X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=2838b9debb0fdaa127ee4bd0cc53c7b5530ed466;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=5b7a2017c8c364695e7e1b1dea370f2a6debb344;hpb=8a864dd19ed838f57d850d72d6c17a5cb02fc3de;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 5b7a201..2838b9d 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; @@ -365,7 +368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // modifyPID.setEnabled(false); } - String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", + String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort"); if (sortby.equals("Id")) @@ -408,7 +411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, wrapMenuItem_actionPerformed(null); } - if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false)) + if (Cache.getDefault("SHOW_OVERVIEW", false)) { this.overviewMenuItem_actionPerformed(null); } @@ -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; @@ -1011,7 +1014,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public String getVersion() { - return jalview.bin.Cache.getProperty("VERSION"); + return Cache.getProperty("VERSION"); } public FeatureRenderer getFeatureRenderer() @@ -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.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.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.trace("ALIGNFRAME setting PrintWriter"); PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { - Cache.log.debug("ALIGNFRAME using temp file " + Cache.trace("ALIGNFRAME about to write to temp file " + backupfiles.getTempFilePath()); } out.print(output); - Cache.log.debug("ALIGNFRAME about to close file"); + Cache.trace("ALIGNFRAME about to close file"); out.close(); - Cache.log.debug("ALIGNFRAME closed file"); + Cache.trace("ALIGNFRAME closed file"); AlignFrame.this.setTitle(file); statusBar.setText(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", @@ -1318,46 +1329,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (IOException e) { lastSaveSuccessful = false; - Cache.log.error( + Cache.error( "ALIGNFRAME Something happened writing the temp file"); - Cache.log.error(e.getMessage()); - Cache.log.debug(e.getStackTrace()); + Cache.error(e.getMessage()); + Cache.debug(Cache.getStackTraceString(e)); } catch (Exception ex) { lastSaveSuccessful = false; - Cache.log.error( - "ALIGNFRAME Something else happened writing the temp file"); - Cache.log.error(ex.getMessage()); - Cache.log.debug(ex.getStackTrace()); + Cache.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Cache.error(ex.getMessage()); + Cache.debug(Cache.getStackTraceString(ex)); } if (doBackup) { backupfiles.setWriteSuccess(lastSaveSuccessful); - Cache.log.debug("ALIGNFRAME writing temp file was " - + (lastSaveSuccessful ? "" : "not ") + "successful"); + Cache.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( + Cache.trace( "ALIGNFRAME about to rollBackupsAndRenameTempFile"); lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); - Cache.log.debug( + Cache.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); - } - } } } }; @@ -1536,7 +1534,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void associatedData_actionPerformed(ActionEvent e) { final JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); String tooltip = MessageManager .getString("label.load_jalview_annotations"); @@ -1548,7 +1546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void run() { String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); } }); @@ -1735,7 +1733,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (originalSource != viewport) { - Cache.log.warn( + Cache.warn( "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); @@ -1775,7 +1773,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != viewport) { - Cache.log.warn( + Cache.warn( "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); @@ -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); } /** @@ -4071,7 +4069,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // Pick the tree file JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); + Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle( MessageManager.getString("label.select_newick_like_tree_file")); @@ -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) { @@ -4335,7 +4333,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { - Cache.log.debug( + Cache.debug( "Exception during web service menu building process.", e); } @@ -4432,7 +4430,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.setEnabled(showp); } catch (Exception e) { - Cache.log.warn( + Cache.warn( "canShowProducts threw an exception - please report to help@jalview.org", e); return false; @@ -4473,7 +4471,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al = dna.translateCdna(codeTable); } catch (Exception ex) { - jalview.bin.Cache.log.error( + Cache.error( "Exception during translation. Please report this !", ex); final String msg = MessageManager.getString( "label.error_when_translating_sequences_submit_bug_report"); @@ -4836,7 +4834,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception x) { - Cache.log.debug( + Cache.debug( "Exception when processing data source as T-COFFEE score file", x); tcf = null;