X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=9f92c42c0117d300eee1a25f68fbf5eabf5cfc18;hp=56b4b875e209a876c7658a46ee92d95caa26df85;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=7d76e402efd4e04e179bc9bb264551bc2d3df936 diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 56b4b87..9f92c42 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,6 +1,6 @@ /* - * 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 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,7 +20,6 @@ */ package jalview.gui; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; @@ -116,6 +115,7 @@ public class SequenceFetcher extends JPanel implements Runnable private static Thread initingThread = null; int debounceTrap = 0; + /** * Blocking method that initialises and returns the shared instance of the * SequenceFetcher client @@ -131,9 +131,11 @@ public class SequenceFetcher extends JPanel implements Runnable { 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. @@ -150,9 +152,11 @@ public class SequenceFetcher extends JPanel implements Runnable } 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 @@ -169,7 +173,8 @@ public class SequenceFetcher extends JPanel implements Runnable */ 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(); @@ -178,8 +183,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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(); @@ -190,9 +194,11 @@ public class SequenceFetcher extends JPanel implements Runnable 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() @@ -201,9 +207,9 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - if (getSequenceFetcherSingleton(guiWindow) != null) + if (getSequenceFetcherSingleton(progressIndicator) != null) { - us.initGui(guiWindow); + us.initGui(progressIndicator); } else { @@ -215,8 +221,10 @@ public class SequenceFetcher extends JPanel implements Runnable 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); } }); @@ -273,7 +281,9 @@ public class SequenceFetcher extends JPanel implements Runnable 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 @@ -359,18 +369,19 @@ public class SequenceFetcher extends JPanel implements Runnable { debounceTrap++; String currentSelection = database.getSelectedItem(); - if (!currentSelection.equalsIgnoreCase("pdb")) { - otherSourceAction(); + otherSourceAction(); } - if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0)) + if (currentSelection.equalsIgnoreCase("pdb") + && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) { pdbSourceAction(); } - + database.action = -1; } }); + dbeg.setText(""); jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH); jPanel2.add(dbeg, java.awt.BorderLayout.CENTER); @@ -390,7 +401,7 @@ public class SequenceFetcher extends JPanel implements Runnable private void pdbSourceAction() { databaseButt.setText(database.getSelectedItem()); - new PDBFetchPanel(this); + new PDBSearchPanel(this); frame.dispose(); } @@ -404,8 +415,7 @@ public class SequenceFetcher extends JPanel implements Runnable : "")); 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()) { @@ -443,8 +453,6 @@ public class SequenceFetcher extends JPanel implements Runnable jPanel3.repaint(); } - - public void close_actionPerformed(ActionEvent e) { try @@ -537,8 +545,13 @@ public class SequenceFetcher extends JPanel implements Runnable try { // update status - guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread - .currentThread().hashCode()); + 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) { @@ -735,11 +748,15 @@ public class SequenceFetcher extends JPanel implements Runnable 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) { @@ -774,7 +791,7 @@ public class SequenceFetcher extends JPanel implements Runnable AlignmentI parseResult(String result, String title) { String format = new IdentifyFile().Identify(result, "Paste"); - Alignment sequences = null; + AlignmentI sequences = null; if (FormatAdapter.isValidFormat(format)) { sequences = null; @@ -816,6 +833,10 @@ public class SequenceFetcher extends JPanel implements Runnable if (al != null && al.getHeight() > 0) { + if (title == null) + { + title = getDefaultRetrievalTitle(); + } if (alignFrame == null) { AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, @@ -828,10 +849,6 @@ public class SequenceFetcher extends JPanel implements Runnable // Alignments? } - if (title == null) - { - title = getDefaultRetrievalTitle(); - } SequenceFeature[] sfs = null; List alsqs; synchronized (alsqs = al.getSequences()) @@ -865,21 +882,7 @@ public class SequenceFetcher extends JPanel implements Runnable } 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; @@ -899,4 +902,14 @@ public class SequenceFetcher extends JPanel implements Runnable } }); } + + public IProgressIndicator getProgressIndicator() + { + return progressIndicator; + } + + public void setProgressIndicator(IProgressIndicator progressIndicator) + { + this.progressIndicator = progressIndicator; + } }