/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.jbgui.GPDBSearchPanel;
import jalview.util.MessageManager;
import jalview.ws.dbsources.PDBRestClient;
import jalview.ws.dbsources.PDBRestClient.PDBDocField;
import jalview.ws.uimodel.PDBRestRequest;
import jalview.ws.uimodel.PDBRestResponse;
import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import javax.swing.DefaultListModel;
@SuppressWarnings("serial")
public class PDBSearchPanel extends GPDBSearchPanel
{
private SequenceFetcher seqFetcher;
private IProgressIndicator progressIdicator;
public PDBSearchPanel(SequenceFetcher seqFetcher)
{
this.seqFetcher = seqFetcher;
this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
.getProgressIndicator();
}
@Override
public void txt_search_ActionPerformed()
{
boolean allowEmptySequence = false;
lst_searchResult.setModel(new DefaultListModel());
mainFrame.setTitle(MessageManager
.getString("label.pdb_sequence_getcher"));
if (txt_search.getText().trim().length() > 0)
{
long startTime = System.currentTimeMillis();
String searchTarget = ((PDBDocField) cmb_searchTarget
.getSelectedItem()).getCode();
List wantedFields = new ArrayList();
wantedFields.add(PDBDocField.MOLECULE_TYPE);
wantedFields.add(PDBDocField.PDB_ID);
// wantedFields.add(PDBDocField.GENUS);
wantedFields.add(PDBDocField.GENE_NAME);
wantedFields.add(PDBDocField.TITLE);
// wantedFields.add(PDBDocField.RESOLUTION);
// wantedFields.add(PDBDocField.EXPERIMENTAL_METHOD);
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)
{
lst_searchResult.setModel(PDBRestResponse
.getListModel(resultList.getSearchSummary()));
}
long endTime = System.currentTimeMillis();
int resultSetCount = resultList.getNumberOfItemsFound();
String result = (resultSetCount > 1) ? MessageManager
.getString("label.results") : MessageManager
.getString("label.result");
mainFrame.setTitle(frameTitle + " - " + resultSetCount + " " + result
+ " (" + (endTime - startTime) + " milli secs)");
}
}
@Override
public void btn_ok_ActionPerformed()
{
loadSelectedPDBSequencesToAlignment();
}
@Override
public void btn_back_ActionPerformed()
{
mainFrame.dispose();
new SequenceFetcher(progressIdicator);
}
@Override
public void btn_cancel_ActionPerformed()
{
mainFrame.dispose();
}
/**
* Add the discovered/selected sequences to a target alignment window
*/
public void loadSelectedPDBSequencesToAlignment()
{
mainFrame.dispose();
StringBuilder selectedIds = new StringBuilder();
for (PDBResponseSummary dataSelected : lst_searchResult
.getSelectedValuesList())
{
selectedIds.append(";").append(dataSelected.getPdbId());
}
String ids = selectedIds.deleteCharAt(0).toString();
seqFetcher.textArea.setText(ids);
Thread worker = new Thread(seqFetcher);
worker.start();
}
/**
* Populates search target combo-box options
*/
public void populateCmbSearchTargetOptions()
{
List searchableTargets = new ArrayList();
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()
{
@Override
public int compare(PDBDocField o1, PDBDocField o2)
{
return o1.getName().compareTo(o2.getName());
}
});
for (PDBDocField searchTarget : searchableTargets)
{
cmb_searchTarget.addItem(searchTarget);
}
}
}