-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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.util.*;\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
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Preferences\r
- extends GPreferences\r
-{\r
- /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
- public static Vector sequenceURLLinks;\r
- static\r
- {\r
- String string = Cache.getDefault("SEQUENCE_LINKS",\r
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");\r
- sequenceURLLinks = new Vector();\r
-\r
- try\r
- {\r
- StringTokenizer st = new StringTokenizer(string, "|");\r
- while (st.hasMoreElements())\r
- {\r
- sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println(ex + "\nError parsing sequence links");\r
- }\r
- }\r
-\r
- Vector nameLinks, urlLinks;\r
-\r
- JInternalFrame frame;\r
-\r
- DasSourceBrowser dasSource;\r
-\r
- /**\r
- * Creates a new Preferences object.\r
- */\r
- public Preferences()\r
- {\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- dasSource = new DasSourceBrowser();\r
- dasPanel.add(dasSource, BorderLayout.CENTER);\r
-\r
- int width = 500, height = 420;\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- width = 570;\r
- height = 460;\r
- }\r
-\r
- Desktop.addInternalFrame(frame, "Preferences", width, height);\r
- frame.setMinimumSize(new Dimension(width, height));\r
-\r
- seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));\r
- rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));\r
- fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));\r
- annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
-\r
- conservation.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
- quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
- identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
-\r
- conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
- quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
- identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
-\r
- for (int i = 0; i < 13; i++)\r
- {\r
- colour.addItem(ColourSchemeProperty.getColourName(i));\r
- }\r
-\r
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
-\r
- colour.setSelectedItem(string);\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(Cache.getDefault("FONT_NAME", "SansSerif"));\r
- fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));\r
-\r
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
-\r
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
-\r
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
-\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
-\r
- gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));\r
-\r
- startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));\r
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
- "http://www.jalview.org/examples/exampleFile.jar"));\r
-\r
- sortby.addItem("No sort");\r
- sortby.addItem("Id");\r
- sortby.addItem("Pairwise Identity");\r
- sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));\r
-\r
- epsRendering.addItem("Prompt each time");\r
- epsRendering.addItem("Lineart");\r
- epsRendering.addItem("Text");\r
- epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",\r
- "Prompt each time"));\r
-\r
- blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));\r
- clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
- fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));\r
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));\r
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));\r
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));\r
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));\r
-\r
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));\r
-\r
- autoCalculateConsCheck.setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));\r
-\r
- /****************************************************\r
- * Set up Connections\r
- */\r
- nameLinks = new Vector();\r
- urlLinks = new Vector();\r
- for (int i = 0; i < sequenceURLLinks.size(); i++)\r
- {\r
- String link = sequenceURLLinks.elementAt(i).toString();\r
- nameLinks.addElement(link.substring(0, link.indexOf("|")));\r
- urlLinks.addElement(link.substring(link.indexOf("|") + 1));\r
- }\r
-\r
- updateLinkData();\r
-\r
- useProxy.setSelected(Cache.getDefault("USE_PROXY", false));\r
- proxyServerTB.setEnabled(useProxy.isSelected());\r
- proxyPortTB.setEnabled(useProxy.isSelected());\r
- proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));\r
- proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
-\r
- defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
-\r
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",\r
- Boolean.toString(seqLimit.\r
- isSelected()));\r
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",\r
- Boolean.toString(rightAlign.\r
- isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",\r
- Boolean.toString(fullScreen.\r
- isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",\r
- Boolean.\r
- toString(annotations.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",\r
- Boolean.\r
- toString(conservation.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_QUALITY",\r
- Boolean.toString(quality.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",\r
- Boolean.toString(identity.\r
- isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR",\r
- colour.getSelectedItem().toString());\r
- Cache.applicationProperties.setProperty("GAP_SYMBOL",\r
- gapSymbolCB.getSelectedItem().\r
- toString());\r
-\r
- Cache.applicationProperties.setProperty("FONT_NAME",\r
- fontNameCB.getSelectedItem().\r
- toString());\r
- Cache.applicationProperties.setProperty("FONT_STYLE",\r
- fontStyleCB.getSelectedItem().\r
- toString());\r
- Cache.applicationProperties.setProperty("FONT_SIZE",\r
- fontSizeCB.getSelectedItem().\r
- toString());\r
-\r
- Cache.applicationProperties.setProperty("ID_ITALICS",\r
- Boolean.toString(idItalics.\r
- isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("ANTI_ALIAS",\r
- Boolean.toString(smoothFont.\r
- isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",\r
- Boolean.toString(wrap.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("STARTUP_FILE",\r
- startupFileTextfield.getText());\r
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",\r
- Boolean.\r
- toString(startupCheckbox.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT",\r
- sortby.getSelectedItem().toString());\r
-\r
- if (epsRendering.getSelectedItem().equals("Prompt each time"))\r
- {\r
- Cache.applicationProperties.remove("EPS_RENDERING");\r
- }\r
- else\r
- {\r
- Cache.applicationProperties.setProperty("EPS_RENDERING",\r
- epsRendering.getSelectedItem().\r
- toString());\r
- }\r
-\r
- if (defaultBrowser.getText().trim().length() < 1)\r
- {\r
- Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
- }\r
- else\r
- {\r
- Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
- defaultBrowser.getText());\r
- }\r
-\r
- jalview.util.BrowserLauncher.resetBrowser();\r
-\r
- if (nameLinks.size() > 0)\r
- {\r
- StringBuffer links = new StringBuffer();\r
- sequenceURLLinks = new Vector();\r
- for (int i = 0; i < nameLinks.size(); i++)\r
- {\r
- sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|" +\r
- urlLinks.elementAt(i));\r
- links.append(sequenceURLLinks.elementAt(i).toString());\r
- links.append("|");\r
- }\r
- // remove last "|"\r
- links.setLength(links.length() - 1);\r
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
- }\r
- else\r
- {\r
- Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
- }\r
-\r
- Cache.applicationProperties.setProperty("USE_PROXY",\r
- Boolean.toString(useProxy.\r
- isSelected()));\r
-\r
- if (proxyServerTB.getText().trim().length() < 1)\r
- {\r
- Cache.applicationProperties.remove("PROXY_SERVER");\r
- }\r
- else\r
- {\r
- Cache.applicationProperties.setProperty("PROXY_SERVER",\r
- proxyServerTB.getText());\r
- }\r
-\r
- if (proxyPortTB.getText().trim().length() < 1)\r
- {\r
- Cache.applicationProperties.remove("PROXY_PORT");\r
- }\r
- else\r
- {\r
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
- }\r
-\r
- if (useProxy.isSelected())\r
- {\r
- System.setProperty("http.proxyHost", proxyServerTB.getText());\r
- System.setProperty("http.proxyPort", proxyPortTB.getText());\r
- }\r
- else\r
- {\r
- System.setProperty("http.proxyHost", "");\r
- System.setProperty("http.proxyPort", "");\r
- }\r
-\r
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX",\r
- Boolean.toString(blcjv.isSelected()));\r
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",\r
- Boolean.\r
- toString(clustaljv.isSelected()));\r
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",\r
- Boolean.toString(fastajv.isSelected()));\r
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX",\r
- Boolean.toString(msfjv.isSelected()));\r
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",\r
- Boolean.toString(pfamjv.isSelected()));\r
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",\r
- Boolean.toString(pileupjv.\r
- isSelected()));\r
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX",\r
- Boolean.toString(pirjv.isSelected()));\r
- Cache.applicationProperties.setProperty("PIR_MODELLER",\r
- Boolean.toString(modellerOutput.\r
- isSelected()));\r
- jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
-\r
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
- Boolean.toString(\r
- autoCalculateConsCheck.isSelected()));\r
- Cache.applicationProperties.setProperty("PAD_GAPS",\r
- Boolean.toString(padGaps.isSelected()));\r
-\r
- dasSource.saveProperties(Cache.applicationProperties);\r
-\r
- Cache.saveProperties();\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\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.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
- chooser.getSelectedFormat());\r
- startupFileTextfield.setText(chooser.getSelectedFile()\r
- .getAbsolutePath());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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
- public void newLink_actionPerformed(ActionEvent e)\r
- {\r
-\r
- GSequenceLink link = new GSequenceLink();\r
- boolean valid = false;\r
- while (!valid)\r
- {\r
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
- "New sequence URL link",\r
- JOptionPane.OK_CANCEL_OPTION\r
- , -1, null)\r
- == JOptionPane.OK_OPTION)\r
- {\r
- if (link.checkValid())\r
- {\r
- nameLinks.addElement(link.getName());\r
