JAL-4257 JAL-4159 JAL-789 tidy up passing of score model to pairwise alignment direct...

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index fd20465..48ec899 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -76,12 +76,9 @@ public class PaSiMap implements Runnable
   {
     this.seqs = sequences;
 
-    //convert ScoreModel name into score matrix, use default if not Blosum or Pam
-    if (sm.getName().equals("BLOSUM62"))
+    if (sm!=null && sm instanceof ScoreMatrix)
     {
-      this.scoreMatrix = ScoreModels.getInstance().getBlosum62();
-    } else if (sm.getName().equals("PAM250")) {
-      this.scoreMatrix = ScoreModels.getInstance().getPam250();
+      this.scoreMatrix = ((ScoreMatrix) sm);
     } else {
       this.scoreMatrix = null;
     }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7116cf3..8336626 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3862,12 +3862,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      JInternalFrame frame = new JInternalFrame();
+      new Thread(new Runnable() {
+        @Override
+        public void run()
+        {
+               JInternalFrame frame = new JInternalFrame();
       frame.setFrameIcon(null);
       frame.setContentPane(new PairwiseAlignPanel(viewport));
       Desktop.addInternalFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
               500);
+        }
+      }).start();
+      
     }
   }
 

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index bf67a44..f8986b6 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -88,17 +88,17 @@ public class CalculationChooser extends JPanel
 
   private static final Font VERDANA_11PT = new Font("Verdana", 0, 11);
 
-
   private static final int MIN_PAIRWISE_SELECTION = 2;
 
   private static final int MIN_TREE_SELECTION = 3;
 
   private static final int MIN_PCA_SELECTION = 4;
-  
+
   private String secondaryStructureModelName;
-  
-  private void getSecondaryStructureModelName() {
-    
+
+  private void getSecondaryStructureModelName()
+  {
+
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
@@ -107,13 +107,14 @@ public class CalculationChooser extends JPanel
         secondaryStructureModelName = sm.getName();
       }
     }
-    
+
   }
 
   /**
-   * minimum number of sequences needed for PASIMAP is 9 (so each has 8 connections)
+   * minimum number of sequences needed for PASIMAP is 9 (so each has 8
+   * connections)
    */
-  private static final int MIN_PASIMAP_SELECTION = 9; 
+  private static final int MIN_PASIMAP_SELECTION = 9;
 
   AlignFrame af;
 
@@ -121,14 +122,14 @@ public class CalculationChooser extends JPanel
 
   JRadioButton pca;
 
-  JRadioButton pasimap;        
+  JRadioButton pasimap;
 
   JRadioButton neighbourJoining;
 
   JRadioButton averageDistance;
 
   JComboBox<String> modelNames;
-  
+
   JComboBox<String> ssSourceDropdown;
 
   JButton calculate;
@@ -164,7 +165,7 @@ public class CalculationChooser extends JPanel
     this.af = alignFrame;
     init();
     af.alignPanel.setCalculationDialog(this);
-    
+
   }
 
   /**
@@ -203,8 +204,9 @@ public class CalculationChooser extends JPanel
             MessageManager.getString("label.principal_component_analysis"));
     pca.setOpaque(false);
 
-    pasimap = new JRadioButton(                        // create the JRadioButton for pasimap with label.pasimap as its text
-           MessageManager.getString("label.pasimap"));
+    pasimap = new JRadioButton( // create the JRadioButton for pasimap with
+                                // label.pasimap as its text
+            MessageManager.getString("label.pasimap"));
     pasimap.setOpaque(false);
 
     neighbourJoining = new JRadioButton(
@@ -215,8 +217,9 @@ public class CalculationChooser extends JPanel
     averageDistance = new JRadioButton(
             MessageManager.getString("label.tree_calc_av"));
     averageDistance.setOpaque(false);
-    
-    pairwise = new JRadioButton(MessageManager.getString("label.pairwise_alignment"));
+
+    pairwise = new JRadioButton(
+            MessageManager.getString("action.pairwise_alignment"));
     pairwise.setOpaque(false);
 
     JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
@@ -240,18 +243,36 @@ public class CalculationChooser extends JPanel
     calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
 
