JAL-2629 add validation for HMMER path

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 2499e79..807f88f 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1315,7 +1315,6 @@ label.occupancy_descr = Number of aligned positions
 label.show_experimental = Enable experimental features
 label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
 label.warning_hidden = Warning: {0} {1} is currently hidden
-label.auto_align_seqs = Automatically Align New Sequences
 label.hmmalign = Align Sequences to HMM
 label.hmmbuild = Build HMM from Alignment
 label.hmmbuild_group = Build HMM from Selected Group
@@ -1325,7 +1324,7 @@ label.change_hmmer_location = HMMER Installation Location
 warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
 label.ignore_below_background_frequency = Ignore Below Background Frequency
 label.information_description = Information content, measured in bits
-label.enter_location = Please enter the path of your HMMER binaries folder.
+label.enter_location = Please enter the path of your HMMER folder.
 label.invalid_hmmer_folder = The folder that you selected does not contain the necessary HMMER binaries.
 warn.no_selected_hmm = Please select a hidden Markov model sequence.
 label.select_hmm = Select HMM
@@ -1337,3 +1336,10 @@ label.freq_alignment = Use Alignment Background Frequencies
 label.freq_uniprot = Use Uniprot Background Frequencies
 label.hmmalign_label = hmmalign Options
 label.hmmsearch_label = hmmsearch Options
+label.hmmbuild_not_found = The hmmbuild binary was not found.
+label.hmmalign_not_found = The hmmalign binary was not found.
+label.hmmsearch_not_found = The hmmsearch binary was not found.
+warn.hmmbuild_failed = hmmbuild was not found. 
+warn.align_failed = hmmalign was not found.
+label.invalid_folder = Invalid Folder
+label.folder_not_exists = HMMER not found. \n Please enter the path to HMMER (if installed).
\ No newline at end of file

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c25fc2f..e11bdec 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -214,7 +214,15 @@ public class Preferences extends GPreferences
     }
     numberOfSequencesToKeepField
             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
-    installationLocationField.setText(Cache.getProperty(HMMER_PATH));
+    hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+    hmmerPath.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        validateHMMERPath();
+      }
+    });
 
     /*
      * Set Visual tab defaults
@@ -665,7 +673,7 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
             numberOfSequencesToKeepField.getText());
     Cache.applicationProperties.setProperty(HMMER_PATH,
-            installationLocationField.getText());
+            hmmerPath.getText());
     trimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
     if (Cache.getDefault("USE_UNIPROT", false))
     {
@@ -677,7 +685,7 @@ public class Preferences extends GPreferences
     }
     numberOfSequencesToKeepField
             .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
-    installationLocationField.setText(Cache.getProperty(HMMER_PATH));
+    hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 
     /*
      * Save Structure settings
@@ -836,6 +844,11 @@ public class Preferences extends GPreferences
       structureTab.requestFocusInWindow();
       return false;
     }
+    if (!validateHMMER())
+    {
+      hmmerTab.requestFocusInWindow();
+      return false;
+    }
     return true;
   }
 