- urlLinks.addElement(link.getURL());\r
- updateLinkData();\r
- valid = true;\r
- }\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
- }\r
-\r
- public void editLink_actionPerformed(ActionEvent e)\r
- {\r
- GSequenceLink link = new GSequenceLink();\r
-\r
- int index = linkNameList.getSelectedIndex();\r
- if (index == -1)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "No link selected!"\r
- , "No link selected",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- link.setName(nameLinks.elementAt(index).toString());\r
- link.setURL(urlLinks.elementAt(index).toString());\r
-\r
- boolean valid = false;\r
- while (!valid)\r
- {\r
-\r
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
- "New sequence URL link",\r
- JOptionPane.OK_CANCEL_OPTION\r
- , -1, null)\r
- == JOptionPane.OK_OPTION)\r
- {\r
- if (link.checkValid())\r
- {\r
- nameLinks.setElementAt(link.getName(), index);\r
- urlLinks.setElementAt(link.getURL(), index);\r
- updateLinkData();\r
- valid = true;\r
- }\r
- }\r
-\r
- else\r
- {\r
- break;\r
- }\r
- }\r
- }\r
-\r
- public void deleteLink_actionPerformed(ActionEvent e)\r
- {\r
- int index = linkNameList.getSelectedIndex();\r
- if (index == -1)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "No link selected!"\r
- , "No link selected",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
- nameLinks.removeElementAt(index);\r
- urlLinks.removeElementAt(index);\r
- updateLinkData();\r
- }\r
-\r
- void updateLinkData()\r
- {\r
- linkNameList.setListData(nameLinks);\r
- linkURLList.setListData(urlLinks);\r
- }\r
-\r
- public void defaultBrowser_mouseClicked(MouseEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(".");\r
- chooser.setDialogTitle("Select default web browser");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JFileChooser.APPROVE_OPTION)\r
- {\r
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
- }\r
-\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+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.Collection;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.help.HelpSetException;
+import javax.swing.JColorChooser;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+
+/**
+ * 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 SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ 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 Vector sequenceURLLinks;
+
+ /**
+ * 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 Vector groupURLLinks;
+ static
+ {
+ String string = Cache
+ .getDefault(
+ "SEQUENCE_LINKS",
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
+ 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("/=$") == -1)
+ {
+ url = url + "|" + st.nextToken();
+ }
+ sequenceURLLinks.addElement(name + "|" + url);
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(ex + "\nError parsing sequence links");
+ }
+ {
+ // upgrade old SRS link
+ int srsPos = sequenceURLLinks
+ .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ if (srsPos > -1)
+ {
+ sequenceURLLinks
+ .setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
+ }
+ }
+
+ /**
+ * TODO: reformulate groupURL encoding so two or more can be stored in the
+ * .properties file as '|' separated strings
+ */
+
+ groupURLLinks = new Vector();
+ }
+
+ Vector nameLinks, urlLinks;
+
+ JInternalFrame frame;
+
+ DasSourceBrowser dasSource;
+
+ private WsPreferences wsPrefs;
+
+ /**
+ * Creates a new Preferences object.
+ */
+ public Preferences()
+ {
+ super();
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ dasSource = new DasSourceBrowser();
+ dasTab.add(dasSource, BorderLayout.CENTER);
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ int width = 500, height = 450;
+ if (new jalview.util.Platform().isAMac())
+ {
+ 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));
+ 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", false));
+ 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
+ */
+ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ {
+ protColour.addItem(ColourSchemeProperty.getColourName(i));
+ nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ }
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR, "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 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);
+ structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name()));
+ chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+ chimeraPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateChimeraPath();
+ }
+ });
+
+ /*
+ * Set Connections tab defaults
+ */
+ 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", ""));
+
+ 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
+ */
+ epsRendering
+ .addItem(MessageManager.getString("label.prompt_each_time"));
+ epsRendering.addItem(MessageManager.getString("label.lineart"));
+ epsRendering.addItem(MessageManager.getString("action.text"));
+ epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
+ "Prompt each time"));
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ userIdWidth.setText(wi == null ? "" : wi.toString());
+ 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
+ }
+
+ /**
+ * Save user selections on the Preferences tabs to the Cache and write out to
+ * file.
