X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=5dae17916d1e7821875d7880661d732760939c87;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=27c455e40ef284484e37808b297c99de5c20bf1b;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 27c455e..5dae179 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -28,7 +29,6 @@ import jalview.bin.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.ws.EnfinEnvision2OneWay;
 
 /**
  * DOCUMENT ME!
@@ -59,7 +59,7 @@ public class Preferences extends GPreferences
     String string = Cache
             .getDefault(
                     "SEQUENCE_LINKS",
-                    "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
     sequenceURLLinks = new Vector();
 
     try
@@ -81,6 +81,18 @@ public class Preferences extends GPreferences
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
+    {
+      // upgrade old SRS link
+      int srsPos = sequenceURLLinks
+              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      if (srsPos > -1)
+      {
+        sequenceURLLinks.setElementAt(
+                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+                srsPos);
+      }
+    }
+
     /**
      * TODO: reformulate groupURL encoding so two or more can be stored in the
      * .properties file as '|' separated strings
@@ -150,8 +162,10 @@ public class Preferences extends GPreferences
     /**
      * default min-max colours for annotation shading
      */
-    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
-    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+            Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+            Color.red));
 
     String[] fonts = java.awt.GraphicsEnvironment
             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
@@ -189,7 +203,8 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            Cache.getDefault("www.jalview.org","http://www.jalview.org")+"/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+                    + "/examples/exampleFile_2_3.jar"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
@@ -201,7 +216,11 @@ public class Preferences extends GPreferences
     epsRendering.addItem("Text");
     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
             "Prompt each time"));
-
+    autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+    userIdWidth.setEnabled(autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+    Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+    userIdWidth.setText(wi == null ? "" : wi.toString());
     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
@@ -335,9 +354,11 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
             .getSelectedItem().toString());
 
-    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground());
-    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground());
-    
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+            minColour.getBackground());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+            maxColour.getBackground());
+
     if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
       Cache.applicationProperties.remove("EPS_RENDERING");
@@ -450,6 +471,12 @@ public class Preferences extends GPreferences
             Boolean.toString(modellerOutput.isSelected()));
     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
+    Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+            Boolean.toString(autoIdWidth.isSelected()));
+    userIdWidth_actionPerformed();
+    Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+            userIdWidth.getText());
+
     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
             Boolean.toString(autoCalculateConsCheck.isSelected()));
     Cache.applicationProperties.setProperty("SORT_BY_TREE",
@@ -653,6 +680,7 @@ public class Preferences extends GPreferences
   {
     return groupURLLinks;
   }
+
   public void minColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
@@ -675,4 +703,38 @@ public class Preferences extends GPreferences
     maxColour.repaint();
   }
 
+  @Override
+  protected void userIdWidth_actionPerformed()
+  {
+    try
+    {
+      String val = userIdWidth.getText().trim();
+      if (val.length() > 0)
+      {
+        Integer iw = Integer.parseInt(val);
+        if (iw.intValue() < 12)
+        {
+          throw new NumberFormatException();
+        }
+        userIdWidth.setText(iw.toString());
+      }
+    } catch (NumberFormatException x)
+    {
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
+                      "Invalid ID Column width",
+                      JOptionPane.WARNING_MESSAGE);
+      userIdWidth.setText("");
+    }
+  }
+
+  @Override
+  protected void autoIdWidth_actionPerformed()
+  {
+    userIdWidth.setEnabled(!autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+  }
+
 }