+/*
+ * 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 java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import javax.help.HelpSetException;
+
+import jalview.bin.Console;
+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;
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";
+
+ private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
- public UniprotFTSPanel(SequenceFetcher seqFetcher)
+ /**
+ * Constructor given an (optional) sequence fetcher panel to revert to on
+ * clicking the 'Back' button
+ *
+ * @param fetcher
+ */
+ public UniprotFTSPanel(SequenceFetcher fetcher)
{
- this.seqFetcher = seqFetcher;
- this.progressIdicator = (seqFetcher == null) ? null : seqFetcher
- .getProgressIndicator();
+ super(fetcher);
+ pageLimit = UniProtFTSRestClient.getInstance()
+ .getDefaultResponsePageSize();
+ this.seqFetcher = fetcher;
+ this.progressIndicator = (fetcher == null) ? null
+ : fetcher.getProgressIndicator();
}
@Override
- public void txt_search_ActionPerformed()
+ public void searchAction(boolean isFreshSearch)
+ {
+ searchAction(null, isFreshSearch);
+ }
+
+ public void searchAction(String cursor, boolean isFreshSearch)
+ {
+ mainFrame.requestFocusInWindow();
+ if (isFreshSearch)
+ {
+ offSet = 0;
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ c.clearCursors();
+ c.setCursorPage(0);
+ c.setCursor(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);
+ UniProtFTSRestClient uniProtRestClient = UniProtFTSRestClient
+ .getInstance();
+ FTSRestResponse resultList;
+ try
+ {
+ resultList = uniProtRestClient.executeRequest(request, cursor);
+ } 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)
+ {
+ updateSearchFrameTitle(
+ defaultFTSFrameTitle + " - " + result + " "
+ + totalNumberformatter
+ .format(Integer.valueOf(offSet + 1))
+ + " to "
+ + totalNumberformatter.format(Integer
+ .valueOf(offSet + resultSetCount))
+ + " of "
+ + totalNumberformatter.format(
+ Integer.valueOf(totalResultSetCount))
+ + " " + " (" + (endTime - startTime)
+ + " milli secs)");
+ }
+ else
+ {
+ updateSearchFrameTitle(defaultFTSFrameTitle + " - "
+ + resultSetCount + " " + result + " ("
+ + (endTime - startTime) + " milli secs)");
+ }
+ setSearchInProgress(false);
+ refreshPaginatorState();
+ updateSummaryTableSelections();
+ }
+ txt_search.updateCache();
+ }
+ }.start();
+
+ }
+
+ 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 btn_ok_ActionPerformed()
+ public void okAction()
{
- // TODO Auto-generated method stub
+ 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();
+ seqFetcher.setQuery(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;
+ }
+
+ @Override
+ public String getAutosearchPreference()
+ {
+ return UNIPROT_AUTOSEARCH;
+ }
+
+ @Override
+ protected void showHelp()
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.UniprotFts);
+ } catch (HelpSetException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+
+ /*
+ * 2022-07-20 bsoares
+ * The new Uniprot API has a strange pagination process described at
+ * https://www.uniprot.org/help/pagination
+ * When a successful request returns results, with more results past the size
+ * limit, the response sends a "Link" header with a URL containing the a "cursor"
+ * parameter with an opaque string that refers to the next page of results.
+ * These are store as nextCursor in the UniProtFTSRestClient along with the currCursor.
+ * When navigation across pages occurs these should be swapped around.
+ */
+ @Override
+ public void refreshPaginatorState()
+ {
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ setNextPageButtonEnabled(c.getNextCursor() != null);
+ setPrevPageButtonEnabled(c.getPrevCursor() != null);
+ }
+
+ @Override
+ public void prevPageAction()
+ {
+ updatePaginatorCart();
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ String prevCursor = c.getPrevCursor();
+ if (prevCursor != null)
+ {
+ if (offSet >= pageLimit)
+ {
+ offSet -= pageLimit;
+ }
+ else
+ {
+ // not sure what's happening if we get here though it wouldn't surprise
+ // me
+ Console.warn(
+ "UniprotFTSPanel: prevCursor exists but offset < pageLimit. This probably shouldn't be happening.");
+ }
+ c.setPrevCursorPage();
+ searchAction(prevCursor, false);
+ }
+ else
+ {
+ refreshPaginatorState();
+ }
+ }
+
+ @Override
+ public void nextPageAction()
+ {
+ UniProtFTSRestClient c = UniProtFTSRestClient.getInstance();
+ String nextCursor = c.getNextCursor();
+ if (nextCursor != null)
+ {
+ offSet += pageLimit;
+ c.setNextCursorPage();
+ searchAction(nextCursor, false);
+ }
+ else
+ {
+ refreshPaginatorState();
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff