/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 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
*/\r
package jalview.gui;\r
\r
-import jalview.bin.*;\r
-\r
import jalview.io.*;\r
\r
import jalview.jbgui.*;\r
public class Preferences extends GPreferences\r
{\r
/** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
- public static Vector sequenceURLLinks = new Vector();\r
- static { sequenceURLLinks.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");}\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
Vector nameLinks, urlLinks;\r
\r
JInternalFrame frame;\r
\r
+ DasSourceBrowser dasSource;\r
+\r
\r
/**\r
* Creates a new Preferences object.\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
- frame.setMinimumSize(new Dimension(480,390));\r
+ dasSource = new DasSourceBrowser();\r
+ dasPanel.add(dasSource, BorderLayout.CENTER);\r
\r
- fullID.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\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_FULL_ID", true));\r
- conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\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
quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\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 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
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
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
"http://www.jalview.org/examples/exampleFile.jar"));\r
\r
- /****************************************************\r
- * Set up Connections\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.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
+ 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
- try{\r
- StringTokenizer st = new StringTokenizer(string, "|");\r
- while (st.hasMoreElements())\r
- {\r
- sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
- }\r
- }catch(Exception ex)\r
- {System.out.println(ex+"\nError parsing sequence links");}\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
public void ok_actionPerformed(ActionEvent e)\r
{\r
\r
- Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
+ Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.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("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
\r
+ Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
+\r
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\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("DEFAULT_BROWSER", defaultBrowser.getText());\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
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
- Cache.applicationProperties.setProperty("PROXY_SERVER",proxyServerTB.getText());\r
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\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
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
\r
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
+ Boolean.toString(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
git://source.jalview.org / jalview.git / blobdiff