X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=9052413245c00b90607583422ea579adef03fa6b;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=24db866810eb546f001dd10dd0af01996d5ad464;hpb=96026e673c3629afa54a0d03be4b0022c7b42869;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 24db866..9052413 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -20,21 +20,6 @@ */ package jalview.gui; -import jalview.api.FeatureSettingsModelI; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.DBRefEntry; -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; -import jalview.io.gff.SequenceOntologyI; -import jalview.util.DBRefUtils; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.seqfetcher.DbSourceProxy; - import java.awt.BorderLayout; import java.awt.Font; import java.awt.event.ActionEvent; @@ -57,6 +42,22 @@ import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.SwingConstants; +import jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.SequenceI; +import jalview.fts.core.GFTSPanel; +import jalview.fts.service.pdb.PDBFTSPanel; +import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel; +import jalview.fts.service.uniprot.UniprotFTSPanel; +import jalview.io.FileFormatI; +import jalview.io.gff.SequenceOntologyI; +import jalview.util.DBRefUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.seqfetcher.DbSourceProxy; + /** * A panel where the use may choose a database source, and enter one or more * accessions, to retrieve entries from the database. @@ -66,11 +67,50 @@ import javax.swing.SwingConstants; */ public class SequenceFetcher extends JPanel implements Runnable { + private class StringPair + { + private String key; + + private String display; + + public StringPair(String s1, String s2) + { + key = s1; + display = s2; + } + + public StringPair(String s) + { + this(s, s); + } + + public String getKey() + { + return key; + } + + public String getDisplay() + { + return display; + } + + @Override + public String toString() + { + return display; + } + + public boolean equals(StringPair other) + { + return other.key == this.key; + } + } + private static jalview.ws.SequenceFetcher sfetch = null; JLabel exampleAccession; - JComboBox database; + JComboBox database; JCheckBox replacePunctuation; @@ -145,8 +185,8 @@ public class SequenceFetcher extends JPanel implements Runnable frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, - Platform.isAMacAndNotJS() ? 240 : 180); + Desktop.addInternalFrame(frame, getFrameTitle(), true, 400, + Platform.isAMacAndNotJS() ? 240 : 180); } private String getFrameTitle() @@ -163,15 +203,25 @@ public class SequenceFetcher extends JPanel implements Runnable database = new JComboBox<>(); database.setFont(JvSwingUtils.getLabelFont()); - database.setPrototypeDisplayValue("ENSEMBLGENOMES "); + StringPair instructionItem = new StringPair( + MessageManager.getString("action.select_ddbb")); + database.setPrototypeDisplayValue(instructionItem); String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb(); Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER); - database.addItem(MessageManager.getString("action.select_ddbb")); + database.addItem(instructionItem); for (String source : sources) { - database.addItem(source); + List slist = sfetch.getSourceProxy(source); + if (slist.size() == 1 && slist.get(0) != null) + { + database.addItem(new StringPair(source, slist.get(0).getDbName())); + } + else + { + database.addItem(new StringPair(source)); + } } - database.setSelectedItem(selectedDb); + setDatabaseSelectedItem(selectedDb); if (database.getSelectedIndex() == -1) { database.setSelectedIndex(0); @@ -182,7 +232,8 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void actionPerformed(ActionEvent e) { - String currentSelection = (String) database.getSelectedItem(); + String currentSelection = ((StringPair) database.getSelectedItem()) + .getKey(); updateExampleQuery(currentSelection); if ("pdb".equalsIgnoreCase(currentSelection)) @@ -195,6 +246,11 @@ public class SequenceFetcher extends JPanel implements Runnable frame.dispose(); new UniprotFTSPanel(SequenceFetcher.this); } + else if ("3d-beacons".equalsIgnoreCase(currentSelection)) + { + frame.dispose(); + new TDBeaconsFTSPanel(SequenceFetcher.this); + } else { otherSourceAction(); @@ -304,6 +360,19 @@ public class SequenceFetcher extends JPanel implements Runnable this.add(databasePanel, BorderLayout.NORTH); } + private void setDatabaseSelectedItem(String db) + { + for (int i = 0; i < database.getItemCount(); i++) + { + StringPair sp = database.getItemAt(i); + if (sp != null && db != null && db.equals(sp.getKey())) + { + database.setSelectedIndex(i); + return; + } + } + } + /** * Answers a semi-colon-delimited string with the example query or queries for * the selected database @@ -375,7 +444,8 @@ public class SequenceFetcher extends JPanel implements Runnable */ protected void example_actionPerformed() { - String eq = getExampleQueries((String) database.getSelectedItem()); + String eq = getExampleQueries( + ((StringPair) database.getSelectedItem()).getKey()); textArea.setText(eq); repaint(); } @@ -417,13 +487,17 @@ public class SequenceFetcher extends JPanel implements Runnable /* * tidy inputs and check there is something to search for */ - String text = textArea.getText(); + String t0 = textArea.getText(); + String text = t0.trim(); if (replacePunctuation.isEnabled() && replacePunctuation.isSelected()) { text = text.replace(",", ";"); } - text = text.replaceAll("(\\s|[,; ])+", ";"); - textArea.setText(text); + text = text.replaceAll("(\\s|[; ])+", ";"); + if (!t0.equals(text)) + { + textArea.setText(text); + } if (text.isEmpty()) { // todo i18n @@ -432,6 +506,14 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); return; } + if (database.getSelectedIndex() == 0) + { + // todo i18n + showErrorMessage("Please choose a database"); + resetDialog(); + return; + } + exampleBtn.setEnabled(false); textArea.setEnabled(false); okBtn.setEnabled(false); @@ -459,12 +541,11 @@ public class SequenceFetcher extends JPanel implements Runnable List presultTitle = new ArrayList<>(); List presult = new ArrayList<>(); List aresult = new ArrayList<>(); - List sources = sfetch - .getSourceProxy((String) database.getSelectedItem()); + List sources = sfetch.getSourceProxy( + ((StringPair) database.getSelectedItem()).getKey()); Iterator proxies = sources.iterator(); - String[] qries; - List nextFetch = Arrays - .asList(qries = textArea.getText().split(";")); + String[] qries = textArea.getText().trim().split(";"); + List nextFetch = Arrays.asList(qries); Iterator en = Arrays.asList(new String[0]).iterator(); int nqueries = qries.length; @@ -513,23 +594,25 @@ public class SequenceFetcher extends JPanel implements Runnable } catch (Exception e) { showErrorMessage("Error retrieving " + textArea.getText() + " from " - + database.getSelectedItem()); + + ((StringPair) database.getSelectedItem()).getDisplay()); // error // +="Couldn't retrieve sequences from "+database.getSelectedItem(); System.err.println("Retrieval failed for source ='" - + database.getSelectedItem() + "' and query\n'" - + textArea.getText() + "'\n"); + + ((StringPair) database.getSelectedItem()).getDisplay() + + "' and query\n'" + textArea.getText() + "'\n"); e.printStackTrace(); } catch (OutOfMemoryError e) { showErrorMessage("Out of Memory when retrieving " - + textArea.getText() + " from " + database.getSelectedItem() + + textArea.getText() + " from " + + ((StringPair) database.getSelectedItem()).getDisplay() + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n"); e.printStackTrace(); } catch (Error e) { showErrorMessage("Serious Error retrieving " + textArea.getText() - + " from " + database.getSelectedItem()); + + " from " + + ((StringPair) database.getSelectedItem()).getDisplay()); e.printStackTrace(); } @@ -676,7 +759,8 @@ public class SequenceFetcher extends JPanel implements Runnable } catch (OutOfMemoryError oome) { new OOMWarning("fetching " + multiacc + " from " - + database.getSelectedItem(), oome, this); + + ((StringPair) database.getSelectedItem()).getDisplay(), + oome, this); } } @@ -727,7 +811,7 @@ public class SequenceFetcher extends JPanel implements Runnable } } catch (Exception e) { - Cache.log.info("Error retrieving " + accession + " from " + Cache.info("Error retrieving " + accession + " from " + proxy.getDbName(), e); } return success; @@ -750,13 +834,14 @@ public class SequenceFetcher extends JPanel implements Runnable for (String q : queries) { - DBRefEntry dbr = new DBRefEntry(); - dbr.setSource(proxy.getDbSource()); - dbr.setVersion(null); + // BH 2019.01.25 dbr is never used. + // DBRefEntry dbr = new DBRefEntry(); + // dbr.setSource(proxy.getDbSource()); + // dbr.setVersion(null); String accId = proxy.getAccessionIdFromQuery(q); - dbr.setAccessionId(accId); + // dbr.setAccessionId(accId); boolean rfound = false; - for (int r = 0; r < rs.length; r++) + for (int r = 0, nr = rs.length; r < nr; r++) { if (rs[r] != null) { @@ -783,10 +868,20 @@ public class SequenceFetcher extends JPanel implements Runnable */ public String getDefaultRetrievalTitle() { - return "Retrieved from " + database.getSelectedItem(); + return "Retrieved from " + + ((StringPair) database.getSelectedItem()).getDisplay(); } - AlignmentI parseResult(AlignmentI al, String title, + /** + * constructs an alignment frame given the data and metadata + * + * @param al + * @param title + * @param currentFileFormat + * @param preferredFeatureColours + * @return the alignment + */ + public AlignmentI parseResult(AlignmentI al, String title, FileFormatI currentFileFormat, FeatureSettingsModelI preferredFeatureColours) { @@ -819,10 +914,7 @@ public class SequenceFetcher extends JPanel implements Runnable } } - if (preferredFeatureColours != null) - { - af.getViewport().applyFeaturesStyle(preferredFeatureColours); - } + af.getViewport().applyFeaturesStyle(preferredFeatureColours); if (Cache.getDefault("HIDE_INTRONS", true)) { af.hideFeatureColumns(SequenceOntologyI.EXON, false);