X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=b42c3423db71c41f1314fd8f9f09b000afc375eb;hpb=75b601c07269d33574fb36f3e128097028e3f7e4;p=jalview.git
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index b42c342..c4dcc6c 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,559 +1,1468 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Preferences
- extends GPreferences
-{
- /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
- public static Vector sequenceURLLinks;
- static
- {
- String string = Cache.getDefault("SEQUENCE_LINKS",
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
- sequenceURLLinks = new Vector();
-
- try
- {
- StringTokenizer st = new StringTokenizer(string, "|");
- while (st.hasMoreElements())
- {
- sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
- }
- }
- catch (Exception ex)
- {
- System.out.println(ex + "\nError parsing sequence links");
- }
- }
-
- Vector nameLinks, urlLinks;
-
- JInternalFrame frame;
-
- DasSourceBrowser dasSource;
-
- /**
- * Creates a new Preferences object.
- */
- public Preferences()
- {
-
- frame = new JInternalFrame();
- frame.setContentPane(this);
- dasSource = new DasSourceBrowser();
- dasPanel.add(dasSource, BorderLayout.CENTER);
-
- int width = 500, height = 420;
- if (System.getProperty("os.name").startsWith("Mac"))
- {
- width = 570;
- height = 460;
- }
-
- Desktop.addInternalFrame(frame, "Preferences", width, height);
- frame.setMinimumSize(new Dimension(width, height));
-
- seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
- rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
- fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
- annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
- identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
- conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
- quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
- identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
- openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
-
- for (int i = 0; i < 13; i++)
- {
- colour.addItem(ColourSchemeProperty.getColourName(i));
- }
-
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
- colour.setSelectedItem(string);
-
- String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
-
- for (int i = 0; i < fonts.length; i++)
- {
- fontNameCB.addItem(fonts[i]);
- }
-
- for (int i = 1; i < 31; i++)
- {
- fontSizeCB.addItem(i + "");
- }
-
- fontStyleCB.addItem("plain");
- fontStyleCB.addItem("bold");
- fontStyleCB.addItem("italic");
-
- fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
- fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
-
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
-
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
-
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
-
- gapSymbolCB.addItem("-");
- gapSymbolCB.addItem(".");
-
- gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
-
- startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile2_3.jar"));
-
- sortby.addItem("No sort");
- sortby.addItem("Id");
- sortby.addItem("Pairwise Identity");
- sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
-
- epsRendering.addItem("Prompt each time");
- epsRendering.addItem("Lineart");
- epsRendering.addItem("Text");
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
- "Prompt each time"));
-
- blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
- clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
- fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
-
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
-
- autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
-
- /****************************************************
- * Set up Connections
- */
- nameLinks = new Vector();
- urlLinks = new Vector();
- for (int i = 0; i < sequenceURLLinks.size(); i++)
- {
- String link = sequenceURLLinks.elementAt(i).toString();
- nameLinks.addElement(link.substring(0, link.indexOf("|")));
- urlLinks.addElement(link.substring(link.indexOf("|") + 1));
- }
-
- updateLinkData();
-
- useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
- proxyServerTB.setEnabled(useProxy.isSelected());
- proxyPortTB.setEnabled(useProxy.isSelected());
- proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
- proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
-
- defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void ok_actionPerformed(ActionEvent e)
- {
-
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
- Boolean.toString(seqLimit.
- isSelected()));
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
- Boolean.toString(rightAlign.
- isSelected()));
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
- Boolean.toString(fullScreen.
- isSelected()));
- Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
- Boolean.toString(openoverv.
- isSelected()));
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
- Boolean.
- toString(annotations.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
- Boolean.
- toString(conservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
- Boolean.toString(quality.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.toString(identity.
- isSelected()));
-
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR",
- colour.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("GAP_SYMBOL",
- gapSymbolCB.getSelectedItem().
- toString());
-
- Cache.applicationProperties.setProperty("FONT_NAME",
- fontNameCB.getSelectedItem().
- toString());
- Cache.applicationProperties.setProperty("FONT_STYLE",
- fontStyleCB.getSelectedItem().
- toString());
- Cache.applicationProperties.setProperty("FONT_SIZE",
- fontSizeCB.getSelectedItem().
- toString());
-
- Cache.applicationProperties.setProperty("ID_ITALICS",
- Boolean.toString(idItalics.
- isSelected()));
-
- Cache.applicationProperties.setProperty("ANTI_ALIAS",
- Boolean.toString(smoothFont.
- isSelected()));
-
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
- Boolean.toString(wrap.isSelected()));
-
- Cache.applicationProperties.setProperty("STARTUP_FILE",
- startupFileTextfield.getText());
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
- Boolean.
- toString(startupCheckbox.isSelected()));
-
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
- sortby.getSelectedItem().toString());
-
- if (epsRendering.getSelectedItem().equals("Prompt each time"))
- {
- Cache.applicationProperties.remove("EPS_RENDERING");
- }
- else
- {
- Cache.applicationProperties.setProperty("EPS_RENDERING",
- epsRendering.getSelectedItem().
- toString());
- }
-
- if (defaultBrowser.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("DEFAULT_BROWSER");
- }
- else
- {
- Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
- defaultBrowser.getText());
- }
-
- jalview.util.BrowserLauncher.resetBrowser();
-
- if (nameLinks.size() > 0)
- {
- StringBuffer links = new StringBuffer();
- sequenceURLLinks = new Vector();
- for (int i = 0; i < nameLinks.size(); i++)
- {
- sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +
- urlLinks.elementAt(i));
- links.append(sequenceURLLinks.elementAt(i).toString());
- links.append("|");
- }
- // remove last "|"
- links.setLength(links.length() - 1);
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
- }
- else
- {
- Cache.applicationProperties.remove("SEQUENCE_LINKS");
- }
-
- Cache.applicationProperties.setProperty("USE_PROXY",
- Boolean.toString(useProxy.
- isSelected()));
-
- if (proxyServerTB.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("PROXY_SERVER");
- }
- else
- {
- Cache.applicationProperties.setProperty("PROXY_SERVER",
- proxyServerTB.getText());
- }
-
- if (proxyPortTB.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("PROXY_PORT");
- }
- else
- {
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
- }
-
- if (useProxy.isSelected())
- {
- System.setProperty("http.proxyHost", proxyServerTB.getText());
- System.setProperty("http.proxyPort", proxyPortTB.getText());
- }
- else
- {
- System.setProperty("http.proxyHost", "");
- System.setProperty("http.proxyPort", "");
- }
-
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
- Boolean.toString(blcjv.isSelected()));
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
- Boolean.
- toString(clustaljv.isSelected()));
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
- Boolean.toString(fastajv.isSelected()));
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
- Boolean.toString(msfjv.isSelected()));
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
- Boolean.toString(pfamjv.isSelected()));
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
- Boolean.toString(pileupjv.
- isSelected()));
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
- Boolean.toString(pirjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_MODELLER",
- Boolean.toString(modellerOutput.
- isSelected()));
- jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
-
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
- Boolean.toString(
- autoCalculateConsCheck.isSelected()));
- Cache.applicationProperties.setProperty("PAD_GAPS",
- Boolean.toString(padGaps.isSelected()));
-
- dasSource.saveProperties(Cache.applicationProperties);
-
- Cache.saveProperties();
- try
- {
- frame.setClosed(true);
- }
- catch (Exception ex)
- {
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void startupFileTextfield_mouseClicked()
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"),
- new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "jar"
- },
- new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select startup file");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
- chooser.getSelectedFormat());
- startupFileTextfield.setText(chooser.getSelectedFile()
- .getAbsolutePath());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void cancel_actionPerformed(ActionEvent e)
- {
- try
- {
- frame.setClosed(true);
- }
- catch (Exception ex)
- {
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void annotations_actionPerformed(ActionEvent e)
- {
- conservation.setEnabled(annotations.isSelected());
- quality.setEnabled(annotations.isSelected());
- identity.setEnabled(annotations.isSelected());
- }
-
- public void newLink_actionPerformed(ActionEvent e)
- {
-
- GSequenceLink link = new GSequenceLink();
- boolean valid = false;
- while (!valid)
- {
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link",
- JOptionPane.OK_CANCEL_OPTION
- , -1, null)
- == JOptionPane.OK_OPTION)
- {
- if (link.checkValid())
- {
- nameLinks.addElement(link.getName());
- urlLinks.addElement(link.getURL());
- updateLinkData();
- valid = true;
- }
- }
- else
- {
- break;
- }
- }
- }
-
- public void editLink_actionPerformed(ActionEvent e)
- {
- GSequenceLink link = new GSequenceLink();
-
- int index = linkNameList.getSelectedIndex();
- if (index == -1)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!"
- , "No link selected",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- link.setName(nameLinks.elementAt(index).toString());
- link.setURL(urlLinks.elementAt(index).toString());
-
- boolean valid = false;
- while (!valid)
- {
-
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link",
- JOptionPane.OK_CANCEL_OPTION
- , -1, null)
- == JOptionPane.OK_OPTION)
- {
- if (link.checkValid())
- {
- nameLinks.setElementAt(link.getName(), index);
- urlLinks.setElementAt(link.getURL(), index);
- updateLinkData();
- valid = true;
- }
- }
-
- else
- {
- break;
- }
- }
- }
-
- public void deleteLink_actionPerformed(ActionEvent e)
- {
- int index = linkNameList.getSelectedIndex();
- if (index == -1)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!"
- , "No link selected",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
- nameLinks.removeElementAt(index);
- urlLinks.removeElementAt(index);
- updateLinkData();
- }
-
- void updateLinkData()
- {
- linkNameList.setListData(nameLinks);
- linkURLList.setListData(urlLinks);
- }
-
- public void defaultBrowser_mouseClicked(MouseEvent e)
- {
- JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle("Select default web browser");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JFileChooser.APPROVE_OPTION)
- {
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
- }
-
- }
-
- private void jbInit()
- throws Exception
- {
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.help.HelpSetException;
+import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JPanel;
+import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
+import javax.swing.RowSorter;
+import javax.swing.SortOrder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.ext.pymol.PymolManager;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.FileFormatI;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.ws.sifts.SiftsSettings;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
+
+ public static final String PYMOL_PATH = "PYMOL_PATH";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
+ public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+ public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+ public static final String GAP_COLOUR = "GAP_COLOUR";
+
+ public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ private static final int MAX_FONT_SIZE = 30;
+
+ /**
+ * Holds name and link separated with | character. Sequence ID must be
+ * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+ */
+ public static UrlProviderI sequenceUrlLinks;
+
+ public static UrlLinkTableModel dataModel;
+
+ /**
+ * Holds name and link separated with | character. Sequence IDS and Sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
+ * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
+ * for first and second token specified after a pipe character at end |,|.
+ * (TODO: proper escape for using | to separate ids or sequences
+ */
+
+ public static List groupURLLinks;
+ static
+ {
+ // get links selected to be in the menu (SEQUENCE_LINKS)
+ // and links entered by the user but not selected (STORED_LINKS)
+ String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
+ String notInMenuString = Cache.getDefault("STORED_LINKS", "");
+ String defaultUrl = Cache.getDefault("DEFAULT_URL",
+ UrlConstants.DEFAULT_LABEL);
+
+ // if both links lists are empty, add the DEFAULT_URL link
+ // otherwise we assume the default link is in one of the lists
+ if (inMenuString.isEmpty() && notInMenuString.isEmpty())
+ {
+ inMenuString = UrlConstants.DEFAULT_STRING;
+ }
+ UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
+ inMenuString, notInMenuString);
+ sequenceUrlLinks = factory.createUrlProvider();
+ dataModel = new UrlLinkTableModel(sequenceUrlLinks);
+
+ /**
+ * TODO: reformulate groupURL encoding so two or more can be stored in the
+ * .properties file as '|' separated strings
+ */
+
+ groupURLLinks = new ArrayList<>();
+ }
+
+ JInternalFrame frame;
+
+ private WsPreferences wsPrefs;
+
+ private OptionsParam promptEachTimeOpt = new OptionsParam(
+ MessageManager.getString("label.prompt_each_time"),
+ "Prompt each time");
+
+ private OptionsParam lineArtOpt = new OptionsParam(
+ MessageManager.getString("label.lineart"), "Lineart");
+
+ private OptionsParam textOpt = new OptionsParam(
+ MessageManager.getString("action.text"), "Text");
+
+ /**
+ * Creates a new Preferences object.
+ */
+ public Preferences()
+ {
+ super();
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ }
+ int width = 500, height = 450;
+ if (Platform.isAMacAndNotJS())
+ {
+ width = 570;
+ height = 480;
+ }
+
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
+ frame.setMinimumSize(new Dimension(width, height));
+
+ /*
+ * Set Visual tab defaults
+ */
+ seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
+ rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
+ annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
+ quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
+ identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+ openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+ showUnconserved
+ .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
+ showGroupConsensus
+ .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+ showGroupConservation.setSelected(
+ Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(
+ Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo
+ .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+ showNpTooltip
+ .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ showDbRefTooltip
+ .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+
+ String[] fonts = java.awt.GraphicsEnvironment
+ .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
+ for (int i = 0; i < fonts.length; i++)
+ {
+ fontNameCB.addItem(fonts[i]);
+ }
+
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
+ {
+ fontSizeCB.addItem(i + "");
+ }
+
+ fontStyleCB.addItem("plain");
+ fontStyleCB.addItem("bold");
+ fontStyleCB.addItem("italic");
+
+ fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+ fontStyleCB.setSelectedItem(
+ Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
+
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
+ scaleProteinToCdna
+ .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
+
+ idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
+ gapSymbolCB.addItem("-");
+ gapSymbolCB.addItem(".");
+
+ gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
+
+ sortby.addItem("No sort");
+ sortby.addItem("Id");
+ sortby.addItem("Pairwise Identity");
+ sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
+
+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
+
+ /*
+ * Set Colours tab defaults
+ */
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
+ {
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
+ }
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+
+ /*
+ * Set overview panel defaults
+ */
+ gapColour.setBackground(
+ Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(
+ Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+ gapLabel.setEnabled(!useLegacyGap.isSelected());
+ gapColour.setEnabled(!useLegacyGap.isSelected());
+ showHiddenAtStart
+ .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
+
+ /*
+ * Set Structure tab defaults
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+
+ /*
+ * set choice of structure viewer, and path if saved as a preference;
+ * default to Jmol (first choice) if an unexpected value is found
+ */
+ String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+ structViewer.setSelectedItem(viewerType);
+ String viewerPath = "";
+ ViewerType type = null;
+ try
+ {
+ type = ViewerType.valueOf(viewerType);
+ switch (type)
+ {
+ case JMOL:
+ break;
+ case CHIMERA:
+ viewerPath = Cache.getDefault(CHIMERA_PATH, "");
+ break;
+ case CHIMERAX:
+ viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
+ break;
+ case PYMOL:
+ viewerPath = Cache.getDefault(PYMOL_PATH, "");
+ break;
+ }
+ } catch (IllegalArgumentException e)
+ {
+ Cache.log.error("Unknown structure viewer type: " + viewerType
+ + ", defaulting to Jmol");
+ type = ViewerType.JMOL;
+ }
+ structureViewerPath.setText(viewerPath);
+
+ structureViewerPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (validateViewerPath())
+ {
+ Cache.setProperty(structViewer.getSelectedItem()
+ .equals(ViewerType.CHIMERAX.name())
+ ? CHIMERAX_PATH
+ : CHIMERA_PATH, structureViewerPath.getText());
+ }
+ }
+ });
+
+ if (Cache.getDefault("MAP_WITH_SIFTS", false))
+ {
+ siftsMapping.setSelected(true);
+ }
+ else
+ {
+ nwMapping.setSelected(true);
+ }
+
+ SiftsSettings
+ .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
+ /*
+ * Set Connections tab defaults
+ */
+
+ // set up sorting
+ linkUrlTable.setModel(dataModel);
+ final TableRowSorter sorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ linkUrlTable.setRowSorter(sorter);
+ List sortKeys = new ArrayList<>();
+
+ UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
+ sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
+ SortOrder.DESCENDING));
+ sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
+ SortOrder.DESCENDING));
+ sortKeys.add(
+ new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
+
+ sorter.setSortKeys(sortKeys);
+ // BH 2018 setSortKeys will do the sort
+ // sorter.sort();
+
+ // set up filtering
+ ActionListener onReset;
+ onReset = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(RowFilter.regexFilter(""));
+ }
+
+ };
+ doReset.addActionListener(onReset);
+
+ // filter to display only custom urls
+ final RowFilter customUrlFilter = new RowFilter<>()
+ {
+ @Override
+ public boolean include(
+ Entry extends TableModel, ? extends Object> entry)
+ {
+ return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
+ }
+ };
+
+ final TableRowSorter customSorter = new TableRowSorter<>(
+ linkUrlTable.getModel());
+ customSorter.setRowFilter(customUrlFilter);
+
+ ActionListener onCustomOnly;
+ onCustomOnly = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterTB.setText("");
+ sorter.setRowFilter(customUrlFilter);
+ }
+ };
+ userOnly.addActionListener(onCustomOnly);
+
+ filterTB.getDocument().addDocumentListener(new DocumentListener()
+ {
+ String caseInsensitiveFlag = "(?i)";
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ sorter.setRowFilter(RowFilter
+ .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+ }
+ });
+
+ // set up list selection functionality
+ linkUrlTable.getSelectionModel()
+ .addListSelectionListener(new UrlListSelectionHandler());
+
+ // set up radio buttons
+ int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+ .getPrimaryColumn();
+ String onClickName = linkUrlTable.getColumnName(onClickCol);
+ linkUrlTable.getColumn(onClickName)
+ .setCellRenderer(new RadioButtonRenderer());
+ linkUrlTable.getColumn(onClickName)
+ .setCellEditor(new RadioButtonEditor());
+
+ // get boolean columns and resize those to min possible
+ for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
+ {
+ if (linkUrlTable.getModel().getColumnClass(column)
+ .equals(Boolean.class))
+ {
+ TableColumn tableColumn = linkUrlTable.getColumnModel()
+ .getColumn(column);
+ int preferredWidth = tableColumn.getMinWidth();
+
+ TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
+ column);
+ Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
+ int cwidth = c.getPreferredSize().width
+ + linkUrlTable.getIntercellSpacing().width;
+ preferredWidth = Math.max(preferredWidth, cwidth);
+
+ tableColumn.setPreferredWidth(preferredWidth);
+ }
+ }
+
+ useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
+ useProxy_actionPerformed(); // make sure useProxy is correctly initialised
+ proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+ proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+ defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+
+ usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ // note antisense here: default is true
+ questionnaire
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
+
+ /*
+ * Set Output tab defaults
+ */
+ setupOutputCombo(epsRendering, "EPS_RENDERING");
+ setupOutputCombo(htmlRendering, "HTML_RENDERING");
+ setupOutputCombo(svgRendering, "SVG_RENDERING");
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
+ userIdWidth.setText(wi == null ? "" : wi.toString());
+ // TODO: refactor to use common enum via FormatAdapter and allow extension
+ // for new flat file formats
+ blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
+ clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
+ fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+ pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+ pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ embbedBioJSON
+ .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
+
+ /*
+ * Set Editing tab defaults
+ */
+ autoCalculateConsCheck
+ .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+
+ annotations_actionPerformed(null); // update the display of the annotation
+ // settings
+
+
+ /*
+ * Set Backups tab defaults
+ */
+ loadLastSavedBackupsOptions();
+ }
+
+ /**
+ * A helper method that sets the items and initial selection in a character
+ * rendering option list (Prompt each time/Lineart/Text)
+ *
+ * @param comboBox
+ * @param propertyKey
+ */
+ protected void setupOutputCombo(JComboBox