Sequence Fetcher

From: jprocter Date: Wed, 22 Sep 2010 09:59:51 +0000 (+0000) Subject: Fix and documentation for JAL-657 X-Git-Tag: Release_2_6~12 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=152aa52bc19a393141cfc19f5852d1fbcd239f16;p=jalview.git Fix and documentation for JAL-657 --- diff --git a/help/html/features/seqfetch.html b/help/html/features/seqfetch.html index d8415c7..c4d671a 100755 --- a/help/html/features/seqfetch.html +++ b/help/html/features/seqfetch.html @@ -16,36 +16,59 @@ * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . --> -Sequence Fetcher + +Sequence Fetcher +

Sequence Fetcher

Jalview can retrieve sequences from certain databases using either the -WSDBFetch service provided by the European Bioinformatics Institute, and, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).

The Sequence Fetcher dialog box can be opened via the "File" - menu on the main desktop in order to retrieve sequences as a new - alignment, or opened via the "File" menu of an existing alignment - to import additional sequences. Please note, there will be a short delay when the sequence fetcher is first opened, - whilst Jalview compiles the list of available sequence datasources from the - currently defined DAS server registry. +

Jalview can retrieve sequences from certain databases using +either the WSDBFetch service provided by the European Bioinformatics +Institute, and, since Jalview 2.4, DAS servers capable of the sequence +command (configured in DAS settings).

The Sequence Fetcher dialog box can be opened via the +"File" menu on the main desktop in order to retrieve sequences +as a new alignment, or opened via the "File" menu of an +existing alignment to import additional sequences. Please note, there +will be a short delay when the sequence fetcher is first opened, whilst +Jalview compiles the list of available sequence datasources from the +currently defined DAS server registry.

First, select the database you want to retrieve sequences from. +Then, enter one or more accession ids (as a semi-colon separated list), +or press the "Example" button to paste the example accession +for the currently selected database into the retrieval box. Finally, +press "OK" to initiate the retrieval.

Fetching Individual PDB Chains
+If you are retrieving sequences from the PDB, you can retrieve specific +chains by appending a colon and the chain id to the PDB id. For example +:
+

 1GAQ:A

+
+When retrieving from DAS sequence sources, coordinate range arguments +can be passed to the server using the standard DAS sequence command +format ( +:<start>,<end> +) +

Retrieving parts of large sequence records
+Some sequence sources allow a range query to be appended to the sequence +ID - e.g. 'Mito:1,85779'. If you know a source understands this type of +query format, then you should untick the checkbox for 'replace commas +with semi-colons' so the range query can be passed to the server +(otherwise the query will be split up into two 'Mito:1' and '85779'). In +some cases, a source that supports range queries usually include a range +qualification in its example query. In this case, Jalview will +automatically disable the 'replace commas with semi-colons' option.
+Support for range queries was added in Jalview 2.6

If you use the WSDBFetch sequence fetcher services (EMBL, +Uniprot, PDB and PFAM) in work for publication, please cite:

Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., +Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez +R.
+SOAP-based services provided by the European Bioinformatics Institute.
+Nucleic Acids Res. 33(1):W25-W28 (2005)
+

First, select the database you want to retrieve sequences from. Then, enter - one or more accession ids (as a semi-colon separated list), or press the - "Example" button to paste the example accession for the currently selected database into the retrieval box. - Finally, press "OK" to initiate the retrieval.

- If you are retrieving sequences from the PDB, you can retrieve - specific chains by appending a colon and the chain id to the PDB - id. For example :

 1GAQ:A

When retrieving from DAS sequence sources, - coordinate range arguments can be passed to the server using the standard DAS - sequence command format (:<start>,<end>)

If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB and PFAM) - in work for publication, please cite:

Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar - S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
- SOAP-based services provided by the European Bioinformatics Institute.
- Nucleic Acids Res. 33(1):W25-W28 (2005)
-
-

diff --git a/help/html/features/seqfetcher.gif b/help/html/features/seqfetcher.gif index 809d719..652976f 100644 Binary files a/help/html/features/seqfetcher.gif and b/help/html/features/seqfetcher.gif differ diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index c5a9235..af8c108 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -57,8 +57,11 @@ public class SequenceFetcher extends JPanel implements Runnable private static jalview.ws.SequenceFetcher sfetch = null; private static String dasRegistry = null; - private static boolean _initingFetcher=false; - private static Thread initingThread=null; + + private static boolean _initingFetcher = false; + + private static Thread initingThread = null; + /** * Blocking method that initialises and returns the shared instance of the * SequenceFetcher client @@ -70,29 +73,39 @@ public class SequenceFetcher extends JPanel implements Runnable public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton( final IProgressIndicator guiWindow) { - if (_initingFetcher && initingThread!=null && initingThread.isAlive()) + if (_initingFetcher && initingThread != null && initingThread.isAlive()) { if (guiWindow != null) { - guiWindow.setProgressBar("Waiting for Sequence Database Fetchers to initialise", + guiWindow.setProgressBar( + "Waiting for Sequence Database Fetchers to initialise", Thread.currentThread().hashCode()); } - // initting happening on another thread - so wait around to see if it finishes. - while (_initingFetcher && initingThread!=null && initingThread.isAlive()) + // initting happening on another thread - so wait around to see if it + // finishes. + while (_initingFetcher && initingThread != null + && initingThread.isAlive()) { - try {Thread.sleep(10);} catch (Exception e){}; + try + { + Thread.sleep(10); + } catch (Exception e) + { + } + ; } if (guiWindow != null) { - guiWindow.setProgressBar("Waiting for Sequence Database Fetchers to initialise", + guiWindow.setProgressBar( + "Waiting for Sequence Database Fetchers to initialise", Thread.currentThread().hashCode()); } } if (sfetch == null || dasRegistry != DasSourceBrowser.getDasRegistryURL()) { - _initingFetcher=true; - initingThread=Thread.currentThread(); + _initingFetcher = true; + initingThread = Thread.currentThread(); /** * give a visual indication that sequence fetcher construction is occuring */ @@ -109,8 +122,8 @@ public class SequenceFetcher extends JPanel implements Runnable initingThread.hashCode()); } sfetch = sf; - _initingFetcher=false; - initingThread=null; + _initingFetcher = false; + initingThread = null; } return sfetch; } @@ -198,11 +211,11 @@ public class SequenceFetcher extends JPanel implements Runnable frame.setContentPane(this); if (new jalview.util.Platform().isAMac()) { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180); + Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240); } else { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140); + Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180); } } @@ -220,8 +233,12 @@ 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("Separate multiple accession ids with semi colon \";\""); + + replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER); + replacePunctuation + .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); + replacePunctuation.setText("Replace commas with semi-colons"); ok.setText("OK"); ok.addActionListener(new ActionListener() { @@ -284,10 +301,13 @@ public class SequenceFetcher extends JPanel implements Runnable { db = sfetch.getSourceProxy((String) sources.get(database .getSelectedItem())); - dbeg.setText("Example query: " + db.getTestQuery()); + String eq = db.getTestQuery(); + dbeg.setText("Example query: " + eq); + replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1)); } catch (Exception ex) { dbeg.setText(""); + replacePunctuation.setEnabled(true); } jPanel2.repaint(); } @@ -295,7 +315,10 @@ public class SequenceFetcher extends JPanel implements Runnable dbeg.setText(""); jPanel2.add(database, java.awt.BorderLayout.NORTH); jPanel2.add(dbeg, java.awt.BorderLayout.CENTER); - jPanel2.add(jLabel1, java.awt.BorderLayout.SOUTH); + JPanel jPanel2a = new JPanel(new BorderLayout()); + jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH); + jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH); + jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH); // jPanel2.setPreferredSize(new Dimension()) jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER); this.add(jPanel1, java.awt.BorderLayout.SOUTH); @@ -331,6 +354,8 @@ public class SequenceFetcher extends JPanel implements Runnable JLabel jLabel1 = new JLabel(); + JCheckBox replacePunctuation = new JCheckBox(); + JButton ok = new JButton(); JButton clear = new JButton(); @@ -393,9 +418,19 @@ public class SequenceFetcher extends JPanel implements Runnable { error += "Please select the source database\n"; } - // TODO: make this transformation optional and configurable - com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex( - "(\\s|[,; ])+", ";"); // \\s+", ""); + // TODO: make this transformation more configurable + com.stevesoft.pat.Regex empty; + if (replacePunctuation.isEnabled() && replacePunctuation.isSelected()) + { + empty = new com.stevesoft.pat.Regex( + // replace commas and spaces with a semicolon + "(\\s|[,; ])+", ";"); + } + else + { + // just turn spaces and semicolons into single semicolons + empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";"); + } textArea.setText(empty.replaceAll(textArea.getText())); // see if there's anthing to search with if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea @@ -414,9 +449,9 @@ public class SequenceFetcher extends JPanel implements Runnable Enumeration en = new StringTokenizer(textArea.getText(), ";"); try { - guiWindow.setProgressBar("Fetching Sequences from " - + database.getSelectedItem(), Thread.currentThread() - .hashCode()); + guiWindow.setProgressBar( + "Fetching Sequences from " + database.getSelectedItem(), + Thread.currentThread().hashCode()); DbSourceProxy proxy = sfetch.getSourceProxy((String) sources .get(source)); if (proxy.getAccessionSeparator() == null) @@ -445,10 +480,8 @@ public class SequenceFetcher extends JPanel implements Runnable indres = proxy.getSequenceRecords(item); } catch (OutOfMemoryError oome) { - new OOMWarning( - "fetching " + item + " from " - + database.getSelectedItem(),oome, - this); + new OOMWarning("fetching " + item + " from " + + database.getSelectedItem(), oome, this); } if (indres != null) { @@ -484,13 +517,10 @@ public class SequenceFetcher extends JPanel implements Runnable aresult = proxy.getSequenceRecords(multiacc.toString()); } catch (OutOfMemoryError oome) { - new OOMWarning( - "fetching " + multiacc + " from " - + database.getSelectedItem(),oome, - this); + new OOMWarning("fetching " + multiacc + " from " + + database.getSelectedItem(), oome, this); } - - + } } catch (Exception e)