */
+ 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);
+ }
+ }
+
+}
protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
-
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
JMenuItem pdbFromFile = new JMenuItem();
- // JBPNote: Commented these out - Should add these services via the web
- // services menu system.
- // JMenuItem ContraFold = new JMenuItem();
-
- // JMenuItem RNAFold = new JMenuItem();
-
JMenuItem enterPDB = new JMenuItem();
JMenuItem discoverPDB = new JMenuItem();
JMenu jMenu1 = new JMenu();
- JMenu structureMenu = new JMenu();
+ JMenuItem structureMenu = new JMenuItem();
JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
-
JMenu groupLinksMenu;
JMenuItem hideInsertions = new JMenuItem();
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
colours.add(RNAInteractionColour);
- // colours.add(covariationColour);
for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
{
{
structureMenu.remove(viewStructureMenu);
}
- // structureMenu.remove(colStructureMenu);
}
if (ap.av.getAlignment().isNucleotide() == true)
{
@Override
public void actionPerformed(ActionEvent e)
{
- // // System.out.println("1:"+structureLine);
- // System.out.println("1:sname" + seq.getName());
- // System.out.println("2:seq" + seq);
- //
- // // System.out.println("3:"+seq.getSequenceAsString());
- // System.out.println("3:strucseq" + rnastruc);
- // // System.out.println("4:struc"+seq.getRNA());
- // System.out.println("5:name" + seq.getName());
- // System.out.println("6:ap" + ap);
new AppVarna(structureLine, seq, seq.getSequenceAsString(),
rnastruc, seq.getName(), ap);
- // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
- // seq.getName(), ap);
System.out.println("end");
}
});
}
}
- // SequenceFeatures[] test = seq.getSequenceFeatures();
if (seq.getAnnotation() != null)
{
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 Object[]
- { sqass.getDisplayId(false) })));
- }
- else
- {
- structureMenu.add(gpdbview = new JMenuItem(MessageManager
- .formatMessage("label.view_all_structures", new Object[]
- { 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 Object[]
- { 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
if (urlset != null)
{
int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
// first two bits ofurlLink type bitfield are sequenceids and sequences
// TODO: FUTURE: ensure the groupURL menu structure can be generalised
addshowLink(linkMenus[type], label
pdbFromFile_actionPerformed();
}
});
- // RNAFold.setText("From RNA Fold with predict2D");
- // RNAFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // RNAFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
- // ContraFold.setText("From Contra Fold with predict2D");
- // ContraFold.addActionListener(new ActionListener()
- // {
- // public void actionPerformed(ActionEvent e)
- // {
- // try {
- // ContraFold_actionPerformed();
- // } catch (Exception e1) {
- // // TODO Auto-generated catch block
- // e1.printStackTrace();
- // }
- // }
- // });
+
enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
enterPDB.addActionListener(new ActionListener()
{
}
});
jMenu1.setText(MessageManager.getString("label.group"));
- structureMenu.setText(MessageManager.getString("label.structure"));
+ structureMenu.setText(MessageManager.getString("label.view_structure"));
+ structureMenu.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[]
+ { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
viewStructureMenu.setText(MessageManager
.getString("label.view_structure"));
// colStructureMenu.setText("Colour By Structure");
if (ap.getAlignment().isNucleotide())
{
// JBPNote - commented since the colourscheme isn't functional
- // colourMenu.add(RNAInteractionColour);
colourMenu.add(purinePyrimidineColour);
}
- // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
colourMenu.add(conservationMenuItem);
- // colourMenu.add(annotationMenuItem);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(showColourText);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
- structureMenu.add(pdbMenu);
- structureMenu.add(viewStructureMenu);
- // structureMenu.add(colStructureMenu);
noColourmenuItem.setText(MessageManager.getString("label.none"));
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
{
}
- // JBNote: commented out - these won't be instantiated here...!
- // public void RNAFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromRNAFold("toto");
- // }
- //
- // public void ContraFold_actionPerformed() throws Exception
- // {
- // Predict2D P2D = new Predict2D();
- // P2D.getStructure2DFromContraFold("toto");
- // }
+
public void enterPDB_actionPerformed()
{
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
public class SequenceFetcher extends JPanel implements Runnable
{
- // ASequenceFetcher sfetch;
+ JLabel dbeg = new JLabel();
+
+ JDatabaseTree database;
+
+ JButton databaseButt;
+
+ JLabel jLabel1 = new JLabel();
+
+ JCheckBox replacePunctuation = new JCheckBox();
+
+ JButton ok = new JButton();
+
+ JButton clear = new JButton();
+
+ JButton example = new JButton();
+
+ JButton close = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JTextArea textArea = new JTextArea();
+
+ JScrollPane jScrollPane1 = new JScrollPane();
+
+ JPanel jPanel2 = new JPanel();
+
+ JPanel jPanel3 = new JPanel();
+
+ JPanel jPanel4 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
JInternalFrame frame;
IProgressIndicator guiWindow;
private static Thread initingThread = null;
+ int debounceTrap = 0;
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
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
{
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
- {
- databaseButt.setText(database.getSelectedItem()
- + (database.getSelectedSources().size() > 1 ? " (and "
- + database.getSelectedSources().size()
- + " others)" : ""));
- String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[]
- { eq }));
- boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
- for (DbSourceProxy dbs : database.getSelectedSources())
- {
- if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
- {
- enablePunct = false;
- break;
- }
- }
- replacePunctuation.setEnabled(enablePunct);
+ debounceTrap++;
+ String currentSelection = database.getSelectedItem();
- } catch (Exception ex)
+ if (!currentSelection.equalsIgnoreCase("pdb"))
+ {
+ otherSourceAction();
+ }
+ if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0))
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ pdbSourceAction();
}
- jPanel2.repaint();
+
}
});
dbeg.setText("");
}
+ private void pdbSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new PDBSearchPanel(this);
+ frame.dispose();
+ }
+
+ private void otherSourceAction()
+ {
+ try
+ {
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size() + " others)"
+ : ""));
+ String eq = database.getExampleQueries();
+ dbeg.setText(MessageManager.formatMessage(
+ "label.example_query_param", new String[]
+ { eq }));
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ for (DbSourceProxy dbs : database.getSelectedSources())
+ {
+ if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ enablePunct = false;
+ break;
+ }
+ }
+ replacePunctuation.setEnabled(enablePunct);
+
+ } catch (Exception ex)
+ {
+ dbeg.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
+ }
+
protected void example_actionPerformed()
{
DbSourceProxy db = null;
jPanel3.repaint();
}
- JLabel dbeg = new JLabel();
-
- JDatabaseTree database;
-
- JButton databaseButt;
- JLabel jLabel1 = new JLabel();
-
- JCheckBox replacePunctuation = new JCheckBox();
-
- JButton ok = new JButton();
-
- JButton clear = new JButton();
-
- JButton example = new JButton();
-
- JButton close = new JButton();
-
- JPanel jPanel1 = new JPanel();
-
- JTextArea textArea = new JTextArea();
-
- JScrollPane jScrollPane1 = new JScrollPane();
-
- JPanel jPanel2 = new JPanel();
-
- JPanel jPanel3 = new JPanel();
-
- JPanel jPanel4 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
public void close_actionPerformed(ActionEvent e)
{
}
});
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
}
