X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=8754fbb59cb3b15653d219a45684d65692ba92b4;hb=bb620cae1e4c44ae9efaf975c7bbbc63b0558db3;hp=e05230bdb71f1e223acf5d7b80e05f9c73cee643;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index e05230b..8754fbb 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.SequenceFeature; 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; @@ -33,7 +34,6 @@ import jalview.io.gff.SequenceOntologyI; import jalview.util.DBRefUtils; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.seqfetcher.DbSourceProxy; import java.awt.BorderLayout; @@ -78,6 +78,8 @@ public class SequenceFetcher extends JPanel implements Runnable JButton close = new JButton(); + JButton back = new JButton(); + JPanel jPanel1 = new JPanel(); JTextArea textArea = new JTextArea(); @@ -108,10 +110,6 @@ public class SequenceFetcher extends JPanel implements Runnable private static jalview.ws.SequenceFetcher sfetch = null; - private static long lastDasSourceRegistry = -3; - - private static DasSourceRegistryI dasRegistry = null; - private static boolean _initingFetcher = false; private static Thread initingThread = null; @@ -162,11 +160,7 @@ public class SequenceFetcher extends JPanel implements Runnable Thread.currentThread().hashCode()); } } - if (sfetch == null || dasRegistry != Cache.getDasSourceRegistry() - || lastDasSourceRegistry != (Cache.getDasSourceRegistry() - .getDasRegistryURL() - + Cache.getDasSourceRegistry().getLocalSourceString()) - .hashCode()) + if (sfetch == null) { _initingFetcher = true; initingThread = Thread.currentThread(); @@ -180,16 +174,12 @@ public class SequenceFetcher extends JPanel implements Runnable "status.init_sequence_database_fetchers"), Thread.currentThread().hashCode()); } - dasRegistry = Cache.getDasSourceRegistry(); - dasRegistry.refreshSources(); jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher(); if (guiWindow != null) { guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); } - lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() - + dasRegistry.getLocalSourceString()).hashCode(); sfetch = sf; _initingFetcher = false; initingThread = null; @@ -270,7 +260,7 @@ public class SequenceFetcher extends JPanel implements Runnable return Collections.emptyList(); } } - sf.newAlframes = new ArrayList(); + sf.newAlframes = new ArrayList<>(); sf.run(); return sf.newAlframes; } @@ -383,6 +373,15 @@ public class SequenceFetcher extends JPanel implements Runnable .getString("label.additional_sequence_fetcher")); } + GFTSPanel parentFTSframe = null; + /** + * change the buttons so they fit with the FTS panel. + */ + public void embedWithFTSPanel(GFTSPanel toClose) + { + back.setVisible(true); + parentFTSframe = toClose; + } private void jbInit() throws Exception { this.setLayout(borderLayout2); @@ -427,7 +426,7 @@ public class SequenceFetcher extends JPanel implements Runnable example_actionPerformed(); } }); - close.setText(MessageManager.getString("action.close")); + close.setText(MessageManager.getString("action.cancel")); close.addActionListener(new ActionListener() { @Override @@ -436,6 +435,17 @@ public class SequenceFetcher extends JPanel implements Runnable close_actionPerformed(e); } }); + back.setText(MessageManager.getString("action.back")); + back.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + parentFTSframe.btn_back_ActionPerformed(); + } + }); + // back not visible unless embedded + back.setVisible(false); textArea.setFont(JvSwingUtils.getLabelFont()); textArea.setLineWrap(true); textArea.addKeyListener(new KeyAdapter() @@ -451,9 +461,10 @@ public class SequenceFetcher extends JPanel implements Runnable }); jPanel3.setLayout(borderLayout1); borderLayout1.setVgap(5); - jPanel1.add(ok); + jPanel1.add(back); jPanel1.add(example); jPanel1.add(clear); + jPanel1.add(ok); jPanel1.add(close); jPanel2.setLayout(borderLayout3); databaseButt = /*database.getDatabaseSelectorButton(); @@ -540,15 +551,10 @@ public class SequenceFetcher extends JPanel implements Runnable dbeg.setText(MessageManager.formatMessage("label.example_query_param", new String[] { eq })); + // TODO this should be a property of the SequenceFetcher whether commas are and + // colons are allowed in the IDs... + 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) @@ -582,6 +588,10 @@ public class SequenceFetcher extends JPanel implements Runnable try { frame.setClosed(true); + if (parentFTSframe!=null) + { + parentFTSframe.btn_cancel_ActionPerformed(); + } } catch (Exception ex) { } @@ -594,7 +604,7 @@ public class SequenceFetcher extends JPanel implements Runnable textArea.setEnabled(false); ok.setEnabled(false); close.setEnabled(false); - + back.setEnabled(false); Thread worker = new Thread(this); worker.start(); } @@ -606,6 +616,7 @@ public class SequenceFetcher extends JPanel implements Runnable textArea.setEnabled(true); ok.setEnabled(true); close.setEnabled(true); + back.setEnabled(parentFTSframe != null); } @Override @@ -645,10 +656,10 @@ public class SequenceFetcher extends JPanel implements Runnable // TODO: Refactor to GUI independent code and write tests. // indicate if successive sources should be merged into one alignment. boolean addToLast = false; - List aresultq = new ArrayList(); - List presultTitle = new ArrayList(); - List presult = new ArrayList(); - List aresult = new ArrayList(); + List aresultq = new ArrayList<>(); + List presultTitle = new ArrayList<>(); + List presult = new ArrayList<>(); + List aresult = new ArrayList<>(); Iterator proxies = database.getSelectedSources() .iterator(); String[] qries; @@ -666,7 +677,7 @@ public class SequenceFetcher extends JPanel implements Runnable nqueries = nextFetch.size(); // save the remaining queries in the original array qries = nextFetch.toArray(new String[nqueries]); - nextFetch = new ArrayList(); + nextFetch = new ArrayList<>(); } DbSourceProxy proxy = proxies.next(); @@ -832,7 +843,7 @@ public class SequenceFetcher extends JPanel implements Runnable List aresult, List nextFetch) throws Exception { StringBuilder multiacc = new StringBuilder(); - List tosend = new ArrayList(); + List tosend = new ArrayList<>(); while (accessions.hasNext()) { String nel = accessions.next(); @@ -1087,4 +1098,9 @@ public class SequenceFetcher extends JPanel implements Runnable { frame.setVisible(false); } + + public void setDatabaseChooserVisible(boolean b) + { + databaseButt.setVisible(b); + } }