<p>
To open the PDB Sequence Fetcher, select PDB as the database from
any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened <em>via</em>
- <strong>"File →Fetch Sequences"</strong>).
+ <strong>"File →Fetch Sequences"</strong>).
</p>
<img src="pdbseqfetcher.png" align="left"
alt="PDB sequence fetcher (introduced in Jalview 2.9)" />
<p>
<strong>Searching the PDB Database</strong>
</p>
+ <p>To search the PDB, begin typing in the text box. If the
+ 'autosearch' checkbox is enabled, then the results of your query
+ will be automatically updated and shown in the search results tab;
+ otherwise, press return to update the results. To access previous
+ searches, press the down-arrow or click the drop down menu icon at
+ the side of the search box. If you just want to paste in a list of
+ IDs, the 'Retrieve IDs' tab provides a batch-retrieval interface.</p>
<p>
- To search the PDB, begin typing in the text box. The results of your
- query are shown in the search results tab, which updates every time
- you type in the search text box. You can sort results according to
- the displayed columns, and select entries with the mouse and
- keyboard. Once you have selected one or more entries, hit the <strong>OK</strong>
- button to retrieve and view them in Jalview.
+ You can sort results according to the displayed columns, and select
+ entries with the mouse and keyboard. Once you have selected one or
+ more entries, hit the <strong>OK</strong> button to retrieve and
+ view them in Jalview.
</p>
<p>
<ul>
1xyz:A</li>
<li><strong>Bulk PDB retrieval</strong><br>Multiple PDB
- IDs can be specified by separating them with a semi-colon.<br />
- e.g. 1xyz;2xyz;3xyz<br />Hitting Return or OK will automatically
- fetch those IDs, like the default Sequence Fetcher interface.</li>
+ IDs can be specified for retrieval via the
+ <strong>Retrieve IDs</strong> tab.</li>
<li><strong>Wild card searching</strong><br>The following
wild cards are supported by the EMBL-EBI PDBe query service:
<p>
<strong>Searching the UniProt Database</strong>
</p>
- <p>
- To search UniProt, simply begin typing in the text box. After a
- short delay (about 1.5 seconds), results will be shown in the table
- below. You can sort results by clicking on the displayed columns,
+ <p>To search UniProt, simply begin typing in the text box. If the
+ 'autosearch' check box is enabled, then after a short delay (about
+ 1.5 seconds), results will be shown in the table below. Results are
+ also updated whenever you press Enter, and you can access previous
+ searches by pressing the 'Down' arrow or clicking the drop-down menu
+ icon at the side of the search box.</p>
+ <p>You can sort results by clicking on the displayed columns,
and select entries with the mouse or keyboard. Once you have
selected one or more entries, hit the <strong>OK</strong> button to
retrieve the sequences.
<li><strong>Bulk UniProt record retrieval</strong><br> To
- retrieve several uniprot accessions at once, first select <strong>UniProt
- ID</strong> from the dropdown menu, then paste in the accession IDs as a
- semi-colon separated list. (e.g. fila_human; mnt_human;
- mnt_mouse).<br />Hitting Return or OK will automatically fetch
- those IDs, like the default Sequence Fetcher interface.</li>
+ retrieve sequences for a list of Uniprot accessions, please enter
+ them via the 'Retrieve IDs' tab.</li>
<li><strong><a name="text-search">Complex queries
with the UniProt query Syntax</a></strong> The text box also allows complex
label.overview = Overview
label.reset_to_defaults = Reset to defaults
label.oview_calc = Recalculating overview...
+option.enable_disable_autosearch = When ticked, search is performed automatically.