--- /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.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+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.awt.event.ItemEvent;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+
+/**
+ * Provides the behaviors for the Structure chooser Panel
+ *
+ * @author tcnofoegbu
+ *
+ */
+@SuppressWarnings("serial")
+public class StructureChooser extends GStructureChooser
+{
+ private boolean structuresDiscovered = false;
+
+ private SequenceI selectedSequence;
+
+ private SequenceI[] selectedSequences;
+
+ private IProgressIndicator progressIndicator;
+
+ private Collection<PDBResponseSummary> discoveredStructuresSet;
+
+ private PDBRestRequest lastPdbRequest;
+
+ private PDBRestClient pdbRestCleint;
+
+ private String selectedPdbFileName;
+
+ private boolean isValidPBDEntry;
+
+ public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+ AlignmentPanel ap)
+ {
+ this.ap = ap;
+ this.selectedSequence = selectedSeq;
+ this.selectedSequences = selectedSeqs;
+ this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+ init();
+ }
+
+ /**
+ * Initializes parameters used by the Structure Chooser Panel
+ */
+ public void init()
+ {
+ Thread discoverPDBStructuresThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ String msg = MessageManager.getString("status.fetching_db_refs");
+ updateProgressIndicator(msg, startTime);
+ fetchStructuresMetaData();
+ populateFilterComboBox();
+ updateProgressIndicator(null, startTime);
+ mainFrame.setVisible(true);
+ updateCurrentView();
+ }
+ });
+ 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);
+ }
+ }
+
+ /**
+ * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
+ * selection group
+ */
+ public void fetchStructuresMetaData()
+ {
+ long startTime = System.currentTimeMillis();
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+
+ discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ for (SequenceI seq : selectedSequences)
+ {
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(500);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ discoveredStructuresSet.addAll(resultList.getSearchSummary());
+ updateSequenceDbRef(seq, resultList.getSearchSummary());
+ }
+ }
+
+ int noOfStructuresFound = 0;
+ if (discoveredStructuresSet != null
+ && !discoveredStructuresSet.isEmpty())
+ {
+ tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+ discoveredStructuresSet));
+ structuresDiscovered = true;
+ noOfStructuresFound = discoveredStructuresSet.size();
+ }
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ + " Found (" + totalTime + ")");
+ }
+
+ /**
+ * 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)
+ {
+ for (PDBResponseSummary response : responseSummaries)
+ {
+ PDBEntry newEntry = new PDBEntry();
+ newEntry.setId(response.getPdbId());
+ newEntry.setType("PDB");
+ seq.getDatasetSequence().addPDBId(newEntry);
+ }
+ }
+
+ /**
+ * 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().replaceAll("GO:", ""))
+ .append(" OR ");
+ ++count;
+ if (count > 10)
+ {
+ break;
+ }
+ }
+ int endIndex = queryBuilder.lastIndexOf(" OR ");
+ query = queryBuilder.toString().substring(5, endIndex);
+ }
+ return query;
+ }
+
+ /**
+ * 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()
+ {
+ @Override
+ public void run()
+ {
+ long startTime = System.currentTimeMillis();
+ try
+ {
+ lbl_loading.setVisible(true);
+
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ for (SequenceI seq : selectedSequences)
+ {
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint
+ .executeRequest(pdbRequest);
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
+ {
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
+
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
+
+ // Update table selection model here
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+
+ }
+
+ lbl_loading.setVisible(false);
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+
+ validateSelections();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ filterThread.start();
+ }
+
+
+ /**
+ * Handles action event for btn_pdbFromFile
+ */
+ 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[]
+ { selectedSequence.getDisplayId(false) }));
+ chooser.setToolTipText(MessageManager.formatMessage(
+ "label.load_pdb_file_associate_with_sequence", new String[]
+ { selectedSequence.getDisplayId(false) }));
+
+ int value = chooser.showOpenDialog(null);
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ selectedPdbFileName = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+ validateSelections();
+ }
+ }
+
+ /**
+ * 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 selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ layout_switchableViews.show(pnl_switchableViews,
+ selectedFilterOpt.getView());
+ String filterTitle = mainFrame.getTitle();
+ mainFrame.setTitle(frameTitle);
+ chk_invertFilter.setVisible(false);
+ if (selectedFilterOpt.getView() == VIEWS_FILTER)
+ {
+ mainFrame.setTitle(filterTitle);
+ chk_invertFilter.setVisible(true);
+ filterResultSet(selectedFilterOpt.getValue());
+ }
+ else
+ {
+ idInputAssSeqPanel.loadCmbAssSeq();
+ fileChooserAssSeqPanel.loadCmbAssSeq();
+ }
+ validateSelections();
+ }
+
+ /**
+ * Validates user selection and activates the view button if all parameters
+ * are correct
+ */
+ public void validateSelections()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ btn_view.setEnabled(false);
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ if (tbl_summary.getSelectedRows().length > 0)
+ {
+ btn_view.setEnabled(true);
+ }
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ validateAssociationEnterPdb();
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ validateAssociationFromFile();
+ }
+ }
+
+ /**
+ * Validates inputs from the Manual PDB entry panel
+ */
+ public void validateAssociationEnterPdb()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-"))
+ {
+ txt_search.setEnabled(true);
+ if (isValidPBDEntry)
+ {
+ btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ txt_search.setEnabled(false);
+ lbl_pdbManualFetchStatus.setIcon(errorImage);
+ }
+ }
+
+ /**
+ * Validates inputs for the manual PDB file selection options
+ */
+ public void validateAssociationFromFile()
+ {
+ AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem();
+ lbl_fromFileStatus.setIcon(errorImage);
+ if (selectedSequences.length == 1
+ || (assSeqOpt != null
+ && !assSeqOpt.getName().equalsIgnoreCase(
+ "-Select Associated Seq-")))
+ {
+ btn_pdbFromFile.setEnabled(true);
+ if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
+ {
+ btn_view.setEnabled(true);
+ lbl_fromFileStatus.setIcon(goodImage);
+ }
+ }
+ else
+ {
+ btn_pdbFromFile.setEnabled(false);
+ lbl_fromFileStatus.setIcon(errorImage);
+ }
+ }
+
+ @Override
+ public void cmbAssSeqStateChanged()
+ {
+ validateSelections();
+ }
+
+ /**
+ * 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();
+ }
+ }
+
+ }
+
+ /**
+ * Handles action event for btn_ok
+ */
+ @Override
+ public void ok_ActionPerformed()
+ {
+ FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+ .getSelectedItem());
+ String currentView = selectedFilterOpt.getView();
+ if (currentView == VIEWS_FILTER)
+ {
+ int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
+ lastPdbRequest.getWantedFields(), true);
+ 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));
+ }
+ else if (currentView == VIEWS_ENTER_ID)
+ {
+ selectedSequence = ((AssociateSeqOptions) idInputAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ PDBEntry pdbEntry = new PDBEntry();
+ pdbEntry.setId(txt_search.getText());
+ pdbEntry.setType("PDB");
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
+ PDBEntry[] pdbEntriesToView = new PDBEntry[]
+ { pdbEntry };
+ new StructureViewer(ap.getStructureSelectionManager())
+ .viewStructures(ap, pdbEntriesToView,
+ ap.av.collateForPDB(pdbEntriesToView));
+ }
+ else if (currentView == VIEWS_FROM_FILE)
+ {
+ selectedSequence = ((AssociateSeqOptions) fileChooserAssSeqPanel
+ .getCmb_assSeq().getSelectedItem()).getSequence();
+ new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
+ }
+ mainFrame.dispose();
+ }
+
+ /**
+ * Populates the combo-box used in associating manually fetched structures to
+ * a unique sequence when more than one sequence selection is made.
