/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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.fts.service.pdb;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.core.GFTSPanel;
import jalview.gui.Help;
import jalview.gui.Help.HelpId;
import jalview.gui.SequenceFetcher;
import jalview.util.MessageManager;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import javax.help.HelpSetException;
@SuppressWarnings("serial")
public class PDBFTSPanel extends GFTSPanel
{
private static String defaultFTSFrameTitle = MessageManager
.getString("label.pdb_sequence_fetcher");
private static Map tempUserPrefs = new HashMap<>();
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
public PDBFTSPanel(SequenceFetcher fetcher)
{
super(fetcher);
pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
this.seqFetcher = fetcher;
this.progressIndicator = (fetcher == null) ? null
: fetcher.getProgressIndicator();
}
@Override
public void searchAction(boolean isFreshSearch)
{
mainFrame.requestFocusInWindow();
if (isFreshSearch)
{
offSet = 0;
}
new Thread()
{
@Override
public void run()
{
reset();
boolean allowEmptySequence = false;
if (getTypedText().length() > 0)
{
setSearchInProgress(true);
long startTime = System.currentTimeMillis();
String searchTarget = ((FTSDataColumnI) cmb_searchTarget
.getSelectedItem()).getCode();
wantedFields = PDBFTSRestClient.getInstance()
.getAllDefaultDisplayedFTSDataColumns();
String searchTerm = decodeSearchTerm(getTypedText(),
searchTarget);
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(allowEmptySequence);
request.setResponseSize(100);
request.setFieldToSearchBy("(" + searchTarget + ":");
request.setSearchTerm(searchTerm + ")");
request.setOffSet(offSet);
request.setWantedFields(wantedFields);
FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
FTSRestResponse resultList;
try
{
resultList = pdbRestClient.executeRequest(request);
} catch (Exception e)
{
setErrorMessage(e.getMessage());
checkForErrors();
setSearchInProgress(false);
return;
}
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
getResultTable().setModel(FTSRestResponse.getTableModel(request,
resultList.getSearchSummary()));
FTSRestResponse.configureTableColumn(getResultTable(),
wantedFields, tempUserPrefs);
getResultTable().setVisible(true);
}
long endTime = System.currentTimeMillis();
totalResultSetCount = resultList.getNumberOfItemsFound();
resultSetCount = resultList.getSearchSummary() == null ? 0
: resultList.getSearchSummary().size();
String result = (resultSetCount > 0)
? MessageManager.getString("label.results")
: MessageManager.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
String f2 = totalNumberformatter
.format(Integer.valueOf(offSet + resultSetCount));
String f3 = totalNumberformatter
.format(Integer.valueOf(totalResultSetCount));
updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+ " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
+ (endTime - startTime) + " milli secs)");
}
else
{
updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+ resultSetCount + " " + result + " ("
+ (endTime - startTime) + " milli secs)");
}
setSearchInProgress(false);
refreshPaginatorState();
updateSummaryTableSelections();
}
txt_search.updateCache();
}
}.start();
}
public static String decodeSearchTerm(String enteredText,
String targetField)
{
String foundSearchTerms = enteredText;
StringBuilder foundSearchTermsBuilder = new StringBuilder();
if (enteredText.contains(";"))
{
String[] searchTerms = enteredText.split(";");
for (String searchTerm : searchTerms)
{
if (searchTerm.contains(":"))
{
foundSearchTermsBuilder.append(targetField).append(":")
.append(searchTerm.split(":")[0]).append(" OR ");
}
else
{
foundSearchTermsBuilder.append(targetField).append(":")
.append(searchTerm).append(" OR ");
}
}
int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
foundSearchTerms = foundSearchTermsBuilder.toString();
if (foundSearchTerms.contains(" OR "))
{
foundSearchTerms = foundSearchTerms
.substring(targetField.length() + 1, endIndex);
}
}
else if (enteredText.contains(":"))
{
foundSearchTerms = foundSearchTerms.split(":")[0];
}
return foundSearchTerms;
}
@Override
public void okAction()
{
// mainFrame.dispose();
disableActionButtons();
StringBuilder selectedIds = new StringBuilder();
HashSet selectedIdsSet = new HashSet<>();
int primaryKeyColIndex = 0;
try
{
primaryKeyColIndex = getFTSRestClient()
.getPrimaryKeyColumIndex(wantedFields, false);
} catch (Exception e)
{
e.printStackTrace();
}
int[] selectedRows = getResultTable().getSelectedRows();
String searchTerm = getTypedText();
for (int summaryRow : selectedRows)
{
String idStr = getResultTable()
.getValueAt(summaryRow, primaryKeyColIndex).toString();
selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
}
for (String idStr : paginatorCart)
{
selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
}
for (String selectedId : selectedIdsSet)
{
selectedIds.append(selectedId).append(";");
}
String ids = selectedIds.toString();
seqFetcher.setQuery(ids);
Thread worker = new Thread(seqFetcher);
worker.start();
delayAndEnableActionButtons();
}
public static String getPDBIdwithSpecifiedChain(String pdbId,
String searchTerm)
{
String pdbIdWithChainCode = "";
if (searchTerm.contains(";"))
{
String[] foundTerms = searchTerm.split(";");
for (String foundTerm : foundTerms)
{
if (foundTerm.contains(pdbId))
{
pdbIdWithChainCode = foundTerm;
}
}
}
else if (searchTerm.contains(pdbId))
{
pdbIdWithChainCode = searchTerm;
}
else
{
pdbIdWithChainCode = pdbId;
}
return pdbIdWithChainCode;
}
@Override
public FTSRestClientI getFTSRestClient()
{
return PDBFTSRestClient.getInstance();
}
@Override
public String getFTSFrameTitle()
{
return defaultFTSFrameTitle;
}
@Override
public boolean isPaginationEnabled()
{
return true;
}
@Override
public Map getTempUserPrefs()
{
return tempUserPrefs;
}
@Override
public String getCacheKey()
{
return PDB_FTS_CACHE_KEY;
}
@Override
public String getAutosearchPreference()
{
return PDB_AUTOSEARCH;
}
@Override
protected void showHelp()
{
try
{
Help.showHelpWindow(HelpId.PdbFts);
} catch (HelpSetException e1)
{
e1.printStackTrace();
}
}
}