Merge branch 'develop' into features/mchmmer

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 9f9d6f8..3259909 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -86,6 +86,15 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  */
 public class Preferences extends GPreferences
 {
+  // suggested list delimiter character
+  public static final String COMMA = ",";
+
+  public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
+
+  public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
+
+  public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
+
   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 
   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
@@ -112,8 +121,6 @@ public class Preferences extends GPreferences
 
   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 
-  public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
-
   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
@@ -222,8 +229,8 @@ public class Preferences extends GPreferences
     /*
      * Set HMMER tab defaults
      */
-    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
-    if (Cache.getDefault("USE_UNIPROT", false))
+    hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+    if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
     {
       hmmerBackgroundUniprot.setSelected(true);
     }
@@ -232,7 +239,7 @@ public class Preferences extends GPreferences
       hmmerBackgroundAlignment.setSelected(true);
     }
     hmmerSequenceCount
-            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+            .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
     hmmerPath.addActionListener(new ActionListener()
     {
@@ -250,23 +257,31 @@ public class Preferences extends GPreferences
         validateHmmerPath();
       }
     });
-    cygwinPath.setText(Cache.getProperty(CYGWIN_PATH));
-    cygwinPath.addActionListener(new ActionListener()
+    if (cygwinPath != null)
     {
-      @Override
-      public void actionPerformed(ActionEvent e)
+      String path = Cache.getProperty(CYGWIN_PATH);
+      if (path == null)
       {
-        validateCygwinPath();
+        path = FileUtils.getPathTo("bash");
       }
-    });
-    cygwinPath.addFocusListener(new FocusAdapter()
-    {
-      @Override
-      public void focusLost(FocusEvent e)
+      cygwinPath.setText(path);
+      cygwinPath.addActionListener(new ActionListener()
       {
-        validateCygwinPath();
-      }
-    });
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          validateCygwinPath();
+        }
+      });
+      cygwinPath.addFocusListener(new FocusAdapter()
+      {
+        @Override
+        public void focusLost(FocusEvent e)
+        {
+          validateCygwinPath();
+        }
+      });
+    }
 
     /*
      * Set Visual tab defaults
@@ -727,14 +742,17 @@ public class Preferences extends GPreferences
     /*
      * Save HMMER settings
      */
-    Cache.applicationProperties.setProperty("TRIM_TERMINI",
+    Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
             Boolean.toString(hmmrTrimTermini.isSelected()));
-    Cache.applicationProperties.setProperty("USE_UNIPROT",
+    Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
-    Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+    Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
             hmmerSequenceCount.getText());
     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
-    Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+    if (cygwinPath != null)
+    {
+      Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+    }
     AlignFrame[] frames = Desktop.getAlignFrames();
     if (frames != null && frames.length > 0)
     {
@@ -744,8 +762,8 @@ public class Preferences extends GPreferences
       }
     }
     
-    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
-    if (Cache.getDefault("USE_UNIPROT", false))
+    hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+    if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
     {
       hmmerBackgroundUniprot.setSelected(true);
     }
@@ -754,7 +772,7 @@ public class Preferences extends GPreferences
       hmmerBackgroundAlignment.setSelected(true);
     }
     hmmerSequenceCount
-            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+            .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 
     /*