/*\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
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
+ "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
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, 395);\r
- frame.setMinimumSize(new Dimension(480,395));\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
fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));\r
\r
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
\r
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
+\r
gapSymbolCB.addItem("-");\r
gapSymbolCB.addItem(".");\r
\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
\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("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