protected JLabel lbl_blank = new JLabel(balnkPlaceholderImage);
- private JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
+ JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
private JPanel pnl_actions = new JPanel();
{
tabs.addTab(MessageManager.getString("label.retrieve_ids"),
fetcher);
- fetcher.setDatabaseChooserVisible(false);
- fetcher.embedWithFTSPanel(this);
+ fetcher.embedIn(this);
}
mainFrame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
final JPanel ftsPanel = this;
}
}
+ /**
+ * Action on Back button is to close this panel and open a new Sequence
+ * Fetcher panel
+ */
public void btn_back_ActionPerformed()
{
closeAction();
public void transferToSequenceFetcher(String ids)
{
- seqFetcher.getTextArea().setText(ids);
+ seqFetcher.setQuery(ids);
Thread worker = new Thread(seqFetcher);
worker.start();
}
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
- + " "
- + totalNumberformatter.format((Number) (offSet + 1))
- + " to "
- + totalNumberformatter
- .format((Number) (offSet + resultSetCount))
- + " of "
- + totalNumberformatter
- .format((Number) totalResultSetCount)
- + " " + " (" + (endTime - startTime) + " milli secs)");
+ + " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
+ + (endTime - startTime) + " milli secs)");
}
else
{
}
String ids = selectedIds.toString();
- // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
- seqFetcher.getTextArea().setText(ids);
+ seqFetcher.setQuery(ids);
Thread worker = new Thread(seqFetcher);
worker.start();
delayAndEnableActionButtons();
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
-//import jalview.javascript.web.Client;
-//import jalview.javascript.web.ClientResponse;
-//import jalview.javascript.web.WebResource;
-
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
-
-import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
/**
* A rest client for querying the Search endpoint of the PDB API
*
- * BH 2018: just a tiny tweak here - for SwingJS, we coerce the classes to be
- * from jalview.javascript.web instead of com.sun.jersey.api.client
- *
- *
* @author tcnofoegbu
- *
*/
public class PDBFTSRestClient extends FTSRestClient
{
{
try
{
- Client client;
- WebResource webResource;
-
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
pdbRestRequest.getWantedFields());
int responseSize = (pdbRestRequest.getResponseSize() == 0)
// BH 2018 the trick here is to coerce the classes in Javascript to be
// different from the ones in Java yet still allow this to be correct for Java
+ Client client;
Class<ClientResponse> clientResponseClass;
if (/** @j2sNative true || */
false)
clientResponseClass = ClientResponse.class;
}
+ WebResource webResource;
if (pdbRestRequest.isFacet())
{
webResource = client.resource(PDB_SEARCH_ENDPOINT)
package jalview.fts.service.uniprot;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
-import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
public class UniProtFTSRestClient extends FTSRestClient
{
try
{
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
uniportRestRequest.getWantedFields());
int responseSize = (uniportRestRequest.getResponseSize() == 0)
+ uniportRestRequest.getSearchTerm();
}
+ // BH 2018 the trick here is to coerce the classes in Javascript to be
+ // different from the ones in Java yet still allow this to be correct for
+ // Java
+ Client client;
+ Class<ClientResponse> clientResponseClass;
+ if (/** @j2sNative true || */
+ false)
+ {
+ // JavaScript only -- coerce types to Java types for Java
+ client = (Client) (Object) new jalview.javascript.web.Client();
+ clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+ }
+ else
+ {
+ // Java only
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
+ }
+
WebResource webResource = null;
webResource = client.resource(uniprotSearchEndpoint)
.queryParam("format", "tab")
.queryParam("sort", "score").queryParam("query", query);
// Execute the REST request
ClientResponse clientResponse = webResource
- .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
+ .accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
String uniProtTabDelimittedResponseString = clientResponse
.getEntity(String.class);
// Make redundant objects eligible for garbage collection to conserve
throw new Exception(errorMessage);
}
- int xTotalResults = Integer.valueOf(
- clientResponse.getHeaders().get("X-Total-Results").get(0));
+ int xTotalResults = Jalview.isJS() ? 1
+ : Integer.valueOf(clientResponse.getHeaders()
+ .get("X-Total-Results").get(0));
clientResponse = null;
client = null;
return parseUniprotResponse(uniProtTabDelimittedResponseString,
private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
+ /**
+ * Constructor given an (optional) sequence fetcher panel to revert to on
+ * clicking the 'Back' button
+ *
+ * @param fetcher
+ */
public UniprotFTSPanel(SequenceFetcher fetcher)
{
super(fetcher);
{
updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
+ " "
- + totalNumberformatter.format((Number) (offSet + 1))
+ + totalNumberformatter
+ .format(Integer.valueOf(offSet + 1))
+ " to "
+ totalNumberformatter
- .format((Number) (offSet + resultSetCount))
+ .format(Integer
+ .valueOf(offSet + resultSetCount))
+ " of "
+ totalNumberformatter
- .format((Number) totalResultSetCount)
+ .format(Integer.valueOf(totalResultSetCount))
+ " " + " (" + (endTime - startTime) + " milli secs)");
}
else
}
String ids = selectedIds.toString();
- // System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
- seqFetcher.getTextArea().setText(ids);
+ seqFetcher.setQuery(ids);
Thread worker = new Thread(seqFetcher);
worker.start();
delayAndEnableActionButtons();
}
@Override
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
@Override
});
rfetch.add(fetchr);
- final AlignFrame me = this;
new Thread(new Runnable()
{
@Override
public void run()
{
final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(me);
+ .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
+ String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
{
continue;
}
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // for (DbSourceProxy db:dbs)
- // {
- // if (!db.isA(DBRefSource.ALIGNMENTDB)
- // }
if (mname == null)
{
mname = "From " + dbclass;
import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import javax.swing.JButton;
import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.SwingConstants;
-import javax.swing.tree.DefaultMutableTreeNode;
+/**
+ * A panel where the use may choose a database source, and enter one or more
+ * accessions, to retrieve entries from the database.
+ * <p>
+ * If the selected source is Uniprot or PDB, a free text search panel is opened
+ * instead to perform the search and selection.
+ */
public class SequenceFetcher extends JPanel implements Runnable
{
- JLabel dbeg = new JLabel();
-
- JDatabaseTree database;
-
- JButton databaseButt;
-
- JLabel jLabel1 = new JLabel();
-
- JCheckBox replacePunctuation = new JCheckBox();
-
- JButton ok = new JButton();
-
- JButton clear = new JButton();
-
- JButton example = new JButton();
-
- JButton close = new JButton();
-
- JButton back = new JButton();
-
- JPanel jPanel1 = new JPanel();
+ private static jalview.ws.SequenceFetcher sfetch = null;
- JTextArea textArea = new JTextArea();
+ JLabel exampleAccession;
- JScrollPane jScrollPane1 = new JScrollPane();
+ JComboBox<String> database;
- JPanel jPanel2 = new JPanel();
+ JCheckBox replacePunctuation;
- JPanel jPanel3 = new JPanel();
+ JButton okBtn;
- JPanel jPanel4 = new JPanel();
+ JButton exampleBtn;
- BorderLayout borderLayout1 = new BorderLayout();
+ JButton closeBtn;
- BorderLayout borderLayout2 = new BorderLayout();
+ JButton backBtn;
- BorderLayout borderLayout3 = new BorderLayout();
+ JTextArea textArea;
JInternalFrame frame;
AlignFrame alignFrame;
- StringBuffer result;
+ GFTSPanel parentSearchPanel;
- final String noDbSelected = "-- Select Database --";
+ IProgressIndicator progressIndicator;
- private static jalview.ws.SequenceFetcher sfetch = null;
-
- private static boolean _initingFetcher = false;
-
- private static Thread initingThread = null;
-
- public JTextArea getTextArea()
- {
- return textArea;
- }
+ volatile boolean _isConstructing = false;
/**
- * Blocking method that initialises and returns the shared instance of the
- * SequenceFetcher client
+ * Returns the shared instance of the SequenceFetcher client
*
- * @param guiWindow
- * - where the initialisation delay message should be shown
- * @return the singleton instance of the sequence fetcher client
+ * @return
*/
- public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
- final IProgressIndicator guiWindow)
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
{
- if (_initingFetcher && initingThread != null && initingThread.isAlive())
- {
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- MessageManager.getString(
- "status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
- }
- // initting happening on another thread - so wait around to see if it
- // finishes.
- while (_initingFetcher && initingThread != null
- && initingThread.isAlive())
- {
- try
- {
- Thread.sleep(10);
- } catch (Exception e)
- {
- }
- ;
- }
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- MessageManager.getString(
- "status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
- }
- }
if (sfetch == null)
{
- _initingFetcher = true;
- initingThread = Thread.currentThread();
- /**
- * give a visual indication that sequence fetcher construction is occuring
- */
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- MessageManager.getString(
- "status.init_sequence_database_fetchers"),
- Thread.currentThread().hashCode());
- }
-
- jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- }
- sfetch = sf;
- _initingFetcher = false;
- initingThread = null;
+ sfetch = new jalview.ws.SequenceFetcher();
}
return sfetch;
}
- private IProgressIndicator progressIndicator;
-
- private volatile boolean _isConstructing = false;
-
- private List<AlignFrame> newAlframes = null;
-
- public SequenceFetcher(IProgressIndicator guiIndic)
- {
- this(guiIndic, null, null);
- }
-
- public SequenceFetcher(IProgressIndicator guiIndic,
- final String selectedDb, final String queryString)
- {
- this._isConstructing = true;
- this.progressIndicator = guiIndic;
- final SequenceFetcher us = this;
- // launch initialiser thread
- Thread sf = new Thread(new Runnable()
- {
-
- @Override
- public void run()
- {
- if (getSequenceFetcherSingleton(progressIndicator) != null)
- {
- us.initGui(progressIndicator, selectedDb, queryString);
- us._isConstructing = false;
- }
- else
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "warn.couldnt_create_sequence_fetcher_client"),
- MessageManager.getString(
- "label.couldnt_create_sequence_fetcher"),
- JvOptionPane.ERROR_MESSAGE);
- }
- });
-
- // raise warning dialog
- }
- }
- });
- sf.start();
- }
-
/**
- * blocking call which creates a new sequence fetcher panel, configures it and
- * presses the OK button with the given database and query.
+ * Constructor given a client to receive any status or progress messages
+ * (currently either the Desktop, or an AlignFrame panel)
*
- * @param database
- * @param query
+ * @param guiIndic
*/
- public static List<AlignFrame> fetchAndShow(String database, String query)
+ public SequenceFetcher(IProgressIndicator guiIndic)
{
- final SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
- database, query);
- while (sf._isConstructing)
- {
- try
- {
- Thread.sleep(50);
- } catch (Exception q)
- {
- return Collections.emptyList();
- }
- }
- sf.newAlframes = new ArrayList<>();
- sf.run();
- return sf.newAlframes;
+ this(guiIndic, null, null);
}
- private class DatabaseAuthority extends DefaultMutableTreeNode
- {
-
- };
-
- private class DatabaseSource extends DefaultMutableTreeNode
- {
-
- };
-
/**
- * initialise the database and query for this fetcher panel
+ * Constructor with specified database and accession(s) to retrieve
*
+ * @param guiIndic
* @param selectedDb
- * - string that should correspond to a sequence fetcher
* @param queryString
- * - string that will be entered in the query dialog
- * @return true if UI was configured with valid database and query string
*/
- protected boolean setInitialQuery(String selectedDb, String queryString)
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
{
- if (selectedDb == null || selectedDb.trim().length() == 0)
- {
- return false;
- }
- try
- {
- List<DbSourceProxy> sp = sfetch.getSourceProxy(selectedDb);
- for (DbSourceProxy sourcep : sp)
- {
- if (sourcep.getTier() == 0)
- {
- database.selection = Arrays
- .asList(new DbSourceProxy[]
- { sourcep });
- break;
- }
- }
- if (database.selection == null || database.selection.size() == 0)
- {
- System.err.println(
- "Ignoring fetch parameter db='" + selectedDb + "'");
- return false;
- }
- textArea.setText(queryString);
- } catch (Exception q)
- {
- System.err.println("Ignoring fetch parameter db='" + selectedDb
- + "' and query='" + queryString + "'");
- return false;
- }
- return true;
- }
+ this.progressIndicator = guiIndic;
+ getSequenceFetcherSingleton();
+ this.guiWindow = progressIndicator;
- /**
- * called by thread spawned by constructor
- *
- * @param guiWindow
- * @param queryString
- * @param selectedDb
- */
- private void initGui(IProgressIndicator guiWindow, String selectedDb,
- String queryString)
- {
- this.guiWindow = guiWindow;
- if (guiWindow instanceof AlignFrame)
- {
- alignFrame = (AlignFrame) guiWindow;
- }
- database = new JDatabaseTree(sfetch);
- try
+ if (progressIndicator instanceof AlignFrame)
{
- jbInit();
- /*
- * configure the UI with any query parameters we were called with
- */
- if (!setInitialQuery(selectedDb, queryString))
- {
- /*
- * none provided, so show the database chooser
- */
- database.waitForInput();
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
+ alignFrame = (AlignFrame) progressIndicator;
}
+ jbInit(selectedDb);
+ textArea.setText(queryString);
+
frame = new JInternalFrame();
frame.setContentPane(this);
- if (Platform.isAMac())
- {
- Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 240);
- }
- else
- {
- Desktop.addInternalFrame(frame, getFrameTitle(), false, 400, 180);
- }
+ int height = Platform.isAMac() ? 240 : 180;
+ Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, height);
}
private String getFrameTitle()
.getString("label.additional_sequence_fetcher"));
}
- GFTSPanel parentFTSframe = null;
- /**
- * change the buttons so they fit with the FTS panel.