@@ -846,6 +859,13 @@ public class Preferences extends GPreferences
 
   }
 
+  @Override
+  protected boolean validateHMMER()
+  {
+    return validateHMMERPath();
+
+  }
+
   /**
    * DOCUMENT ME!
    */
@@ -1143,18 +1163,74 @@ public class Preferences extends GPreferences
    */
   private boolean validateHMMERPath()
   {
-    String path = Cache.getProperty("HMMERPATH");
-    if (path.length() > 0)
+    int missing = 0;
+    String message = "";
+    String path = hmmerPath.getText();
+    if (path.length() < 1)
+    {
+      return false;
+    }
+    else
     {
       File f = new File(path);
-      if (!f.canExecute())
+      if (!f.exists())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                MessageManager.getString("label.invalid_hmmer_folder"),
-                MessageManager.getString("Invalid folder"),
+                MessageManager.getString("label.folder_not_exists"),
+                MessageManager.getString("label.invalid_folder"),
                 JvOptionPane.ERROR_MESSAGE);
         return false;
       }
+
+      File hmmbuild = new File(path + "/binaries/hmmbuild.exe");
+      {
+        if (!hmmbuild.canExecute())
+        {
+          message += MessageManager.getString("label.hmmbuild_not_found")
+                  + "\n";
+          missing++;
+        }
+      }
+
+      File hmmalign = new File(path + "/binaries/hmmalign.exe");
+      {
+        if (!hmmalign.canExecute())
+        {
+          message += MessageManager.getString("label.hmmalign_not_found")
+                  + "\n";
+          missing++;
+        }
+      }
+
+      File hmmsearch = new File(path + "/binaries/hmmsearch.exe");
+      {
+        if (!hmmsearch.canExecute())
+        {
+          message += MessageManager.getString("label.hmmsearch_not_found")
+                  + "\n";
+          missing++;
+        }
+      }
+
+      if (missing > 0)
+      {
+        if (missing < 3)
+        {
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop, message,
+                  MessageManager.getString("label.invalid_folder"),
+                  JvOptionPane.ERROR_MESSAGE);
+          return false;
+        }
+        else
+        {
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  MessageManager.getString("label.no_binaries"),
+                  MessageManager.getString("label.invalid_folder"),
+                  JvOptionPane.ERROR_MESSAGE);
+          return false;
+        }
+      }
+
     }
     return true;
   }

diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
index c424cf0..4f4e46c 100644 (file)
--- a/src/jalview/hmmer/HMMAlignThread.java
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -10,6 +10,7 @@ import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.gui.SplitFrame;
 import jalview.io.DataSourceType;
@@ -123,7 +124,13 @@ public class HMMAlignThread implements Runnable
       }
       try
       {
-        runCommand();
+        boolean ran = runCommand();
+        if (!ran)
+        {
+          JvOptionPane.showInternalMessageDialog(af,
+                  MessageManager.getString("warn.hmmalign_failed"));
+          return;
+        }
       } catch (IOException | InterruptedException e)
       {
         e.printStackTrace();
@@ -156,8 +163,13 @@ public class HMMAlignThread implements Runnable
     inputTemp.deleteOnExit();
   }
 
-  private void runCommand() throws IOException, InterruptedException
+  private boolean runCommand() throws IOException, InterruptedException
   {
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmalign.exe");
+    if (!file.canExecute())
+    {
+      return false;
+    }
     String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
     if (!hmm.getFileHeader().contains("HMMER3/f"))
     {
@@ -176,7 +188,7 @@ public class HMMAlignThread implements Runnable
     command += " -o" + inputTemp.getAbsolutePath() + cmds.SPACE
             + hmmTemp.getAbsolutePath() + cmds.SPACE
             + outTemp.getAbsolutePath();
-    cmds.runCommand(command);
+    return cmds.runCommand(command);
   }
 
   private void importData(int index)

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index e9f691b..d1039f9 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -5,6 +5,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -98,7 +99,13 @@ public class HMMBuildThread implements Runnable
     }
     try
     {
-      runCommand();
+        boolean ran = runCommand();
+        if (!ran)
+        {
+          JvOptionPane.showInternalMessageDialog(af,
+                  MessageManager.getString("warn.hmmbuild_failed"));
+          return;
+        }
     } catch (IOException | InterruptedException e)
     {
       // TODO Auto-generated catch block
@@ -126,8 +133,13 @@ public class HMMBuildThread implements Runnable
   
 
   
-  private void runCommand() throws IOException, InterruptedException
+  private boolean runCommand() throws IOException, InterruptedException
   {
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
+    if (!file.canExecute())
+    {
+      return false;
+    }
     String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
             + af.getName() + cmds.SPACE;
     if (!alignment.isNucleotide())
@@ -141,7 +153,7 @@ public class HMMBuildThread implements Runnable
 
     command += hmmTemp.getAbsolutePath()
             + cmds.SPACE + stoTemp.getAbsolutePath() + cmds.SPACE;
-    cmds.runCommand(command);
+    return cmds.runCommand(command);
   }
   
   private void importData() throws IOException, InterruptedException

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index bcd0662..136ad5c 100644 (file)
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -24,11 +24,11 @@ public class HMMERCommands
   public String JALVIEWDIRECTORY = System.getProperty("user.dir")
           + "/";
 
-  public final String HMMALIGN = "/hmmalign ";
+  public final String HMMALIGN = "/binaries/hmmalign ";
 
-  public final String HMMBUILD = "/hmmbuild ";
+  public final String HMMBUILD = "/binaries/hmmbuild ";
 
-  public final String HMMSEARCH = "/hmmsearch ";
+  public final String HMMSEARCH = "/binaries/hmmsearch ";
 
   public String HMMBUFFER;
 
@@ -73,7 +73,7 @@ public class HMMERCommands
    * @throws IOException
    * @throws InterruptedException
    */
-  public void runCommand(String command)
+  public boolean runCommand(String command)
           throws IOException, InterruptedException
   {
     try
@@ -106,7 +106,9 @@ public class HMMERCommands
     } catch (Exception e)
     {
       e.printStackTrace();
+      return false;
     }
+    return true;
   }
 
   /**

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 40f8616..25742b4 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -276,7 +276,7 @@ public class GPreferences extends JPanel
 
   protected JLabel installationLocation = new JLabel();
 
-  protected JTextField installationLocationField = new JTextField();
+  protected JTextField hmmerPath = new JTextField();
 
   protected JLabel hmmsearch = new JLabel();
 
@@ -376,6 +376,15 @@ public class GPreferences extends JPanel
             return;
           }
         }
+        else if (lastTab == hmmerTab
+                && tabbedPane.getSelectedComponent() != hmmerTab)
+        {
+          if (!validateHMMER())
+          {
+            tabbedPane.setSelectedComponent(hmmerTab);
+          }
+          return;
+        }
         lastTab = tabbedPane.getSelectedComponent();
       }
 
@@ -443,8 +452,8 @@ public class GPreferences extends JPanel
     installationLocation.setText(
             MessageManager.getString("label.change_hmmer_location"));
     installationLocation.setBounds(new Rectangle(22, 200, 200, 23));
-    installationLocationField.setBounds(new Rectangle(22, 220, 200, 23));
-    installationLocationField.addMouseListener(new MouseAdapter()
+    hmmerPath.setBounds(new Rectangle(22, 220, 200, 23));
+    hmmerPath.addMouseListener(new MouseAdapter()
     {
       @Override
       public void mouseClicked(MouseEvent e)
@@ -454,7 +463,7 @@ public class GPreferences extends JPanel
           String chosen = openFileChooser();
           if (chosen != null)
           {
-            installationLocationField.setText(chosen);
+            hmmerPath.setText(chosen);
           }
         }
       }
@@ -477,7 +486,7 @@ public class GPreferences extends JPanel
     hmmerTab.add(hmmalign);
     hmmerTab.add(hmmsearch);
     hmmerTab.add(installationLocation);
-    hmmerTab.add(installationLocationField);
+    hmmerTab.add(hmmerPath);
     hmmerTab.add(trimTermini);
     hmmerTab.add(sequencesToKeep);
     hmmerTab.add(sequencesToKeep);
@@ -1247,11 +1256,31 @@ public class GPreferences extends JPanel
     return true;
   }
 
+  /**
+   * Validate the hmmer tab preferences; if invalid, set focus on this tab.
+   * 
+   * @param e
+   */
+  protected boolean validateHMMER(FocusEvent e)
+  {
+    if (!validateHMMER())
+    {
+      e.getComponent().requestFocusInWindow();
+      return false;
+    }
+    return true;
+  }
+
   protected boolean validateStructure()
   {
     return false;
   }
 
+  protected boolean validateHMMER()
+  {
+    return false;
+  }
+
   /**
    * Initialises the Visual tabbed panel.
    * 
@@ -1741,4 +1770,9 @@ public class GPreferences extends JPanel
       }
 
   }
+
+  public void hmmerPath_actionPerformed(ActionEvent e)
+  {
+
+  }
 }