+option.autosearch = Autosearch
+label.retrieve_ids = Retrieve IDs
\ No newline at end of file
* @return
*/
public String getCacheKey();
+
+ /**
+ *
+ * @return user preference name for configuring this FTS search's autosearch
+ * checkbox
+ */
+ public String getAutosearchPreference();
}
import javax.swing.ImageIcon;
import javax.swing.JButton;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFrame;
import javax.swing.JInternalFrame;
protected JInternalFrame mainFrame = new JInternalFrame(
getFTSFrameTitle());
+ protected JTabbedPane tabs = new JTabbedPane();
protected IProgressIndicator progressIndicator;
protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
protected JButton btn_cancel = new JButton();
+ protected JCheckBox btn_autosearch = new JCheckBox();
+
protected JvCacheableInputBox<String> txt_search;
protected SequenceFetcher seqFetcher;
public GFTSPanel()
{
+ this(null);
+ }
+
+ public GFTSPanel(SequenceFetcher fetcher)
+ {
try
{
+ if (fetcher == null)
+ {
+ tabs = null;
+ }
jbInit();
+ if (fetcher != null)
+ {
+ tabs.addTab(MessageManager.getString("label.retrieve_ids"),
+ fetcher);
+ fetcher.setDatabaseChooserVisible(false);
+ fetcher.embedWithFTSPanel(this);
+ }
mainFrame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ final JPanel ftsPanel = this;
mainFrame.addFocusListener(new FocusAdapter()
{
@Override
public void focusGained(FocusEvent e)
{
- txt_search.requestFocusInWindow();
+ // TODO: make selected tab gain focus in correct widget
+ if (tabs != null
+ && tabs.getSelectedComponent() == ftsPanel)
+ {
+ txt_search.requestFocusInWindow();
+ }
}
});
mainFrame.invalidate();
}
});
+ btn_autosearch.setText(MessageManager.getString("option.autosearch"));
+ btn_autosearch.setToolTipText(
+ MessageManager.getString("option.enable_disable_autosearch"));
+ btn_autosearch.setSelected(
+ jalview.bin.Cache.getDefault(getAutosearchPreference(), true));
+ btn_autosearch.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ jalview.bin.Cache.setProperty(getAutosearchPreference(),
+ Boolean.toString(btn_autosearch.isSelected()));
+ }
+ });
btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
btn_back.setText(MessageManager.getString("action.back"));
btn_back.addActionListener(new java.awt.event.ActionListener()
if (primaryKeyName.equalsIgnoreCase(getCmbSearchTarget()
.getSelectedItem().toString()))
{
+ // TODO: nicer to show the list in the result set before
+ // viewing in Jalview perhaps ?
transferToSequenceFetcher(getTypedText());
}
+ else
+ {
+ performSearchAction();
+ }
}
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- String typed = getTypedText();
- if (!typed.equalsIgnoreCase(lastSearchTerm))
+ if (btn_autosearch.isSelected()
+ || txt_search.wasEnterPressed())
{
- searchAction(true);
- paginatorCart.clear();
- lastSearchTerm = typed;
+ performSearchAction();
}
}
}, false);
}
});
+ txt_search.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ performSearchAction();
+ }
+ });
final String searchTabTitle = MessageManager
.getString("label.search_result");
final String configureCols = MessageManager
pnl_results.add(tabbedPane);
pnl_inputs.add(cmb_searchTarget);
pnl_inputs.add(txt_search);
+ pnl_inputs.add(btn_autosearch);
pnl_inputs.add(lbl_loading);
pnl_inputs.add(lbl_warning);
pnl_inputs.add(lbl_blank);
this.add(pnl_results, java.awt.BorderLayout.CENTER);
this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
mainFrame.setVisible(true);
- mainFrame.setContentPane(this);
+ if (tabs != null)
+ {
+ tabs.setOpaque(true);
+ tabs.insertTab("Free Text Search", null, this, "", 0);
+ mainFrame.setContentPane(tabs);
+ tabs.setVisible(true);
+ }
+ else
+ {
+ mainFrame.setContentPane(this);
+ }
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
mainFrame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
closeAction();
}
});
- mainFrame.setVisible(true);
- mainFrame.setContentPane(this);
mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
Integer x = getTempUserPrefs().get("FTSPanel.x");
Integer y = getTempUserPrefs().get("FTSPanel.y");
}
+ void performSearchAction()
+ {
+ String typed = getTypedText();
+ if (typed != null && typed.length() > 0
+ && !typed.equalsIgnoreCase(lastSearchTerm))
+ {
+ searchAction(true);
