/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.io.*;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
+import javax.swing.tree.DefaultMutableTreeNode;
+import javax.swing.tree.MutableTreeNode;
+import javax.swing.tree.TreeModel;
-import MCview.*;
import jalview.datamodel.*;
-import jalview.datamodel.xdb.embl.*;
-import java.io.File;
import jalview.io.*;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.seqfetcher.DbSourceProxy;
-import java.awt.Rectangle;
import java.awt.BorderLayout;
-import java.awt.Dimension;
public class SequenceFetcher extends JPanel implements Runnable
{
final String noDbSelected = "-- Select Database --";
- Hashtable sources = new Hashtable();
-
private static jalview.ws.SequenceFetcher sfetch = null;
- private static String dasRegistry = null;
+ private static long lastDasSourceRegistry = -3;
+
+ private static DasSourceRegistryI dasRegistry = null;
private static boolean _initingFetcher = false;
}
}
if (sfetch == null
- || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (jalview.bin.Cache
+ .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ .getDasSourceRegistry().getLocalSourceString())
+ .hashCode())
{
_initingFetcher = true;
initingThread = Thread.currentThread();
guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
Thread.currentThread().hashCode());
}
- dasRegistry = DasSourceBrowser.getDasRegistryURL();
+ dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry.refreshSources();
+
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
- initingThread.hashCode());
+ Thread.currentThread().hashCode());
}
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
+ .getLocalSourceString()).hashCode();
sfetch = sf;
_initingFetcher = false;
initingThread = null;
sf.start();
}
+ private class DatabaseAuthority extends DefaultMutableTreeNode
+ {
+
+ };
+
+ private class DatabaseSource extends DefaultMutableTreeNode
+ {
+
+ };
+
/**
* called by thread spawned by constructor
*
{
alignFrame = (AlignFrame) guiWindow;
}
-
- database.addItem(noDbSelected);
- /*
- * Dynamically generated database list will need a translation function from
- * internal source to externally distinct names. UNIPROT and UP_NAME are
- * identical DB sources, and should be collapsed.
- */
-
- String dbs[] = sfetch.getOrderedSupportedSources();
- for (int i = 0; i < dbs.length; i++)
- {
- if (!sources.containsValue(dbs[i]))
- {
- String name = sfetch.getSourceProxy(dbs[i]).getDbName();
- // duplicate source names are thrown away, here.
- if (!sources.containsKey(name))
- {
- database.addItem(name);
- }
- // overwrite with latest version of the retriever for this source
- sources.put(name, dbs[i]);
- }
- }
+ database = new JDatabaseTree(sfetch);
try
{
jbInit();
{
this.setLayout(borderLayout2);
- database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ 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);
close_actionPerformed(e);
}
});
- textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
jPanel1.add(close);
jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
-
+ databaseButt = database.getDatabaseSelectorButton();
+ databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- String eq = db.getTestQuery();
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size()
+ + " others)" : ""));
+ String eq = database.getExampleQueries();
dbeg.setText("Example query: " + eq);
replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
} catch (Exception ex)
}
});
dbeg.setText("");
- jPanel2.add(database, java.awt.BorderLayout.NORTH);
+ jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
JPanel jPanel2a = new JPanel(new BorderLayout());
jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- textArea.setText(db.getTestQuery());
+ textArea.setText(database.getExampleQueries());
} catch (Exception ex)
{
}
JLabel dbeg = new JLabel();
- JComboBox database = new JComboBox();
+ JDatabaseTree database;
+
+ JButton databaseButt;
JLabel jLabel1 = new JLabel();
public void run()
{
String error = "";
- if (database.getSelectedItem().equals(noDbSelected))
+ if (!database.hasSelection())
{
error += "Please select the source database\n";
}
resetDialog();
return;
}
- AlignmentI aresult = null;
- Object source = database.getSelectedItem();
+ ArrayList<String> aresultq = new ArrayList<String>();
+ ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
+ DbSourceProxy proxy = database.getSelectedSources().get(0);
Enumeration en = new StringTokenizer(textArea.getText(), ";");
+ boolean isAliSource = false;
try
{
guiWindow.setProgressBar(
- "Fetching Sequences from " + database.getSelectedItem(),
- Thread.currentThread().hashCode());
- DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
- .get(source));
+ "Fetching Sequences from " + proxy.getDbName(), Thread
+ .currentThread().hashCode());
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
if (proxy.getAccessionSeparator() == null)
{
while (en.hasMoreElements())
} catch (OutOfMemoryError oome)
{
new OOMWarning("fetching " + item + " from "
- + database.getSelectedItem(), oome, this);
+ + proxy.getDbName(), oome, this);
}
if (indres != null)
{
- if (aresult == null)
- {
- aresult = indres;
- }
- else
- {
- aresult.append(indres);
- }
+ aresultq.add(item);
+ aresult.add(indres);
}
} catch (Exception e)
{
jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + source, e);
+ + " from " + proxy.getDbName(), e);
}
}
}
}
try
{
- aresult = proxy.getSequenceRecords(multiacc.toString());
+ aresultq.add(multiacc.toString());
+ aresult.add(proxy.getSequenceRecords(multiacc.toString()));
} catch (OutOfMemoryError oome)
{
new OOMWarning("fetching " + multiacc + " from "
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
- if (aresult != null)
+ if (aresult != null && aresult.size() > 0)
{
- parseResult(aresult, null, null);
+ AlignmentI ar = null;
+ if (isAliSource)
+ {
+ // new window for each result
+ while (aresult.size() > 0)
+ {
+ parseResult(aresult.remove(0), aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle(), null);
+ }
+ }
+ else
+ {
+ // concatenate all results in one window
+ while (aresult.size() > 0)
+ {
+ if (ar == null)
+ {
+ ar = aresult.remove(0);
+ }
+ else
+ {
+ ar.append(aresult.remove(0));
+ }
+ ;
+ }
+ parseResult(ar, null, null);
+ }
}
// only remove visual delay after we finished parsing.
guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
return null;
}
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
+ */
+ public String getDefaultRetrievalTitle()
+ {
+ return "Retrieved from " + database.getSelectedItem();
+ }
+
AlignmentI parseResult(AlignmentI al, String title,
String currentFileFormat)
{
if (title == null)
{
- title = "Retrieved from " + database.getSelectedItem();
+ title = getDefaultRetrievalTitle();
}
SequenceFeature[] sfs = null;
for (Enumeration sq = al.getSequences().elements(); sq
{
for (int i = 0; i < al.getHeight(); i++)
{
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this
+ alignFrame.viewport.getAlignment().addSequence(
+ al.getSequenceAt(i)); // this
// also
// creates
// dataset
// sequence
// entries
}
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
.getHeight());
- alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.getAlignment().getWidth();
alignFrame.viewport.firePropertyChange("alignment", null,
alignFrame.viewport.getAlignment().getSequences());
}
git://source.jalview.org / jalview.git / blobdiff