+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.fts.service.uniprot;
+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.SequenceFetcher;
import jalview.util.MessageManager;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
@SuppressWarnings("serial")
public class UniprotFTSPanel extends GFTSPanel
{
+ private static String defaultFTSFrameTitle = MessageManager
+ .getString("label.uniprot_sequence_fetcher");
+
+ private static Map<String, Integer> tempUserPrefs = new HashMap<>();
+
+ private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
public UniprotFTSPanel(SequenceFetcher seqFetcher)
{
+ super();
+ pageLimit = UniProtFTSRestClient.getInstance()
+ .getDefaultResponsePageSize();
this.seqFetcher = seqFetcher;
- this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
- .getProgressIndicator();
+ this.progressIndicator = (seqFetcher == null) ? null
+ : seqFetcher.getProgressIndicator();
}
@Override
- public void txt_search_ActionPerformed()
+ public void searchAction(boolean isFreshSearch)
{
- // TODO Auto-generated method stub
+ mainFrame.requestFocusInWindow();
+ if (isFreshSearch)
+ {
+ offSet = 0;
+ }
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ reset();
+ String searchInput = getTypedText();
+ if (searchInput.length() > 0)
+ {
+ setSearchInProgress(true);
+ long startTime = System.currentTimeMillis();
+ searchInput = getTypedText();
+ String searchTarget = ((FTSDataColumnI) cmb_searchTarget
+ .getSelectedItem()).getAltCode();
+ wantedFields = UniProtFTSRestClient.getInstance()
+ .getAllDefaultDisplayedFTSDataColumns();
+ String searchTerm = decodeSearchTerm(searchInput, searchTarget);
+
+ FTSRestRequest request = new FTSRestRequest();
+ request.setFieldToSearchBy(searchTarget);
+ request.setSearchTerm(searchTerm);
+ request.setOffSet(offSet);
+ request.setWantedFields(wantedFields);
+ FTSRestClientI uniProtRestCleint = UniProtFTSRestClient
+ .getInstance();
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = uniProtRestCleint.executeRequest(request);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ 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)
+ {
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+ + " "
+ + totalNumberformatter.format((Number) (offSet + 1))
+ + " to "
+ + totalNumberformatter
+ .format((Number) (offSet + resultSetCount))
+ + " of "
+ + totalNumberformatter
+ .format((Number) totalResultSetCount)
+ + " " + " (" + (endTime - startTime) + " milli secs)");
+ }
+ else
+ {
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+ + resultSetCount + " " + result + " ("
+ + (endTime - startTime) + " milli secs)");
+ }
+ setSearchInProgress(false);
+ refreshPaginatorState();
+ updateSummaryTableSelections();
+ }
+ txt_search.updateCache();
+ }
+ }.start();
}
- @Override
- public void btn_ok_ActionPerformed()
+ public String decodeSearchTerm(String enteredText, String targetField)
{
- // TODO Auto-generated method stub
+ int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
+ : targetField.length() + 1;
+ String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
+ : targetField + ":";
+ String foundSearchTerms = enteredText;
+ StringBuilder foundSearchTermsBuilder = new StringBuilder();
+ if (enteredText.contains(";"))
+ {
+ String[] searchTerms = enteredText.split(";");
+ for (String searchTerm : searchTerms)
+ {
+ foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
+ .append(" OR ");
+ }
+ int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
+ foundSearchTerms = foundSearchTermsBuilder.toString();
+ if (foundSearchTerms.contains(" OR "))
+ {
+ foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
+ endIndex);
+ }
+ }
+ return foundSearchTerms;
+ }
+ @Override
+ public boolean isPaginationEnabled()
+ {
+ return true;
}
+ @Override
+ public void okAction()
+ {
+ disableActionButtons();
+ StringBuilder selectedIds = new StringBuilder();
+ HashSet<String> selectedIdsSet = new HashSet<>();
+ int primaryKeyColIndex = 0;
+ try
+ {
+ primaryKeyColIndex = getFTSRestClient()
+ .getPrimaryKeyColumIndex(wantedFields, false);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ int[] selectedRows = getResultTable().getSelectedRows();
+ for (int summaryRow : selectedRows)
+ {
+ String idStr = getResultTable()
+ .getValueAt(summaryRow, primaryKeyColIndex).toString();
+ selectedIdsSet.add(idStr);
+ }
+ selectedIdsSet.addAll(paginatorCart);
+ for (String selectedId : selectedIdsSet)
+ {
+ selectedIds.append(selectedId).append(";");
+ }
+
+ String ids = selectedIds.toString();
+ // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
+ seqFetcher.getTextArea().setText(ids);
+ Thread worker = new Thread(seqFetcher);
+ worker.start();
+ delayAndEnableActionButtons();
+ }
@Override
public FTSRestClientI getFTSRestClient()
{
- return UniProtRestClient.getInstance();
+ return UniProtFTSRestClient.getInstance();
}
@Override
public String getFTSFrameTitle()
{
- return MessageManager.getString("label.uniprot_sequence_fetcher");
+ return defaultFTSFrameTitle;
}
+ @Override
+ public Map<String, Integer> getTempUserPrefs()
+ {
+ return tempUserPrefs;
+ }
+
+ @Override
+ public String getCacheKey()
+ {
+ return UNIPROT_FTS_CACHE_KEY;
+ }
}
git://source.jalview.org / jalview.git / blobdiff