+ */
+ public void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq)
+ {
+ cmb_assSeq.removeAllItems();
+ cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
+ null));
+ // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
+ lbl_associateSeq.setVisible(false);
+ if (selectedSequences.length > 1)
+ {
+ for (SequenceI seq : selectedSequences)
+ {
+ cmb_assSeq.addItem(new AssociateSeqOptions(seq));
+ }
+ }
+ else
+ {
+ String seqName = selectedSequence.getDisplayId(false);
+ seqName = seqName.length() <= 40 ? seqName : seqName.substring(0, 39);
+ lbl_associateSeq.setText(seqName);
+ lbl_associateSeq.setVisible(true);
+ cmb_assSeq.setVisible(false);
+ }
+ }
+
+ public boolean isStructuresDiscovered()
+ {
+ return structuresDiscovered;
+ }
+
+ public void setStructuresDiscovered(boolean structuresDiscovered)
+ {
+ this.structuresDiscovered = structuresDiscovered;
+ }
+
+ public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ {
+ return discoveredStructuresSet;
+ }
+
+ @Override
+ protected void txt_search_ActionPerformed()
+ {
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
+ validateSelections();
+ }
+
+ @Override
+ public void tabRefresh()
+ {
+ if (selectedSequences != null)
+ {
+ Thread refreshThread = new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ fetchStructuresMetaData();
+ filterResultSet(((FilterOption) cmb_filterOption
+ .getSelectedItem()).getValue());
+ }
+ });
+ refreshThread.start();
+ }
+ }
+
+}
--- /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.jbgui.PDBDocFieldPreferences.PreferenceSource;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+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.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+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 JTable tbl_summary = new JTable();
+
+ protected JScrollPane scrl_searchResult = new JScrollPane(
+tbl_summary);
+
+ private JTabbedPane tabbedPane = new JTabbedPane();
+
+ private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
+ PreferenceSource.SEARCH_SUMMARY);
+
+ 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
+ {
+ tbl_summary.setAutoCreateRowSorter(true);
+ 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();
+ }
+ });
+
+ scrl_searchResult.setPreferredSize(new Dimension(500, 300));
+ scrl_searchResult
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ 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();
+ }
+ });
+
+ final String searchTabTitle = MessageManager
+ .getString("label.search_result");
+ ChangeListener changeListener = new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent changeEvent)
+ {
+ JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
+ .getSource();
+ int index = sourceTabbedPane.getSelectedIndex();
+ if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
+ {
+ txt_search_ActionPerformed();
+ }
+ }
+ };
+ tabbedPane.addChangeListener(changeListener);
+ tabbedPane.setPreferredSize(new Dimension(500, 300));
+ tabbedPane.add(searchTabTitle, scrl_searchResult);
+ tabbedPane.add(
+ MessageManager.getString("label.configure_displayed_columns"),
+ pdbDocFieldPrefs);
+
+ pnl_actions.add(btn_back);
+ pnl_actions.add(btn_ok);
+ pnl_actions.add(btn_cancel);
+
+ pnl_results.add(tabbedPane);
+ 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 JComboBox<PDBDocField> getCmbSearchTarget()
+ {
+ return cmb_searchTarget;
+ }
+
+ public JTextField getTxtSearch()
+ {
+ return txt_search;
+ }
+
+ public JInternalFrame getMainFrame()
+ {
+ return mainFrame;
+ }
+
+ public abstract void txt_search_ActionPerformed();
+
+ public abstract void btn_ok_ActionPerformed();
+
+ public abstract void btn_back_ActionPerformed();
+
+ public abstract void btn_cancel_ActionPerformed();
+
+ public abstract void populateCmbSearchTargetOptions();
+
+}
import jalview.gui.JvSwingUtils;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
protected JTextField chimeraPath = new JTextField();
+
/*
* Colours tab components
*/
.getString("label.structure_options")));
structureTab.setLayout(null);
final int width = 400;
- final int height = 23;
- final int lineSpacing = 30;
+ final int height = 22;
+ final int lineSpacing = 25;
int ypos = 30;
structFromPdb.setFont(verdana11);
});
structureTab.add(chimeraPath);
+ ypos += lineSpacing;
+ // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
+ // scrl_pdbDocFieldConfig
+ // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+ // scrl_pdbDocFieldConfig.setBounds();
+ PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
+ PreferenceSource.PREFERENCES);
+ docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
+ structureTab.add(docFieldPref);
+
+
+
+
return structureTab;
}
+
/**
* Action on choosing a structure viewer from combobox options.
*
--- /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.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
+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.ImageIcon;
+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.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+
+@SuppressWarnings("serial")
+/**
+ * GUI layout for structure chooser
+ * @author tcnofoegbu
+ *
+ */
+public abstract class GStructureChooser extends JPanel implements
+ ItemListener
+{
+ protected String frameTitle = MessageManager
+ .getString("label.structure_chooser");
+
+ protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+
+ protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
+
+ protected AlignmentPanel ap;
+
+ protected JLabel lbl_result = new JLabel(
+ MessageManager.getString("label.select"));
+
+ protected JButton btn_view = new JButton();
+
+ protected JButton btn_cancel = new JButton();
+
+ protected JButton btn_pdbFromFile = new JButton();
+
+ protected JTextField txt_search = new JTextField(14);
+
+ private JPanel pnl_actions = new JPanel();
+
+ private JPanel pnl_filter = new JPanel();
+
+ private JPanel pnl_idInput = new JPanel(new FlowLayout());
+
+ private JPanel pnl_fileChooser = new JPanel(new FlowLayout());
+
+ private JPanel pnl_idInputBL = new JPanel(new BorderLayout());
+
+ private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
+
+ protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
+
+ protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
+ .getLayout());
+
+ private BorderLayout mainLayout = new BorderLayout();
+
+ protected JCheckBox chk_rememberSettings = new JCheckBox(
+ MessageManager.getString("label.dont_ask_me_again"));
+
+ protected JCheckBox chk_invertFilter = new JCheckBox(
+ MessageManager.getString("label.invert"));
+
+ protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
+ "/images/loading.gif"));
+
+ protected ImageIcon goodImage = new ImageIcon(getClass().getResource(
+ "/images/good.png"));
+
+ protected ImageIcon errorImage = new ImageIcon(getClass().getResource(
+ "/images/error.png"));
+
+ protected JLabel lbl_loading = new JLabel(loadingImage);
+
+ protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
+
+ protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
+
+
+ protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
+
+ protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
+
+ protected static final String VIEWS_FILTER = "VIEWS_FILTER";
+
+ protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
+
+ protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
+
+ protected JTable tbl_summary = new JTable();
+
+ protected JScrollPane scrl_foundStructures = new JScrollPane(
+ tbl_summary);
+
+ private JTabbedPane tabbedPane = new JTabbedPane();
+
+ private PDBDocFieldPreferences pdbDocFieldPrefs = new PDBDocFieldPreferences(
+ PreferenceSource.STRUCTURE_CHOOSER);
+
+ public GStructureChooser()
+ {
+ try
+ {
+ jbInit();
+ mainFrame.setVisible(false);
+ mainFrame.invalidate();
+ mainFrame.pack();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Initializes the GUI default properties
+ *
+ * @throws Exception
+ */
+ private void jbInit() throws Exception
+ {
+ tbl_summary.setAutoCreateRowSorter(true);
+ btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
+ btn_view.setText(MessageManager.getString("action.view"));
+ btn_view.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ 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)
+ {
+ mainFrame.dispose();
+ }
+ });
+
+ 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)
+ {
+ pdbFromFile_actionPerformed();
+ }
+ });
+
+ scrl_foundStructures.setPreferredSize(new Dimension(500, 300));
+ scrl_foundStructures
+ .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+
+ 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));
+
+
+ txt_search.setToolTipText(MessageManager
+ .getString("label.enter_pdb_id"));
+ cmb_filterOption.setToolTipText(MessageManager
+ .getString("info.select_filter_option"));
+ 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();
+ }
+ });
+
+ cmb_filterOption.addItemListener(this);
+ chk_invertFilter.addItemListener(this);
+
+ pnl_actions.add(chk_rememberSettings);
+ pnl_actions.add(btn_view);
+ pnl_actions.add(btn_cancel);
+
+ // pnl_filter.add(lbl_result);
+ pnl_filter.add(cmb_filterOption);
+ pnl_filter.add(lbl_loading);
+ pnl_filter.add(chk_invertFilter);
+ lbl_loading.setVisible(false);
+
+ pnl_idInput.add(txt_search);
+ pnl_idInput.add(lbl_pdbManualFetchStatus);
+
+ pnl_fileChooser.add(btn_pdbFromFile);
+ pnl_fileChooser.add(lbl_fromFileStatus);
+
+ pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
+ pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
+
+ pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
+ pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
+
+ final String foundStructureSummary = MessageManager
+ .getString("label.found_structures_summary");
+
+ ChangeListener changeListener = new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent changeEvent)
+ {
+ JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
+ .getSource();
+ int index = sourceTabbedPane.getSelectedIndex();
+ if (sourceTabbedPane.getTitleAt(index)
+ .equals(foundStructureSummary))
+ {
+ tabRefresh();
+ }
+ }
+ };
+ tabbedPane.addChangeListener(changeListener);
+ tabbedPane.setPreferredSize(new Dimension(500, 300));
+ tabbedPane.add(foundStructureSummary, scrl_foundStructures);
+ tabbedPane.add(
+ MessageManager.getString("label.configure_displayed_columns"),
+ pdbDocFieldPrefs);
+
+
+ pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
+ pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
+ pnl_switchableViews.add(tabbedPane, VIEWS_FILTER);
+
+ this.setLayout(mainLayout);
+ 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);
+ mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ Desktop.addInternalFrame(mainFrame, frameTitle, 800, 400);
+ }
+
+
+ @Override
+ /**
+ * Event listener for the 'filter' combo-box and 'invert' check-box
+ */
+ public void itemStateChanged(ItemEvent e)
+ {
+ stateChanged(e);
+ }
+
+ /**
+ * This inner class provides the data model for the structure filter combo-box
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class FilterOption
+ {
+ private String name;
+
+ private String value;
+
+ private String view;
+
+ public FilterOption(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;
+ }
+ }
+
+ /**
+ * This inner class provides the provides the data model for associate
