/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import jalview.datamodel.Alignment;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import javax.swing.SwingConstants;
import javax.swing.tree.DefaultMutableTreeNode;
-import com.stevesoft.pat.Regex;
-
public class SequenceFetcher extends JPanel implements Runnable
{
JLabel dbeg = new JLabel();
private static Thread initingThread = null;
- int x = 0;
+ int debounceTrap = 0;
+
+ public JTextArea getTextArea()
+ {
+ return textArea;
+ }
+
/**
* Blocking method that initialises and returns the shared instance of the
* SequenceFetcher client
{
if (guiWindow != null)
{
- guiWindow.setProgressBar(
- MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ 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.
}
if (guiWindow != null)
{
- guiWindow.setProgressBar(
- MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
- Thread.currentThread().hashCode());
+ guiWindow
+ .setProgressBar(
+ MessageManager
+ .getString("status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
}
if (sfetch == null
- || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (jalview.bin.Cache
- .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ || dasRegistry != Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (Cache.getDasSourceRegistry()
+ .getDasRegistryURL() + Cache
.getDasSourceRegistry().getLocalSourceString())
.hashCode())
{
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
+ guiWindow.setProgressBar(MessageManager
+ .getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
- dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry = Cache.getDasSourceRegistry();
dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
- guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
}
lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
.getLocalSourceString()).hashCode();
return sfetch;
}
+ private IProgressIndicator progressIndicator;
+
public SequenceFetcher(IProgressIndicator guiIndic)
{
- final IProgressIndicator guiWindow = guiIndic;
+ this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
Thread sf = new Thread(new Runnable()
@Override
public void run()
{
- if (getSequenceFetcherSingleton(guiWindow) != null)
+ if (getSequenceFetcherSingleton(progressIndicator) != null)
{
- us.initGui(guiWindow);
+ us.initGui(progressIndicator);
}
else
{
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
- MessageManager.getString("label.couldnt_create_sequence_fetcher"),
+ MessageManager
+ .getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager
+ .getString("label.couldnt_create_sequence_fetcher"),
JOptionPane.ERROR_MESSAGE);
}
});
private String getFrameTitle()
{
- return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
+ return ((alignFrame == null) ? MessageManager
+ .getString("label.new_sequence_fetcher") : MessageManager
+ .getString("label.additional_sequence_fetcher"));
}
private void jbInit() throws Exception
@Override
public void actionPerformed(ActionEvent e)
{
- x++;
+ debounceTrap++;
String currentSelection = database.getSelectedItem();
- if (!currentSelection.equalsIgnoreCase("pdb"))
+ if (currentSelection.equalsIgnoreCase("pdb")
+ && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
{
- otherSourceAction();
+ pdbSourceAction();
}
- if (currentSelection.equalsIgnoreCase("pdb") && ((x % 2) == 0))
+ // else if (currentSelection.equalsIgnoreCase("uniprot")
+ // && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) ==
+ // 0)))
+ // {
+ // uniprotSourceAction();
+ // }
+ else
{
- frame.dispose();
- new EBIFetchPanel();
+ otherSourceAction();
}
-
+ database.action = -1;
}
});
+
dbeg.setText("");
jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
}
- private void hideX()
+ private void pdbSourceAction()
{
- this.setVisible(false);
+ databaseButt.setText(database.getSelectedItem());
+ new PDBFTSPanel(this);
+ frame.dispose();
+ }
+
+ private void uniprotSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new UniprotFTSPanel(this);
+ frame.dispose();
}
private void otherSourceAction()
{
: ""));
String eq = database.getExampleQueries();
dbeg.setText(MessageManager.formatMessage(
- "label.example_query_param", new String[]
- { eq }));
+ "label.example_query_param", new String[] { eq }));
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
jPanel3.repaint();
}
-
-
public void close_actionPerformed(ActionEvent e)
{
try
resetDialog();
return;
}
+ // TODO: Refactor to GUI independent code and write tests.
