Updated with latest from mchmmer branch

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index aa8369a..df35b5e 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.hmmer.HmmerCommand;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -48,6 +49,8 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.MouseEvent;
 import java.io.File;
 import java.util.ArrayList;
@@ -102,6 +105,12 @@ public class Preferences extends GPreferences
   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 
   public static final String CHIMERA_PATH = "CHIMERA_PATH";
+  
+  public static final String HMMER_PATH = "HMMER_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";
 
@@ -207,6 +216,38 @@ public class Preferences extends GPreferences
     frame.setMinimumSize(new Dimension(width, height));
 
     /*
+     * Set HMMER tab defaults
+     */
+    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+    if (Cache.getDefault("USE_UNIPROT", false))
+    {
+      hmmerBackgroundUniprot.setSelected(true);
+    }
+    else
+    {
+      hmmerBackgroundAlignment.setSelected(true);
+    }
+    hmmerSequenceCount
+            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+    hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+    hmmerPath.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        validateHMMERPath(true);
+      }
+    });
+    hmmerPath.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        validateHMMERPath(true);
+      }
+    });
+
+    /*
      * Set Visual tab defaults
      */
     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
@@ -229,6 +270,9 @@ public class Preferences extends GPreferences
             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
     showConsensLogo
             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+    showInformationHistogram.setSelected(
+            Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+    showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
     showNpTooltip
             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
     showDbRefTooltip
@@ -525,7 +569,7 @@ public class Preferences extends GPreferences
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
-    Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+    Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
     userIdWidth.setText(wi == null ? "" : wi.toString());
     // TODO: refactor to use common enum via FormatAdapter and allow extension
     // for new flat file formats
@@ -610,6 +654,10 @@ public class Preferences extends GPreferences
             Boolean.toString(showConsensHistogram.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
             Boolean.toString(showConsensLogo.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
+            Boolean.toString(showConsensHistogram.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
+            Boolean.toString(showHMMLogo.isSelected()));
     Cache.applicationProperties.setProperty("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
@@ -656,6 +704,39 @@ public class Preferences extends GPreferences
             maxColour.getBackground());
 
     /*
+     * Save HMMER settings
+     */
+    Cache.applicationProperties.setProperty("TRIM_TERMINI",
+            Boolean.toString(hmmrTrimTermini.isSelected()));
+    Cache.applicationProperties.setProperty("USE_UNIPROT",
+            Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+    Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+            hmmerSequenceCount.getText());
+    Cache.applicationProperties.setProperty(HMMER_PATH,
+            hmmerPath.getText());
+    AlignFrame[] frames = Desktop.getAlignFrames();
+    if (frames != null && frames.length > 0)
+    {
+      for (AlignFrame f : frames)
+      {
+        f.updateHMMERStatus();
+      }
+    }
+    
+    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+    if (Cache.getDefault("USE_UNIPROT", false))
+    {
+      hmmerBackgroundUniprot.setSelected(true);
+    }
+    else
+    {
+      hmmerBackgroundAlignment.setSelected(true);
+    }
+    hmmerSequenceCount
+            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+    hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+    /*
      * Save Overview settings
      */
     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
@@ -784,7 +865,7 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
-    Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+    Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
             userIdWidth.getText());
 
     /*
@@ -898,6 +979,8 @@ public class Preferences extends GPreferences
             && (identity.isSelected() || showGroupConsensus.isSelected()));
     showConsensLogo.setEnabled(annotations.isSelected()
             && (identity.isSelected() || showGroupConsensus.isSelected()));
+    showInformationHistogram.setEnabled(annotations.isSelected());
+    showHMMLogo.setEnabled(annotations.isSelected());
   }
 
   @Override
@@ -1179,6 +1262,53 @@ public class Preferences extends GPreferences
     }
     return true;
   }
+  
+  /**
+   * Returns true if hmmer path is to a folder that contains an executable
+   * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
+   * dialog)
+   */
+  @Override
+  protected boolean validateHMMERPath(boolean showWarning)
+  {
+    String folder = hmmerPath.getText().trim();
+
+    if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
+    {
+      return true;
+    }
+    if (showWarning && folder.length() > 0)
+    {
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.hmmbuild_not_found"),
+              MessageManager.getString("label.invalid_folder"),
+              JvOptionPane.ERROR_MESSAGE);
+    }
+    return false;
+  }
+
+  /**
+   * Checks if a file can be executed
+   * 
+   * @param path
+   *          the path to the file
+   * @return
+   */
+  public boolean canExecute(String path)
+  {
+    File file = new File(path);
+    if (!file.canExecute())
+    {
+      file = new File(path + ".exe");
+      {
+        if (!file.canExecute())
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
 
   /**
    * If Chimera is selected, check it can be found on default or user-specified