+ *
+ * @param e
+ */
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ if (!validateSettings())
+ {
+ return;
+ }
+
+ /*
+ * Save Visual settings
+ */
+ 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("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("SHOW_GROUP_CONSENSUS",
+ Boolean.toString(showGroupConsensus.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+ Boolean.toString(showGroupConservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+ Boolean.toString(showConsensHistogram.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("ANTI_ALIAS",
+ Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Boolean.toString(scaleProteinToCdna.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Boolean.toString(showNpTooltip.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Boolean.toString(showDbRefTooltip.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());
+
+ // convert description of sort order to enum name for save
+ SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
+ .forDescription(sortAnnBy.getSelectedItem().toString());
+ if (annSortOrder != null)
+ {
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+ annSortOrder.name());
+ }
+
+ final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+ .valueOf(showAutocalcFirst).toString());
+
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
+ .getSelectedItem().toString());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
+
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+ .getSelectedItem().toString());
+ Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+
+ /*
+ * Save Output settings
+ */
+ if (epsRendering.getSelectedItem().equals("Prompt each time"))
+ {
+ Cache.applicationProperties.remove("EPS_RENDERING");
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
+ .getSelectedItem().toString());
+ }
+
+ /*
+ * Save Connections settings
+ */
+ Cache.setOrRemove("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()));
+
+ Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
+
+ Cache.setOrRemove("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.setProperty("VERSION_CHECK",
+ Boolean.toString(versioncheck.isSelected()));
+ if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
+ {
+ // default is false - we only set this if the user has actively agreed
+ Cache.setProperty("USAGESTATS",
+ Boolean.toString(usagestats.isSelected()));
+ }
+ if (!questionnaire.isSelected())
+ {
+ Cache.setProperty("NOQUESTIONNAIRES", "true");
+ }
+ else
+ {
+ // special - made easy to edit a property file to disable questionnaires
+ // by just adding the given line
+ Cache.removeProperty("NOQUESTIONNAIRES");
+ }
+
+ /*
+ * Save Output settings
+ */
+ 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()));
+ Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Boolean.toString(embbedBioJSON.isSelected()));
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+ Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Boolean.toString(autoIdWidth.isSelected()));
+ userIdWidth_actionPerformed();
+ Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ userIdWidth.getText());
+
+ /*
+ * Save Editing settings
+ */
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+ Boolean.toString(autoCalculateConsCheck.isSelected()));
+ Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Boolean.toString(sortByTree.isSelected()));
+ Cache.applicationProperties.setProperty("PAD_GAPS",
+ Boolean.toString(padGaps.isSelected()));
+
+ dasSource.saveProperties(Cache.applicationProperties);
+ wsPrefs.updateAndRefreshWsMenuConfig(false);
+ Cache.saveProperties();
+ Desktop.instance.doConfigureStructurePrefs();
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * Do any necessary validation before saving settings. Return focus to the
+ * first tab which fails validation.
+ *
+ * @return
+ */
+ private boolean validateSettings()
+ {
+ if (!validateStructure())
+ {
+ structureTab.requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean validateStructure()
+ {
+ return validateChimeraPath();
+
+ }
+
+ /**
+ * 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(MessageManager
+ .getString("label.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
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ 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());
+ showGroupConsensus.setEnabled(annotations.isSelected());
+ showGroupConservation.setEnabled(annotations.isSelected());
+ showConsensHistogram.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ showConsensLogo.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ }
+
+ public void newLink_actionPerformed(ActionEvent e)
+ {
+
+ GSequenceLink link = new GSequenceLink();
+ boolean valid = false;
+ while (!valid)
+ {
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ MessageManager.getString("label.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,
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.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,
+ MessageManager.getString("label.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,
+ MessageManager.getString("label.no_link_selected"),
+ MessageManager.getString("label.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(MessageManager
+ .getString("label.select_default_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);
+ }
+
+ public static Collection getGroupURLLinks()
+ {
+ return groupURLLinks;
+ }
+
+ @Override
+ public void minColour_actionPerformed(JPanel panel)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
+ if (col != null)
+ {
+ panel.setBackground(col);
+ }
+ panel.repaint();
+ }
+
+ @Override
+ public void maxColour_actionPerformed(JPanel panel)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
+ if (col != null)
+ {
+ panel.setBackground(col);
+ }
+ panel.repaint();
+ }
+
+ @Override
+ protected void userIdWidth_actionPerformed()
+ {
+ try
+ {
+ String val = userIdWidth.getText().trim();
+ if (val.length() > 0)
+ {
+ Integer iw = Integer.parseInt(val);
+ if (iw.intValue() < 12)
+ {
+ throw new NumberFormatException();
+ }
+ userIdWidth.setText(iw.toString());
+ }
+ } catch (NumberFormatException x)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JOptionPane.WARNING_MESSAGE);
+ userIdWidth.setText("");
+ }
+ }
+
+ @Override
+ protected void autoIdWidth_actionPerformed()
+ {
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ }
+
+ /**
+ * Returns true if chimera path is to a valid executable, else show an error
+ * dialog.
+ */
+ private boolean validateChimeraPath()
+ {
+ if (chimeraPath.getText().trim().length() > 0)
+ {
+ File f = new File(chimeraPath.getText());
+ if (!f.canExecute())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.invalid_chimera_path"),
+ MessageManager.getString("label.invalid_name"),
+ JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * If Chimera is selected, check it can be found on default or user-specified
+ * path, if not show a warning/help dialog.
+ */
+ @Override
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+ {
+ return;
+ }
+ boolean found = false;
+
+ /*
+ * Try user-specified and standard paths for Chimera executable.
+ */
+ List<String> paths = StructureManager.getChimeraPaths();
+ paths.add(0, chimeraPath.getText());
+ for (String path : paths)
+ {
+ if (new File(path.trim()).canExecute())
+ {
+ found = true;
+ break;
+ }
+ }
+ if (!found)
+ {
+ String[] options = { "OK", "Help" };
+ int showHelp = JOptionPane.showInternalOptionDialog(
+ Desktop.desktop,
+ JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_missing")),
+ "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ if (showHelp == JOptionPane.NO_OPTION)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.StructureViewer);
+ } catch (HelpSetException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff