jog pixels for OSX

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6273fbc..ac2c59c 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -29,6 +29,7 @@ import jalview.bin.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
+import jalview.ws.EnfinEnvision2OneWay;
 
 /**
  * DOCUMENT ME!
@@ -84,8 +85,8 @@ public class Preferences extends GPreferences
      */
     
     groupURLLinks = new Vector();
-    groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
-    groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+    //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+    //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
     
   }
 
@@ -126,6 +127,8 @@ public class Preferences extends GPreferences
     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
     showUnconserved.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+    showNpTooltip.setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 
     for (int i = 0; i < 13; i++)
     {
@@ -200,7 +203,7 @@ public class Preferences extends GPreferences
     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",false));
     showGroupConservation.setSelected(Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
     showConsensHistogram.setSelected(Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",true));
-    showConsensProfile.setSelected(Cache.getDefault("SHOW_CONSENSUS_PROFILE",false));
+    showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",false));
     
     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 
@@ -284,9 +287,11 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",Boolean.toString(showGroupConsensus.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",Boolean.toString(showGroupConservation.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",Boolean.toString(showConsensHistogram.isSelected()));
-    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_PROFILE",Boolean.toString(showConsensProfile.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",Boolean.toString(showConsensLogo.isSelected()));
     Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
             .toString(smoothFont.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean.toString(showNpTooltip.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean.toString(showDbRefTooltip.isSelected()));
 
     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
             .toString(wrap.isSelected()));
@@ -475,10 +480,10 @@ public class Preferences extends GPreferences
     conservation.setEnabled(annotations.isSelected());
     quality.setEnabled(annotations.isSelected());
     identity.setEnabled(annotations.isSelected());
-    showConsensHistogram.setEnabled(annotations.isSelected());
-    showConsensProfile.setEnabled(annotations.isSelected());
     showGroupConsensus.setEnabled(annotations.isSelected());
     showGroupConservation.setEnabled(annotations.isSelected());
+    showConsensHistogram.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
+    showConsensLogo.setEnabled(annotations.isSelected() && (identity.isSelected() || showGroupConsensus.isSelected()));
   }
 
   public void newLink_actionPerformed(ActionEvent e)
@@ -593,4 +598,9 @@ public class Preferences extends GPreferences
   private void jbInit() throws Exception
   {
   }
+
+  public static Collection getGroupURLLinks()
+  {
+    return groupURLLinks;
+  }
 }