+/*\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 jalview.io.*;\r
+\r
import jalview.jbgui.*;\r
+\r
import jalview.schemes.*;\r
\r
-import jalview.bin.Cache;\r
-import javax.swing.*;\r
-import java.awt.event.ActionEvent;\r
import java.awt.*;\r
+import java.awt.event.*;\r
\r
+import javax.swing.*;\r
+\r
+import java.util.*;\r
+\r
+import jalview.bin.Cache;\r
+\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class Preferences extends GPreferences\r
{\r
- AlignViewport av;\r
- JInternalFrame frame;\r
- public Preferences(AlignViewport av)\r
- {\r
- this.av = av;\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480,350 );\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
- fullID.setSelected(av.getShowFullId());\r
- String string = Cache.getProperty("SHOW_FULLSCREEN");\r
- boolean value = false;\r
- if(string!=null)\r
- value = Boolean.valueOf(string).booleanValue();\r
+ JInternalFrame frame;\r
\r
- fullScreen.setSelected(value);\r
- annotations.setSelected(av.getShowAnnotation());\r
\r
- conservation.setEnabled(av.getShowAnnotation());\r
- quality.setEnabled(av.getShowAnnotation());\r
- identity.setEnabled(av.getShowAnnotation());\r
+ /**\r
+ * Creates a new Preferences object.\r
+ */\r
+ public Preferences()\r
+ {\r
\r
- conservation.setSelected(av.showConservation);\r
- quality.setSelected(av.showQuality);\r
- identity.setSelected(av.showIdentity);\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
+ frame.setMinimumSize(new Dimension(480,390));\r
\r
- for(int i=0; i<12; i++)\r
- colour.addItem( ColourSchemeProperty.getColourName(i) );\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 = Cache.getProperty("DEFAULT_COLOUR");\r
- if(string!=null)\r
- colour.setSelectedItem( string );\r
- else\r
- colour.setSelectedIndex( 11 );\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
- String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();\r
- for(int i=0; i<fonts.length; i++)\r
- fontName.addItem(fonts[i]);\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=1; i<31; i++)\r
- fontSize.addItem(i+"");\r
+ for (int i = 0; i < 13; i++)\r
+ {\r
+ colour.addItem(ColourSchemeProperty.getColourName(i));\r
+ }\r
\r
- fontStyle.addItem("plain");\r
- fontStyle.addItem("bold");\r
- fontStyle.addItem("italic");\r
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
\r
- Font oldFont = av.getFont();\r
- fontName.setSelectedItem(oldFont.getName());\r
- fontSize.setSelectedItem(oldFont.getSize() + "");\r
- fontStyle.setSelectedIndex(oldFont.getStyle());\r
+ colour.setSelectedItem(string);\r
\r
- gapSymbol.addItem("-");\r
- gapSymbol.addItem(".");\r
+ String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
+ .getAvailableFontFamilyNames();\r
\r
- gapSymbol.setSelectedItem( av.getGapCharacter()+"" );\r
+ for (int i = 0; i < fonts.length; i++)\r
+ {\r
+ fontNameCB.addItem(fonts[i]);\r
+ }\r
\r
- }\r
+ for (int i = 1; i < 31; i++)\r
+ {\r
+ fontSizeCB.addItem(i + "");\r
+ }\r
\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- Cache.setProperty("SHOW_FULL_ID", Boolean.toString( fullID.isSelected() ));\r
- Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( fullScreen.isSelected() ));\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
+ gapSymbolCB.addItem("-");\r
+ gapSymbolCB.addItem(".");\r
\r
- Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( annotations.isSelected() ));\r
- Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( conservation.isSelected() ));\r
- Cache.setProperty("SHOW_QUALITY", Boolean.toString( quality.isSelected() ));\r
- Cache.setProperty("SHOW_IDENTITY", Boolean.toString( identity.isSelected() ));\r
+ gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
\r
- Cache.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString() );\r
- Cache.setProperty("GAP_SYMBOL", gapSymbol.getSelectedItem().toString());\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
- Cache.setProperty("FONT_NAME", fontName.getSelectedItem().toString());\r
- Cache.setProperty("FONT_STYLE", fontStyle.getSelectedIndex()+"");\r
- Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());\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
- try {\r
- frame.setClosed(true);\r
- } catch (Exception ex) {}\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
- av.updateFromPreferences();\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
- repaint();\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
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\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_FULL_ID", Boolean.toString(fullID.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\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
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\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
+ Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
+\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(defaultBrowser.getText().trim().length()<1)\r
+ Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
+ else\r
+ Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
+ defaultBrowser.getText());\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)+"|"+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
+\r
+ Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\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
+ 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(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
+\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.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
+\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
- public void annotations_actionPerformed(ActionEvent e)\r
+ private void jbInit()\r
+ throws Exception\r
{\r
- conservation.setEnabled(annotations.isSelected());\r
- quality.setEnabled(annotations.isSelected());\r
- identity.setEnabled(annotations.isSelected());\r
}\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff