label.example_param = Example: {0}
label.select_file_format_before_saving = You must select a file format before saving!
label.file_format_not_specified = File format not specified
-label.couldnt_save_file = Couldn't save file: {0}
+label.couldnt_save_file = Couldn''t save file: {0}
label.error_saving_file = Error Saving File
label.remove_from_default_list = Remove from default list?
label.remove_user_defined_colour = Remove user defined colour
label.couldnt_load_file = Couldn't load file
label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
label.no_pdb_id_in_file = No PDB Id in File
-label.couldnt_read_pasted_text = Couldn't read the pasted text {0}
+label.couldnt_read_pasted_text = Couldn''t read the pasted text {0}
label.error_parsing_text = Error parsing text
label.input_alignment_from_url = Input Alignment From URL
label.input_alignment = Input Alignment
-label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas session.
+label.couldnt_import_as_vamsas_session = Couldn''t import {0} as a new vamsas session.
label.vamsas_document_import_failed = Vamsas Document Import Failed
label.couldnt_locate = Could not locate {0}
label.url_not_found = URL not found
label.set_proxy_settings = Please set up your proxy settings in the 'Connections' tab of the Preferences window
label.proxy_authorization_failed = Proxy Authorization Failed
label.internal_jalview_error = Internal Jalview Error
-label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn't be located.
+label.secondary_structure_prediction_service_couldnt_be_located = The Secondary Structure Prediction Service named {0} at {1} couldn''t be located.
label.service_called_is_not_msa_service = The Service called \n{0}\nis not a \nMultiple Sequence Alignment Service\!
label.msa_service_is_unknown = The Multiple Sequence Alignment Service named {0} is unknown
label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!
error.implementation_error_runner_config_not_available = Implementation Error: Runner Config not available for a JABAWS service of type {0} ({1})
error.implementation_error_cannot_handle_jaba_param = Implementation Error: Cannot handle Jaba parameter object {0}
error.implementation_error_attempt_to_delete_service_preset = Implementation error: Attempt to delete a service preset!
-error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can't locate either oldname ({0}) or presetName ({1}in the datastore!"
+error.implementation_error_cannot_locate_oldname_presetname = Implementation error: Can''t locate either oldname ({0}) or presetName ({1}in the datastore!"
error.implementation_error_jabaws_param_set_only_handled_by = Implementation error: JabaWsParamSets can only be handled by JabaParamStore
error.cannot_set_source_file_for = Cannot set source file for {0}
error.mismatch_service_instance_preset = Probable mismatch between service instance and preset!
error.implementation_error_can_only_instantiate_jaba_param_sets = Implementation error: Can only instantiate Jaba parameter sets
error.no_aacon_service_found = No AACon service found
error.implementation_error_couldnt_copy_value_constraint = Implementation error: could not copy ValueConstrain!
-error.couldnt_encode_as_utf8 = Couldn't encode {0} as UTF-8.
+error.couldnt_encode_as_utf8 = Couldn''t encode {0} as UTF-8.
error.tree_inputtype_not_yet_implemented = Tree InputType not yet implemented
error.implementation_error_need_to_have_httpresponse = Implementation Error: need to have an HttpResponse to process
error.dbrefsource_implementation_exception =DBRefSource Implementation Exception
exception.number_of_residues_in_query_sequence_differ_from_prediction = Number of residues in {0} supposed query sequence ({1}\n{2})\ndiffer from number of prediction sites in prediction ({3})
label.mapped = mapped
exception.jpredconcide_entry_has_unexpected_number_of_columns = JPredConcise: Entry ({0}) has an unexpected number of columns
-exception.couldnt_parse_concise_annotation_for_prediction = Couldn't parse concise annotation for prediction profile.\n{0}
+exception.couldnt_parse_concise_annotation_for_prediction = Couldn''t parse concise annotation for prediction profile.\n{0}
exception.newfile = NewickFile\: {0}\n
label.no_tree_read_in = No Tree read in
-exception.rnaml_couldnt_access_datasource = Couldn't access datasource ({0})
-exception.ranml_couldnt_process_data = Couldn't process data as RNAML file ({0})
+exception.rnaml_couldnt_access_datasource = Couldn''t access datasource ({0})
+exception.ranml_couldnt_process_data = Couldn''t process data as RNAML file ({0})
exception.ranml_invalid_file = Invalid RNAML file ({0})
exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
exception.pfam_no_sequences_found = No sequences found (PFAM input)
exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
-exception.couldnt_store_sequence_mappings = Couldn't store sequence mappings for {0}
+exception.couldnt_store_sequence_mappings = Couldn''t store sequence mappings for {0}
exception.matrix_too_many_iteration = Too many iterations in {0} (max is {1})
exception.browser_not_found = Exception in finding browser: {0}
exception.browser_unable_to_locate = Unable to locate browser: {0}
warn.input_is_too_big = Input is too big!