// indicate if successive sources should be merged into one alignment.
boolean addToLast = false;
- ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
- ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
+ List<String> aresultq = new ArrayList<String>();
+ List<String> presultTitle = new ArrayList<String>();
+ List<AlignmentI> presult = new ArrayList<AlignmentI>();
+ List<AlignmentI> aresult = new ArrayList<AlignmentI>();
Iterator<DbSourceProxy> proxies = database.getSelectedSources()
.iterator();
String[] qries;
- List<String> nextfetch = Arrays.asList(qries = textArea.getText()
+ List<String> nextFetch = Arrays.asList(qries = textArea.getText()
.split(";"));
Iterator<String> en = Arrays.asList(new String[0]).iterator();
int nqueries = qries.length;
- while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
+
+ FeatureSettingsModelI preferredFeatureColours = null;
+ while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
{
- if (!en.hasNext() && nextfetch.size() > 0)
+ if (!en.hasNext() && nextFetch.size() > 0)
{
- en = nextfetch.iterator();
- nqueries = nextfetch.size();
+ en = nextFetch.iterator();
+ nqueries = nextFetch.size();
// save the remaining queries in the original array
- qries = nextfetch.toArray(new String[nqueries]);
- nextfetch = new ArrayList<String>();
+ qries = nextFetch.toArray(new String[nqueries]);
+ nextFetch = new ArrayList<String>();
}
DbSourceProxy proxy = proxies.next();
- boolean isAliSource = false;
try
{
// update status
- guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
- .currentThread().hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ guiWindow
+ .setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from",
+ new String[] {
+ Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }), Thread.currentThread()
+ .hashCode());
+ if (proxy.getMaximumQueryCount() == 1)
{
+ /*
+ * proxy only handles one accession id at a time
+ */
while (en.hasNext())
{
- String item = en.next();
- try
- {
- if (aresult != null)
- {
- try
- {
- // give the server a chance to breathe
- Thread.sleep(5);
- } catch (Exception e)
- {
- //
- }
-
- }
-
- AlignmentI indres = null;
- try
- {
- indres = proxy.getSequenceRecords(item);
- } catch (OutOfMemoryError oome)
- {
- new OOMWarning("fetching " + item + " from "
- + proxy.getDbName(), oome, this);
- }
- if (indres != null)
- {
- aresultq.add(item);
- aresult.add(indres);
- }
- else
- {
- nextfetch.add(item);
- }
- } catch (Exception e)
+ String acc = en.next();
+ if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
{
- jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + proxy.getDbName(), e);
- nextfetch.add(item);
+ nextFetch.add(acc);
}
}
}
else
{
- StringBuffer multiacc = new StringBuffer();
- ArrayList<String> tosend = new ArrayList<String>();
- while (en.hasNext())
- {
- String nel = en.next();
- tosend.add(nel);
- multiacc.append(nel);
- if (en.hasNext())
- {
- multiacc.append(proxy.getAccessionSeparator());
- }
- }
- try
- {
- AlignmentI rslt;
- SequenceI[] rs;
- List<String> nores = new ArrayList<String>();
- rslt = proxy.getSequenceRecords(multiacc.toString());
- if (rslt == null || rslt.getHeight() == 0)
- {
- // no results - pass on all queries to next source
- nextfetch.addAll(tosend);
- }
- else
- {
- aresultq.add(multiacc.toString());
- aresult.add(rslt);
-
- rs = rslt.getSequencesArray();
- // search for each query in the dbrefs associated with each
- // sequence
- // returned.