- */
- public void embedWithFTSPanel(GFTSPanel toClose)
+ private void jbInit(String selectedDb)
{
- back.setVisible(true);
- parentFTSframe = toClose;
- }
- private void jbInit() throws Exception
- {
- this.setLayout(borderLayout2);
+ this.setLayout(new BorderLayout());
+ database = new JComboBox<>();
database.setFont(JvSwingUtils.getLabelFont());
- dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
- jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText(MessageManager
+ database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
+ String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
+ Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
+ database.addItem(MessageManager.getString("action.select_ddbb"));
+ for (String source : sources)
+ {
+ database.addItem(source);
+ }
+ database.setSelectedItem(selectedDb);
+ if (database.getSelectedIndex() == -1)
+ {
+ database.setSelectedIndex(0);
+ }
+ database.setMaximumRowCount(database.getItemCount());
+ database.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ String currentSelection = (String) database.getSelectedItem();
+ updateExampleQuery(currentSelection);
+
+ if ("pdb".equalsIgnoreCase(currentSelection))
+ {
+ new PDBFTSPanel(SequenceFetcher.this);
+ frame.dispose();
+ }
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ new UniprotFTSPanel(SequenceFetcher.this);
+ frame.dispose();
+ }
+ else
+ {
+ otherSourceAction();
+ }
+ }
+ });
+
+ exampleAccession = new JLabel("");
+ exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
+ JLabel jLabel1 = new JLabel(MessageManager
.getString("label.separate_multiple_accession_ids"));
+ jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
- replacePunctuation
- .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText(
+ replacePunctuation = new JCheckBox(
MessageManager.getString("label.replace_commas_semicolons"));
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
+ replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+ replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
+ okBtn = new JButton(MessageManager.getString("action.ok"));
+ okBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
ok_actionPerformed();
}
});
- clear.setText(MessageManager.getString("action.clear"));
+ JButton clear = new JButton(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
@Override
}
});
- example.setText(MessageManager.getString("label.example"));
- example.addActionListener(new ActionListener()
+ exampleBtn = new JButton(MessageManager.getString("label.example"));
+ exampleBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
example_actionPerformed();
}
});
- close.setText(MessageManager.getString("action.cancel"));
- close.addActionListener(new ActionListener()
+ closeBtn = new JButton(MessageManager.getString("action.cancel"));
+ closeBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
close_actionPerformed(e);
}
});
- back.setText(MessageManager.getString("action.back"));
- back.addActionListener(new ActionListener()
+ backBtn = new JButton(MessageManager.getString("action.back"));
+ backBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- parentFTSframe.btn_back_ActionPerformed();
+ parentSearchPanel.btn_back_ActionPerformed();
}
});
// back not visible unless embedded
- back.setVisible(false);
+ backBtn.setVisible(false);
+
+ textArea = new JTextArea();
textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
}
}
});
- jPanel3.setLayout(borderLayout1);
- borderLayout1.setVgap(5);
- jPanel1.add(back);
- jPanel1.add(example);
- jPanel1.add(clear);
- jPanel1.add(ok);
- jPanel1.add(close);
- jPanel2.setLayout(borderLayout3);
- databaseButt = /*database.getDatabaseSelectorButton();
- final JButton viewdbs =*/new JButton(
- MessageManager.getString("action.select_ddbb"));
- databaseButt.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- hidePanel();
- database.showDialog();
- }
- });
- databaseButt.setFont(JvSwingUtils.getLabelFont());
- database.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- String currentSelection = database.getSelectedItem();
- if (currentSelection == null)
- {
- close_actionPerformed(null);
- }
-
- showPanel();
-
- if ("pdb".equalsIgnoreCase(currentSelection))
- {
- pdbSourceAction();
- }
- else if ("uniprot".equalsIgnoreCase(currentSelection))
- {
- uniprotSourceAction();
- }
- else
- {
- otherSourceAction();
- }
- database.action = -1;
- }
- });
-
- dbeg.setText("");
- jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
- jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+ JPanel actionPanel = new JPanel();
+ actionPanel.add(backBtn);
+ actionPanel.add(exampleBtn);
+ actionPanel.add(clear);
+ actionPanel.add(okBtn);
+ actionPanel.add(closeBtn);
+
+ JPanel databasePanel = new JPanel();
+ databasePanel.setLayout(new BorderLayout());
+ databasePanel.add(database, BorderLayout.NORTH);
+ databasePanel.add(exampleAccession, BorderLayout.CENTER);
JPanel jPanel2a = new JPanel(new BorderLayout());
- jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
- jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
- jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
- // jPanel2.setPreferredSize(new Dimension())
- jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(jLabel1, BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
+ databasePanel.add(jPanel2a, BorderLayout.SOUTH);
+
+ JPanel idsPanel = new JPanel();
+ idsPanel.setLayout(new BorderLayout(0, 5));
+ JScrollPane jScrollPane1 = new JScrollPane();
jScrollPane1.getViewport().add(textArea);
- }
+ idsPanel.add(jScrollPane1, BorderLayout.CENTER);
- private void pdbSourceAction()
- {
- databaseButt.setText(database.getSelectedItem());
- new PDBFTSPanel(this);
- frame.dispose();
+ this.add(actionPanel, BorderLayout.SOUTH);
+ this.add(idsPanel, BorderLayout.CENTER);
+ this.add(databasePanel, BorderLayout.NORTH);
}
- private void uniprotSourceAction()
+ /**
+ * Answers a semi-colon-delimited string with the example query or queries for
+ * the selected database
+ *
+ * @param db
+ * @return
+ */
+ protected String getExampleQueries(String db)
{
- databaseButt.setText(database.getSelectedItem());
- new UniprotFTSPanel(this);
- frame.dispose();
+ StringBuilder sb = new StringBuilder();
+ HashSet<String> hs = new HashSet<>();
+ for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
+ {
+ String tq = dbs.getTestQuery();
+ if (hs.add(tq)) // not a duplicate source
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(";");
+ }
+ sb.append(tq);
+ }
+ }
+ return sb.toString();
}
- private void otherSourceAction()
+ /**
+ * Action on selected a database other than Uniprot or PDB is to enable or
+ * disable 'Replace commas', and await input in the query field
+ */
+ protected void otherSourceAction()
{
try
{
- databaseButt.setText(database.getSelectedItem()
- + (database.getSelectedSources().size() > 1 ? " (and "
- + database.getSelectedSources().size() + " others)"
- : ""));
- String eq = database.getExampleQueries();
- dbeg.setText(MessageManager.formatMessage("label.example_query_param",
- new String[]
- { eq }));
- // TODO this should be a property of the SequenceFetcher whether commas are and
+ String eq = exampleAccession.getText();
+ // TODO this should be a property of the SequenceFetcher whether commas
+ // are and
// colons are allowed in the IDs...