warn.invalid_job_param_set = Invalid job parameter set!
warn.oneseq_msainput_selection = The current selection only contains a single sequence. Do you want to submit all sequences for alignment instead ?
-info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn't support this program.\n{0}
+info.job_couldnt_be_run_server_doesnt_support_program = Job could not be run because the server doesn''t support this program.\n{0}
info.job_couldnt_be_run_exceeded_hard_limit = Job could not be run because it exceeded a hard limit on the server.\n{0}
info.job_couldnt_be_run_incorrect_param_setting = Job could not be run because some of the parameter settings are not supported by the server.\n{0}\nPlease check to make sure you have used the correct parameter set for this service\!\n
info.no_jobs_ran = No jobs ran
label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file.
label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay.
label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay.
+label.continue_operation = Continue operation?
label.backups = Backups
label.backup = Backup
label.backup_files = Backup Files
label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
label.features_not_shown = {0} feature(s) not shown
label.no_features_to_sort_by = No features to sort by
+label.log_level = Log level
+label.log_level_tooltip = Temporarily set the log level for this console
+label.copy_to_clipboard = Copy to clipboard
+label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard
label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Posiblemente algo está mal con los archivos de respaldos.
label.backupfiles_confirm_save_new_saved_file_ok = El nuevo archivo guardado parece estar bien.
label.backupfiles_confirm_save_new_saved_file_not_ok = El nuevo archivo guardado podría no estar bien.
+label.continue_operation = ¿Continuar operación?
label.backups = Respaldos
label.backup = Respaldo
label.backup_files = Archivos de respaldos
label.include_linked_tooltip = Incluir características de {0}<br>convertidas a coordenadas de secuencia local
label.features_not_shown = {0} característica(s) no mostradas
label.no_features_to_sort_by = No hay características para ordenar
+label.log_level = Nivel del registro
+label.log_level_tooltip = Establezca temporalmente el nivel de registro para esta consola
+label.copy_to_clipboard = Copiar en el portapapeles
+label.copy_to_clipboard_tooltip = Copie todo el texto de registro en esta consola al portapapeles del sistema
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Collections;
String jnlpVersion = System.getProperty("jalview.version");
// jnlpVersion will be null if a latest version check for the channel needs
- // to
- // be done
+ // to be done
// Dont do this check if running in headless mode
if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
appendIfNotNull(sb, "Launcher version: ",
System.getProperty("launcher_version"), "\n", null);
LookAndFeel laf = UIManager.getLookAndFeel();
- String lafName = laf == null?"Not obtained":laf.getName();
- String lafClass = laf == null?"unknown":laf.getClass().getName();
- appendIfNotNull(sb, "LookAndFeel: ", lafName+" ("+lafClass+")", "\n", null);
- // Not displayed in release version ( determined by possible version number regex 9[9.]*9[.-_a9]* )
- if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", jalview.bin.Cache.getDefault("VERSION", "TEST"))) {
+ String lafName = laf == null ? "Not obtained" : laf.getName();
+ String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+ appendIfNotNull(sb, "LookAndFeel: ", lafName + " (" + lafClass + ")",
+ "\n", null);
+ // Not displayed in release version ( determined by possible version number
+ // regex 9[9.]*9[.-_a9]* )
+ if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+ jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ {
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdownappdir"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
// eg 'built from Source' or update channel
return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
}
+
+ public static String getStackTraceString(Throwable t)
+ {
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw);
+ t.printStackTrace(pw);
+ return sw.toString();
+ }
}
*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+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;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.seqfetcher.DbSourceProxy;
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
/**
* DOCUMENT ME!
