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;
.getProgressIndicator();
}
-
/**
* Action performed when an input is detected on txt_search field.
*/
@Override
public void txt_search_ActionPerformed()
{
- boolean allowEmptySequence = false;
- mainFrame.setTitle(MessageManager
- .getString("label.pdb_sequence_getcher"));
- tbl_summary.setModel(new DefaultTableModel());
- if (txt_search.getText().trim().length() > 0)
+ new Thread()
{
- long startTime = System.currentTimeMillis();
+ 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();
+ String searchTarget = ((PDBDocField) cmb_searchTarget
+ .getSelectedItem()).getCode();
- wantedFields = PDBDocFieldPreferences
- .getSearchSummaryFields();
+ wantedFields = PDBDocFieldPreferences.getSearchSummaryFields();
- String searchTerm = txt_search.getText();
- if (searchTerm.contains(":"))
- {
- searchTerm = searchTerm.split(":")[0];
- }
+ 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);
+ 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;
+ }
- PDBRestClient pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(request);
- if (resultList.getSearchSummary() != null)
- {
- tbl_summary.setModel(PDBRestResponse.getTableModel(request,
- resultList.getSearchSummary()));
+ if (resultList.getSearchSummary() != null)
+ {
+ tbl_summary.setModel(PDBRestResponse.getTableModel(request,
+ 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)");
+ lbl_loading.setVisible(false);
+ }
}
+ }.start();
+ }
- 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)");
+ 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
mainFrame.dispose();
}
+ 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();
+ // 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();
- if (searchTerm.contains(":"))
- {
- selectedIds.append(";").append(pdbIdStr).append(":")
- .append(searchTerm.split(":")[1].toUpperCase());
- }
- else
- {
- selectedIds.append(";").append(pdbIdStr);
- }
+ selectedIdsSet.add(getPDBIdwithSpecifiedChain(pdbIdStr, searchTerm));
}
- String ids = selectedIds.deleteCharAt(0).toString();
+ 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()
+ {
+ 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;
}
/**
}
}
+ 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