X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=8deff013e14e91509ce5028a5d39dacd1ecb18b1;hb=038cd8338ccca1cec7e00979f796740add7c4aed;hp=5b7a2017c8c364695e7e1b1dea370f2a6debb344;hpb=8a864dd19ed838f57d850d72d6c17a5cb02fc3de;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 5b7a201..8deff01 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import java.util.Locale; + import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; @@ -144,6 +146,7 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; +import jalview.util.HttpUtils; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; @@ -483,9 +486,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } }); - if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("devel") > -1 - || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase() + || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT) .indexOf("test") > -1) { formatMenu.add(vsel); @@ -564,7 +567,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown()); } break; @@ -575,7 +578,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown()); } break; @@ -588,7 +591,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -600,7 +603,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; @@ -1062,7 +1065,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") + DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName) ? DataSourceType.URL : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); @@ -1078,9 +1081,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (fileObject == null) { - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); + DataSourceType protocol = HttpUtils.startsWithHttpOrHttps( + fileName) ? DataSourceType.URL : DataSourceType.FILE; newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); } @@ -1131,7 +1133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void save_actionPerformed(ActionEvent e) { if (fileName == null || (currentFileFormat == null) - || fileName.startsWith("http")) + || HttpUtils.startsWithHttpOrHttps(fileName)) { saveAs_actionPerformed(); } @@ -1204,11 +1206,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!lastSaveSuccessful) { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", new Object[] - { lastFilenameSaved }), - MessageManager.getString("label.error_saving_file"), - JvOptionPane.WARNING_MESSAGE); + if (!Platform.isHeadless()) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } + else + { + Cache.log.error(MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { lastFilenameSaved })); + } } else { @@ -1250,7 +1261,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format })); + { file, format })); return; } @@ -1288,7 +1299,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, BackupFiles backupfiles = null; if (doBackup) { - Cache.log.debug( + Cache.log.trace( "ALIGNFRAME making backupfiles object for " + file); backupfiles = new BackupFiles(file); } @@ -1296,19 +1307,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; - Cache.log.debug("ALIGNFRAME setting PrintWriter"); + Cache.log.trace("ALIGNFRAME setting PrintWriter"); PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { - Cache.log.debug("ALIGNFRAME using temp file " + Cache.log.trace("ALIGNFRAME about to write to temp file " + backupfiles.getTempFilePath()); } out.print(output); - Cache.log.debug("ALIGNFRAME about to close file"); + Cache.log.trace("ALIGNFRAME about to close file"); out.close(); - Cache.log.debug("ALIGNFRAME closed file"); + Cache.log.trace("ALIGNFRAME closed file"); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", @@ -1321,23 +1332,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Cache.log.error( "ALIGNFRAME Something happened writing the temp file"); Cache.log.error(e.getMessage()); - Cache.log.debug(e.getStackTrace()); + Cache.log.debug(Cache.getStackTraceString(e)); } catch (Exception ex) { lastSaveSuccessful = false; Cache.log.error( - "ALIGNFRAME Something else happened writing the temp file"); + "ALIGNFRAME Something unexpected happened writing the temp file"); Cache.log.error(ex.getMessage()); - Cache.log.debug(ex.getStackTrace()); + Cache.log.debug(Cache.getStackTraceString(ex)); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); Cache.log.debug("ALIGNFRAME writing temp file was " - + (lastSaveSuccessful ? "" : "not ") + "successful"); + + (lastSaveSuccessful ? "" : "NOT ") + "successful"); // do the backup file roll and rename the temp file to actual file - Cache.log.debug( + Cache.log.trace( "ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); Cache.log.debug( @@ -1345,19 +1356,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + (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); - } - } } } }; @@ -2829,7 +2827,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(alignPanel); + new Finder(alignPanel, false, null); } /** @@ -4301,7 +4299,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jws2servs.attachWSMenuEntry(webService, me); for (Jws2Instance sv : jws2servs.getServices()) { - if (sv.description.toLowerCase().contains("jpred")) + if (sv.description.toLowerCase(Locale.ROOT).contains("jpred")) { for (JMenuItem jmi : legacyItems) {