- // ones we do not find will be used to query next source (if any)
- for (String q : tosend)
- {
- DBRefEntry dbr = new DBRefEntry(), found[] = null;
- dbr.setSource(proxy.getDbSource());
- dbr.setVersion(null);
- if (proxy.getAccessionValidator() != null)
- {
- Regex vgr = proxy.getAccessionValidator();
- vgr.search(q);
- if (vgr.numSubs() > 0)
- {
- dbr.setAccessionId(vgr.stringMatched(1));
- }
- else
- {
- dbr.setAccessionId(vgr.stringMatched());
- }
- }
- else
- {
- dbr.setAccessionId(q);
- }
- boolean rfound = false;
- for (int r = 0; r < rs.length; r++)
- {
- if (rs[r] != null
- && (found = DBRefUtils.searchRefs(
- rs[r].getDBRef(), dbr)) != null
- && found.length > 0)
- {
- rfound = true;
- rs[r] = null;
- continue;
- }
- }
- if (!rfound)
- {
- nextfetch.add(q);
- }
- }
- }
- } catch (OutOfMemoryError oome)
- {
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
- }
+ /*
+ * proxy can fetch multiple accessions at one time
+ */
+ fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
}
-
} catch (Exception e)
{
showErrorMessage("Error retrieving " + textArea.getText()
e.printStackTrace();
} catch (OutOfMemoryError e)
{
- // resets dialog box - so we don't use OOMwarning here.
showErrorMessage("Out of Memory when retrieving "
+ textArea.getText()
+ " from "
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
+
// Stack results ready for opening in alignment windows
if (aresult != null && aresult.size() > 0)
{
+ FeatureSettingsModelI proxyColourScheme = proxy
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ preferredFeatureColours = proxyColourScheme;
+ }
+
AlignmentI ar = null;
- if (isAliSource)
+ if (proxy.isAlignmentSource())
{
addToLast = false;
// new window for each result
{
ar.append(aresult.remove(0));
}
- ;
}
addToLast = true;
presult.add(ar);
presultTitle.add(titl);
}
}
- guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
+ guiWindow.setProgressBar(MessageManager
+ .getString("status.finshed_querying"), Thread.currentThread()
.hashCode());
}
- guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
- : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(
+ (presult.size() > 0) ? MessageManager
+ .getString("status.parsing_results") : MessageManager
+ .getString("status.processing"), Thread.currentThread()
+ .hashCode());
// process results
while (presult.size() > 0)
{
- parseResult(presult.remove(0), presultTitle.remove(0), null);
+ parseResult(presult.remove(0), presultTitle.remove(0), null,
+ preferredFeatureColours);
}
// only remove visual delay after we finished parsing.
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- if (nextfetch.size() > 0)
+ if (nextFetch.size() > 0)
{
StringBuffer sb = new StringBuffer();
sb.append("Didn't retrieve the following "
- + (nextfetch.size() == 1 ? "query" : nextfetch.size()
+ + (nextFetch.size() == 1 ? "query" : nextFetch.size()
+ " queries") + ": \n");
int l = sb.length(), lr = 0;
- for (String s : nextfetch)
+ for (String s : nextFetch)
{
if (l != sb.length())
{
resetDialog();
}
- AlignmentI parseResult(String result, String title)
+ /**
+ * Tries to fetch one or more accession ids from the database proxy
+ *
+ * @param proxy
+ * @param accessions
+ * the queries to fetch
+ * @param aresultq
+ * a successful queries list to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @param nextFetch
+ * failed queries are added to this list
+ * @throws Exception
+ */
+ void fetchMultipleAccessions(DbSourceProxy proxy,
+ Iterator<String> accessions, List<String> aresultq,
+ List<AlignmentI> aresult, List<String> nextFetch)
+ throws Exception
{
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
- if (FormatAdapter.isValidFormat(format))
+ StringBuilder multiacc = new StringBuilder();
+ List<String> tosend = new ArrayList<String>();
+ while (accessions.hasNext())
+ {
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+
+ try
{
- sequences = null;
- try
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
{
- sequences = new FormatAdapter().readFile(result.toString(),
- "Paste", format);
- } catch (Exception ex)
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
+ }
+ else
+ {
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
+ {
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
+ }
+ }
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+ }
+
+ /**
+ * Query for a single accession id via the database proxy
+ *
+ * @param proxy
+ * @param accession
+ * @param aresultq
+ * a list of successful queries to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @return true if the fetch was successful, else false
+ */
+ boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
+ List<String> aresultq, List<AlignmentI> aresult)
+ {
+ boolean success = false;
+ try
+ {
+ if (aresult != null)
{
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
}
- if (sequences != null)
+ AlignmentI indres = null;
+ try
{
- return parseResult(sequences, title, format);
+ indres = proxy.getSequenceRecords(accession);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + accession + " from "
+ + proxy.getDbName(), oome, this);
}
- }
- else
+ if (indres != null)
+ {
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
+ }
+ } catch (Exception e)
+ {
+ Cache.log.info(
+ "Error retrieving " + accession
+ + " from " + proxy.getDbName(), e);
+ } finally
{
- showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
+ return success;
}
+ }
- return null;
+ /**
+ * Checks which of the queries were successfully retrieved by searching the
+ * DBRefs of the retrieved sequences for a match. Any not found are added to
+ * the 'nextFetch' list.
+ *
+ * @param rslt
+ * @param queries
+ * @param nextFetch
+ * @param proxy
+ */
+ void checkResultForQueries(AlignmentI rslt, List<String> queries,
+ List<String> nextFetch, DbSourceProxy proxy)
+ {
+ SequenceI[] rs = rslt.getSequencesArray();
+
+ for (String q : queries)
+ {
+ DBRefEntry[] found = null;
+ DBRefEntry dbr = new DBRefEntry();
+ dbr.setSource(proxy.getDbSource());
+ dbr.setVersion(null);
+ String accId = proxy.getAccessionIdFromQuery(q);
+ dbr.setAccessionId(accId);
+ boolean rfound = false;
+ for (int r = 0; r < rs.length; r++)
+ {
+ if (rs[r] != null)
+ {
+ found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
+ if (found != null && found.length > 0)
+ {
+ rfound = true;
+ break;
+ }
+ }
+ }
+ if (!rfound)
+ {
+ nextFetch.add(q);
+ }
+ }
}
/**
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat)
+ String currentFileFormat,
+ FeatureSettingsModelI preferredFeatureColours)
{
if (al != null && al.getHeight() > 0)
{
+ if (title == null)
+ {
+ title = getDefaultRetrievalTitle();
+ }
if (alignFrame == null)
{
AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
// Alignments?
}
- if (title == null)
- {
- title = getDefaultRetrievalTitle();
- }
SequenceFeature[] sfs = null;
List<SequenceI> alsqs;
synchronized (alsqs = al.getSequences())
}
}
+
+ if (preferredFeatureColours != null)
+ {
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
+ }
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ hideIntronsIfPresent(af);
+ }
+
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
false));
} catch (Exception ex)
{
}
else
{
- for (int i = 0; i < al.getHeight(); i++)
- {
- alignFrame.viewport.getAlignment().addSequence(
- al.getSequenceAt(i)); // this
- // also
- // creates
- // dataset
- // sequence
- // entries
- }
- alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
- .getHeight());
- alignFrame.viewport.getAlignment().getWidth();
- alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.getAlignment().getSequences());
+ alignFrame.viewport.addAlignment(al, title);
}
}
return al;
}
+ /**
+ * Hide columns not containing 'exon' features, provided there are exon
+ * features on the alignment
+ *
+ * @param af
+ */
+ public void hideIntronsIfPresent(AlignFrame af)
+ {
+ boolean hasExons = af.avc.markColumnsContainingFeatures(false, false,
+ false,
+ SequenceOntologyI.EXON);
+ if (hasExons)
+ {
+ af.avc.markColumnsContainingFeatures(true, false, true,
+ SequenceOntologyI.EXON);
+ af.getViewport().hideSelectedColumns();
+ }
+ }
+
void showErrorMessage(final String error)
{
resetDialog();
}
});
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
}
git://source.jalview.org / jalview.git / blobdiff