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;
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;
*/
void init()
{
-// setBackground(Color.white); // BH 2019
-
+ // setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
addKeyListener();
- final List<AlignmentPanel> selviews = new ArrayList<>();
+ final List<AlignmentViewPanel> selviews = new ArrayList<>();
final List<AlignmentPanel> origview = new ArrayList<>();
final String menuLabel = MessageManager
.getString("label.copy_format_from");
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 protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
- : DataSourceType.FILE);
+ : 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.log.error(MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }));
+ }
}
else
{
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 }));
-
+ { file, format }));
+
return;
}
{
// 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.trace(
+ "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.trace("ALIGNFRAME setting PrintWriter");
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+ if (backupfiles != null)
+ {
+ Cache.log.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
+ }
out.print(output);
+ Cache.log.trace("ALIGNFRAME about to close file");
out.close();
+ Cache.log.trace("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(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- ex.printStackTrace();
+ Cache.log.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
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.trace(
+ "ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Cache.log.debug(
+ "ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un")
+ + "successfully");
}
}
}
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()
}
/**
- * 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)
{
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);
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();
+ }
}
/**
}
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
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);
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
}
/**
- * DOCUMENT ME!
+ * Opens a Finder dialog
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder();
+ new Finder(alignPanel);
}
/**
if (viewport.getViewName() == null)
{
- viewport.setViewName(MessageManager
- .getString("label.view_name_original"));
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
JLabel textLabel = new JLabel();
textLabel.setText(content);
textLabel.setBackground(Color.WHITE);
-
+
pane = new JPanel(new BorderLayout());
((JPanel) pane).setOpaque(true);
pane.setBackground(Color.WHITE);
* 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);
}
Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- labels.nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.setResponseHandler(0,new Runnable()
+ chooser.setResponseHandler(0, new Runnable()
{
@Override
public void run()
// 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();
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();
}
private Rectangle lastFeatureSettingsBounds = null;
+
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
git://source.jalview.org / jalview.git / blobdiff