X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=71348ef9bf5349dc212d042d9ec6c9d5842aad14;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d596183b28d12732a9dfe69b144c0858441d67d1;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index d596183..71348ef 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,43 +1,43 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.io.*;
import java.util.*;
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
-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.util.DBRefUtils;
+import jalview.util.MessageManager;
+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
{
@@ -52,11 +52,11 @@ 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;
@@ -78,7 +78,7 @@ public class SequenceFetcher extends JPanel implements Runnable
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
@@ -97,12 +97,16 @@ public class SequenceFetcher extends JPanel implements Runnable
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
}
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();
@@ -111,16 +115,20 @@ public class SequenceFetcher extends JPanel implements Runnable
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ guiWindow.setProgressBar(MessageManager.getString("status.init_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",
+ guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
+ .getLocalSourceString()).hashCode();
sfetch = sf;
_initingFetcher = false;
initingThread = null;
@@ -136,6 +144,7 @@ public class SequenceFetcher extends JPanel implements Runnable
Thread sf = new Thread(new Runnable()
{
+ @Override
public void run()
{
if (getSequenceFetcherSingleton(guiWindow) != null)
@@ -146,13 +155,14 @@ public class SequenceFetcher extends JPanel implements Runnable
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Could not create the sequence fetcher client. Check error logs for details.",
- "Couldn't create SequenceFetcher",
+ MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString("label.couldnt_create_sequence_fetcher"),
JOptionPane.ERROR_MESSAGE);
}
});
@@ -164,6 +174,16 @@ public class SequenceFetcher extends JPanel implements Runnable
sf.start();
}
+ private class DatabaseAuthority extends DefaultMutableTreeNode
+ {
+
+ };
+
+ private class DatabaseSource extends DefaultMutableTreeNode
+ {
+
+ };
+
/**
* called by thread spawned by constructor
*
@@ -176,29 +196,7 @@ public class SequenceFetcher extends JPanel implements Runnable
{
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();
@@ -221,8 +219,7 @@ public class SequenceFetcher extends JPanel implements Runnable
private String getFrameTitle()
{
- return ((alignFrame == null) ? "New " : "Additional ")
- + "Sequence Fetcher";
+ return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
}
private void jbInit() throws Exception
@@ -233,40 +230,46 @@ public class SequenceFetcher extends JPanel implements Runnable
dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
- jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+ jLabel1.setText(MessageManager
+ .getString("label.separate_multiple_accession_ids"));
replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
replacePunctuation
.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- replacePunctuation.setText("Replace commas with semi-colons");
- ok.setText("OK");
+ replacePunctuation.setText(MessageManager
+ .getString("label.replace_commas_semicolons"));
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed();
}
});
- clear.setText("Clear");
+ clear.setText(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
}
});
- example.setText("Example");
+ example.setText(MessageManager.getString("label.example"));
example.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
}
});
- close.setText("Close");
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
@@ -276,6 +279,7 @@ public class SequenceFetcher extends JPanel implements Runnable
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
@@ -290,20 +294,35 @@ public class SequenceFetcher extends JPanel implements Runnable
jPanel1.add(close);
jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
jPanel2.setLayout(borderLayout3);
-
+ databaseButt = database.getDatabaseSelectorButton();
+ databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- String eq = db.getTestQuery();
- dbeg.setText("Example query: " + eq);
- replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size()
+ + " others)" : ""));
+ String eq = database.getExampleQueries();
+ dbeg.setText(MessageManager.formatMessage(
+ "label.example_query_param", new String[]
+ { eq }));
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ for (DbSourceProxy dbs : database.getSelectedSources())
+ {
+ if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ enablePunct = false;
+ break;
+ }
+ }
+ replacePunctuation.setEnabled(enablePunct);
+
} catch (Exception ex)
{
dbeg.setText("");
@@ -313,7 +332,7 @@ public class SequenceFetcher extends JPanel implements Runnable
}
});
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);
@@ -333,9 +352,7 @@ public class SequenceFetcher extends JPanel implements Runnable
DbSourceProxy db = null;
try
{
- db = sfetch.getSourceProxy((String) sources.get(database
- .getSelectedItem()));
- textArea.setText(db.getTestQuery());
+ textArea.setText(database.getExampleQueries());
} catch (Exception ex)
{
}
@@ -350,7 +367,9 @@ public class SequenceFetcher extends JPanel implements Runnable
JLabel dbeg = new JLabel();
- JComboBox database = new JComboBox();
+ JDatabaseTree database;
+
+ JButton databaseButt;
JLabel jLabel1 = new JLabel();
@@ -394,7 +413,8 @@ public class SequenceFetcher extends JPanel implements Runnable
public void ok_actionPerformed()
{
- database.setEnabled(false);
+ databaseButt.setEnabled(false);
+ example.setEnabled(false);
textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
@@ -405,16 +425,18 @@ public class SequenceFetcher extends JPanel implements Runnable
private void resetDialog()
{
- database.setEnabled(true);
+ databaseButt.setEnabled(true);
+ example.setEnabled(true);
textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
}
+ @Override
public void run()
{
String error = "";
- if (database.getSelectedItem().equals(noDbSelected))
+ if (!database.hasSelection())
{
error += "Please select the source database\n";
}
@@ -444,274 +466,267 @@ public class SequenceFetcher extends JPanel implements Runnable
resetDialog();
return;
}
- ArrayList aresultq=new ArrayList();
- ArrayList aresult = new ArrayList();
- Object source = database.getSelectedItem();
- 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));
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ // indicate if successive sources should be merged into one alignment.
+ boolean addToLast = false;
+ ArrayList aresultq = new ArrayList(), presultTitle = new ArrayList();
+ ArrayList presult = new ArrayList(), aresult = new ArrayList();
+ Iterator proxies = database.getSelectedSources()
+ .iterator();
+ String[] qries;
+ List nextfetch = Arrays.asList(qries = textArea.getText()
+ .split(";"));
+ Iterator en = Arrays.asList(new String[0]).iterator();
+ int nqueries = qries.length;
+ while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
+ {
+ if (!en.hasNext() && nextfetch.size() > 0)
{
- while (en.hasMoreElements())
+ en = nextfetch.iterator();
+ nqueries = nextfetch.size();
+ // save the remaining queries in the original array
+ qries = nextfetch.toArray(new String[nqueries]);
+ nextfetch = new ArrayList();
+ }
+
+ 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)
{
- String item = (String) en.nextElement();
- try
+ while (en.hasNext())
{
- if (aresult != null)
+ 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
{
- // give the server a chance to breathe
- Thread.sleep(5);
- } catch (Exception e)
+ 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)
+ {
+ jalview.bin.Cache.log.info("Error retrieving " + item
+ + " from " + proxy.getDbName(), e);
+ nextfetch.add(item);
}
-
- AlignmentI indres = null;
- try
+ }
+ }
+ else
+ {
+ StringBuffer multiacc = new StringBuffer();
+ ArrayList tosend = new ArrayList();
+ while (en.hasNext())
+ {
+ String nel = en.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (en.hasNext())
{
- indres = proxy.getSequenceRecords(item);
- } catch (OutOfMemoryError oome)
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+ try
+ {
+ AlignmentI rslt;
+ SequenceI[] rs;
+ List nores = new ArrayList();
+ rslt = proxy.getSequenceRecords(multiacc.toString());
+ if (rslt == null || rslt.getHeight() == 0)
{
- new OOMWarning("fetching " + item + " from "
- + database.getSelectedItem(), oome, this);
+ // no results - pass on all queries to next source
+ nextfetch.addAll(tosend);
}
- if (indres != null)
+ else
{
- aresultq.add(item);
- aresult.add(indres);
+ 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 (Exception e)
+ } catch (OutOfMemoryError oome)
{
- jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + source, e);
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
}
+
+ } catch (Exception e)
+ {
+ showErrorMessage("Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ // error
+ // +="Couldn't retrieve sequences from "+database.getSelectedItem();
+ System.err.println("Retrieval failed for source ='"
+ + database.getSelectedItem() + "' and query\n'"
+ + textArea.getText() + "'\n");
+ e.printStackTrace();
+ } catch (OutOfMemoryError e)
+ {
+ // resets dialog box - so we don't use OOMwarning here.
+ showErrorMessage("Out of Memory when retrieving "
+ + textArea.getText()
+ + " from "
+ + database.getSelectedItem()
+ + "\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());
+ e.printStackTrace();
}
- else
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
{
- StringBuffer multiacc = new StringBuffer();
- while (en.hasMoreElements())
+ AlignmentI ar = null;
+ if (isAliSource)
{
- multiacc.append(en.nextElement());
- if (en.hasMoreElements())
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
{
- multiacc.append(proxy.getAccessionSeparator());
+ presult.add(aresult.remove(0));
+ presultTitle.add(aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle());
}
}
- try
- {
- aresultq.add(multiacc.toString());
- aresult.add(proxy.getSequenceRecords(multiacc.toString()));
- } catch (OutOfMemoryError oome)
+ else
{
- new OOMWarning("fetching " + multiacc + " from "
- + database.getSelectedItem(), oome, this);
+ String titl = null;
+ if (addToLast && presult.size() > 0)
+ {
+ ar = presult.remove(presult.size() - 1);
+ titl = presultTitle.remove(presultTitle.size() - 1);
+ }
+ // concatenate all results in one window
+ while (aresult.size() > 0)
+ {
+ if (ar == null)
+ {
+ ar = aresult.remove(0);
+ }
+ else
+ {
+ ar.append(aresult.remove(0));
+ }
+ ;
+ }
+ addToLast = true;
+ presult.add(ar);
+ presultTitle.add(titl);
}
-
}
-
- } catch (Exception e)
- {
- showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
- // error +="Couldn't retrieve sequences from "+database.getSelectedItem();
- System.err.println("Retrieval failed for source ='"
- + database.getSelectedItem() + "' and query\n'"
- + textArea.getText() + "'\n");
- e.printStackTrace();
- } catch (OutOfMemoryError e)
- {
- // resets dialog box - so we don't use OOMwarning here.
- showErrorMessage("Out of Memory when retrieving "
- + textArea.getText()
- + " from "
- + database.getSelectedItem()
- + "\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());
- e.printStackTrace();
+ guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
+ .hashCode());
}
- if (aresult != null && aresult.size()>0)
+ guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
+ : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
+ // process results
+ while (presult.size() > 0)
{
- AlignmentI ar=null;
- if (isAliSource) {
- // new window for each result
- while (aresult.size()>0)
+ parseResult(presult.remove(0), presultTitle.remove(0), null);
+ }
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+ if (nextfetch.size() > 0)
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Didn't retrieve the following "
+ + (nextfetch.size() == 1 ? "query" : nextfetch.size()
+ + " queries") + ": \n");
+ int l = sb.length(), lr = 0;
+ for (String s : nextfetch)
+ {
+ if (l != sb.length())
{
- parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
+ sb.append("; ");
}
- } else {
- // concatenate all results in one window
- while (aresult.size()>0)
+ if (lr - sb.length() > 40)
{
- if (ar==null) { ar = aresult.remove(0);}
- else { ar.append(aresult.remove(0)); };
+ sb.append("\n");
}
- parseResult(ar, null, null);
- }
+ sb.append(s);
+ }
+ showErrorMessage(sb.toString());
}
- // only remove visual delay after we finished parsing.
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
resetDialog();
}
- /*
- * result = new StringBuffer(); if
- * (database.getSelectedItem().equals("Uniprot")) {
- * getUniprotFile(textArea.getText()); } else if
- * (database.getSelectedItem().equals("EMBL") ||
- * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
- * database.getSelectedItem().equals("EMBLCDS") ?
- * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
- *
- * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
- * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch
- * = new EBIFetchClient(); String qry =
- * database.getSelectedItem().toString().toLowerCase( ) + ":" +
- * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
- *
- * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
- * reply.exists()) { efile =
- * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null)
- * { for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
- * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
- * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
- * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
- * SequenceI[seqparts.length]; } else { newseqs = new
- * SequenceI[seqs.length+seqparts.length];
- *
- * for (;si0) { if (parseResult(new Alignment(seqs), null,
- * null)!=null) { result.append("# Successfully parsed the
- * "+database.getSelectedItem()+" Queries into an Alignment"); } } } else if
- * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
- * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
- * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
- * SequenceI[] seqparts = getPDBFile(query.toUpperCase()); if (seqparts !=
- * null) { if (seqs == null) { seqs = seqparts; } else { SequenceI[] newseqs =
- * new SequenceI[seqs.length+seqparts.length]; int i=0; for (; i <
- * seqs.length; i++) { newseqs[i] = seqs[i]; seqs[i] = null; } for (int
- * j=0;j 0) { if (parseResult(new
- * Alignment(seqs), null, null)!=null) { result.append( "# Successfully parsed
- * the PDB File Queries into an
- * Alignment"); } } } else if( database.getSelectedItem().equals("PFAM")) {
- * try { result.append(new FastaFile(
- * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
- * textArea.getText().toUpperCase(), "URL").print() );
- *
- * if(result.length()>0) { parseResult( result.toString(),
- * textArea.getText().toUpperCase() ); } } catch (java.io.IOException ex) {
- * result = null; } }
- *
- * if (result == null || result.length() == 0) { showErrorMessage("Error