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
} catch (Exception ex)
{
- dbeg.setText("");
+ exampleAccession.setText("");
replacePunctuation.setEnabled(true);
}
- jPanel2.repaint();
+ repaint();
+ }
+
+ /**
+ * Sets the text of the example query to incorporate the example accession
+ * provided by the selected database source
+ *
+ * @param selectedDatabase
+ * @return
+ */
+ protected String updateExampleQuery(String selectedDatabase)
+ {
+ String eq = getExampleQueries(selectedDatabase);
+ exampleAccession.setText(MessageManager
+ .formatMessage("label.example_query_param", new String[]
+ { eq }));
+ return eq;
}
+ /**
+ * Action on clicking the 'Example' button is to write the example accession
+ * as the query text field value
+ */
protected void example_actionPerformed()
{
- DbSourceProxy db = null;
- try
- {
- textArea.setText(database.getExampleQueries());
- } catch (Exception ex)
- {
- }
- jPanel3.repaint();
+ String eq = getExampleQueries((String) database.getSelectedItem());
+ textArea.setText(eq);
+ repaint();
}
+ /**
+ * Clears the query input field
+ */
protected void clear_actionPerformed()
{
textArea.setText("");
- jPanel3.repaint();
+ repaint();
}
- public void close_actionPerformed(ActionEvent e)
+ /**
+ * Action on Close button is to close this frame, and also (if it is embedded
+ * in a search panel) to close the search panel
+ *
+ * @param e
+ */
+ protected void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
- if (parentFTSframe!=null)
+ if (parentSearchPanel != null)
{
- parentFTSframe.btn_cancel_ActionPerformed();
+ parentSearchPanel.btn_cancel_ActionPerformed();
}
} catch (Exception ex)
{
}
}
+ /**
+ * Action on OK is to start the fetch for entered accession(s)
+ */
public void ok_actionPerformed()
{
- databaseButt.setEnabled(false);
- example.setEnabled(false);
+ /*
+ * tidy inputs and check there is something to search for
+ */
+ String text = textArea.getText();
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ text = text.replace(",", ";");
+ }
+ text = text.replaceAll("(\\s|[,; ])+", ";");
+ textArea.setText(text);
+ if (text.isEmpty())
+ {
+ // todo i18n
+ showErrorMessage(
+ "Please enter a (semi-colon separated list of) database id(s)");
+ resetDialog();
+ return;
+ }
+ exampleBtn.setEnabled(false);
textArea.setEnabled(false);
- ok.setEnabled(false);
- close.setEnabled(false);
- back.setEnabled(false);
+ okBtn.setEnabled(false);
+ closeBtn.setEnabled(false);
+ backBtn.setEnabled(false);
+
Thread worker = new Thread(this);
worker.start();
}
private void resetDialog()
{
- databaseButt.setEnabled(true);
- example.setEnabled(true);
+ exampleBtn.setEnabled(true);
textArea.setEnabled(true);
- ok.setEnabled(true);
- close.setEnabled(true);
- back.setEnabled(parentFTSframe != null);
+ okBtn.setEnabled(true);
+ closeBtn.setEnabled(true);
+ backBtn.setEnabled(parentSearchPanel != null);
}
@Override
public void run()
{
- String error = "";
- if (!database.hasSelection())
- {
- error += "Please select the source database\n";
- }
- // TODO: make this transformation more configurable
- com.stevesoft.pat.Regex empty;
- if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
- {
- empty = new com.stevesoft.pat.Regex(
- // replace commas and spaces with a semicolon
- "(\\s|[,; ])+", ";");
- }
- else
- {
- // just turn spaces and semicolons into single semicolons
- empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
- }
- textArea.setText(empty.replaceAll(textArea.getText()));
- // see if there's anthing to search with
- if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]")
- .search(textArea.getText()))
- {
- error += "Please enter a (semi-colon separated list of) database id(s)";
- }
- if (error.length() > 0)
- {
- showErrorMessage(error);
- resetDialog();
- return;
- }
- // TODO: Refactor to GUI independent code and write tests.
- // indicate if successive sources should be merged into one alignment.
boolean addToLast = false;
List<String> aresultq = new ArrayList<>();
List<String> presultTitle = new ArrayList<>();
List<AlignmentI> presult = new ArrayList<>();
List<AlignmentI> aresult = new ArrayList<>();
- Iterator<DbSourceProxy> proxies = database.getSelectedSources()
- .iterator();
+ List<DbSourceProxy> sources = sfetch
+ .getSourceProxy((String) database.getSelectedItem());
+ Iterator<DbSourceProxy> proxies = sources.iterator();
String[] qries;
List<String> nextFetch = Arrays
.asList(qries = textArea.getText().split(";"));
AlignFrame.DEFAULT_HEIGHT);
if (currentFileFormat != null)
{
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
- // FORMAT FOR
- // NON-FormatAdapter Sourced
- // Alignments?
+ af.currentFileFormat = currentFileFormat;
}
List<SequenceI> alsqs = al.getSequences();
{
af.hideFeatureColumns(SequenceOntologyI.EXON, false);
}
- if (newAlframes != null)
- {
- newAlframes.add(af);
- }
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
}
/**
- * Make this panel visible (after a selection has been made in the database
- * chooser)
- */
- void showPanel()
- {
- frame.setVisible(true);
- }
-
- /**
* Hide this panel (on clicking the database button to open the database
* chooser)
*/
frame.setVisible(false);
}
- public void setDatabaseChooserVisible(boolean b)
+ public void setQuery(String ids)
+ {
+ textArea.setText(ids);
+ }
+
+ /**
+ * Called to modify the search panel for embedding as an alternative tab of a
+ * free text search panel. The database choice list is hidden (since the
+ * choice has been made), and a Back button is made visible (which reopens the
+ * Sequence Fetcher panel).
+ *
+ * @param parentPanel
+ */
+ public void embedIn(GFTSPanel parentPanel)
{
- databaseButt.setVisible(b);
+ database.setVisible(false);
+ backBtn.setVisible(true);
+ parentSearchPanel = parentPanel;
}
}
featureSettings_actionPerformed(e);
}
});
+
+ /*
+ * add sub-menu of database we can fetch from
+ */
JMenuItem fetchSequence = new JMenuItem(
MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
@Override
public void actionPerformed(ActionEvent e)
{
- fetchSequence_actionPerformed(e);
+ fetchSequence_actionPerformed();
}
});
}
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
}
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
- sfetcher = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(progressIndicatorFrame);
+ sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
// set default behaviour for transferring excess sequence data to the
// dataset
trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
import jalview.ws.seqfetcher.DbSourceProxy;
import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
/**
* This implements the run-time discovery of sequence database clients.
/**
* return an ordered list of database sources excluding alignment only databases
*/
- public String[] getOrderedSupportedSources()
+ public String[] getNonAlignmentSources()
{
String[] srcs = this.getSupportedDb();
- ArrayList<String> src = new ArrayList<>();
+ List<String> src = new ArrayList<>();
for (int i = 0; i < srcs.length; i++)
{
- boolean skip = false;
+ boolean accept = true;
for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
{
// Skip the alignment databases for the moment - they're not useful for
// verifying a single sequence against its reference source
if (dbs.isAlignmentSource())
{
- skip = true;
+ accept = false;
+ break;
}
}
- if (skip)
- {
- continue;
- }
+ if (accept)
{
src.add(srcs[i]);
}
}
- String[] tosort = src.toArray(new String[0]),
- sorted = src.toArray(new String[0]);
- for (int j = 0, jSize = sorted.length; j < jSize; j++)
- {
- tosort[j] = tosort[j].toLowerCase();
- }
- jalview.util.QuickSort.sort(tosort, sorted);
- // construct array with all sources listed
- int i = 0;
- for (int j = sorted.length - 1; j >= 0; j--, i++)
- {
- srcs[i] = sorted[j];
- }
- return srcs;
+ Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+ return src.toArray(new String[src.size()]);
}
}
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
import jalview.util.DBRefUtils;
import java.io.File;
import java.util.List;
import java.util.Map;
-import junit.extensions.PA;
-
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import junit.extensions.PA;
+
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
List<String> failedXrefMenuItems = new ArrayList<>();
List<String> failedProjectRecoveries = new ArrayList<>();
// only search for ensembl or Uniprot crossrefs
- List<String> limit=Arrays.asList(new String[] {
- DBRefUtils.getCanonicalName("ENSEMBL"),
- DBRefUtils.getCanonicalName("Uniprot")});
+ List<String> limit = Arrays
+ .asList(new String[]
+ { DBRefUtils.getCanonicalName("ENSEMBL"),
+ DBRefUtils.getCanonicalName("Uniprot") });
// for every set of db queries
// retrieve db query
// verify presence of expected xrefs
List<String> keyseq = new ArrayList<>();
Map<String, File> savedProjects = new HashMap<>();
-// for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
-// {
- // pass counters - 0 - first pass, 1 means retrieve project rather than
- // perform action
- int pass1 = 0, pass2 = 0, pass3 = 0;
- // each do loop performs two iterations in the first outer loop pass, but
- // only performs one iteration on the second outer loop
- // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
- // { pass 2 = 0 { pass 3 = 0 } }
- do
+ // for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+ // {
+ // pass counters - 0 - first pass, 1 means retrieve project rather than
+ // perform action
+ int pass1 = 0, pass2 = 0, pass3 = 0;
+ // each do loop performs two iterations in the first outer loop pass, but
+ // only performs one iteration on the second outer loop
+ // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
+ // { pass 2 = 0 { pass 3 = 0 } }
+ do
+ {
+ String first = forSource + " " + forAccession;// did[0] + " " + did[1];
+ AlignFrame af = null;
+ boolean dna;
+ AlignmentI retral;
+ AlignmentI dataset;
+ SequenceI[] seqs;
+ List<String> ptypes = null;
+ if (pass1 == 0)
{
- String first = forSource + " " + forAccession;//did[0] + " " + did[1];
- AlignFrame af = null;
- boolean dna;
- AlignmentI retral;
- AlignmentI dataset;
- SequenceI[] seqs;
- List<String> ptypes = null;
- if (pass1 == 0)
- {
- // retrieve dbref
+ // retrieve dbref
- List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
+ SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
forSource, forAccession);
- // did[0], did[1]);
- if (afs.size() == 0)
- {
- failedDBRetr.add("Didn't retrieve " + first);
- break;
- }
- keyseq.add(first);
- af = afs.get(0);
-
- // verify references for retrieved data
- AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
- .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
- + pass3 + "): Fetch " + first + ":");
- assertDatasetIsNormalisedKnownDefect(af.getViewport()
- .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
- + pass3 + "): Fetch " + first + ":");
- dna = af.getViewport().getAlignment().isNucleotide();
- retral = af.getViewport().getAlignment();
- dataset = retral.getDataset();
- seqs = retral.getSequencesArray();
-
- }
- else
+ sf.run();
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ if (afs.length == 0)
{
- Desktop.instance.closeAll_actionPerformed(null);
- // recover stored project
- af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
- .get(first).toString(), DataSourceType.FILE);
- System.out.println("Recovered view for '" + first + "' from '"
- + savedProjects.get(first).toString() + "'");
- dna = af.getViewport().getAlignment().isNucleotide();
- retral = af.getViewport().getAlignment();
- dataset = retral.getDataset();
- seqs = retral.getSequencesArray();
-
- // verify references for recovered data
- AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
- .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
- + pass3 + "): Recover " + first + ":");
- assertDatasetIsNormalisedKnownDefect(af.getViewport()
- .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
- + pass3 + "): Recover " + first + ":");
-
+ failedDBRetr.add("Didn't retrieve " + first);
+ break;
}
+ keyseq.add(first);
+ af = afs[0];
+
+ // verify references for retrieved data
+ AlignmentTest.assertAlignmentDatasetRefs(
+ af.getViewport().getAlignment(), "Pass (" + pass1 + ","
+ + pass2 + "," + pass3 + "): Fetch " + first + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ af.getViewport().getAlignment(), "Pass (" + pass1 + ","
+ + pass2 + "," + pass3 + "): Fetch " + first + ":");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
- // store project on first pass, compare next pass
- stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
+ }
+ else
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ af = new FileLoader(false).LoadFileWaitTillLoaded(
+ savedProjects.get(first).toString(), DataSourceType.FILE);
+ System.out.println("Recovered view for '" + first + "' from '"
+ + savedProjects.get(first).toString() + "'");
+ dna = af.getViewport().getAlignment().isNucleotide();
+ retral = af.getViewport().getAlignment();
+ dataset = retral.getDataset();
+ seqs = retral.getSequencesArray();
+
+ // verify references for recovered data
+ AlignmentTest.assertAlignmentDatasetRefs(
+ af.getViewport().getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover "
+ + first + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ af.getViewport().getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover "
+ + first + ":");
- ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
- seqs, dataset).findXrefSourcesForSequences(dna);
- filterDbRefs(ptypes, limit);
-
- // start of pass2: retrieve each cross-ref for fetched or restored
- // project.
- do // first cross ref and recover crossref loop
- {
+ }
+
+ // store project on first pass, compare next pass
+ stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
+
+ ptypes = (seqs == null || seqs.length == 0) ? null
+ : new CrossRef(seqs, dataset)
+ .findXrefSourcesForSequences(dna);
+ filterDbRefs(ptypes, limit);
+
+ // start of pass2: retrieve each cross-ref for fetched or restored
+ // project.
+ do // first cross ref and recover crossref loop
+ {
- for (String db : ptypes)
+ for (String db : ptypes)
+ {
+ // counter for splitframe views retrieved via crossref
+ int firstcr_ap = 0;
+ // build next key so we an retrieve all views
+ String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
+ // perform crossref action, or retrieve stored project
+ List<AlignmentViewPanel> cra_views = new ArrayList<>();
+ CrossRefAction cra = null;
+
+ if (pass2 == 0)
+ { // retrieve and show cross-refs in this thread
+ cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
+ cra.run();
+ cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
+ "xrefViews");
+ if (cra_views.size() == 0)
+ {
+ failedXrefMenuItems.add(
+ "No crossrefs retrieved for " + first + " -> " + db);
+ continue;
+ }
+ assertNucleotide(cra_views.get(0),
+ "Nucleotide panel included proteins for " + first
+ + " -> " + db);
+ assertProtein(cra_views.get(1),
+ "Protein panel included nucleotides for " + first
+ + " -> " + db);
+ }
+ else
{
- // counter for splitframe views retrieved via crossref
- int firstcr_ap = 0;
- // build next key so we an retrieve all views
- String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
- // perform crossref action, or retrieve stored project
- List<AlignmentViewPanel> cra_views = new ArrayList<>();
- CrossRefAction cra = null;
-
- if (pass2 == 0)
- { // retrieve and show cross-refs in this thread
- cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
- cra.run();
- cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
- "xrefViews");
- if (cra_views.size() == 0)
- {
- failedXrefMenuItems.add("No crossrefs retrieved for "
- + first + " -> " + db);
- continue;
- }
- assertNucleotide(cra_views.get(0),
- "Nucleotide panel included proteins for " + first
- + " -> " + db);
- assertProtein(cra_views.get(1),
- "Protein panel included nucleotides for " + first
- + " -> " + db);
+ Desktop.instance.closeAll_actionPerformed(null);
+ pass3 = 0;
+ // recover stored project
+ File storedProject = savedProjects.get(nextxref);
+ if (storedProject == null)
+ {
+ failedProjectRecoveries
+ .add("Failed to store a view for '" + nextxref + "'");
+ continue;
}
- else
+
+ // recover stored project
+ AlignFrame af2 = new FileLoader(false).LoadFileWaitTillLoaded(
+ savedProjects.get(nextxref).toString(),
+ DataSourceType.FILE);
+ System.out
+ .println("Recovered view for '" + nextxref + "' from '"
+ + savedProjects.get(nextxref).toString() + "'");
+ // gymnastics to recover the alignPanel/Complementary alignPanel
+ if (af2.getViewport().isNucleotide())
{
- Desktop.instance.closeAll_actionPerformed(null);
- pass3 = 0;
- // recover stored project
- File storedProject = savedProjects.get(nextxref);
- if (storedProject == null)
- {
- failedProjectRecoveries.add("Failed to store a view for '"
- + nextxref + "'");
- continue;
- }
-
- // recover stored project
- AlignFrame af2 = new FileLoader(false)
- .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
- .toString(), DataSourceType.FILE);
- System.out.println("Recovered view for '" + nextxref
- + "' from '" + savedProjects.get(nextxref).toString()
- + "'");
- // gymnastics to recover the alignPanel/Complementary alignPanel
- if (af2.getViewport().isNucleotide())
- {
- // top view, then bottom
- cra_views.add(af2.getViewport().getAlignPanel());
- cra_views.add(((jalview.gui.AlignViewport) af2
- .getViewport().getCodingComplement())
- .getAlignPanel());
-
- }
- else
- {
- // bottom view, then top
- cra_views.add(((jalview.gui.AlignViewport) af2
- .getViewport().getCodingComplement())
- .getAlignPanel());
- cra_views.add(af2.getViewport().getAlignPanel());
+ // top view, then bottom
+ cra_views.add(af2.getViewport().getAlignPanel());
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
- }
}
- HashMap<String, List<String>> xrptypes = new HashMap<>();
- // first save/verify views.
- for (AlignmentViewPanel avp : cra_views)
+ else
{
- nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
- // verify references for this panel
- AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
- "Pass (" + pass1 + "," + pass2 + "," + pass3
- + "): before start of pass3: " + nextxref
- + ":");
- assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
- "Pass (" + pass1 + "," + pass2 + "," + pass3
- + "): before start of pass3: " + nextxref
- + ":");
-
- SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
-
- List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
- : new CrossRef(xrseqs, dataset)
- .findXrefSourcesForSequences(avp
- .getAlignViewport().isNucleotide());
-
- stringify(dbtoviewBit, savedProjects, nextxref, avp);
- xrptypes.put(nextxref, _xrptypes);
+ // bottom view, then top
+ cra_views.add(((jalview.gui.AlignViewport) af2.getViewport()
+ .getCodingComplement()).getAlignPanel());
+ cra_views.add(af2.getViewport().getAlignPanel());
}
+ }
+ HashMap<String, List<String>> xrptypes = new HashMap<>();
+ // first save/verify views.
+ for (AlignmentViewPanel avp : cra_views)
+ {
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+ assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
+ "Pass (" + pass1 + "," + pass2 + "," + pass3
+ + "): before start of pass3: " + nextxref
+ + ":");
+
+ SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
+
+ List<String> _xrptypes = (seqs == null || seqs.length == 0)
+ ? null
+ : new CrossRef(xrseqs, dataset)
+ .findXrefSourcesForSequences(
+ avp.getAlignViewport().isNucleotide());
+
+ stringify(dbtoviewBit, savedProjects, nextxref, avp);
+ xrptypes.put(nextxref, _xrptypes);
+
+ }
- // now do the second xref pass starting from either saved or just
- // recovered split pane, in sequence
- do // retrieve second set of cross refs or recover and verify
+ // now do the second xref pass starting from either saved or just
+ // recovered split pane, in sequence
+ do // retrieve second set of cross refs or recover and verify
+ {
+ firstcr_ap = 0;
+ for (AlignmentViewPanel avp : cra_views)
{
- firstcr_ap = 0;
- for (AlignmentViewPanel avp : cra_views)
+ nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
+ for (String xrefdb : xrptypes.get(nextxref))
{
- nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
- for (String xrefdb : xrptypes.get(nextxref))
- {
- List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
- int q = 0;
- String nextnextxref = nextxref + " -> " + xrefdb + "{"
- + q + "}";
+ List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
+ int q = 0;
+ String nextnextxref = nextxref + " -> " + xrefdb + "{" + q
+ + "}";
- if (pass3 == 0)
+ if (pass3 == 0)
+ {
+ SequenceI[] xrseqs = avp.getAlignment()
+ .getSequencesArray();
+ AlignFrame nextaf = Desktop
+ .getAlignFrameFor(avp.getAlignViewport());
+
+ cra = CrossRefAction.getHandlerFor(xrseqs,
+ avp.getAlignViewport().isNucleotide(), xrefdb,
+ nextaf);
+ cra.run();
+ cra_views2 = (List<AlignmentViewPanel>) PA.getValue(cra,
+ "xrefViews");
+ if (cra_views2.size() == 0)
{
- SequenceI[] xrseqs = avp.getAlignment()
- .getSequencesArray();
- AlignFrame nextaf = Desktop.getAlignFrameFor(avp
- .getAlignViewport());
-
- cra = CrossRefAction.getHandlerFor(xrseqs, avp
- .getAlignViewport().isNucleotide(), xrefdb,
- nextaf);
- cra.run();
- cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
- cra, "xrefViews");
- if (cra_views2.size() == 0)
- {
- failedXrefMenuItems
- .add("No crossrefs retrieved for '"
- + nextxref + "' to " + xrefdb
- + " via '" + nextaf.getTitle() + "'");
- continue;
- }
- assertNucleotide(cra_views2.get(0),
- "Nucleotide panel included proteins for '"
- + nextxref + "' to " + xrefdb
- + " via '" + nextaf.getTitle() + "'");
- assertProtein(cra_views2.get(1),
- "Protein panel included nucleotides for '"
- + nextxref + "' to " + xrefdb
- + " via '" + nextaf.getTitle() + "'");
-
+ failedXrefMenuItems.add("No crossrefs retrieved for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+ continue;
}
- else
+ assertNucleotide(cra_views2.get(0),
+ "Nucleotide panel included proteins for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+ assertProtein(cra_views2.get(1),
+ "Protein panel included nucleotides for '"
+ + nextxref + "' to " + xrefdb + " via '"
+ + nextaf.getTitle() + "'");
+
+ }
+ else
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ // recover stored project
+ File storedProject = savedProjects.get(nextnextxref);
+ if (storedProject == null)
{
- Desktop.instance.closeAll_actionPerformed(null);
- // recover stored project
- File storedProject = savedProjects.get(nextnextxref);
- if (storedProject == null)
- {
- failedProjectRecoveries
- .add("Failed to store a view for '"
- + nextnextxref + "'");
- continue;
- }
- AlignFrame af2 = new FileLoader(false)
- .LoadFileWaitTillLoaded(
- savedProjects.get(nextnextxref)
- .toString(),
- DataSourceType.FILE);
- System.out.println("Recovered view for '"
- + nextnextxref + "' from '"
- + savedProjects.get(nextnextxref).toString()
- + "'");
- // gymnastics to recover the alignPanel/Complementary
- // alignPanel
- if (af2.getViewport().isNucleotide())
- {
- // top view, then bottom
- cra_views2.add(af2.getViewport().getAlignPanel());
- cra_views2.add(((jalview.gui.AlignViewport) af2
- .getViewport().getCodingComplement())
- .getAlignPanel());
-
- }
- else
- {
- // bottom view, then top
- cra_views2.add(((jalview.gui.AlignViewport) af2
- .getViewport().getCodingComplement())
- .getAlignPanel());
- cra_views2.add(af2.getViewport().getAlignPanel());
- }
- Assert.assertEquals(cra_views2.size(), 2);