+ * sequence combo-box - cmb_assSeq
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class AssociateSeqOptions
+ {
+ private SequenceI sequence;
+ private String name;
+
+ public AssociateSeqOptions(SequenceI seq)
+ {
+ this.sequence = seq;
+ this.name = (seq.getName().length() >= 23) ? seq.getName().substring(
+ 0, 23) : seq.getName();
+ }
+
+ public AssociateSeqOptions(String name, SequenceI seq)
+ {
+ this.name = name;
+ this.sequence = seq;
+ }
+
+ public String toString()
+ {
+ return name;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public void setSequence(SequenceI sequence)
+ {
+ this.sequence = sequence;
+ }
+
+ }
+
+ /**
+ * This inner class holds the Layout and configuration of the panel which
+ * handles association of manually fetched structures to a unique sequence
+ * when more than one sequence selection is made
+ *
+ * @author tcnofoegbu
+ *
+ */
+ public class AssciateSeqPanel extends JPanel implements ItemListener
+ {
+ private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<AssociateSeqOptions>();
+
+ private JLabel lbl_associateSeq = new JLabel();
+
+ public AssciateSeqPanel()
+ {
+ this.setLayout(new FlowLayout());
+ this.add(cmb_assSeq);
+ this.add(lbl_associateSeq);
+ cmb_assSeq.setToolTipText(MessageManager
+ .getString("info.associate_wit_sequence"));
+ cmb_assSeq.addItemListener(this);
+ }
+
+ public void loadCmbAssSeq()
+ {
+ populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
+ }
+
+ public JComboBox<AssociateSeqOptions> getCmb_assSeq()
+ {
+ return cmb_assSeq;
+ }
+
+ public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
+ {
+ this.cmb_assSeq = cmb_assSeq;
+ }
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (e.getStateChange() == ItemEvent.SELECTED)
+ {
+ cmbAssSeqStateChanged();
+ }
+ }
+ }
+
+ public JComboBox<FilterOption> getCmbFilterOption()
+ {
+ return cmb_filterOption;
+ }
+
+ protected abstract void stateChanged(ItemEvent e);
+
+ protected abstract void updateCurrentView();
+
+ protected abstract void populateFilterComboBox();
+
+ protected abstract void ok_ActionPerformed();
+
+ protected abstract void pdbFromFile_actionPerformed();
+
+ protected abstract void txt_search_ActionPerformed();
+
+ public abstract void populateCmbAssociateSeqOptions(
+ JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq);
+
+ public abstract void cmbAssSeqStateChanged();
+
+ public abstract void tabRefresh();
+}
--- /dev/null
+package jalview.jbgui;
+
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.table.AbstractTableModel;
+
+@SuppressWarnings("serial")
+public class PDBDocFieldPreferences extends JScrollPane
+{
+ protected JTable tbl_pdbDocFieldConfig = new JTable();
+
+ protected JScrollPane scrl_pdbDocFieldConfig = new JScrollPane(
+ tbl_pdbDocFieldConfig);
+
+ private HashMap<String, PDBDocField> map = new HashMap<String, PDBDocField>();
+
+ private static Collection<PDBDocField> searchSummaryFields = new HashSet<PDBDocField>();
+
+ private static Collection<PDBDocField> structureSummaryFields = new HashSet<PDBDocField>();
+
+ public enum PreferenceSource
+ {
+ SEARCH_SUMMARY, STRUCTURE_CHOOSER, PREFERENCES;
+ }
+
+ private PreferenceSource currentSource;
+
+ static
+ {
+ searchSummaryFields.add(PDBDocField.PDB_ID);
+ searchSummaryFields.add(PDBDocField.TITLE);
+
+ structureSummaryFields.add(PDBDocField.PDB_ID);
+ structureSummaryFields.add(PDBDocField.TITLE);
+ }
+
+ public PDBDocFieldPreferences(PreferenceSource source)
+ {
+ tbl_pdbDocFieldConfig.setAutoCreateRowSorter(true);
+ this.getViewport().add(tbl_pdbDocFieldConfig);
+ this.currentSource = source;
+
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[]
+ { "PDB Feild", "Show in search summary" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[]
+ { "PDB Feild", "Show in structure summary" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[]
+ { "PDB Feild", "Show in search summary", "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+
+ Object[][] data = new Object[PDBDocField.values().length - 1][3];
+ int x = 0;
+ for (PDBDocField field : PDBDocField.values())
+ {
+ if (field.getName().equalsIgnoreCase("all"))
+ {
+ continue;
+ }
+
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ data[x++] = new Object[]
+ { field.getName(), searchSummaryFields.contains(field) };
+ break;
+ case STRUCTURE_CHOOSER:
+ data[x++] = new Object[]
+ { field.getName(), structureSummaryFields.contains(field) };
+ break;
+ case PREFERENCES:
+ data[x++] = new Object[]
+ { field.getName(), searchSummaryFields.contains(field),
+ structureSummaryFields.contains(field) };
+ break;
+ default:
+ break;
+ }
+ map.put(field.getName(), field);
+ }
+
+ PDBFieldTableModel model = new PDBFieldTableModel(columnNames, data);
+ tbl_pdbDocFieldConfig.setModel(model);
+ }
+
+ public static Collection<PDBDocField> getSearchSummaryFields()
+ {
+ return searchSummaryFields;
+ }
+
+ public static void setSearchSummaryFields(
+ Collection<PDBDocField> searchSummaryFields)
+ {
+ PDBDocFieldPreferences.searchSummaryFields = searchSummaryFields;
+ }
+
+ public static Collection<PDBDocField> getStructureSummaryFields()
+ {
+ return structureSummaryFields;
+ }
+
+ public static void setStructureSummaryFields(
+ Collection<PDBDocField> structureSummaryFields)
+ {
+ PDBDocFieldPreferences.structureSummaryFields = structureSummaryFields;
+ }
+
+ class PDBFieldTableModel extends AbstractTableModel
+ {
+
+ public PDBFieldTableModel(String[] columnNames, Object[][] data)
+ {
+ this.data = data;
+ this.columnNames = columnNames;
+ }
+
+ private Object[][] data;
+
+ private String[] columnNames;
+
+ public int getColumnCount()
+ {
+ return columnNames.length;
+ }
+
+ public int getRowCount()
+ {
+ return data.length;
+ }
+
+ public String getColumnName(int col)
+ {
+ return columnNames[col];
+ }
+
+ public Object getValueAt(int row, int col)
+ {
+ return data[row][col];
+ }
+
+ /*
+ * JTable uses this method to determine the default renderer/ editor for
+ * each cell. If we didn't implement this method, then the last column would
+ * contain text ("true"/"false"), rather than a check box.
+ */
+ public Class getColumnClass(int c)
+ {
+ return getValueAt(0, c).getClass();
+ }
+
+ /*
+ * Don't need to implement this method unless your table's editable.
+ */
+ public boolean isCellEditable(int row, int col)
+ {
+ // Note that the data/cell address is constant,
+ // no matter where the cell appears onscreen.
+ return col == 1 || col == 2;
+
+ }
+
+ /*
+ * Don't need to implement this method unless your table's data can change.
+ */
+ public void setValueAt(Object value, int row, int col)
+ {
+ data[row][col] = value;
+ fireTableCellUpdated(row, col);
+
+ String name = getValueAt(row, 0).toString();
+ boolean selected = ((Boolean) value).booleanValue();
+
+ PDBDocField pdbField = map.get(name);
+
+ if (currentSource == PreferenceSource.SEARCH_SUMMARY)
+ {
+ updatePrefs(searchSummaryFields, pdbField, selected);
+ }
+ else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
+ {
+ updatePrefs(structureSummaryFields, pdbField, selected);
+ }
+ else if (currentSource == PreferenceSource.PREFERENCES)
+ {
+ if (col == 1)
+ {
+ updatePrefs(searchSummaryFields, pdbField, selected);
+ }
+ else if (col == 2)
+ {
+ updatePrefs(structureSummaryFields, pdbField, selected);
+ }
+ }
+ }
+
+ private void updatePrefs(Collection<PDBDocField> prefConfig,
+ PDBDocField pdbField,
+ boolean selected)
+ {
+ if (prefConfig.contains(pdbField) && !selected)
+ {
+ prefConfig.remove(pdbField);
+ }
+
+ if (!prefConfig.contains(pdbField) && selected)
+ {
+ prefConfig.add(pdbField);
+ }
+ }
+
+ }
+}
/**
* Formats a character into a string (like sprintf in C)
*
- * @param x
+ * @param debounceTrap
* the value to format
* @return the formatted string
*/
/**
* Formats a string into a larger string (like sprintf in C)
*
- * @param x
+ * @param debounceTrap
* the value to format
* @return the formatted string
*/
public static String formatMessage(String key, Object... params)
{
+ return MessageFormat.format(rb.getString(key), params);
+ }
+
+ public static String formatMessage(String key, String[] params)
+ {
return MessageFormat.format(rb.getString(key), (Object[]) params);
}
--- /dev/null
+package jalview.ws.dbsources;
+
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.ws.rs.core.MediaType;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.WebResource;
+import com.sun.jersey.api.client.config.ClientConfig;
+import com.sun.jersey.api.client.config.DefaultClientConfig;
+import com.sun.jersey.api.json.JSONConfiguration;
+
+/**
+ * A rest client for querying the Search endpoing of the PDB REST API
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestClient
+{
+ private static String PDB_SEARCH_ENDPOINT = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
+
+ private static int DEFAULT_RESPONSE_SIZE = 200;
+
+ /**
+ * Takes a PDBRestRequest object and returns a response upon execution
+ *
+ * @param pdbRestRequest
+ * the PDBRestRequest instance to be processed
+ * @return the pdbResponse object for the given request
+ */
+ public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
+ Boolean.TRUE);
+ Client client = Client.create(clientConfig);
+
+ String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
+ .getWantedFields());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ : pdbRestRequest.getResponseSize();
+ String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
+ .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
+ .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+ : " desc"));
+
+ // Build request parameters for the REST Request
+ WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", String.valueOf(responseSize))
+ .queryParam("q", pdbRestRequest.getQuery())
+ .queryParam("sort", sortParam);
+
+ // Execute the REST request
+ ClientResponse clientResponse = webResource.accept(
+ MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+ // Get the JSON string from the response object
+ String responseString = clientResponse.getEntity(String.class);
+
+ // Check the response status and report exception if one occurs
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = "";
+ if (clientResponse.getStatus() == 400)
+ {
+ errorMessage = parseJsonExceptionString(responseString);
+ throw new RuntimeException(errorMessage);
+ }
+ else
+ {
+ errorMessage = "Failed : HTTP error code : "
+ + clientResponse.getStatus();
+ throw new RuntimeException(errorMessage);
+ }
+ }
+
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+
+ // Process the response and return the result to the caller.
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
+ }
+
+ /**
+ * 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(jsonErrorResponse);
+ JSONObject errorResponse = (JSONObject) jsonObj.get("error");
+ errorMessage = errorResponse.get("msg").toString();
+
+ JSONObject responseHeader = (JSONObject) jsonObj
+ .get("responseHeader");
+ errorMessage += responseHeader.get("params").toString();
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return errorMessage;
+ }
+
+ /**
+ * Parses the JSON response string from PDB REST API. The response is dynamic
+ * hence, only fields specifically requested for in the 'wantedFields'
+ * parameter is fetched/processed
+ *
+ * @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")
+ public static PDBRestResponse parsePDBJsonResponse(
+ String pdbJsonResponseString, PDBRestRequest pdbRestRequest)
+ {
+ PDBRestResponse searchResult = new PDBRestResponse();
+ List<PDBResponseSummary> result = null;
+ try
+ {
+ JSONParser jsonParser = new JSONParser();
+ JSONObject jsonObj = (JSONObject) jsonParser
+ .parse(pdbJsonResponseString);
+
+ JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
+ String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
+ "QTime").toString();
+ int numFound = Integer
+ .valueOf(pdbResponse.get("numFound").toString());
+ if (numFound > 0)
+ {
+ result = new ArrayList<PDBResponseSummary>();
+ JSONArray docs = (JSONArray) pdbResponse.get("docs");
+ for (Iterator<JSONObject> docIter = docs.iterator(); docIter
+ .hasNext();)
+ {
+ JSONObject doc = docIter.next();
+ result.add(searchResult.new PDBResponseSummary(doc,
+ pdbRestRequest));
+ }
+ searchResult.setNumberOfItemsFound(numFound);
+ searchResult.setResponseTime(queryTime);
+ searchResult.setSearchSummary(result);
+ }
+ } catch (ParseException e)
+ {
+ e.printStackTrace();
+ }
+ return searchResult;
+ }
+
+ /**
+ * Takes a collection of PDBDocField and converts its 'code' Field values into
+ * a comma delimited string.