- * retrieving " + textArea.getText() + " from " + database.getSelectedItem());
- * }
- *
- * resetDialog(); return; }
- *
- * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
- * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
- *
- * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
- * dbref.getUniprotEntries(file);
- *
- * if (entries != null) { //First, make the new sequences Enumeration en =
- * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
- * (UniprotEntry) en.nextElement();
- *
- * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
- * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
- * name.append("|"); name.append(en2.nextElement()); } en2 =
- * entry.getName().elements(); while (en2.hasMoreElements()) {
- * name.append("|"); name.append(en2.nextElement()); }
- *
- * if (entry.getProtein() != null) { name.append(" " +
- * entry.getProtein().getName().elementAt(0)); }
- *
- * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- * "\n"); }
- *
- * //Then read in the features and apply them to the dataset Alignment al =
- * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
- * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
- * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
- * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
- *
- * onlyPdbEntries.addElement(pdb); }
- *
- * Enumeration en2 = entry.getAccession().elements(); while
- * (en2.hasMoreElements()) {
- * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
- *
- *
- *
- *
- * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
- * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
- * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
- * e.nextElement(); sf.setFeatureGroup("Uniprot");
- * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } }
- * }
- *
- * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
- * chain = null; if (id.indexOf(":") > -1) { chain =
- * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
- *
- * EBIFetchClient ebi = new EBIFetchClient(); String file =
- * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file
- * == null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
- * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
- * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
- * pdbfile.chains.elementAt(i)).id. toUpperCase().equals(chain)) { PDBChain
- * pdbchain = (PDBChain) pdbfile.chains.elementAt(i); // Get the Chain's
- * Sequence - who's dataset includes any special features added from the PDB
- * file SequenceI sq = pdbchain.sequence; // Specially formatted name for the
- * PDB chain sequences retrieved from the PDB
- * sq.setName("PDB|"+id+"|"+sq.getName()); // Might need to add more metadata
- * to the PDBEntry object // like below /* PDBEntry entry = new PDBEntry(); //
- * Construct the PDBEntry entry.setId(id); if (entry.getProperty() == null)
- * entry.setProperty(new Hashtable()); entry.getProperty().put("chains",
- * pdbchain.id + "=" + sq.getStart() + "-" + sq.getEnd());
- * sq.getDatasetSequence().addPDBId(entry); // Add PDB DB Refs // We make a
- * DBRefEtntry because we have obtained the PDB file from a verifiable source
- * // JBPNote - PDB DBRefEntry should also carry the chain and mapping
- * information DBRefEntry dbentry = new
- * DBRefEntry(jalview.datamodel.DBRefSource.PDB, "0", id + pdbchain.id);
- * sq.addDBRef(dbentry); // and add seuqence to the retrieved set
- * result.addElement(sq.deriveSequence()); } }
- *
- * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
- * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file
- * { jalview.bin.Cache.log.warn("Exception when retrieving " +
- * textArea.getText() + " from " + database.getSelectedItem(), ex); return
- * null; }
- *
- *
- * SequenceI[] results = new SequenceI[result.size()]; for (int i = 0, j =
- * result.size(); i < j; i++) { results[i] = (SequenceI) result.elementAt(i);
- * result.setElementAt(null,i); } return results; }
- */
AlignmentI parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
@@ -743,11 +758,14 @@ public class SequenceFetcher extends JPanel implements Runnable
/**
*
- * @return a standard title for any results retrieved using the currently selected source and settings
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
*/
- public String getDefaultRetrievalTitle() {
+ public String getDefaultRetrievalTitle()
+ {
return "Retrieved from " + database.getSelectedItem();
}
+
AlignmentI parseResult(AlignmentI al, String title,
String currentFileFormat)
{
@@ -771,24 +789,27 @@ public class SequenceFetcher extends JPanel implements Runnable
title = getDefaultRetrievalTitle();
}
SequenceFeature[] sfs = null;
- for (Enumeration sq = al.getSequences().elements(); sq
- .hasMoreElements();)
+ List alsqs;
+ synchronized (alsqs = al.getSequences())
{
- if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
- .getSequenceFeatures()) != null)
+ for (SequenceI sq : alsqs)
{
- if (sfs.length > 0)
+ if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
{
- af.setShowSeqFeatures(true);
- break;
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
}
- }
+ }
}
Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
@@ -802,7 +823,8 @@ public class SequenceFetcher extends JPanel implements Runnable
{
for (int i = 0; i < al.getHeight(); i++)
{
- alignFrame.viewport.getAlignment().addSequence(al.getSequenceAt(i)); // this
+ alignFrame.viewport.getAlignment().addSequence(
+ al.getSequenceAt(i)); // this
// also
// creates
// dataset
@@ -824,10 +846,12 @@ public class SequenceFetcher extends JPanel implements Runnable
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.error_retrieving_data"),
+ JOptionPane.WARNING_MESSAGE);
}
});
}