*/\r
package jalview.gui;\r
\r
-import jalview.bin.*;\r
-\r
import jalview.io.*;\r
\r
import jalview.jbgui.*;\r
\r
import javax.swing.*;\r
\r
+import java.util.*;\r
+\r
+import jalview.bin.Cache;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class Preferences extends GPreferences\r
{\r
- static boolean preferencesLoaded = false;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showFullscreen = false;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showFullId = true;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showAnnotation = true;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showConservation = true;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showQuality = true;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showIdentity = true;\r
-\r
- /** DOCUMENT ME!! */\r
- public static String fontName = "SansSerif";\r
-\r
- /** DOCUMENT ME!! */\r
- public static String fontSize = "10";\r
-\r
- /** DOCUMENT ME!! */\r
- public static String fontStyle = Font.PLAIN + "";\r
-\r
- /** DOCUMENT ME!! */\r
- public static char gapSymbol = '-';\r
-\r
- /** DOCUMENT ME!! */\r
- public static String defaultColour = null;\r
-\r
- /** DOCUMENT ME!! */\r
- public static boolean showStartupFile = true;\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/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\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
+ Vector nameLinks, urlLinks;\r
\r
- /** DOCUMENT ME!! */\r
- public static String startupFile = "http://www.jalview.org/examples/exampleFile.jar";\r
JInternalFrame frame;\r
\r
+\r
/**\r
* Creates a new Preferences object.\r
*/\r
public Preferences()\r
{\r
- initPreferences();\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
+ frame.setMinimumSize(new Dimension(480,390));\r
\r
- fullID.setSelected(showFullId);\r
+ fullID.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\r
+ fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));\r
+ annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
\r
- String string = Cache.getProperty("SHOW_FULLSCREEN");\r
- boolean value = false;\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
- 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
+ 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
- conservation.setSelected(showConservation);\r
- quality.setSelected(showQuality);\r
- identity.setSelected(showIdentity);\r
-\r
- for (int i = 0; i < 12; i++)\r
+ for (int i = 0; i < 13; i++)\r
{\r
colour.addItem(ColourSchemeProperty.getColourName(i));\r
}\r
\r
- string = Cache.getProperty("DEFAULT_COLOUR");\r
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
\r
- if (string != null)\r
- {\r
- colour.setSelectedItem(string);\r
- }\r
- else\r
- {\r
- colour.setSelectedIndex(11);\r
- }\r
+ colour.setSelectedItem(string);\r
\r
String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
.getAvailableFontFamilyNames();\r
fontStyleCB.addItem("bold");\r
fontStyleCB.addItem("italic");\r
\r
- fontNameCB.setSelectedItem(fontName);\r
- fontSizeCB.setSelectedItem(fontSize);\r
- fontStyleCB.setSelectedItem(fontStyle);\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
gapSymbolCB.addItem("-");\r
gapSymbolCB.addItem(".");\r
\r
- gapSymbolCB.setSelectedItem(gapSymbol + "");\r
+ gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
\r
- startupCheckbox.setSelected(showStartupFile);\r
- startupFileTextfield.setText(startupFile);\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
- /**\r
- * DOCUMENT ME!\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
+ sortby.addItem("No sort");\r
+ sortby.addItem("Id");\r
+ sortby.addItem("Pairwise Identity");\r
+ sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
\r
- string = Cache.getProperty("SHOW_FULLSCREEN");\r
+ epsRendering.addItem("Prompt each time");\r
+ epsRendering.addItem("Lineart");\r
+ epsRendering.addItem("Text");\r
+ epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
\r
- if (string != null)\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
- showFullscreen = Boolean.valueOf(string).booleanValue();\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
- string = Cache.getProperty("SHOW_ANNOTATIONS");\r
+ updateLinkData();\r
\r
- if (string != null)\r
- {\r
- showAnnotation = Boolean.valueOf(string).booleanValue();\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
- string = Cache.getProperty("SHOW_CONSERVATION");\r
+ defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
\r
- if (string != null)\r
- {\r
- showConservation = Boolean.valueOf(string).booleanValue();\r
- }\r
+ }\r
\r
- string = Cache.getProperty("SHOW_QUALITY");\r
\r
- if (string != null)\r
- {\r
- showQuality = Boolean.valueOf(string).booleanValue();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void ok_actionPerformed(ActionEvent e)\r
+ {\r
\r
- string = Cache.getProperty("SHOW_IDENTITY");\r
+ Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
\r
- if (string != null)\r
- {\r
- showIdentity = Boolean.valueOf(string).booleanValue();\r
- }\r
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
\r
- string = Cache.getProperty("GAP_SYMBOL");\r
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
\r
- if (string != null)\r
- {\r
- gapSymbol = string.charAt(0);\r
- }\r
+ Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
\r
- string = Cache.getProperty("SHOW_FULL_ID");\r
+ Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));\r
\r
- if (string != null)\r
- {\r
- showFullId = Boolean.valueOf(string).booleanValue();\r
- }\r
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
\r
- string = Cache.getProperty("FONT_NAME");\r
+ if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
+ Cache.applicationProperties.remove("EPS_RENDERING");\r
+ else\r
+ Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
\r
- if (string != null)\r
- {\r
- fontName = string;\r
- }\r
+ if(defaultBrowser.getText().trim().length()<1)\r
+ Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
+ else\r
+ Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
+ defaultBrowser.getText());\r
\r
- string = Cache.getProperty("FONT_STYLE");\r
+ jalview.util.BrowserLauncher.resetBrowser();\r
\r
- if (string != null)\r
+ if(nameLinks.size()>0)\r
{\r
- fontStyle = string;\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)+"|"+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
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");\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
+ Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
\r
- if (string != null)\r
- {\r
- defaultColour = string;\r
- }\r
+ if (proxyServerTB.getText().trim().length() < 1)\r
+ Cache.applicationProperties.remove("PROXY_SERVER");\r
+ else\r
+ Cache.applicationProperties.setProperty("PROXY_SERVER",\r
+ proxyServerTB.getText());\r
\r
- string = Cache.getProperty("STARTUP_FILE");\r
+ if (proxyPortTB.getText().trim().length() < 1)\r
+ Cache.applicationProperties.remove("PROXY_PORT");\r
+ else\r
+ Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
\r
- if (string != null)\r
+ if(useProxy.isSelected())\r
{\r
- startupFile = string;\r
+ System.setProperty("http.proxyHost", proxyServerTB.getText());\r
+ System.setProperty("http.proxyPort", proxyPortTB.getText());\r
}\r
-\r
- string = Cache.getProperty("SHOW_STARTUP_FILE");\r
-\r
- if (string != null)\r
+ else\r
{\r
- showStartupFile = Boolean.valueOf(string).booleanValue();\r
+ System.setProperty("http.proxyHost","");\r
+ System.setProperty("http.proxyPort","");\r
}\r
\r
- preferencesLoaded = true;\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\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
+ Cache.saveProperties();\r
try\r
{\r
frame.setClosed(true);\r
\r
if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
+ jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
chooser.getSelectedFormat());\r
startupFileTextfield.setText(chooser.getSelectedFile()\r
.getAbsolutePath());\r
quality.setEnabled(annotations.isSelected());\r
identity.setEnabled(annotations.isSelected());\r
}\r
+\r
+\r
+ public void newLink_actionPerformed(ActionEvent e) {\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
+ break;\r
+ }\r
+ }\r
+\r
+ public void editLink_actionPerformed(ActionEvent e) {\r
+ GSequenceLink link = new GSequenceLink();\r
+\r
+ int index = linkNameList.getSelectedIndex();\r
+ if(index==-1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
+ ,"No link selected", 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
+ break;\r
+ }\r
+ }\r
+\r
+ public void deleteLink_actionPerformed(ActionEvent e) {\r
+ int index = linkNameList.getSelectedIndex();\r
+ if(index==-1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
+ ,"No link selected", 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
git://source.jalview.org / jalview.git / blobdiff