/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
*/\r
package jalview.gui;\r
\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
+import java.util.*;\r
\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
+import jalview.bin.*;\r
+import jalview.io.*;\r
+import jalview.jbgui.*;\r
+import jalview.schemes.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class Preferences extends GPreferences\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
+ /** 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
+ try\r
+ {\r
+ StringTokenizer st = new StringTokenizer(string, "|");\r
+ while (st.hasMoreElements())\r
{\r
- System.out.println(ex + "\nError parsing sequence links");\r
+ sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
}\r
}\r
- Vector nameLinks, urlLinks;\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println(ex + "\nError parsing sequence links");\r
+ }\r
+ }\r
\r
- JInternalFrame frame;\r
+ Vector nameLinks, urlLinks;\r
\r
- DasSourceBrowser dasSource;\r
+ JInternalFrame frame;\r
\r
+ DasSourceBrowser dasSource;\r
\r
- /**\r
- * Creates a new Preferences object.\r
- */\r
- public Preferences()\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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ 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
+ String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
\r
- colour.setSelectedItem(string);\r
+ colour.setSelectedItem(string);\r
\r
- String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
- .getAvailableFontFamilyNames();\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
+ 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
+ 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
+ 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
+ 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
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
\r
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
+ idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
\r
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
+ gapSymbolCB.addItem("-");\r
+ gapSymbolCB.addItem(".");\r
\r
- gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\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
+ 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
+ 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", "Prompt each time"));\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
+ 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
+ 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
+ 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
+ * 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
+ 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
+ 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
+ defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));\r
try\r
{\r
jbInit();\r
\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void ok_actionPerformed(ActionEvent e)\r
+ {\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void ok_actionPerformed(ActionEvent e)\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
- 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("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("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("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
+ 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
- if(defaultBrowser.getText().trim().length()<1)\r
- Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
- else\r
- Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
- defaultBrowser.getText());\r
+ jalview.util.BrowserLauncher.resetBrowser();\r
\r
- jalview.util.BrowserLauncher.resetBrowser();\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
- 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
+ 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
- Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\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 (proxyServerTB.getText().trim().length() < 1)\r
- Cache.applicationProperties.remove("PROXY_SERVER");\r
- else\r
- Cache.applicationProperties.setProperty("PROXY_SERVER",\r
- proxyServerTB.getText());\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
- if (proxyPortTB.getText().trim().length() < 1)\r
- Cache.applicationProperties.remove("PROXY_PORT");\r
- else\r
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\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
- if(useProxy.isSelected())\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
- System.setProperty("http.proxyHost", proxyServerTB.getText());\r
- System.setProperty("http.proxyPort", proxyPortTB.getText());\r
- }\r
- else\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\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
+ "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
- 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
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
+ int value = chooser.showOpenDialog(this);\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void startupFileTextfield_mouseClicked()\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\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
+ 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
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void cancel_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
{\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
+ frame.setClosed(true);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void annotations_actionPerformed(ActionEvent e)\r
+ catch (Exception ex)\r
{\r
- conservation.setEnabled(annotations.isSelected());\r
- quality.setEnabled(annotations.isSelected());\r
- identity.setEnabled(annotations.isSelected());\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
+ public void newLink_actionPerformed(ActionEvent e)\r
+ {\r
\r
- GSequenceLink link = new GSequenceLink();\r
- boolean valid = false;\r
- while( !valid )\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 (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
- "New sequence URL link",\r
- JOptionPane.OK_CANCEL_OPTION\r
- ,-1, null)\r
- == JOptionPane.OK_OPTION)\r
+ if (link.checkValid())\r
{\r
- if (link.checkValid())\r
- {\r
- nameLinks.addElement(link.getName());\r
- urlLinks.addElement(link.getURL());\r
- updateLinkData();\r
- valid = true;\r
- }\r
+ nameLinks.addElement(link.getName());\r
+ urlLinks.addElement(link.getURL());\r
+ updateLinkData();\r
+ valid = true;\r
}\r
- else\r
- break;\r
+ }\r
+ else\r
+ {\r
+ break;\r
}\r
}\r
+ }\r
\r
- public void editLink_actionPerformed(ActionEvent e) {\r
- GSequenceLink link = new GSequenceLink();\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, "No link selected!"\r
- ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
- return;\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
+ link.setName(nameLinks.elementAt(index).toString());\r
+ link.setURL(urlLinks.elementAt(index).toString());\r
\r
- boolean valid = false;\r
- while (!valid)\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
+ 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
- if (link.checkValid())\r
- {\r
- nameLinks.setElementAt(link.getName(), index);\r
- urlLinks.setElementAt(link.getURL(), index);\r
- updateLinkData();\r
- valid = true;\r
- }\r
+ nameLinks.setElementAt(link.getName(), index);\r
+ urlLinks.setElementAt(link.getURL(), index);\r
+ updateLinkData();\r
+ valid = true;\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
+ else\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
- ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
- return;\r
+ break;\r
}\r
- nameLinks.removeElementAt(index);\r
- urlLinks.removeElementAt(index);\r
- updateLinkData();\r
}\r
+ }\r
\r
- void updateLinkData()\r
+ public void deleteLink_actionPerformed(ActionEvent e)\r
+ {\r
+ int index = linkNameList.getSelectedIndex();\r
+ if (index == -1)\r
{\r
- linkNameList.setListData(nameLinks);\r
- linkURLList.setListData(urlLinks);\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
- public void defaultBrowser_mouseClicked(MouseEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(".");\r
- chooser.setDialogTitle("Select default web browser");\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
+ int value = chooser.showOpenDialog(this);\r
\r
- if (value == JFileChooser.APPROVE_OPTION)\r
- {\r
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
- }\r
+ if (value == JFileChooser.APPROVE_OPTION)\r
+ {\r
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
+ }\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff