JAL-2629 add ability to add and select a DB for hmmsearch

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 0749a23..a7623f7 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1360,4 +1360,8 @@ label.seq_e_value_desc = The E-value cutoff for returned sequences.
 label.seq_score_desc = The score threshold for returned sequences.
 label.dom_e_value_desc = The E-value cutoff for returned domains.
 label.dom_score_desc = The score threshold for returned domains.
-label.not_enough_sequences = There are not enough sequences to run {0}
\ No newline at end of file
+label.not_enough_sequences = There are not enough sequences to run {0}
+label.add_database = Add Database
+warn.file_not_exists = File does not exist
+warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
+label.database_for_hmmsearch = The database hmmsearch will search through.
\ No newline at end of file

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 85e3db5..d1d8a61 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -93,6 +93,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -143,10 +144,12 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Scanner;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
+import javax.swing.JFileChooser;
 import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
@@ -172,9 +175,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public static final int DEFAULT_HEIGHT = 500;
 
-  boolean autoAlignNewSequences;
-
-
   /*
    * The currently displayed panel (selected tabbed view if more than one)
    */
@@ -1163,6 +1163,78 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void addDatabase_actionPerformed(ActionEvent e) throws IOException
+  {
+    if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
+    {
+      Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+      Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+    }
+
+    String path = openFileChooser(false);
+    if (new File(path).exists())
+    {
+      IdentifyFile identifier = new IdentifyFile();
+      FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+      if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+              || format == FileFormat.Pfam)
+      {
+        String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+        String currentDbPaths = Cache
+                .getProperty(Preferences.HMMSEARCH_DB_PATHS);
+        currentDbPaths += " " + path;
+
+        String fileName = StringUtils.getLastToken(path, new String("/"));
+        Scanner scanner = new Scanner(fileName).useDelimiter(".");
+        String name = scanner.next();
+        scanner.close();
+        currentDbs += " " + path; // TODO remove path from file name
+        scanner.close();
+
+        Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+        Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+      }
+      else
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("warn.invalid_format"));
+      }
+    }
+    else
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("warn.not_enough_sequences"));
+    }
+  }
+
+  /**
+   * Opens a file chooser
+   * 
+   * @param forFolder
+   * @return
+   */
+  protected String openFileChooser(boolean forFolder)
+  {
+    String choice = null;
+    JFileChooser chooser = new JFileChooser();
+    if (forFolder)
+    {
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+    }
+    chooser.setDialogTitle(
+            MessageManager.getString("label.open_local_file"));
+    chooser.setToolTipText(MessageManager.getString("action.open"));
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JFileChooser.APPROVE_OPTION)
+    {
+      choice = chooser.getSelectedFile().getPath();
+    }
+    return choice;
+  }
+
+  @Override
   public void reload_actionPerformed(ActionEvent e)
   {
     if (fileName != null)

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7af3abc..bb226a0 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -112,6 +112,10 @@ public class Preferences extends GPreferences
   
   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";
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 1bfc72f..3dad581 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -1,6 +1,8 @@
 package jalview.hmmer;
 
 
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
@@ -8,10 +10,13 @@ import jalview.ws.params.WsParamSetI;
 import jalview.ws.params.simple.BooleanOption;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.LogarithmicParameter;
+import jalview.ws.params.simple.Option;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
+import java.util.Scanner;
 
 
 public class HMMERParamStore implements ParamDatastoreI
@@ -51,6 +56,34 @@ public class HMMERParamStore implements ParamDatastoreI
               MessageManager
                       .getString("label.number_of_results_desc"),
               true, 100, 0, 100000));
+      String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+      if (names != null && !names.isEmpty())
+      {
+        Collection<String> databases = new ArrayList<>();
+        databases.add("This Alignment");
+        Scanner nameScanner = new Scanner(names);
+
+        if (nameScanner.hasNext())
+        {
+          while (nameScanner.hasNext())
+          {
+            String next = nameScanner.next();
+            if (next == "null")
+            {
+              Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+              Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+            }
+            else
+            {
+              databases.add(next);
+            }
+          }
+        }
+        nameScanner.close();
+        args.add(new Option(MessageManager.getString("label.database"),
+                MessageManager.getString("label.database_for_hmmsearch"),
+                true, "This Alignment", "This Alignment", databases, null));
+      }
       args.add(new BooleanOption(
               MessageManager.getString("label.auto_align_seqs"),
               MessageManager.getString("label.auto_align_seqs_desc"),

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index cf6c487..c2d19d7 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.io.FileFormatException;
 import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -82,6 +83,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem hmmSearchSettings = new JMenuItem();
 
+  protected JMenuItem addDatabase = new JMenuItem();
+
   protected JMenu hmmBuild = new JMenu();
 
   protected JMenuItem hmmBuildRun = new JMenuItem();
@@ -1833,6 +1836,24 @@ public class GAlignFrame extends JInternalFrame
       }
 
     });
+    addDatabase.setText(MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed(e);
+        } catch (IOException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
+      }
+
+    });
     hmmSearchSettings.setText(
             MessageManager.getString("label.edit_settings_and_run"));
     hmmSearchSettings.addActionListener(new ActionListener()
@@ -2055,8 +2076,11 @@ public class GAlignFrame extends JInternalFrame
             MessageManager.getString("label.edit_settings_and_run"));
     hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
             "label.action_with_default_settings", "hmmsearch"));
+    addDatabase = new JMenuItem(
+            MessageManager.getString("label.add_database"));
     hmmSearch.add(hmmSearchSettings);
     hmmSearch.add(hmmSearchRun);
+    hmmSearch.add(addDatabase);
   }
 
   /**
@@ -2552,6 +2576,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void addDatabase_actionPerformed(ActionEvent e)
+          throws FileFormatException, IOException
+  {
+  }
+
   protected void hmmAlignRun_actionPerformed(ActionEvent e)
           throws IOException, InterruptedException
   {