*
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
+ { file, format }));
}
else
else
{
// create backupfiles object and get new temp filename destination
+ Cache.log.debug("ALIGNFRAME making backupfiles object for " + file);
BackupFiles backupfiles = new BackupFiles(file);
try
{
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
+ String tempFilePath = backupfiles.getTempFilePath();
+ Cache.log.debug(
+ "ALIGNFRAME setting PrintWriter to " + tempFilePath);
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+ Cache.log.debug(
+ "ALIGNFRAME about to write to temp file " + tempFilePath);
out.print(output);
+ Cache.log.debug("ALIGNFRAME about to close file");
out.close();
+ Cache.log.debug("ALIGNFRAME closed file");
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
+ { file, format.getName() }));
+ } catch (IOException e)
+ {
+ success = 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)
{
success = false;
- ex.printStackTrace();
+ Cache.log.error(
+ "ALIGNFRAME Something else happened writing the temp file");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
backupfiles.setWriteSuccess(success);
+ Cache.log.debug("ALIGNFRAME writing temp file was "
+ + (success ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
+ Cache.log.debug("ALIGNFRAME about to rollBackupsAndRenameTempFile");
success = backupfiles.rollBackupsAndRenameTempFile();
+ Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (success ? "" : "un") + "successfully");
}
}
if (!success)
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
+ if (!Platform.isHeadless())
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { file }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
return success;
if (viewport.getViewName() == null)
{
- viewport.setViewName(MessageManager
- .getString("label.view_name_original"));
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
* 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);
}
}
private Rectangle lastFeatureSettingsBounds = null;
+
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
*/
package jalview.gui;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Dimension;
import java.awt.GraphicsEnvironment;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
import java.awt.Rectangle;
import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import java.io.PrintStream;
import javax.swing.JButton;
+import javax.swing.JComboBox;
import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
+import org.apache.log4j.Level;
import org.apache.log4j.SimpleLayout;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
/**
* Simple Jalview Java Console. Version 1 - allows viewing of console output
* after desktop is created. Acquired with thanks from RJHM's site
private int MIN_HEIGHT = 250;
+ private JComboBox logLevelCombo = new JComboBox();
+
public Console()
{
// create all components and add them
// textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
- JButton button = new JButton(MessageManager.getString("action.clear"));
+ JButton clearButton = new JButton(
+ MessageManager.getString("action.clear"));
+ JButton copyToClipboardButton = new JButton(
+ MessageManager.getString("label.copy_to_clipboard"));
+ copyToClipboardButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copyConsoleTextToClipboard();
+ }
+ });
+ copyToClipboardButton.addMouseListener(new MouseAdapter()
+ {
+ private Color bg = textArea.getBackground();
+
+ private Color fg = textArea.getForeground();
+
+ public void mousePressed(MouseEvent e)
+ {
+ textArea.setBackground(textArea.getSelectionColor());
+ textArea.setForeground(textArea.getSelectedTextColor());
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ textArea.setBackground(bg);
+ textArea.setForeground(fg);
+ }
+
+ });
+ copyToClipboardButton.setToolTipText(
+ MessageManager.getString("label.copy_to_clipboard_tooltip"));
+
+ JLabel logLevelLabel = new JLabel(
+ MessageManager.getString("label.log_level") + ":");
+
+ // logLevelCombo.addItem(Level.ALL);
+ logLevelCombo.addItem(Level.TRACE);
+ logLevelCombo.addItem(Level.DEBUG);
+ logLevelCombo.addItem(Level.INFO);
+ logLevelCombo.addItem(Level.WARN);
+ // logLevelCombo.addItem(Level.ERROR);
+ // logLevelCombo.addItem(Level.FATAL);
+ // logLevelCombo.addItem(Level.OFF);
+ setChosenLogLevelCombo();
+ logLevelCombo.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if (Cache.log != null)
+ {
+ Cache.log.setLevel((Level) logLevelCombo.getSelectedItem());
+ }
+ }
+
+ });
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
frame.getContentPane().add(new JScrollPane(textArea),
BorderLayout.CENTER);
- frame.getContentPane().add(button, BorderLayout.SOUTH);
+ JPanel southPanel = new JPanel();
+ southPanel.setLayout(new GridBagLayout());
+
+ JPanel logLevelPanel = new JPanel();
+ logLevelPanel.setAlignmentX(JPanel.LEFT_ALIGNMENT);
+ logLevelPanel.add(logLevelLabel);
+ logLevelPanel.add(logLevelCombo);
+ logLevelLabel.setToolTipText(
+ MessageManager.getString("label.log_level_tooltip"));
+ logLevelCombo.setToolTipText(
+ MessageManager.getString("label.log_level_tooltip"));
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+ gbc.weightx = 0.1;
+ southPanel.add(logLevelPanel, gbc);
+
+ gbc.gridx++;
+ gbc.weightx = 0.8;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ southPanel.add(clearButton, gbc);
+
+ gbc.gridx++;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.NONE;
+ southPanel.add(copyToClipboardButton, gbc);
+
+ southPanel.setVisible(true);
+ frame.getContentPane().add(southPanel, BorderLayout.SOUTH);
frame.setVisible(visible);
updateConsole = visible;
frame.addWindowListener(this);
- button.addActionListener(this);
+ clearButton.addActionListener(this);
+
if (redirect)
{
redirectStreams();
textAppender.start();
}
+ private void setChosenLogLevelCombo()
+ {
+ Level currentLogLevel = Cache.log == null ? Level.INFO
+ : Cache.log.getLevel();
+ logLevelCombo.setSelectedItem(currentLogLevel);
+ if (!logLevelCombo.getSelectedItem().equals(currentLogLevel)) // currentLogLevel
+ // not in list
+ {
+ if (currentLogLevel != null && currentLogLevel instanceof Level)
+ {
+ // add new item to list (might be set via .jalview_properties)
+ boolean added = false;
+ for (int i = 0; i < logLevelCombo.getItemCount(); i++)
+ {
+ Level l = (Level) logLevelCombo.getItemAt(i);
+ if (l.isGreaterOrEqual(currentLogLevel))
+ {
+ logLevelCombo.insertItemAt(currentLogLevel, i);
+ added = true;
+ break;
+ }
+ }
+ if (!added) // lower priority than others or some confusion -- add to
+ // end of list
+ {
+ logLevelCombo.addItem(currentLogLevel);
+ }
+ logLevelCombo.setSelectedItem(currentLogLevel);
+ }
+ else
+ {
+ logLevelCombo.setSelectedItem(Level.INFO);
+ }
+ }
+ }
+
+ private void copyConsoleTextToClipboard()
+ {
+ String consoleText = textArea.getText();
+ StringSelection consoleTextSelection = new StringSelection(consoleText);
+ Clipboard cb = Toolkit.getDefaultToolkit().getSystemClipboard();
+ cb.setContents(consoleTextSelection, null);
+ }
+
PipedOutputStream pout = null, perr = null;
public void redirectStreams()
frame.setVisible(selected);
if (selected == true)
{
+ setChosenLogLevelCombo();
redirectStreams();
updateConsole = true;
frame.toFront();
}
else
{
+ // reset log level to user preference
+ if (Cache.log != null)
+ {
+ String userLogLevel = Cache.getDefault("logs.Jalview.level",
+ Level.INFO.toString());
+ Cache.log.setLevel(Level.toLevel(userLogLevel));
+ }
+
unredirectStreams();
updateConsole = false;
}
*/
package jalview.io;
-import jalview.bin.Cache;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.util.MessageManager;
-
import java.io.File;
import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.TreeMap;
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/*
* BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
* User configurable options are:
private static final SimpleDateFormat sdf = new SimpleDateFormat(
"yyyy-MM-dd HH:mm:ss");
+ private static final String newTempFileSuffix = "_newfile";
+
+ private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+
public BackupFiles(String filename)
{
this(new File(filename));
{
classInit();
this.file = file;
- BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
this.suffix = bfpe.suffix;
this.noMax = bfpe.keepAll;
this.max = bfpe.rollMax;
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
- tempdir);
+ Cache.log.debug(
+ "BACKUPFILES [file!=null] attempting to create temp file for "
+ + tempfilename + " in dir " + tempdir);
+ temp = File.createTempFile(tempfilename,
+ TEMP_FILE_EXT + newTempFileSuffix, tempdir);
+ Cache.log.debug(
+ "BACKUPFILES using temp file " + temp.getAbsolutePath());
}
else
{
+ Cache.log.debug(
+ "BACKUPFILES [file==null] attempting to create default temp file "
+ + DEFAULT_TEMP_FILE + " with extension "
+ + TEMP_FILE_EXT);
temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
}
} catch (IOException e)
{
- System.out.println(
- "Could not create temp file to save into (IOException)");
+ Cache.log
+ .error("Could not create temp file to save to (IOException)");
+ Cache.log.error(e.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
- System.out.println("Exception ctreating temp file for saving");
+ Cache.log.error("Exception ctreating temp file for saving");
+ Cache.log.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
- setEnabled(Cache.getDefault(ENABLED, true));
+ Cache.log.debug("BACKUPFILES classInit");
+ boolean e = Cache.getDefault(ENABLED, true);
+ setEnabled(e);
+ Cache.log.debug("BACKUPFILES " + (e ? "enabled" : "disabled"));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
+ Cache.log.debug("BACKUPFILES preset scheme " + bfpe.toString());
setConfirmDelete(bfpe.confirmDelete);
+ Cache.log.debug("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
- System.out.println(
+ Cache.log.error(
"IOException when getting Canonical Path of temp file '"
+ this.getTempFile().getName() + "'");
+ Cache.log.debug(Cache.getStackTraceString(e));
}
return path;
}
public boolean renameTempFile()
{
- return tempFile.renameTo(file);
+ return moveFileToFile(tempFile, file);
}
// roll the backupfiles
|| suffix.length() == 0)
{
// nothing to do
+ Cache.log.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ + "filename: " + (file != null ? file.getName() : "null")
+ + ", " + "file exists: " + file.exists() + ", " + "enabled: "
+ + enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
+ + "'");
return true;
}
+ Cache.log.debug("BACKUPFILES rollBackupFiles starting");
+
String dir = "";
File dirFile;
try
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
+ Cache.log.debug("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Could not get canonical path for file '" + file + "'");
+ Cache.log.error(e.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(e));
return false;
}
String filename = file.getName();
String basename = filename;
+ Cache.log.debug("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
+ Cache.log
+ .debug("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
+ Cache.log.debug(
+ "BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
else
if (reverseOrder)
{
// backup style numbering
-
+ Cache.log.debug("BACKUPFILES rolling files in reverse order");
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
tempMax = i;
}
}
-
+
File previousFile = null;
File fileToBeDeleted = null;
for (int n = tempMax; n > 0; n--)
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
+ Cache.log.debug("BACKUPFILES No oldest file to delete");
continue;
}
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
+ Cache.log.debug("BACKUPFILES fileToBeDeleted is "
+ + fileToBeDeleted.getAbsolutePath());
+ Cache.log.debug("BACKUPFILES replacementFile is "
+ + backupfile_n.getAbsolutePath());
try
{
File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
dirFile);
-
+
if (fileToBeDeletedLMT > replacementFileLMT)
{
String fileToBeDeletedLMTString = sdf
.format(fileToBeDeletedLMT);
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- System.out.println("WARNING! I am set to delete backupfile "
+ Cache.log.warn("WARNING! I am set to delete backupfile "
+ fileToBeDeleted.getName()
+ " has modification time "
+ fileToBeDeletedLMTString
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
+ Cache.log.debug("BACKUPFILES "
+ + (delete ? "confirmed" : "not") + " deleting file "
+ + fileToBeDeleted.getAbsolutePath()
+ + " which is newer than "
+ + replacementFile.getAbsolutePath());
if (delete)
{
}
else
{
- fileToBeDeleted.renameTo(oldestTempFile);
+ Cache.log.debug("BACKUPFILES moving "
+ + fileToBeDeleted.getAbsolutePath() + " to "
+ + oldestTempFile.getAbsolutePath());
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
}
}
else
{
- fileToBeDeleted.renameTo(oldestTempFile);
+ Cache.log.debug("BACKUPFILES going to move "
+ + fileToBeDeleted.getAbsolutePath() + " to "
+ + oldestTempFile.getAbsolutePath());
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
addDeleteFile(oldestTempFile);
}
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
- e.printStackTrace();
+ Cache.log.error(Cache.getStackTraceString(e));
}
// reset
{
if (previousFile != null)
{
- ret = ret && backupfile_n.renameTo(previousFile);
+ // using boolean '&' instead of '&&' as don't want moveFileToFile
+ // attempt to be conditional (short-circuit)
+ ret = ret & moveFileToFile(backupfile_n, previousFile);
}
}
// index to use for the latest backup
nextIndexNum = 1;
}
- else
+ else // not reverse numbering
{
// version style numbering (with earliest file deletion if max files
// reached)
bfTreeMap.values().toArray(backupFiles);
+ StringBuilder bfsb = new StringBuilder();
+ for (int i = 0; i < backupFiles.length; i++)
+ {
+ if (bfsb.length() > 0)
+ {
+ bfsb.append(", ");
+ }
+ bfsb.append(backupFiles[i].getName());
+ }
+ Cache.log.debug("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
+ Cache.log.debug("BACKUPFILES noMax: " + noMax + ", " + "max: "
+ + max + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
- // max
- int numToDelete = bfTreeMap.size() - max + 1;
+ // max.
