*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
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;
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = Cache.getDefault("SORT_ALIGNMENT",
"No sort");
if (sortby.equals("Id"))
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (Cache.getDefault("SHOW_OVERVIEW", false))
{
this.overviewMenuItem_actionPerformed(null);
}
}
}
});
- 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);
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1);
+ alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1);
+ alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(-1, 0);
+ alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(1, 0);
+ alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
*/
public String getVersion()
{
- return jalview.bin.Cache.getProperty("VERSION");
+ return Cache.getProperty("VERSION");
}
public FeatureRenderer getFeatureRenderer()
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);
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);
}
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed();
}
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
{
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
+ { file, format }));
return;
}
BackupFiles backupfiles = null;
if (doBackup)
{
- Cache.log.debug(
+ Cache.trace(
"ALIGNFRAME making backupfiles object for " + file);
backupfiles = new BackupFiles(file);
}
{
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",
} 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);
- }
- }
}
}
};
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");
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);
}
});
{
if (originalSource != viewport)
{
- Cache.log.warn(
+ Cache.warn(
"Implementation worry: mismatch of viewport origin for undo");
}
originalSource.updateHiddenColumns();
if (originalSource != viewport)
{
- Cache.log.warn(
+ Cache.warn(
"Implementation worry: mismatch of viewport origin for redo");
}
originalSource.updateHiddenColumns();
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder(alignPanel);
+ new Finder(alignPanel, false, null);
}
/**
{
// 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"));
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)
{
}
} catch (Exception e)
{
- Cache.log.debug(
+ Cache.debug(
"Exception during web service menu building process.",
e);
}
showProducts.setEnabled(showp);
} catch (Exception e)
{
- Cache.log.warn(
+ Cache.warn(
"canShowProducts threw an exception - please report to help@jalview.org",
e);
return false;
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");
}
} catch (Exception x)
{
- Cache.log.debug(
+ Cache.debug(
"Exception when processing data source as T-COFFEE score file",
x);
tcf = null;
git://source.jalview.org / jalview.git / blobdiff