X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5b7a2017c8c364695e7e1b1dea370f2a6debb344;hb=8a864dd19ed838f57d850d72d6c17a5cb02fc3de;hp=ef402615a9f0f3d789c5c00ae2e447dfed72f34e;hpb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index ef40261..5b7a201 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -48,6 +48,7 @@ import java.awt.print.PrinterJob; import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; +import java.io.IOException; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; @@ -345,8 +346,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { -// setBackground(Color.white); // BH 2019 - + // setBackground(Color.white); // BH 2019 + if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); @@ -1241,15 +1242,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String shortName = title; if (shortName.indexOf(File.separatorChar) > -1) { - shortName = shortName.substring( - shortName.lastIndexOf(File.separatorChar) + 1); + shortName = shortName + .substring(shortName.lastIndexOf(File.separatorChar) + 1); } - lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); - + lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, + shortName); + statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { fileName, format })); - + return; } @@ -1283,31 +1285,78 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // create backupfiles object and get new temp filename destination boolean doBackup = BackupFiles.getEnabled(); - BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null; + BackupFiles backupfiles = null; + if (doBackup) + { + Cache.log.debug( + "ALIGNFRAME making backupfiles object for " + file); + backupfiles = new BackupFiles(file); + } try { - String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; - PrintWriter out = new PrintWriter( - new FileWriter(tempFilePath)); + String tempFilePath = doBackup ? backupfiles.getTempFilePath() + : file; + Cache.log.debug("ALIGNFRAME setting PrintWriter"); + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + + if (backupfiles != null) + { + Cache.log.debug("ALIGNFRAME using temp file " + + backupfiles.getTempFilePath()); + } out.print(output); + Cache.log.debug("ALIGNFRAME about to close file"); out.close(); + Cache.log.debug("ALIGNFRAME closed file"); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format.getName() })); + "label.successfully_saved_to_file_in_format", + new Object[] + { fileName, format.getName() })); lastSaveSuccessful = true; + } catch (IOException e) + { + lastSaveSuccessful = false; + Cache.log.error( + "ALIGNFRAME Something happened writing the temp file"); + Cache.log.error(e.getMessage()); + Cache.log.debug(e.getStackTrace()); } catch (Exception ex) { lastSaveSuccessful = false; - ex.printStackTrace(); + Cache.log.error( + "ALIGNFRAME Something else happened writing the temp file"); + Cache.log.error(ex.getMessage()); + Cache.log.debug(ex.getStackTrace()); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); + Cache.log.debug("ALIGNFRAME writing temp file was " + + (lastSaveSuccessful ? "" : "not ") + "successful"); // do the backup file roll and rename the temp file to actual file + Cache.log.debug( + "ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); + Cache.log.debug( + "ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (lastSaveSuccessful ? "" : "un") + + "successfully"); + } + + if (!lastSaveSuccessful) + { + if (!Platform.isHeadless()) + { + JvOptionPane.showInternalMessageDialog(AlignFrame.this, + MessageManager.formatMessage( + "label.couldnt_save_file", new Object[] + { fileName }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } } } } @@ -1489,7 +1538,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - String tooltip = MessageManager.getString("label.load_jalview_annotations"); + String tooltip = MessageManager + .getString("label.load_jalview_annotations"); chooser.setDialogTitle(tooltip); chooser.setToolTipText(tooltip); chooser.setResponseHandler(0, new Runnable() @@ -1782,10 +1832,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection + * or the sequence under cursor in keyboard mode * * @param up - * DOCUMENT ME! + * or down (if !up) */ public void moveSelectedSequences(boolean up) { @@ -1793,8 +1844,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (sg == null) { + if (viewport.cursorMode) + { + sg = new SequenceGroup(); + sg.addSequence(viewport.getAlignment().getSequenceAt( + alignPanel.getSeqPanel().seqCanvas.cursorY), false); + } + else + { + return; + } + } + + if (sg.getSize() < 1) + { return; } + + // TODO: JAL-3733 - add an event to the undo buffer for this ! + viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true, false); @@ -2404,56 +2472,61 @@ 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()]); - - 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.