+++ /dev/null
-/*
- * 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.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.HashSet;
-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()
- {
- new Thread()
- {
- @Override
- public void run()
- {
- lbl_loading.setVisible(false);
- errorWarning.setLength(0);
- lbl_warning.setVisible(false);
- btn_ok.setEnabled(false);
- boolean allowEmptySequence = false;
- mainFrame.setTitle(MessageManager
- .getString("label.pdb_sequence_getcher"));
- tbl_summary.setModel(new DefaultTableModel());
- if (txt_search.getText().trim().length() > 0)
- {
- lbl_loading.setVisible(true);
- long startTime = System.currentTimeMillis();
-
- String searchTarget = ((PDBDocField) cmb_searchTarget
- .getSelectedItem()).getCode();
-
- wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
-
- String searchTerm = decodeSearchTerm(txt_search.getText(),
- searchTarget);
-
- PDBRestRequest request = new PDBRestRequest();
- request.setAllowEmptySeq(allowEmptySequence);
- request.setResponseSize(100);
- request.setFieldToSearchBy("(" + searchTarget + ":");
- request.setSearchTerm(searchTerm + ")");
- request.setWantedFields(wantedFields);
- // System.out.println(">>>>>>>>>>>>>> " + request.getQuery());
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(request);
- } catch (Exception e)
- {
- // e.printStackTrace();
- errorWarning.append(e.getMessage());
- checkForErrors();
- return;
- }
-
- if (resultList.getSearchSummary() != null)
- {
- tbl_summary.setModel(PDBRestResponse.getTableModel(request,
- resultList.getSearchSummary()));
- }
-
- PDBRestResponse.configureTableColumn(tbl_summary, wantedFields);
-
- 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)");
- lbl_loading.setVisible(false);
- }
- }
- }.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 btn_ok_ActionPerformed()
- {
- loadSelectedPDBSequencesToAlignment();
- }
-
- @Override
- public void btn_back_ActionPerformed()
- {
- mainFrame.dispose();
- new SequenceFetcher(progressIdicator);
- }
-
- @Override
- public void btn_cancel_ActionPerformed()
- {
- mainFrame.dispose();
- }
-
- @Override
- public void transferToSequenceFetcher(String ids)
- {
- // mainFrame.dispose();
- seqFetcher.textArea.setText(ids);
- Thread worker = new Thread(seqFetcher);
- worker.start();
- }
-
- /**
- * Add the discovered/selected sequences to a target alignment window
- */
- public void loadSelectedPDBSequencesToAlignment()
- {
- // mainFrame.dispose();
- disableActionButtons();
- StringBuilder selectedIds = new StringBuilder();
- HashSet<String> selectedIdsSet = new HashSet<String>();
- int pdbIdCol = PDBRestClient.getPDBIdColumIndex(wantedFields, false);
- int[] selectedRows = tbl_summary.getSelectedRows();
- for (int summaryRow : selectedRows)
- {
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
- .toString();
- String searchTerm = txt_search.getText();
- selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
- }
-
- for (String selectedId : selectedIdsSet)
- {
- selectedIds.append(selectedId).append(";");
- }
-
- String ids = selectedIds.toString();
- // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
- seqFetcher.textArea.setText(ids);
- Thread worker = new Thread(seqFetcher);
- worker.start();
- delayAndEnableActionButtons();
-
- }
-
- private void disableActionButtons()
- {
- btn_ok.setEnabled(false);
- btn_back.setEnabled(false);
- btn_cancel.setEnabled(false);
- }
-
- private void delayAndEnableActionButtons()
- {
- new Thread()
- {
- @Override
- public void run()
- {
- try
- {
- Thread.sleep(1500);
- } catch (InterruptedException e)
- {
- e.printStackTrace();
- }
- btn_ok.setEnabled(true);
- btn_back.setEnabled(true);
- btn_cancel.setEnabled(true);
- }
- }.start();
- }
-
- 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;
- }
-
- /**
- * Populates search target combo-box options
- */
- @Override
- 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);
- }
- }
-
- public void checkForErrors()
- {
- lbl_warning.setVisible(false);
- if (errorWarning.length() > 0)
- {
- lbl_loading.setVisible(false);
- lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
- errorWarning.toString()));
- lbl_warning.setVisible(true);
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff