X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPreferences.java;h=a1e5c611034486957c269d3585423aa6628ae6e6;hb=c9c74c082bdd9323850a864144dc8a9b36399157;hp=f322daa78a49e2a44204ce9d06f3db4814fec2c7;hpb=dc1d2d1779b2ccd4d67b2afa094f269db77732e2;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index f322daa..a1e5c61 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -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.
@@ -76,8 +78,18 @@ 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));
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
@@ -123,6 +135,8 @@ public class Preferences extends GPreferences
 
         smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
+        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
         gapSymbolCB.addItem("-");
         gapSymbolCB.addItem(".");
 
@@ -150,6 +164,11 @@ 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
    */
@@ -208,6 +227,8 @@ 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()));
 
@@ -276,7 +297,15 @@ 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