+ *
+ * @param pdbDocfields
+ * the collection of PDBDocField to process
+ * @return the comma delimited string from the pdbDocFields collection
+ */
+ public static String getPDBDocFieldsAsCommaDelimitedString(
+ Collection<PDBDocField> pdbDocfields)
+ {
+ String result = "";
+ if (pdbDocfields != null && !pdbDocfields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (PDBDocField field : pdbDocfields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+ /**
+ * Determines the column index for 'PDB Id' Fields in the dynamic 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, boolean hasRefSeq)
+ {
+
+ // If a reference sequence is attached then start counting from 1 else
+ // start from zero
+ int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
+
+ for (PDBDocField feild : wantedFeilds)
+ {
+ if (feild.equals(PDBDocField.PDB_ID))
+ {
+ break; // Once PDB Id index is determined exit iteration
+ }
+ ++pdbFeildIndexCounter;
+ }
+ return pdbFeildIndexCounter;
+ }
+
+ /**
+ * This enum represents the fields available in the PDB JSON response
+ *
+ */
+ 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"), PFAM_ACCESSION("PFAM Accession",
+ "pfam_accession"), PFAM_NAME("PFAM Name", "pfam_name"), INTERPRO_NAME(
+ "InterPro Name", "interpro_name"), INTERPRO_ACCESSION(
+ "InterPro Accession", "interpro_accession"), UNIPROT_ID(
+ "UniProt Id", "uniprot_id"), UNIPROT_ACCESSION(
+ "UniProt Accession", "uniprot_accession"), UNIPROT_COVERAGE(
+ "UniProt Coverage", "uniprot_coverage"), UNIPROT_FEATURES(
+ "Uniprot Features", "uniprot_features"), R_FACTOR("R Factor",
+ "r_factor"), RESOLUTION("Resolution", "resolution"), DATA_QUALITY(
+ "Data Quality", "data_quality"), OVERALL_QUALITY(
+ "Overall Quality", "overall_quality"), POLYMER_COUNT(
+ "Number of Polymers", "number_of_polymers"), PROTEIN_CHAIN_COUNT(
+ "Number of Protein Chains", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
+ "Number of Bound Molecule", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
+ "Number of Polymer Residue", "number_of_polymer_residues"), GENUS(
+ "GENUS", "genus"), GENE_NAME("Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method"), GO_ID("GO Id",
+ "go_id"), ASSEMBLY_ID("Assembly Id", "assembly_form"), ASSEMBLY_FORM(
+ "Assembly Form", "assembly_id"), ASSEMBLY_TYPE("Assembly Type",
+ "assembly_type"), SPACE_GROUP("Space Group", "spacegroup"), CATH_CODE(
+ "Cath Code", "cath_code"), TAX_ID("Tax Id", "tax_id"), TAX_QUERY(
+ "Tax Query", "tax_query"), INTERACTING_ENTRY_ID(
+ "Interacting Entry Id", "interacting_entry_id"), INTERACTING_ENTITY_ID(
+ "Interacting Entity Id", "interacting_entity_id"), INTERACTING_MOLECULES(
+ "Interacting Molecules", "interacting_molecules"), PUBMED_ID(
+ "Pubmed Id", "pubmed_id"), STATUS("Status", "status"), MODEL_QUALITY(
+ "Model Quality", "model_quality"), PIVOT_RESOLUTION(
+ "Pivot Resolution", "pivot_resolution"), DATA_REDUCTION_SOFTWARE(
+ "Data reduction software", "data_reduction_software"), MAX_OBSERVED_RES(
+ "Max observed residues", "max_observed_residues"), ORG_SCI_NAME(
+ "Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM(
+ "Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH(
+ "Crystallisation Ph", "crystallisation_ph"), BIOLOGICAL_FUNCTION(
+ "Biological Function", "biological_function"), BIOLOGICAL_PROCESS(
+ "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT(
+ "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
+ "Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
+ "compound_id"), COMPOUND_WEIGHT("Compound Weight",
+ "compound_weight"), COMPOUND_SYSTEMATIC_NAME(
+ "Compound Systematic Name", "compound_systematic_name"), INTERACTING_LIG(
+ "Interacting Ligands", "interacting_ligands"), JOURNAL(
+ "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
+ "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
+ "Diffraction Protocol", "diffraction_protocol"), REFINEMENT_SOFTWARE(
+ "Refinement Software", "refinement_software"), STRUCTURE_DETERMINATION_METHOD(
+ "Structure Determination Method",
+ "structure_determination_method"), SYNCHROTON_SITE(
+ "Synchrotron Site", "synchrotron_site"), SAMPLE_PREP_METHOD(
+ "Sample Preparation Method", "sample_preparation_method"), ENTRY_AUTHORS(
+ "Entry Authors", "entry_authors"), CITATION_TITLE(
+ "Citation Title", "citation_title"), STRUCTURE_SOLUTION_SOFTWARE(
+ "Structure Solution Software", "structure_solution_software"), ENTRY_ENTITY(
+ "Entry Entity", "entry_entity"), R_FREE("R Free", "r_free"), NO_OF_POLYMER_ENTITIES(
+ "Number of Polymer Entities", "number_of_polymer_entities"), NO_OF_BOUND_ENTITIES(
+ "Number of Bound Entities", "number_of_bound_entities"), CRYSTALLISATION_RESERVOIR(
+ "Crystallisation Reservoir", "crystallisation_reservoir"), DATA_SCALING_SW(
+ "Data Scalling Software", "data_scaling_software"), DETECTOR(
+ "Detector", "detector"), DETECTOR_TYPE("Detector Type",
+ "detector_type"), MODIFIED_RESIDUE_FLAG(
+ "Modified Residue Flag", "modified_residue_flag"), NUMBER_OF_COPIES(
+ "Number of Copies", "number_of_copies"), STRUCT_ASYM_ID(
+ "Struc Asym Id", "struct_asym_id"), HOMOLOGUS_PDB_ENTITY_ID(
+ "Homologus PDB Entity Id", "homologus_pdb_entity_id"), MOLECULE_SYNONYM(
+ "Molecule Synonym", "molecule_synonym"), DEPOSITION_SITE(
+ "Deposition Site", "deposition_site"), SYNCHROTRON_BEAMLINE(
+ "Synchrotron Beamline", "synchrotron_beamline"), ENTITY_ID(
+ "Entity Id", "entity_id"), BEAM_SOURCE_NAME("Beam Source Name",
+ "beam_source_name"), PROCESSING_SITE("Processing Site",
+ "processing_site"), ENTITY_WEIGHT("Entity Weight",
+ "entity_weight"), VERSION("Version", "_version_"), ALL("ALL",
+ "text");
+
+ 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;
+ }
+ }
+}
\ No newline at end of file
--- /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.ws.uimodel;
+
+
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.Collection;
+
+/**
+ * Represents the PDB request to be consumed by the PDBRestClient
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestRequest
+{
+ private String fieldToSearchBy;
+
+ private String searchTerm;
+
+ private String fieldToSortBy;
+
+ private String associatedSequence;
+
+ private boolean allowEmptySequence;
+
+ private int responseSize;
+
+ private boolean isSortAscending;
+
+ private Collection<PDBDocField> wantedFields;// = new
+ // Collection<PDBDocField>();
+
+ public String getFieldToSearchBy()
+ {
+ return fieldToSearchBy;
+ }
+
+ public void setFieldToSearchBy(String fieldToSearchBy)
+ {
+ this.fieldToSearchBy = fieldToSearchBy;
+ }
+
+ public String getSearchTerm()
+ {
+ return searchTerm;
+ }
+
+ public void setSearchTerm(String searchTerm)
+ {
+ this.searchTerm = searchTerm;
+ }
+
+ public boolean isAllowEmptySeq()
+ {
+ return allowEmptySequence;
+ }
+
+ public void setAllowEmptySeq(boolean allowEmptySeq)
+ {
+ this.allowEmptySequence = allowEmptySeq;
+ }
+
+ public int getResponseSize()
+ {
+ return responseSize;
+ }
+
+ public void setResponseSize(int responseSize)
+ {
+ this.responseSize = responseSize;
+ }
+
+ public Collection<PDBDocField> getWantedFields()
+ {
+ return wantedFields;
+ }
+
+ public void setWantedFields(Collection<PDBDocField> wantedFields)
+ {
+ this.wantedFields = wantedFields;
+ }
+
+ public String getFieldToSortBy()
+ {
+ return fieldToSortBy;
+ }
+
+ public void setFieldToSortBy(String fieldToSortBy, boolean isSortAscending)
+ {
+ this.fieldToSortBy = fieldToSortBy;
+ this.isSortAscending = isSortAscending;
+ }
+
+ public boolean isAscending()
+ {
+ return isSortAscending;
+ }
+
+ public String getAssociatedSequence()
+ {
+ return associatedSequence;
+ }
+
+ public void setAssociatedSequence(String associatedSequence)
+ {
+ this.associatedSequence = associatedSequence;
+ }
+
+ public String getQuery()
+ {
+ return fieldToSearchBy + searchTerm
+ + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]");
+ }
+
+ public String toString()
+ {
+ return "Query : " + getQuery() + " sort field: " + fieldToSortBy
+ + " isAsc: " + isAscending() + " Associated Seq : "
+ + associatedSequence;
+ }
+}
--- /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.ws.uimodel;
+
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+
+import java.util.Collection;
+import java.util.Objects;
+
+import javax.swing.table.DefaultTableModel;
+
+import org.json.simple.JSONObject;
+
+/**
+ * Represents the response model produced by the PDBRestClient upon successful
+ * execution of a given request
+ *
+ * @author tcnofoegbu
+ *
+ */
+public class PDBRestResponse
+{
+ private int numberOfItemsFound;
+
+ private String responseTime;
+
+ private Collection<PDBResponseSummary> searchSummary;
+
+ public int getNumberOfItemsFound()
+ {
+ return numberOfItemsFound;
+ }
+
+ public void setNumberOfItemsFound(int itemFound)
+ {
+ this.numberOfItemsFound = itemFound;
+ }
+
+ public String getResponseTime()
+ {
+ return responseTime;
+ }
+
+ public void setResponseTime(String responseTime)
+ {
+ this.responseTime = responseTime;
+ }
+
+ public Collection<PDBResponseSummary> getSearchSummary()
+ {
+ return searchSummary;
+ }
+
+ public void setSearchSummary(Collection<PDBResponseSummary> searchSummary)
+ {
+ this.searchSummary = searchSummary;
+ }
+
+
+ /**
+ * Convenience method to obtain a Table model for a given summary List based
+ * on the request parameters
+ *
+ * @param request
+ * the PDBRestRequest object which holds useful information for
+ * 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 tableModel = new DefaultTableModel();
+
+ if (request.getAssociatedSequence() != null)
+ {
+ tableModel.addColumn("Sequence"); // Create sequence column header if
+ // exists in the request
+ }
+ for (PDBDocField field : request.getWantedFields())
+ {
+ tableModel.addColumn(field.getName()); // Create sequence column header if
+ // exists in the request
+ }
+
+ for (PDBResponseSummary res : summariesList)
+ {
+ tableModel.addRow(res.getSummaryData()); // Populate table rows with
+ // summary list
+ }
+
+ return tableModel;
+ }
+
+ /**
+ * Model for a unique response summary
+ *
+ */
+ public class PDBResponseSummary
+ {
+ private String pdbId;
+
+ private String[] summaryRowData;
+
+ private String associatedSequence;
+
+ public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request)
+ {
+ Collection<PDBDocField> diplayFields = request.getWantedFields();
+ String associatedSeq = request.getAssociatedSequence();
+ int colCounter = 0;
+ summaryRowData = new String[(associatedSeq != null) ? diplayFields
+ .size() + 1 : diplayFields.size()];
+ if (associatedSeq != null)
+ {
+ this.associatedSequence = (associatedSeq.length() > 18) ? associatedSeq
+ .substring(0, 18) : associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (PDBDocField field : diplayFields)
+ {
+ String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? ""
+ : pdbJsonDoc
+ .get(field.getCode()).toString();
+ if (field.equals(PDBDocField.PDB_ID))
+ {
+ this.pdbId = fieldData;
+ summaryRowData[colCounter++] = this.pdbId;
+ }
+ else
+ {
+ summaryRowData[colCounter++] = fieldData;
+ }
+ }
+ }
+
+ public String getPdbId()
+ {
+ return pdbId;
+ }
+
+ public void setPdbId(String pdbId)
+ {
+ this.pdbId = pdbId;
+ }
+
+ public String[] getSummaryData()
+ {
+ return summaryRowData;
+ }
+
+ public void setSummaryData(String[] summaryData)
+ {
+ this.summaryRowData = summaryData;
+ }
+
+ /**
+ * Returns a string representation of this object;
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder summaryFieldValues = new StringBuilder();
+ for (String summaryField : summaryRowData)
+ {
+ summaryFieldValues.append(summaryField).append("\t");
+ }
+ return summaryFieldValues.toString();
+ }
+
+ /**
+ * Returns hash code value for this object
+ */
+ @Override
+ public int hashCode()
+ {
+ return Objects.hash(this.pdbId, this.toString());
+ }
+
+ /**
+ * Indicates whether some object is equal to this one
+ */
+ @Override
+ public boolean equals(Object that)
+ {
+ if (!(that instanceof PDBResponseSummary))
+ {
+ return false;
+ }
+ PDBResponseSummary another = (PDBResponseSummary) that;
+ return this.toString().equals(another.toString());
+ }
+
+ }
+
+}
+
--- /dev/null
+package jalview.gui;
+
+import static org.junit.Assert.assertTrue;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JTextField;
+
+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 populateCmbSearchTargetOptionsTest()
+ {
+ PDBSearchPanel searchPanel = new PDBSearchPanel(null);
+ assertTrue(searchPanel.getCmbSearchTarget().getItemCount() > 0);
+ searchPanel.populateCmbSearchTargetOptions();
+ }
+
+ @Test
+ public void txt_search_ActionPerformedTest()
+ {
+ PDBSearchPanel searchPanel = new PDBSearchPanel(null);
+ JInternalFrame mainFrame = searchPanel.getMainFrame();
+ JTextField txt_search = searchPanel.getTxtSearch();
+
+ assertTrue(mainFrame.getTitle().length() == 20);
+ assertTrue(mainFrame.getTitle()
+ .equalsIgnoreCase("PDB Sequence Fetcher"));
+
+ txt_search.setText("ABC");
+
+ assertTrue(mainFrame.getTitle().length() > 20);
+ assertTrue(!mainFrame.getTitle().equalsIgnoreCase(
+ "PDB Sequence Fetcher"));
+ }
+}
--- /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 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 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);
+ }
+
+ @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, PDBRestClient.getPDBIdColumIndex(wantedFields, true));
+ assertEquals(4, PDBRestClient.getPDBIdColumIndex(wantedFields, false));
+ }
+
+ 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