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - if (viewport.getAlignment().getHeight() < 1) - { - try - { - AlignFrame.this.setClosed(true); - } catch (Exception ex) - { - } - } - }}; + Runnable okAction = new Runnable() + { + @Override + public void run() + { + 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())); + + viewport.setSelectionGroup(null); + viewport.sendSelection(); + viewport.getAlignment().deleteGroup(sg); + + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + if (viewport.getAlignment().getHeight() < 1) + { + try + { + AlignFrame.this.setClosed(true); + } catch (Exception ex) + { + } + } + } + }; /* * If the cut affects all sequences, prompt for confirmation */ - boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight(); + boolean wholeHeight = sg.getSize() == viewport.getAlignment() + .getHeight(); boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport.getAlignment().getWidth()) ? true : false; - if (wholeHeight && wholeWidth) - { - JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); - dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION - Object[] options = new Object[] { MessageManager.getString("action.ok"), - MessageManager.getString("action.cancel") }; - dialog.showDialog(MessageManager.getString("warn.delete_all"), - MessageManager.getString("label.delete_all"), - JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, - options, options[0]); - } else - { - okAction.run(); - } + if (wholeHeight && wholeWidth) + { + JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop); + dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION + Object[] options = new Object[] { + MessageManager.getString("action.ok"), + MessageManager.getString("action.cancel") }; + dialog.showDialog(MessageManager.getString("warn.delete_all"), + MessageManager.getString("label.delete_all"), + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, + options, options[0]); + } + else + { + okAction.run(); + } } /** @@ -2512,7 +2585,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); + viewport.setSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; // JAL-2034 - should delegate to // alignPanel to decide if overview needs @@ -2625,8 +2698,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - setStatus(MessageManager - .formatMessage("label.removed_columns", new String[] + setStatus(MessageManager.formatMessage("label.removed_columns", + new String[] { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2675,8 +2748,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - setStatus(MessageManager - .formatMessage("label.removed_empty_columns", new Object[] + setStatus(MessageManager.formatMessage("label.removed_empty_columns", + new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue @@ -2749,15 +2822,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel); } /** @@ -2798,8 +2870,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getViewName() == null) { - viewport.setViewName(MessageManager - .getString("label.view_name_original")); + viewport.setViewName( + MessageManager.getString("label.view_name_original")); } /* @@ -3325,7 +3397,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JLabel textLabel = new JLabel(); textLabel.setText(content); textLabel.setBackground(Color.WHITE); - + pane = new JPanel(new BorderLayout()); ((JPanel) pane).setOpaque(true); pane.setBackground(Color.WHITE); @@ -3455,8 +3527,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, - viewport, - viewport.getAlignment(), viewport.getHiddenRepSequences()); + viewport, viewport.getAlignment(), + viewport.getHiddenRepSequences()); changeColour(cs); } @@ -3839,8 +3911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Enumeration labels = scoreSorts.keys(); while (labels.hasMoreElements()) { - addSortByAnnotScoreMenuItem(sortByAnnotScore, - labels.nextElement()); + addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); @@ -4007,7 +4078,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.setResponseHandler(0,new Runnable() + chooser.setResponseHandler(0, new Runnable() { @Override public void run() @@ -4175,8 +4246,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Add any secondary structure prediction services for (int i = 0, j = secstrpr.size(); i < j; i++) { - final ext.vamsas.ServiceHandle sh = secstrpr - .get(i); + final ext.vamsas.ServiceHandle sh = secstrpr.get(i); jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); int p = secstrmenu.getItemCount(); @@ -4555,10 +4625,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (protocol == DataSourceType.FILE) { File fl; - if (file instanceof File) { + if (file instanceof File) + { fl = (File) file; Platform.cacheFileData(fl); - } else { + } + else + { fl = new File(fileName); } pdbfn = fl.getName(); @@ -5795,6 +5868,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } private Rectangle lastFeatureSettingsBounds = null; + @Override public void setFeatureSettingsGeometry(Rectangle bounds) {