- Assert.assertNotNull(cra_views2.get(0));
- Assert.assertNotNull(cra_views2.get(1));
+ failedProjectRecoveries
+ .add("Failed to store a view for '"
+ + nextnextxref + "'");
+ continue;
}
+ AlignFrame af2 = new FileLoader(false)
+ .LoadFileWaitTillLoaded(savedProjects
+ .get(nextnextxref).toString(),
+ DataSourceType.FILE);
+ System.out
+ .println("Recovered view for '" + nextnextxref
+ + "' from '" + savedProjects
+ .get(nextnextxref).toString()
+ + "'");
+ // gymnastics to recover the alignPanel/Complementary
+ // alignPanel
+ if (af2.getViewport().isNucleotide())
+ {
+ // top view, then bottom
+ cra_views2.add(af2.getViewport().getAlignPanel());
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
- for (AlignmentViewPanel nextavp : cra_views2)
+ }
+ else
{
- nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
- + "}";
-
- // verify references for this panel
- AlignmentTest.assertAlignmentDatasetRefs(
- nextavp.getAlignment(), "" + "Pass (" + pass1
- + "," + pass2 + "): For "
- + nextnextxref + ":");
- assertDatasetIsNormalisedKnownDefect(
- nextavp.getAlignment(), "" + "Pass (" + pass1
- + "," + pass2 + "): For "
- + nextnextxref + ":");
-
- stringify(dbtoviewBit, savedProjects, nextnextxref,
- nextavp);
- keyseq.add(nextnextxref);
+ // bottom view, then top
+ cra_views2.add(((jalview.gui.AlignViewport) af2
+ .getViewport().getCodingComplement())
+ .getAlignPanel());
+ cra_views2.add(af2.getViewport().getAlignPanel());
}
- } // end of loop around showing all xrefdb for crossrf2
-
- } // end of loop around all viewpanels from crossrf1
- } while (pass2 == 2 && pass3++ < 2);
- // fetchdb->crossref1->crossref-2->verify for xrefs we
- // either loop twice when pass2=0, or just once when pass2=1
- // (recovered project from previous crossref)
-
- } // end of loop over db-xrefs for crossref-2
-
- // fetchdb-->crossref1
- // for each xref we try to retrieve xref, store and verify when
- // pass1=0, or just retrieve and verify when pass1=1
- } while (pass1 == 1 && pass2++ < 2);
- // fetchdb
- // for each ref we
- // loop twice: first, do the retrieve, second recover from saved project
-
- // increment pass counters, so we repeat traversal starting from the
- // oldest saved project first.
- if (pass1 == 0)
- {
- // verify stored projects for first set of cross references
- pass1 = 1;
- // and verify cross-references retrieved from stored projects
- pass2 = 0;
- pass3 = 0;
- }
- else
- {
- pass1++;
- }
- } while (pass1 < 3);
+ Assert.assertEquals(cra_views2.size(), 2);
+ Assert.assertNotNull(cra_views2.get(0));
+ Assert.assertNotNull(cra_views2.get(1));
+ }
+
+ for (AlignmentViewPanel nextavp : cra_views2)
+ {
+ nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+ + "}";
+
+ // verify references for this panel
+ AlignmentTest.assertAlignmentDatasetRefs(
+ nextavp.getAlignment(),
+ "" + "Pass (" + pass1 + "," + pass2 + "): For "
+ + nextnextxref + ":");
+ assertDatasetIsNormalisedKnownDefect(
+ nextavp.getAlignment(),
+ "" + "Pass (" + pass1 + "," + pass2 + "): For "
+ + nextnextxref + ":");
+
+ stringify(dbtoviewBit, savedProjects, nextnextxref,
+ nextavp);
+ keyseq.add(nextnextxref);
+ }
+ } // end of loop around showing all xrefdb for crossrf2
+
+ } // end of loop around all viewpanels from crossrf1
+ } while (pass2 == 2 && pass3++ < 2);
+ // fetchdb->crossref1->crossref-2->verify for xrefs we
+ // either loop twice when pass2=0, or just once when pass2=1
+ // (recovered project from previous crossref)
+
+ } // end of loop over db-xrefs for crossref-2
+
+ // fetchdb-->crossref1
+ // for each xref we try to retrieve xref, store and verify when
+ // pass1=0, or just retrieve and verify when pass1=1
+ } while (pass1 == 1 && pass2++ < 2);
+ // fetchdb
+ // for each ref we
+ // loop twice: first, do the retrieve, second recover from saved project
+
+ // increment pass counters, so we repeat traversal starting from the
+ // oldest saved project first.
+ if (pass1 == 0)
+ {
+ // verify stored projects for first set of cross references
+ pass1 = 1;
+ // and verify cross-references retrieved from stored projects
+ pass2 = 0;
+ pass3 = 0;
+ }
+ else
+ {
+ pass1++;
+ }
+ } while (pass1 < 3);
if (failedXrefMenuItems.size() > 0)
{
{
System.err.println(s);
}
- Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
- + failedProjectRecoveries.size() + " counts)");
+ Assert.fail(
+ "Didn't recover projects for some retrievals (did they retrieve ?) ("
+ + failedProjectRecoveries.size() + " counts)");
}
if (failedDBRetr.size() > 0)
{
}
else
{
- System.out
- .println("Ignored exception for known defect: JAL-2179 : "
- + message);
+ System.out.println("Ignored exception for known defect: JAL-2179 : "
+ + message);
}
}
AlignmentViewPanel alignmentViewPanel, String message)
{
List<SequenceI> nonType = new ArrayList<>();
- for (SequenceI sq : alignmentViewPanel.getAlignViewport()
- .getAlignment().getSequences())
+ for (SequenceI sq : alignmentViewPanel.getAlignViewport().getAlignment()
+ .getSequences())
{
if (sq.isProtein() != expectProtein)
{
}
else
{
- Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
- + xrefpath);
+ Assert.assertEquals(sbr.toString(), dbt,
+ "stringify mismatch for " + xrefpath);
}
}
}
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.MediaTracker;
-import java.awt.MenuItem;
+import java.text.DecimalFormat;
import javax.swing.ImageIcon;
import javax.swing.JButton;
*/
void doTest()
{
+ new DecimalFormat("###,###").format((Integer) 1);
JFrame main = new JFrame();
main.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
JMenu menu = new JMenu("testing");
git://source.jalview.org / jalview.git / commitdiff