     // create pasimap panel
-    JPanel pasimapBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));    // create new JPanel (button) for pasimap
+    JPanel pasimapBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT)); // create
+                                                                            // new
+                                                                            // JPanel
+                                                                            // (button)
+                                                                            // for
+                                                                            // pasimap
     pasimapBorderless.setBorder(
-           BorderFactory.createEmptyBorder(2, b.left, 2, b.right));    // set border (margin) for button (same as treePanel and pca)
-    pasimapBorderless.setOpaque(false);                // false -> stops every pixel inside border from being painted
-    pasimapBorderless.add(pasimap, FlowLayout.LEFT);   // add pasimap button to the JPanel
-    calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT);   // add button with border and everything to the overall ChoicePanel
+            BorderFactory.createEmptyBorder(2, b.left, 2, b.right)); // set
+                                                                     // border
+                                                                     // (margin)
+                                                                     // for
+                                                                     // button
+                                                                     // (same as
+                                                                     // treePanel
+                                                                     // and pca)
+    pasimapBorderless.setOpaque(false); // false -> stops every pixel inside
+                                        // border from being painted
+    pasimapBorderless.add(pasimap, FlowLayout.LEFT); // add pasimap button to
+                                                     // the JPanel
+    calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button with
+                                                             // border and
+                                                             // everything to
+                                                             // the overall
+                                                             // ChoicePanel
 
     treePanel.add(neighbourJoining);
     treePanel.add(averageDistance);
 
     calcChoicePanel.add(treePanel);
-    calcChoicePanel.add(pairwise,FlowLayout.CENTER);
+    calcChoicePanel.add(pairwise, FlowLayout.CENTER);
 
     ButtonGroup calcTypes = new ButtonGroup();
     calcTypes.add(pca);
@@ -269,12 +290,13 @@ public class CalculationChooser extends JPanel
       }
     };
     pca.addActionListener(calcChanged);
-    pasimap.addActionListener(calcChanged);    // add the calcChanged ActionListener to pasimap --> <++> idk
+    pasimap.addActionListener(calcChanged); // add the calcChanged
+                                            // ActionListener to pasimap -->
+                                            // <++> idk
     neighbourJoining.addActionListener(calcChanged);
     averageDistance.addActionListener(calcChanged);
-    
-    
-    //to do    
+
+    // to do
     ssSourceDropdown = buildSSSourcesOptionsList();
     ssSourceDropdown.setVisible(false); // Initially hide the dropdown
     pairwise.addActionListener(calcChanged);
@@ -282,27 +304,31 @@ public class CalculationChooser extends JPanel
      * score models drop-down - with added tooltips!
      */
     modelNames = buildModelOptionsList();
-    
+
     // Step 3: Show or Hide Dropdown Based on Selection
-    modelNames.addActionListener(new ActionListener() {
-        @Override
-        public void actionPerformed(ActionEvent e) {
-            String selectedModel = modelNames.getSelectedItem().toString();
-            
-            if (selectedModel.equals(secondaryStructureModelName)) {
-              ssSourceDropdown.setVisible(true);
-            } else {
-              ssSourceDropdown.setVisible(false);
-            }
+    modelNames.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        String selectedModel = modelNames.getSelectedItem().toString();
+
+        if (selectedModel.equals(secondaryStructureModelName))
+        {
+          ssSourceDropdown.setVisible(true);
         }
+        else
+        {
+          ssSourceDropdown.setVisible(false);
+        }
+      }
     });
 
-
     JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
     scoreModelPanel.setOpaque(false);
     scoreModelPanel.add(modelNames);
     scoreModelPanel.add(ssSourceDropdown);
-    
+
     /*
      * score model parameters
      */
@@ -317,7 +343,7 @@ public class CalculationChooser extends JPanel
     paramsPanel.add(matchGaps);
     paramsPanel.add(includeGappedColumns);
     paramsPanel.add(shorterSequence);
-    
+
     /*
      * OK / Cancel buttons
      */
@@ -400,7 +426,9 @@ public class CalculationChooser extends JPanel
      * return value of true means enabled and selected
      */
     boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION);
-    boolean checkPasimap = checkEnabled(pasimap, size, MIN_PASIMAP_SELECTION);         // check if pasimap is enabled and min_size is fulfilled
+    boolean checkPasimap = checkEnabled(pasimap, size,
+            MIN_PASIMAP_SELECTION); // check if pasimap is enabled and min_size
+                                    // is fulfilled
     boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size,
             MIN_TREE_SELECTION);
     boolean checkAverageDistance = checkEnabled(averageDistance, size,
@@ -408,7 +436,8 @@ public class CalculationChooser extends JPanel
     boolean checkPairwise = checkEnabled(pairwise, size,
             MIN_PAIRWISE_SELECTION);
 
-    if (checkPca || checkPasimap || checkPca || checkNeighbourJoining || checkAverageDistance || checkPairwise)
+    if (checkPca || checkPasimap || checkPca || checkNeighbourJoining
+            || checkAverageDistance || checkPairwise)
     {
       calculate.setToolTipText(null);
       calculate.setEnabled(true);
@@ -506,7 +535,6 @@ public class CalculationChooser extends JPanel
 
     return scoreModelsCombo;
   }
-  
 
   private JComboBox<String> buildSSSourcesOptionsList()
   {
@@ -525,7 +553,7 @@ public class CalculationChooser extends JPanel
         curSel = source;
       }
       sourcesModel.addElement(source);
-      
+
     }
 
