-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-\r
-import jalview.bin.*;\r
-import jalview.io.*;\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-\r
-public class Preferences\r
- extends GPreferences\r
-{\r
- static boolean preferencesLoaded = false;\r
- public static boolean showFullscreen = false;\r
- public static boolean showFullId = true;\r
- public static boolean showAnnotation = true;\r
- public static boolean showConservation = true;\r
- public static boolean showQuality = true;\r
- public static boolean showIdentity = true;\r
- public static String fontName = "SansSerif";\r
- public static String fontSize = "10";\r
- public static String fontStyle = Font.PLAIN + "";\r
- public static char gapSymbol = '-';\r
- public static String defaultColour = null;\r
- public static boolean showStartupFile = true;\r
- public static String startupFile =\r
- "http://www.jalview.org/examples/exampleFile.jar";\r
- JInternalFrame frame;\r
-\r
- public Preferences()\r
- {\r
- initPreferences();\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
-\r
- fullID.setSelected(showFullId);\r
-\r
- String string = Cache.getProperty("SHOW_FULLSCREEN");\r
- boolean value = false;\r
-\r
- if (string != null)\r
- {\r
- value = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- fullScreen.setSelected(value);\r
- annotations.setSelected(showAnnotation);\r
-\r
- conservation.setEnabled(showAnnotation);\r
- quality.setEnabled(showAnnotation);\r
- identity.setEnabled(showAnnotation);\r
-\r
- conservation.setSelected(showConservation);\r
- quality.setSelected(showQuality);\r
- identity.setSelected(showIdentity);\r
-\r
- for (int i = 0; i < 12; i++)\r
- {\r
- colour.addItem(ColourSchemeProperty.getColourName(i));\r
- }\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
-\r
- if (string != null)\r
- {\r
- colour.setSelectedItem(string);\r
- }\r
- else\r
- {\r
- colour.setSelectedIndex(11);\r
- }\r
-\r
- String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
- .getAvailableFontFamilyNames();\r
-\r
- for (int i = 0; i < fonts.length; i++)\r
- {\r
- fontNameCB.addItem(fonts[i]);\r
- }\r
-\r
- for (int i = 1; i < 31; i++)\r
- {\r
- fontSizeCB.addItem(i + "");\r
- }\r
-\r
- fontStyleCB.addItem("plain");\r
- fontStyleCB.addItem("bold");\r
- fontStyleCB.addItem("italic");\r
-\r
- fontNameCB.setSelectedItem(fontName);\r
- fontSizeCB.setSelectedItem(fontSize);\r
- fontStyleCB.setSelectedItem(fontStyle);\r
-\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
-\r
- gapSymbolCB.setSelectedItem(gapSymbol + "");\r
-\r
- startupCheckbox.setSelected(showStartupFile);\r
- startupFileTextfield.setText(startupFile);\r
- }\r
-\r
- public static void initPreferences()\r
- {\r
- String string = Cache.getProperty("SHOW_FULL_ID");\r
-\r
- if (string != null)\r
- {\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("SHOW_FULLSCREEN");\r
-\r
- if (string != null)\r
- {\r
- showFullscreen = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("SHOW_ANNOTATIONS");\r
-\r
- if (string != null)\r
- {\r
- showAnnotation = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("SHOW_CONSERVATION");\r
-\r
- if (string != null)\r
- {\r
- showConservation = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("SHOW_QUALITY");\r
-\r
- if (string != null)\r
- {\r
- showQuality = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("SHOW_IDENTITY");\r
-\r
- if (string != null)\r
- {\r
- showIdentity = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("GAP_SYMBOL");\r
-\r
- if (string != null)\r
- {\r
- gapSymbol = string.charAt(0);\r
- }\r
-\r
- string = Cache.getProperty("SHOW_FULL_ID");\r
-\r
- if (string != null)\r
- {\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- string = Cache.getProperty("FONT_NAME");\r
-\r
- if (string != null)\r
- {\r
- fontName = string;\r
- }\r
-\r
- string = Cache.getProperty("FONT_STYLE");\r
-\r
- if (string != null)\r
- {\r
- fontStyle = string;\r
- }\r
-\r
- string = Cache.getProperty("FONT_SIZE");\r
-\r
- if (string != null)\r
- {\r
- fontSize = string;\r
- }\r
-\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
-\r
- if (string != null)\r
- {\r
- defaultColour = string;\r
- }\r
-\r
- string = Cache.getProperty("STARTUP_FILE");\r
-\r
- if (string != null)\r
- {\r
- startupFile = string;\r
- }\r
-\r
- string = Cache.getProperty("SHOW_STARTUP_FILE");\r
-\r
- if (string != null)\r
- {\r
- showStartupFile = Boolean.valueOf(string).booleanValue();\r
- }\r
-\r
- preferencesLoaded = true;\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- showFullId = fullID.isSelected();\r
- showFullscreen = fullScreen.isSelected();\r
- showAnnotation = annotations.isSelected();\r
- showConservation = conservation.isSelected();\r
- showQuality = quality.isSelected();\r
- showIdentity = identity.isSelected();\r
- defaultColour = colour.getSelectedItem().toString();\r
- gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);\r
- fontName = fontNameCB.getSelectedItem().toString();\r
- fontSize = fontSizeCB.getSelectedItem().toString();\r
- fontStyle = fontStyleCB.getSelectedItem().toString();\r
- startupFile = startupFileTextfield.getText();\r
- showStartupFile = startupCheckbox.isSelected();\r
-\r
- Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));\r
- Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen));\r
-\r
- Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation));\r
- Cache.setProperty("SHOW_CONSERVATION",\r
- Boolean.toString(showConservation));\r
- Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality));\r
- Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity));\r
-\r
- Cache.setProperty("DEFAULT_COLOUR", defaultColour);\r
- Cache.setProperty("GAP_SYMBOL", gapSymbol + "");\r
-\r
- Cache.setProperty("FONT_NAME", fontName);\r
- Cache.setProperty("FONT_STYLE", fontStyle);\r
- Cache.setProperty("FONT_SIZE", fontSize);\r
-\r
- Cache.setProperty("STARTUP_FILE", startupFile);\r
- Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));\r
-\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- public void startupFileTextfield_mouseClicked()\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
- new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select startup file");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
- chooser.getSelectedFormat());\r
- startupFileTextfield.setText(chooser.getSelectedFile()\r
- .getAbsolutePath());\r
- }\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
- conservation.setEnabled(annotations.isSelected());\r
- quality.setEnabled(annotations.isSelected());\r
- identity.setEnabled(annotations.isSelected());\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
+ * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+ */
+ 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())
+ {
+ String name = st.nextToken();
+ String url = st.nextToken();
+ // check for '|' within a regex
+ int rxstart = url.indexOf("$SEQUENCE_ID$");
+ while (rxstart == -1 && url.indexOf("/=$") == -1)
+ {
+ url = url + "|" + st.nextToken();
+ }
+ sequenceURLLinks.addElement(name + "|" + url);
+ }
+ } 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 (new jalview.util.Platform().isAMac())
+ {
+ 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));
+ showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", 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/exampleFile_2_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("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.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());
+ }
+
+ }
+ /* (non-Javadoc)
+ * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
+ */
+ protected void showunconserved_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+ super.showunconserved_actionPerformed(e);
+ }
+
+ private void jbInit() throws Exception
+ {
+ }
+}
git://source.jalview.org / jalview.git / blobdiff