X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d8fec3aeb886adee209cd16d2f3e9c95ccf47efa;hb=b364e1e6d199002069dab615d1007799b5bb71e1;hp=8a6907cb9749688a62e9b506dad23e6f801220a7;hpb=0980e87380e2922790d01bde3f616115f1916a43;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 8a6907c..d8fec3a 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -59,6 +59,7 @@ import java.util.Hashtable; import java.util.List; import java.util.Locale; import java.util.Vector; +import java.util.concurrent.Callable; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; @@ -1272,103 +1273,89 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - Runnable cancelAction = new Runnable() - { - @Override - public void run() + Callable cancelAction = () -> { + lastSaveSuccessful = false; + return null; + }; + Callable outputAction = () -> { + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport.getAlignExportData(options); + String output = new FormatAdapter(alignPanel, options) + .formatSequences(format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns()); + if (output == null) { lastSaveSuccessful = false; } - }; - Runnable outputAction = new Runnable() - { - @Override - public void run() + else { - // todo defer this to inside formatSequences (or later) - AlignmentExportData exportData = viewport - .getAlignExportData(options); - String output = new FormatAdapter(alignPanel, options) - .formatSequences(format, exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getAlignment().getHiddenColumns()); - if (output == null) + // create backupfiles object and get new temp filename destination + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = null; + if (doBackup) { - lastSaveSuccessful = false; + Console.trace("ALIGNFRAME making backupfiles object for " + file); + backupfiles = new BackupFiles(file); } - else + try { - // create backupfiles object and get new temp filename destination - boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = null; - if (doBackup) - { - Console.trace( - "ALIGNFRAME making backupfiles object for " + file); - backupfiles = new BackupFiles(file); - } - try - { - String tempFilePath = doBackup ? backupfiles.getTempFilePath() - : file; - Console.trace("ALIGNFRAME setting PrintWriter"); - PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + String tempFilePath = doBackup ? backupfiles.getTempFilePath() + : file; + Console.trace("ALIGNFRAME setting PrintWriter"); + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); - if (backupfiles != null) - { - Console.trace("ALIGNFRAME about to write to temp file " - + backupfiles.getTempFilePath()); - } - - out.print(output); - Console.trace("ALIGNFRAME about to close file"); - out.close(); - Console.trace("ALIGNFRAME closed file"); - AlignFrame.this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", - new Object[] - { fileName, format.getName() })); - lastSaveSuccessful = true; - } catch (IOException e) - { - lastSaveSuccessful = false; - Console.error( - "ALIGNFRAME Something happened writing the temp file"); - Console.error(e.getMessage()); - Console.debug(Cache.getStackTraceString(e)); - } catch (Exception ex) + if (backupfiles != null) { - lastSaveSuccessful = false; - Console.error( - "ALIGNFRAME Something unexpected happened writing the temp file"); - Console.error(ex.getMessage()); - Console.debug(Cache.getStackTraceString(ex)); + Console.trace("ALIGNFRAME about to write to temp file " + + backupfiles.getTempFilePath()); } - if (doBackup) - { - backupfiles.setWriteSuccess(lastSaveSuccessful); - Console.debug("ALIGNFRAME writing temp file was " - + (lastSaveSuccessful ? "" : "NOT ") + "successful"); - // do the backup file roll and rename the temp file to actual file - Console.trace( - "ALIGNFRAME about to rollBackupsAndRenameTempFile"); - lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); - Console.debug( - "ALIGNFRAME performed rollBackupsAndRenameTempFile " - + (lastSaveSuccessful ? "" : "un") - + "successfully"); - } + out.print(output); + Console.trace("ALIGNFRAME about to close file"); + out.close(); + Console.trace("ALIGNFRAME closed file"); + AlignFrame.this.setTitle(file); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new Object[] + { fileName, format.getName() })); + lastSaveSuccessful = true; + } catch (IOException e) + { + lastSaveSuccessful = false; + Console.error( + "ALIGNFRAME Something happened writing the temp file"); + Console.error(e.getMessage()); + Console.debug(Cache.getStackTraceString(e)); + } catch (Exception ex) + { + lastSaveSuccessful = false; + Console.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); + } - Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); - if (lastSaveSuccessful) - { - AlignFrame.this.getViewport().setSavedUpToDate(true); - } + if (doBackup) + { + backupfiles.setWriteSuccess(lastSaveSuccessful); + Console.debug("ALIGNFRAME writing temp file was " + + (lastSaveSuccessful ? "" : "NOT ") + "successful"); + // do the backup file roll and rename the temp file to actual file + Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); + lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); + Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (lastSaveSuccessful ? "" : "un") + "successfully"); + } + + Console.debug("lastSaveSuccessful=" + lastSaveSuccessful); + if (lastSaveSuccessful) + { + AlignFrame.this.getViewport().setSavedUpToDate(true); } } + return null; }; /* @@ -1384,7 +1371,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - outputAction.run(); + try + { + outputAction.call(); + } catch (Exception e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } } } @@ -1401,34 +1395,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FileFormatI fileFormat = FileFormats.getInstance() .forName(fileFormatName); AlignExportSettingsI options = new AlignExportSettingsAdapter(false); - Runnable outputAction = new Runnable() - { - @Override - public void run() + Callable outputAction = () -> { + // todo defer this to inside formatSequences (or later) + AlignmentExportData exportData = viewport.getAlignExportData(options); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + try { - // todo defer this to inside formatSequences (or later) - AlignmentExportData exportData = viewport - .getAlignExportData(options); - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(null); - try - { - FileFormatI format = fileFormat; - cap.setText(new FormatAdapter(alignPanel, options) - .formatSequences(format, exportData.getAlignment(), - exportData.getOmitHidden(), - exportData.getStartEndPostions(), - viewport.getAlignment().getHiddenColumns())); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.alignment_output_command", new Object[] - { fileFormat.getName() }), 600, 500); - } catch (OutOfMemoryError oom) - { - new OOMWarning("Outputting alignment as " + fileFormat.getName(), - oom); - cap.dispose(); - } + FileFormatI format = fileFormat; + cap.setText(new FormatAdapter(alignPanel, options).formatSequences( + format, exportData.getAlignment(), + exportData.getOmitHidden(), + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new Object[] + { fileFormat.getName() }), 600, 500); + } catch (OutOfMemoryError oom) + { + new OOMWarning("Outputting alignment as " + fileFormat.getName(), + oom); + cap.dispose(); } + return null; }; /* @@ -1443,7 +1432,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - outputAction.run(); + try + { + outputAction.call(); + } catch (Exception e) + { + e.printStackTrace(); + } } } @@ -1551,15 +1546,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.load_jalview_annotations"); chooser.setDialogTitle(tooltip); chooser.setToolTipText(tooltip); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); - } + chooser.setResponseHandler(0, () -> { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); + return null; }); chooser.showOpenDialog(this); @@ -2481,36 +2472,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Runnable okAction = new Runnable() - { - @Override - public void run() - { - SequenceI[] cut = sg.getSequences() - .toArray(new SequenceI[sg.getSize()]); + Callable okAction = () -> { + SequenceI[] cut = sg.getSequences() + .toArray(new SequenceI[sg.getSize()]); - addHistoryItem(new EditCommand( - MessageManager.getString("label.cut_sequences"), Action.CUT, - cut, sg.getStartRes(), - sg.getEndRes() - sg.getStartRes() + 1, - viewport.getAlignment())); + addHistoryItem(new EditCommand( + MessageManager.getString("label.cut_sequences"), Action.CUT, + cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, + viewport.getAlignment())); - viewport.setSelectionGroup(null); - viewport.sendSelection(); - viewport.getAlignment().deleteGroup(sg); + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - if (viewport.getAlignment().getHeight() < 1) + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + AlignFrame.this.setClosed(true); + } catch (Exception ex) { - try - { - AlignFrame.this.setClosed(true); - } catch (Exception ex) - { - } } } + return null; }; /* @@ -2534,7 +2520,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - okAction.run(); + try + { + okAction.call(); + } catch (Exception e) + { + e.printStackTrace(); + } } } @@ -4087,36 +4079,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() + chooser.setResponseHandler(0, () -> { + String filePath = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", filePath); + NewickFile fin = null; + try { - String filePath = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", filePath); - NewickFile fin = null; - try - { - fin = new NewickFile(new FileParse(chooser.getSelectedFile(), - DataSourceType.FILE)); - viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); - } catch (Exception ex) - { - JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - MessageManager - .getString("label.problem_reading_tree_file"), - JvOptionPane.WARNING_MESSAGE); - ex.printStackTrace(); - } - if (fin != null && fin.hasWarningMessage()) - { - JvOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), - MessageManager.getString( - "label.possible_problem_with_tree_file"), - JvOptionPane.WARNING_MESSAGE); - } + fin = new NewickFile(new FileParse(chooser.getSelectedFile(), + DataSourceType.FILE)); + viewport.setCurrentTree(showNewickTree(fin, filePath).getTree()); + } catch (Exception ex) + { + JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), + MessageManager.getString("label.problem_reading_tree_file"), + JvOptionPane.WARNING_MESSAGE); + ex.printStackTrace(); } + if (fin != null && fin.hasWarningMessage()) + { + JvOptionPane.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager + .getString("label.possible_problem_with_tree_file"), + JvOptionPane.WARNING_MESSAGE); + } + return null; }); chooser.showOpenDialog(this); } @@ -5888,16 +5875,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); final AlignFrame us = this; - chooser.setResponseHandler(0, new Runnable() - { - @Override - public void run() - { - String choice = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", choice); - SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); - new VCFLoader(choice).loadVCF(seqs, us); - } + chooser.setResponseHandler(0, () -> { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, us); + return null; }); chooser.showOpenDialog(null);