+ paginatorCart.clear();
+ lastSearchTerm = typed;
+ }
+ }
+
public boolean wantedFieldsUpdated()
{
if (previousWantedFields == null)
}
}
- protected void btn_back_ActionPerformed()
+ public void btn_back_ActionPerformed()
{
closeAction();
new SequenceFetcher(progressIndicator);
btn_cancel.setEnabled(false);
}
- protected void btn_cancel_ActionPerformed()
+ public void btn_cancel_ActionPerformed()
{
closeAction();
}
private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
+ private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
+
public PDBFTSPanel(SequenceFetcher fetcher)
{
- super();
+ super(fetcher);
pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
this.seqFetcher = fetcher;
this.progressIndicator = (fetcher == null) ? null
return PDB_FTS_CACHE_KEY;
}
-}
+ @Override
+ public String getAutosearchPreference()
+ {
+ return PDB_AUTOSEARCH;
+ }
+}
\ No newline at end of file
private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
+ private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
+
public UniprotFTSPanel(SequenceFetcher fetcher)
{
- super();
+ super(fetcher);
pageLimit = UniProtFTSRestClient.getInstance()
.getDefaultResponsePageSize();
this.seqFetcher = fetcher;
{
return UNIPROT_FTS_CACHE_KEY;
}
+
+ @Override
+ public String getAutosearchPreference()
+ {
+ return UNIPROT_AUTOSEARCH;
+ }
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
import jalview.fts.service.pdb.PDBFTSPanel;
import jalview.fts.service.uniprot.UniprotFTSPanel;
import jalview.io.FileFormatI;
JButton close = new JButton();
+ JButton back = new JButton();
+
JPanel jPanel1 = new JPanel();
JTextArea textArea = new JTextArea();
.getString("label.additional_sequence_fetcher"));
}
+ GFTSPanel parentFTSframe = null;
+ /**
+ * change the buttons so they fit with the FTS panel.
+ */
+ public void embedWithFTSPanel(GFTSPanel toClose)
+ {
+ back.setVisible(true);
+ parentFTSframe = toClose;
+ }
private void jbInit() throws Exception
{
this.setLayout(borderLayout2);
example_actionPerformed();
}
});
- close.setText(MessageManager.getString("action.close"));
+ close.setText(MessageManager.getString("action.cancel"));
close.addActionListener(new ActionListener()
{
@Override
close_actionPerformed(e);
}
});
+ back.setText(MessageManager.getString("action.back"));
+ back.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentFTSframe.btn_back_ActionPerformed();
+ }
+ });
+ // back not visible unless embedded
+ back.setVisible(false);
textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
});
jPanel3.setLayout(borderLayout1);
borderLayout1.setVgap(5);
- jPanel1.add(ok);
+ jPanel1.add(back);
jPanel1.add(example);
jPanel1.add(clear);
+ jPanel1.add(ok);
jPanel1.add(close);
jPanel2.setLayout(borderLayout3);
databaseButt = /*database.getDatabaseSelectorButton();
try
{
frame.setClosed(true);
+ if (parentFTSframe!=null)
+ {
+ parentFTSframe.btn_cancel_ActionPerformed();
+ }
} catch (Exception ex)
{
}
textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
-
+ back.setEnabled(false);
Thread worker = new Thread(this);
worker.start();
}
textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
+ back.setEnabled(parentFTSframe != null);
}
@Override
{
frame.setVisible(false);
}
+
+ public void setDatabaseChooserVisible(boolean b)
+ {
+ databaseButt.setVisible(b);
+ }
}
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
private JMenuItem menuItemClearCache = new JMenuItem();
+ volatile boolean enterWasPressed = false;
+
+ /**
+ * @return flag indicating if the most recent keypress was enter
+ */
+ public boolean wasEnterPressed()
+ {
+ return enterWasPressed;
+ }
+
public JvCacheableInputBox(String newCacheKey)
{
super();
this.cacheKey = newCacheKey;
setEditable(true);
+ addKeyListener(new KeyListener()
+ {
+
+ @Override
+ public void keyTyped(KeyEvent e)
+ {
+ enterWasPressed = false;
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ enterWasPressed = true;
+ }
+ // let event bubble up
+ }
+
+ @Override
+ public void keyReleased(KeyEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+ });
setPrototypeDisplayValue(
"XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
appCache = AppCache.getInstance();
git://source.jalview.org / jalview.git / commitdiff
