X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=742a10940d73a7ac8b753eb6ae23f2d9798784d4;hb=ef9282b464dc189faf9ce40a4b7420a204266668;hp=6a0d0102b6b92cc1c9bfe8d1863f908659c7f15c;hpb=08643e75e18b16562e90e9b42c0b327f9c46226b;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 6a0d010..742a109 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -22,7 +22,6 @@ package jalview.gui; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; @@ -54,8 +53,6 @@ import javax.swing.JTextArea; import javax.swing.SwingConstants; import javax.swing.tree.DefaultMutableTreeNode; -import com.stevesoft.pat.Regex; - public class SequenceFetcher extends JPanel implements Runnable { JLabel dbeg = new JLabel(); @@ -115,6 +112,7 @@ 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 @@ -130,9 +128,11 @@ 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. @@ -149,9 +149,11 @@ 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 @@ -168,7 +170,8 @@ 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(); @@ -189,6 +192,7 @@ public class SequenceFetcher extends JPanel implements Runnable } private IProgressIndicator progressIndicator; + public SequenceFetcher(IProgressIndicator guiIndic) { this.progressIndicator = guiIndic; @@ -214,8 +218,10 @@ 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); } }); @@ -272,7 +278,9 @@ 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 @@ -360,7 +368,7 @@ public class SequenceFetcher extends JPanel implements Runnable String currentSelection = database.getSelectedItem(); if (!currentSelection.equalsIgnoreCase("pdb")) { - otherSourceAction(); + otherSourceAction(); } if (currentSelection.equalsIgnoreCase("pdb") && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0))) @@ -404,8 +412,7 @@ 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 +450,6 @@ public class SequenceFetcher extends JPanel implements Runnable jPanel3.repaint(); } - - public void close_actionPerformed(ActionEvent e) { try @@ -510,6 +515,7 @@ public class SequenceFetcher extends JPanel implements Runnable resetDialog(); return; } + // TODO: Refactor to GUI independent code and write tests. // indicate if successive sources should be merged into one alignment. boolean addToLast = false; ArrayList aresultq = new ArrayList(), presultTitle = new ArrayList(); @@ -537,9 +543,14 @@ 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()); - isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB); + guiWindow + .setProgressBar(MessageManager.formatMessage( + "status.fetching_sequence_queries_from", + new String[] { + Integer.valueOf(nqueries).toString(), + proxy.getDbName() }), Thread.currentThread() + .hashCode()); + isAliSource = proxy.isAlignmentSource(); if (proxy.getAccessionSeparator() == null) { while (en.hasNext()) @@ -626,34 +637,18 @@ public class SequenceFetcher extends JPanel implements Runnable 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); - } + String accId = proxy.getAccessionIdFromQuery(q); + dbr.setAccessionId(accId); boolean rfound = false; for (int r = 0; r < rs.length; r++) { if (rs[r] != null && (found = DBRefUtils.searchRefs( - rs[r].getDBRef(), dbr)) != null + rs[r].getDBRefs(), dbr)) != null && found.length > 0) { rfound = true; rs[r] = null; - continue; } } if (!rfound) @@ -735,11 +730,15 @@ 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) { @@ -773,7 +772,7 @@ public class SequenceFetcher extends JPanel implements Runnable AlignmentI parseResult(String result, String title) { - String format = new IdentifyFile().Identify(result, "Paste"); + String format = new IdentifyFile().identify(result, "Paste"); AlignmentI sequences = null; if (FormatAdapter.isValidFormat(format)) { @@ -891,8 +890,6 @@ public class SequenceFetcher extends JPanel implements Runnable return progressIndicator; } - - public void setProgressIndicator(IProgressIndicator progressIndicator) { this.progressIndicator = progressIndicator;