X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=840598bfd9402db2a9ccb7301d4e3dcc88fd2474;hb=99bd0585b045d25fa719ee007e3310d27e53ac88;hp=8cbe03fb3c12f170a54310e6af928fd9014b2af0;hpb=92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8cbe03f..840598b 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -47,7 +47,7 @@ public class Preferences extends GPreferences
     static
     {
       String string = Cache.getDefault("SEQUENCE_LINKS",
-                                       "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
+                                       "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
       sequenceURLLinks = new Vector();
 
       try
@@ -67,6 +67,8 @@ public class Preferences extends GPreferences
 
     JInternalFrame frame;
 
+    DasSourceBrowser dasSource;
+
 
     /**
      * Creates a new Preferences object.
@@ -76,10 +78,21 @@ public class Preferences extends GPreferences
 
         frame = new JInternalFrame();
         frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "Preferences", 480, 395);
-        frame.setMinimumSize(new Dimension(480,395));
+        dasSource = new DasSourceBrowser();
+        dasPanel.add(dasSource, BorderLayout.CENTER);
+
+        int width = 500, height = 420;
+        if(System.getProperty("os.name").startsWith("Mac"))
+        {
+          width = 570;
+          height = 460;
+        }
+
+        Desktop.addInternalFrame(frame, "Preferences", width, height);
+        frame.setMinimumSize(new Dimension(width, height));
 
         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
+        rightAlign.setSelected(  Cache.getDefault("RIGHT_ALIGN_IDS", false));
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
         annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
 
@@ -123,6 +136,8 @@ public class Preferences extends GPreferences
 
         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
+        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
         gapSymbolCB.addItem("-");
         gapSymbolCB.addItem(".");
 
@@ -150,7 +165,10 @@ public class Preferences extends GPreferences
         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
 
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
         autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
 
   /****************************************************
    * Set up Connections
@@ -194,6 +212,7 @@ public class Preferences extends GPreferences
     {
 
       Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
+      Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.isSelected()));
       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
 
       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
@@ -210,6 +229,8 @@ public class Preferences extends GPreferences
 
       Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
 
+      Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));
+
       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
 
@@ -278,9 +299,15 @@ public class Preferences extends GPreferences
         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
         Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
                                                 Boolean.toString(autoCalculateConsCheck.isSelected()));
+        Cache.applicationProperties.setProperty("PAD_GAPS",
+                                                Boolean.toString(padGaps.isSelected()));
+
+        dasSource.saveProperties(Cache.applicationProperties);
 
         Cache.saveProperties();
         try