+ // Note that if the suffix is not numbered then do not delete any
+ // backup files later or we'll delete the new backup file (there can
+ // be only one).
+ int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
+ ? bfTreeMap.size() - max + 1
+ : 0;
+ Cache.log.debug("BACKUPFILES numToDelete: " + numToDelete);
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
+ Cache.log.debug(
+ "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+
boolean newer = false;
if (replacementFile != null)
{
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- System.out
- .println("WARNING! I am set to delete backupfile '"
- + fileToBeDeleted.getName()
- + "' has modification time "
+ Cache.log.warn("WARNING! I am set to delete backupfile '"
+ + fileToBeDeleted.getName()
+ + "' has modification time "
+ fileToBeDeletedLMTString
- + " which is newer than the oldest backupfile being kept '"
+ + " which is newer than the oldest backupfile being kept '"
+ replacementFile.getName()
- + "' with modification time "
+ + "' with modification time "
+ replacementFileLMTString);
delete = confirmNewerDeleteFile(fileToBeDeleted,
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
+ Cache.log.debug("BACKUPFILES deleting fileToBeDeleted: "
+ + fileToBeDeleted);
delete = false;
}
else
{
// keeping file, nothing to do!
+ Cache.log.debug("BACKUPFILES keeping fileToBeDeleted: "
+ + fileToBeDeleted);
}
}
}
if (delete)
{
addDeleteFile(fileToBeDeleted);
+ Cache.log.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ + fileToBeDeleted);
}
}
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- ret |= file.renameTo(new File(latestBackupFilename));
-
+ Cache.log.debug("BACKUPFILES Moving old file [" + file
+ + "] to latestBackupFilename [" + latestBackupFilename + "]");
+ // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
+ // be conditional (short-circuit)
+ ret = ret & moveFileToFile(file, new File(latestBackupFilename));
+ Cache.log.debug(
+ "BACKUPFILES moving " + file + " to " + latestBackupFilename
+ + " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
+ Cache.log.debug("BACKUPFILES tidying up files");
tidyUpFiles();
}
saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Error when confirming to keep backup file newer than other backup files.");
e.printStackTrace();
}
"label.newerdelete_replacement_line", new String[]
{ ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
rfSize }));
+ // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and
+ // replaced by apparently older file \n''{1}''\t(modified {3}, size
+ // {5}).""
messageSB.append("\n\n");
messageSB.append(MessageManager.formatMessage(
"label.confirm_deletion_or_rename", new String[]
{ ftbd.getName(), saveFile.getName() }));
+ // "Confirm deletion of ''{0}'' or rename to ''{1}''?"
String[] options = new String[] {
MessageManager.getString("label.delete"),
MessageManager.getString("label.rename") };
- confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager.getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
- null, options, options[0]);
+ confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
}
else
{
.formatMessage("label.newerdelete_line", new String[]
{ ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
rfSize }));
+ // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but
+ // is newer than the oldest remaining backup file \n''{1}''\t(modified
+ // {3}, size {5})."
messageSB.append("\n\n");
messageSB.append(MessageManager
.formatMessage("label.confirm_deletion", new String[]
{ ftbd.getName() }));
+ // "Confirm deletion of ''{0}''?"
String[] options = new String[] {
MessageManager.getString("label.delete"),
MessageManager.getString("label.keep") };
- confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager.getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
- null, options, options[0]);
+ confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
}
-
// return should be TRUE if file is to be deleted
return (confirmButton == JvOptionPane.YES_OPTION);
}
messageSB = new StringBuilder();
messageSB.append(MessageManager
.getString("label.backupfiles_confirm_delete_old_files"));
+ // "Delete the following older backup files? (see the Backups tab in
+ // Preferences for more options)"
for (int i = 0; i < deleteFiles.size(); i++)
{
File df = deleteFiles.get(i);
new String[]
{ sdf.format(df.lastModified()),
Long.toString(df.length()) }));
+ // "(modified {0}, size {1})"
}
- int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager
- .getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+ int confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE);
doDelete = (confirmButton == JvOptionPane.YES_OPTION);
}
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
+ Cache.log.debug(
+ "BACKUPFILES deleting fileToDelete:" + fileToDelete);
fileToDelete.delete();
- System.out.println("DELETING '" + fileToDelete.getName() + "'");
+ Cache.log.warn("deleting '" + fileToDelete.getName() + "'");
}
}
}
private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
- File[] backupFiles,
- String basename)
+ File[] backupFiles, String basename)
{
// sort the backup files (based on integer found in the suffix) using a
// precomputed Hashmap for speed
boolean rename = false;
if (write)
{
- roll = this.rollBackupFiles(false);
+ roll = this.rollBackupFiles(false); // tidyUpFiles at the end
rename = this.renameTempFile();
}
if (!okay)
{
StringBuilder messageSB = new StringBuilder();
- messageSB.append(MessageManager.getString( "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ messageSB.append(MessageManager.getString(
+ "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ // "Something possibly went wrong with the backups of this file."
if (rename)
{
if (messageSB.length() > 0)
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_ok"));
+ // "The new saved file seems okay."
}
else
{
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_not_ok"));
+ // "The new saved file might not be okay."
}
-
- int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager
- .getString("label.backupfiles_confirm_save_file"),
- JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
+ if (messageSB.length() > 0)
+ {
+ messageSB.append("\n");
+ }
+ messageSB
+ .append(MessageManager.getString("label.continue_operation"));
+
+ int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
+ : JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_save_file"),
+ // "Confirm save file"
+ JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
okay = confirmButton == JvOptionPane.OK_OPTION;
}
if (okay)
dirFile = file.getParentFile();
} catch (Exception e)
{
- System.out.println(
+ Cache.log.error(
"Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
int pos = deleteFiles.indexOf(fileToBeDeleted);
if (pos > -1)
{
+ Cache.log.debug("BACKUPFILES not adding file "
+ + fileToBeDeleted.getAbsolutePath()
+ + " to the delete list (already at index" + pos + ")");
return true;
}
else
{
+ Cache.log.debug("BACKUPFILES adding file "
+ + fileToBeDeleted.getAbsolutePath() + " to the delete list");
deleteFiles.add(fileToBeDeleted);
}
return ret;
}
+ public static boolean moveFileToFile(File oldFile, File newFile)
+ {
+ boolean ret = false;
+ Path oldPath = Paths.get(oldFile.getAbsolutePath());
+ Path newPath = Paths.get(newFile.getAbsolutePath());
+ try
+ {
+ // delete destination file - not usually necessary but Just In Case...
+ Cache.log.debug("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ newFile.delete();
+ Cache.log.debug("BACKUPFILES moving " + oldFile.getAbsolutePath()
+ + " to " + newFile.getAbsolutePath());
+ Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
+ ret = true;
+ Cache.log.debug("BACKUPFILES move seems to have succeeded");
+ } catch (IOException e)
+ {
+ Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
+ + newPath.toString() + "'");
+ Cache.log.error(e.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(e));
+ ret = false;
+ } catch (Exception e)
+ {
+ Cache.log.error(e.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(e));
+ ret = false;
+ }
+ return ret;
+ }
}
*/
package jalview.io;
-import jalview.bin.Cache;
-import jalview.util.MessageManager;
-
import java.util.HashMap;
import java.util.Map;
import java.util.StringTokenizer;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
public class BackupFilesPresetEntry
{
{
String savedPresetString = Cache
.getDefault(BackupFilesPresetEntry.SAVEDCONFIG, null);
+ Cache.log.debug("BACKUPFILESPRESETENTRY saved preset string is "
+ + savedPresetString);
BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
.createBackupFilesPresetEntry(savedPresetString);
if (savedPreset == null)
*/
package jalview.ws.sifts;
-import jalview.analysis.AlignSeq;
-import jalview.analysis.scoremodels.ScoreMatrix;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.DBRefEntryI;
-import jalview.api.SiftsClientI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.Format;
-import jalview.xml.binding.sifts.Entry;
-import jalview.xml.binding.sifts.Entry.Entity;
-import jalview.xml.binding.sifts.Entry.Entity.Segment;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
-
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import MCview.Atom;
import MCview.PDBChain;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.DBRefEntryI;
+import jalview.api.SiftsClientI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.Format;
+import jalview.xml.binding.sifts.Entry;
+import jalview.xml.binding.sifts.Entry.Entity;
+import jalview.xml.binding.sifts.Entry.Entity.Segment;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
public class SiftsClient implements SiftsClientI
{
private enum CoordinateSys
{
UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+
private String name;
private CoordinateSys(String name)
{
NAME_SEC_STRUCTURE("nameSecondaryStructure"),
CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
+
private String code;
private ResidueDetailType(String code)
SiftsSettings.getCacheThresholdInDays()))
{
File oldSiftsFile = new File(siftsFileName + "_old");
- siftsFile.renameTo(oldSiftsFile);
+ BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
try
{
siftsFile = downloadSiftsFile(pdbId.toLowerCase());
} catch (IOException e)
{
e.printStackTrace();
- oldSiftsFile.renameTo(siftsFile);
+ BackupFiles.moveFileToFile(oldSiftsFile, siftsFile);
return new File(siftsFileName);
}
}
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
List<Integer> omitNonObserved = new ArrayList<>();
- int nonObservedShiftIndex = 0,pdbeNonObserved=0;
+ int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
// System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
- omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
+ omitNonObserved, nonObservedShiftIndex, pdbeNonObserved);
processSegments(segments, shp);
try
{
{
throw new SiftsException("SIFTS mapping failed");
}
- // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
+ // also construct a mapping object between the seq-coord sys and the PDB
+ // seq's coord sys
Integer[] keys = mapping.keySet().toArray(new Integer[0]);
Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
- List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
- int[]_cfrom=null,_cto=null;
+ List<int[]> from = new ArrayList<>(), to = new ArrayList<>();
+ int[] _cfrom = null, _cto = null;
String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
+ if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb
+ // sequence that starts <-1
{
- for (int seqps:keys)
+ for (int seqps : keys)
{
int pdbpos = mapping.get(seqps)[PDBE_POS];
if (pdbpos == UNASSIGNED)
// not correct - pdbpos might be -1, but leave it for now
continue;
}
- if (_cfrom==null || seqps!=_cfrom[1]+1)
+ if (_cfrom == null || seqps != _cfrom[1] + 1)
{
- _cfrom = new int[] { seqps,seqps};
+ _cfrom = new int[] { seqps, seqps };
from.add(_cfrom);
_cto = null; // discontinuity
- } else {
- _cfrom[1]= seqps;
}
- if (_cto==null || pdbpos!=1+_cto[1])
+ else
+ {
+ _cfrom[1] = seqps;
+ }
+ if (_cto == null || pdbpos != 1 + _cto[1])
{
- _cto = new int[] { pdbpos,pdbpos};
+ _cto = new int[] { pdbpos, pdbpos };
to.add(_cto);
- } else {
+ }
+ else
+ {
_cto[1] = pdbpos;
}
}
;
seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
- 1,
- 1);
+ 1, 1);
pdbStart = mapping.get(seqStart)[PDB_RES_POS];
pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
int orignalSeqStart = seq.getStart();
}
// if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
// true
- // numbering
- // is
- // not
- // up
- // to
- // seq.getEnd()
+ // numbering
+ // is
+ // not
+ // up
+ // to
+ // seq.getEnd()
{
int resNum = (pdbRefDb == null)
{
return pdbeNonObserved;
}
+
public SequenceI getSeq()
{
return seq;
git://source.jalview.org / jalview.git / commitdiff