X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=a429eceb3b1b850ea6550c5b5842979413722e56;hb=0d519ae0c45b0b9962b4589e84c262a71bb2f346;hp=bd9f661cfd4c1afe7775c01e6f3428bc841d5b77;hpb=994a386819147f73fa47f3c29ba6c438f0e4b15a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bd9f661..a429ece 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -63,6 +63,13 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
+import jalview.hmmer.JackHMMER;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BackupFiles;
@@ -97,6 +104,9 @@ import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -126,23 +136,26 @@ import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.io.FileWriter;
+import java.io.IOException;
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
+import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
@@ -155,7 +168,6 @@ import javax.swing.SwingUtilities;
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
-
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -181,6 +193,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   String fileName = null;
 
+
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -765,6 +778,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
       ap.av.updateStrucConsensus(ap);
+      ap.av.initInformationWorker(ap);
     }
   }
 
@@ -907,6 +921,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
     showSequenceLogo.setSelected(av.isShowSequenceLogo());
     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+    showInformationHistogram.setSelected(av.isShowInformationHistogram());
+    showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+    normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 
     ColourMenuHelper.setColourSelected(colourMenu,
             av.getGlobalColourScheme());
@@ -974,7 +991,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setStatus(String text)
   {
-    statusBar.setText(text);
+    statusBar.setText(text == null || text.isEmpty() ? " " : text);
   }
 
   /*
@@ -1003,6 +1020,258 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void hmmBuild_actionPerformed(boolean withDefaults)
+  {
+    if (!alignmentIsSufficient(1))
+    {
+      return;
+    }
+
+    /*
+     * get default parameters, and optionally show a dialog
+     * to allow them to be modified
+     */
+    ParamDatastoreI store = HMMERParamStore.forBuild(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new HMMBuild(this, args)).start();
+  }
+
+  @Override
+  public void hmmAlign_actionPerformed(boolean withDefaults)
+  {
+    if (!(checkForHMM() && alignmentIsSufficient(2)))
+    {
+      return;
+    }
+
+    /*
+     * get default parameters, and optionally show a dialog
+     * to allow them to be modified
+     */
+    ParamDatastoreI store = HMMERParamStore.forAlign(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new HMMAlign(this, args)).start();
+  }
+
+  @Override
+  public void hmmSearch_actionPerformed(boolean withDefaults)
+  {
+    if (!checkForHMM())
+    {
+      return;
+    }
+
+    /*
+     * get default parameters, and (if requested) show 
+     * dialog to allow modification
+     */
+    ParamDatastoreI store = HMMERParamStore.forSearch(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new HMMSearch(this, args)).start();
+    alignPanel.repaint();
+  }
+  
+  @Override
+  public void jackhmmer_actionPerformed(boolean withDefaults)
+  {
+    
+    /*
+     * get default parameters, and (if requested) show 
+     * dialog to allow modification
+     */
+    
+    ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
+    List<ArgumentI> args = store.getServiceParameters();
+
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      WsJobParameters params = new WsJobParameters(store, set, args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new JackHMMER(this, args)).start();
+    alignPanel.repaint();
+    
+  }
+
+  /**
+   * Checks if the alignment has at least one hidden Markov model, if not shows
+   * a dialog advising to run hmmbuild or load an HMM profile
+   * 
+   * @return
+   */
+  private boolean checkForHMM()
+  {
+    if (viewport.getAlignment().getHmmSequences().isEmpty())
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("warn.no_hmm"));
+      return false;
+    }
+    return true;
+  }
+  
+  @Override
+  protected void filterByEValue_actionPerformed()
+  {
+    viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+  }
+  
+  @Override
+  protected void filterByScore_actionPerformed()
+  {
+    viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+  }
+  
+  private double inputDouble(String message)
+  {
+    String str = null;
+    Double d = null;
+    while(d == null || d <= 0)
+    {
+      str = JOptionPane.showInputDialog(this.alignPanel, message);
+      try
+      {
+        d = Double.valueOf(str);
+      }
+      catch (NumberFormatException e)
+      {
+      }
+    }
+    return d;
+  }
+
+  /**
+   * Checks if the alignment contains the required number of sequences.
+   * 
+   * @param required
+   * @return
+   */
+  public boolean alignmentIsSufficient(int required)
+  {
+      if (getViewport().getSequenceSelection().length < required)
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("label.not_enough_sequences"));
+        return false;
+      }
+      return true;
+  }
+
+  /**
+   * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+   * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+   * comma-separated list)
+   */
+  @Override
+  public void addDatabase_actionPerformed() throws IOException
+  {
+    if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
+    {
+      Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+    }
+
+    String path = openFileChooser(false);
+    if (path != null && 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 currentDbPaths = Cache
+                .getProperty(Preferences.HMMSEARCH_DBS);
+        currentDbPaths += Preferences.COMMA + path;
+        Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+      }
+      else
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("warn.invalid_format"));
+      }
+    }
+  }
+
+  /**
+   * Opens a file chooser, optionally restricted to selecting folders
+   * (directories) only. Answers the path to the selected file or folder, or
+   * null if none is chosen.
+   * 
+   * @param
+   * @return
+   */
+  protected String openFileChooser(boolean forFolder)
+  {
+    // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
+    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)
@@ -1203,23 +1472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           PrintWriter out = new PrintWriter(
                   new FileWriter(backupfiles.getTempFilePath()));
 
-          // TESTING code here
-          boolean TESTING = true;
-          if (TESTING)
-          {
-            out.print("; TESTSTART\n");
-            int count = 20;
-            for (int i = 0; i < count; i++)
-            {
-              // Thread.sleep(1000);
-              out.println("; TEST: " + (count - 1 - i));
-            }
-          }
           out.print(output);
-          if (TESTING)
-          {
-            out.print("; TESTEND\n");
-          }
           out.close();
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
@@ -1437,6 +1690,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   @Override
   public void associatedData_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -1922,9 +2176,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws InterruptedException
+   * @throws IOException
    */
   @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     paste(true);
   }
@@ -1934,9 +2191,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws InterruptedException
+   * @throws IOException
    */
   @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     paste(false);
   }
@@ -1946,8 +2206,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
+   * @throws InterruptedException
+   * @throws IOException
    */
-  void paste(boolean newAlignment)
+  void paste(boolean newAlignment) throws IOException, InterruptedException
   {
     boolean externalPaste = true;
     try
@@ -2108,7 +2370,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2155,7 +2417,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2275,7 +2537,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       System.out.println("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     }
-
   }
 
   @Override
@@ -3120,7 +3381,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    // TODO: do we actually need to update overview for scale above change ?
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3134,6 +3395,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3147,6 +3409,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3732,35 +3995,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     if (viewport.getAlignment().getAlignmentAnnotation()
-            .hashCode() != _annotationScoreVectorHash)
+            .hashCode() == _annotationScoreVectorHash)
+    {
+      return;
+    }
+
+    sortByAnnotScore.removeAll();
+    Set<String> scoreSorts = new HashSet<>();
+    for (SequenceI sqa : viewport.getAlignment().getSequences())
     {
-      sortByAnnotScore.removeAll();
-      // almost certainly a quicker way to do this - but we keep it simple
-      Hashtable scoreSorts = new Hashtable();
-      AlignmentAnnotation aann[];
-      for (SequenceI sqa : viewport.getAlignment().getSequences())
+      AlignmentAnnotation[] anns = sqa.getAnnotation();
+      for (int i = 0; anns != null && i < anns.length; i++)
       {
-        aann = sqa.getAnnotation();
-        for (int i = 0; aann != null && i < aann.length; i++)
+        AlignmentAnnotation aa = anns[i];
+        if (aa != null && aa.hasScore() && aa.sequenceRef != null)
         {
-          if (aann[i].hasScore() && aann[i].sequenceRef != null)
-          {
-            scoreSorts.put(aann[i].label, aann[i].label);
-          }
+          scoreSorts.add(aa.label);
         }
       }
-      Enumeration labels = scoreSorts.keys();
-      while (labels.hasMoreElements())
-      {
-        addSortByAnnotScoreMenuItem(sortByAnnotScore,
-                (String) labels.nextElement());
-      }
-      sortByAnnotScore.setVisible(scoreSorts.size() > 0);
-      scoreSorts.clear();
-
-      _annotationScoreVectorHash = viewport.getAlignment()
-              .getAlignmentAnnotation().hashCode();
     }
+    for (String label : scoreSorts)
+    {
+      addSortByAnnotScoreMenuItem(sortByAnnotScore, label);
+    }
+    sortByAnnotScore.setVisible(!scoreSorts.isEmpty());
+
+    _annotationScoreVectorHash = viewport.getAlignment()
+            .getAlignmentAnnotation().hashCode();
   }
 
   /**
@@ -4601,6 +4862,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    *          either a filename or a URL string.
+   * @throws InterruptedException
+   * @throws IOException
    */
   public void loadJalviewDataFile(String file, DataSourceType sourceType,
           FileFormatI format, SequenceI assocSeq)
@@ -4707,7 +4970,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       if (isAnnotation)
       {
-
         alignPanel.adjustAnnotationHeight();
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
@@ -5640,6 +5902,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  /**
+   * Sets the status of the HMMER menu
+   */
+  public void updateHMMERStatus()
+  {
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+  }
+
   @Override
   protected void loadVcf_actionPerformed()
   {