X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=8e1d5498554f4b9de439cbdc5beb13f82ed5456c;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=cc8c46e77d599500c4b3be4488a19d5e6223b4f9;hpb=1fea862e99e1fdd5eb85d5feaec2d28de58828b4;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index cc8c46e..8e1d549 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -28,6 +28,7 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.fts.service.pdb.PDBFTSPanel; import jalview.fts.service.uniprot.UniprotFTSPanel; +import jalview.io.FileFormatI; import jalview.io.gff.SequenceOntologyI; import jalview.util.DBRefUtils; import jalview.util.MessageManager; @@ -43,6 +44,7 @@ import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.Iterator; import java.util.List; @@ -115,8 +117,6 @@ public class SequenceFetcher extends JPanel implements Runnable private static Thread initingThread = null; - int debounceTrap = 0; - public JTextArea getTextArea() { return textArea; @@ -168,9 +168,8 @@ public class SequenceFetcher extends JPanel implements Runnable if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry() || lastDasSourceRegistry != (Cache.getDasSourceRegistry() - .getDasRegistryURL() + Cache - .getDasSourceRegistry().getLocalSourceString()) - .hashCode()) + .getDasRegistryURL() + Cache.getDasSourceRegistry() + .getLocalSourceString()).hashCode()) { _initingFetcher = true; initingThread = Thread.currentThread(); @@ -202,8 +201,19 @@ public class SequenceFetcher extends JPanel implements Runnable private IProgressIndicator progressIndicator; + private volatile boolean _isConstructing = false; + + private List 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 @@ -215,7 +225,8 @@ public class SequenceFetcher extends JPanel implements Runnable { if (getSequenceFetcherSingleton(progressIndicator) != null) { - us.initGui(progressIndicator); + us.initGui(progressIndicator, selectedDb, queryString); + us._isConstructing = false; } else { @@ -224,14 +235,14 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("warn.couldnt_create_sequence_fetcher_client"), MessageManager .getString("label.couldnt_create_sequence_fetcher"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } }); @@ -242,6 +253,32 @@ public class SequenceFetcher extends JPanel implements Runnable sf.start(); } + /** + * blocking call which creates a new sequence fetcher panel, configures it and + * presses the OK button with the given database and query. + * + * @param database + * @param query + */ + public static List fetchAndShow(String database, String query) + { + 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; + } + private class DatabaseAuthority extends DefaultMutableTreeNode { @@ -253,11 +290,57 @@ public class SequenceFetcher extends JPanel implements Runnable }; /** + * initialise the database and query for this fetcher panel + * + * @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) + { + if (selectedDb == null || selectedDb.trim().length() == 0) + { + return false; + } + try + { + List 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; + } + + /** * called by thread spawned by constructor * * @param guiWindow + * @param queryString + * @param selectedDb */ - private void initGui(IProgressIndicator guiWindow) + private void initGui(IProgressIndicator guiWindow, String selectedDb, + String queryString) { this.guiWindow = guiWindow; if (guiWindow instanceof AlignFrame) @@ -268,6 +351,16 @@ public class SequenceFetcher extends JPanel implements Runnable try { 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(); @@ -364,16 +457,26 @@ public class SequenceFetcher extends JPanel implements Runnable jPanel1.add(example); jPanel1.add(clear); jPanel1.add(close); - jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER); jPanel2.setLayout(borderLayout3); - databaseButt = database.getDatabaseSelectorButton(); + 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) { - debounceTrap++; String currentSelection = database.getSelectedItem(); if (currentSelection == null) { @@ -382,13 +485,11 @@ public class SequenceFetcher extends JPanel implements Runnable showPanel(); - if (currentSelection.equalsIgnoreCase("pdb") - && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) + if ("pdb".equalsIgnoreCase(currentSelection)) { pdbSourceAction(); } - else if (currentSelection.equalsIgnoreCase("uniprot") - && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) + else if ("uniprot".equalsIgnoreCase(currentSelection)) { uniprotSourceAction(); } @@ -413,11 +514,6 @@ public class SequenceFetcher extends JPanel implements Runnable this.add(jPanel3, java.awt.BorderLayout.CENTER); this.add(jPanel2, java.awt.BorderLayout.NORTH); jScrollPane1.getViewport().add(textArea); - - /* - * open the database tree - */ - database.waitForInput(); } private void pdbSourceAction() @@ -433,6 +529,7 @@ public class SequenceFetcher extends JPanel implements Runnable new UniprotFTSPanel(this); frame.dispose(); } + private void otherSourceAction() { try @@ -822,12 +919,10 @@ public class SequenceFetcher extends JPanel implements Runnable } catch (Exception e) { Cache.log.info( - "Error retrieving " + accession - + " from " + proxy.getDbName(), e); - } finally - { - return success; + "Error retrieving " + accession + " from " + + proxy.getDbName(), e); } + return success; } /** @@ -847,7 +942,6 @@ public class SequenceFetcher extends JPanel implements Runnable for (String q : queries) { - DBRefEntry[] found = null; DBRefEntry dbr = new DBRefEntry(); dbr.setSource(proxy.getDbSource()); dbr.setVersion(null); @@ -858,8 +952,9 @@ public class SequenceFetcher extends JPanel implements Runnable { if (rs[r] != null) { - found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId); - if (found != null && found.length > 0) + List found = DBRefUtils.searchRefs(rs[r].getDBRefs(), + accId); + if (!found.isEmpty()) { rfound = true; break; @@ -884,7 +979,7 @@ public class SequenceFetcher extends JPanel implements Runnable } AlignmentI parseResult(AlignmentI al, String title, - String currentFileFormat, + FileFormatI currentFileFormat, FeatureSettingsModelI preferredFeatureColours) { @@ -932,7 +1027,10 @@ public class SequenceFetcher extends JPanel implements Runnable { af.hideFeatureColumns(SequenceOntologyI.EXON, false); } - + if (newAlframes != null) + { + newAlframes.add(af); + } Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); @@ -941,8 +1039,7 @@ public class SequenceFetcher extends JPanel implements Runnable try { - af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", - false)); + af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (Exception ex) { } @@ -963,9 +1060,9 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, error, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, error, MessageManager.getString("label.error_retrieving_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -988,4 +1085,13 @@ public class SequenceFetcher extends JPanel implements Runnable { frame.setVisible(true); } + + /** + * Hide this panel (on clicking the database button to open the database + * chooser) + */ + void hidePanel() + { + frame.setVisible(false); + } }