     if (selectedIsPresent)
@@ -533,11 +561,10 @@ public class CalculationChooser extends JPanel
       sourcesModel.setSelectedItem(curSel);
     }
     comboBox.setModel(sourcesModel);
-    
+
     return comboBox;
   }
-  
-  
+
   private void updateScoreModels(JComboBox<String> comboBox,
           List<String> toolTips)
   {
@@ -549,12 +576,14 @@ public class CalculationChooser extends JPanel
      * select the score models applicable to the alignment type
      */
     boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
-    AlignmentAnnotation[] alignmentAnnotations = af.getViewport().getAlignment().getAlignmentAnnotation();
+    AlignmentAnnotation[] alignmentAnnotations = af.getViewport()
+            .getAlignment().getAlignmentAnnotation();
 
-    boolean ssPresent = AlignmentUtils.isSecondaryStructurePresent(alignmentAnnotations);
+    boolean ssPresent = AlignmentUtils
+            .isSecondaryStructurePresent(alignmentAnnotations);
 
-    List<ScoreModelI> models = getApplicableScoreModels(nucleotide, pca.isSelected(),
-            ssPresent, pasimap.isSelected());
+    List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+            pca.isSelected(), ssPresent, pasimap.isSelected());
 
     /*
      * now we can actually add entries to the combobox,
@@ -589,8 +618,8 @@ public class CalculationChooser extends JPanel
     }
     // finally, update the model
     comboBox.setModel(model);
-    comboBox.setEnabled(model.getSize()>0);
-    
+    comboBox.setEnabled(model.getSize() > 0);
+
   }
 
   /**
@@ -605,32 +634,27 @@ public class CalculationChooser extends JPanel
    * 
    * @param nucleotide
    * @param forPca
+   * @param ssPresent - include secondary structure similarity model
+   * @param forPasimap - limit to ScoreMatrix based models - allows use of AlignSeq
    * @return
    */
   protected static List<ScoreModelI> getApplicableScoreModels(
-          boolean nucleotide, boolean forPca, boolean ssPresent, boolean forPasimap)
+          boolean nucleotide, boolean forPca, boolean ssPresent,
+          boolean forPasimap)
   {
     List<ScoreModelI> filtered = new ArrayList<>();
 
     ScoreModels scoreModels = ScoreModels.getInstance();
     for (ScoreModelI sm : scoreModels.getModels())
     {
-      if (!forPasimap && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() 
-              || sm.isSecondaryStructure() && ssPresent))
-              
+      if ((!forPasimap || sm instanceof ScoreMatrix)  
+              && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
+                      || sm.isSecondaryStructure() && ssPresent))
+
       {
         filtered.add(sm);
       }
     }
-    
-    /*
-     * make PaSiMap only use Blosum62 and Pam250
-     */
-    if (forPasimap && !nucleotide && !forPca)
-    {
-      filtered.add(scoreModels.getBlosum62());
-      filtered.add(scoreModels.getPam250());
-    }
 
     /*
      * special case: add BLOSUM62 as last option for nucleotide PCA, 
@@ -641,22 +665,23 @@ public class CalculationChooser extends JPanel
     {
       filtered.add(scoreModels.getBlosum62());
     }
-    
+
     return filtered;
   }
 
-  
   protected List<String> getApplicableSecondaryStructureSources()
   {
-    AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation();
-    
-    List<String> ssSources = AlignmentUtils.getSecondaryStructureSources(annotations);
-    //List<String> ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
-    
-                 
+    AlignmentAnnotation[] annotations = af.getViewport().getAlignment()
+            .getAlignmentAnnotation();
+
+    List<String> ssSources = AlignmentUtils
+            .getSecondaryStructureSources(annotations);
+    // List<String> ssSources =
+    // AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+
     return ssSources;
   }
-  
+
   /**
    * Open and calculate the selected tree or PCA on 'OK'
    */
@@ -664,15 +689,17 @@ public class CalculationChooser extends JPanel
   {
     boolean doPCA = pca.isSelected();
     boolean doPaSiMap = pasimap.isSelected();
-    boolean doPairwise= pairwise.isSelected();
-    String modelName = modelNames.getSelectedItem() == null ? "" : modelNames.getSelectedItem().toString();
+    boolean doPairwise = pairwise.isSelected();
+    String modelName = modelNames.getSelectedItem() == null ? ""
+            : modelNames.getSelectedItem().toString();
     String ssSource = "";
     Object selectedItem = ssSourceDropdown.getSelectedItem();
-    if (selectedItem != null) {
-        ssSource = selectedItem.toString();
+    if (selectedItem != null)
+    {
+      ssSource = selectedItem.toString();
     }
     SimilarityParams params = getSimilarityParameters(doPCA);
-    if(ssSource.length()>0)
+    if (ssSource.length() > 0)
     {
       params.setSecondaryStructureSource(ssSource);
     }
@@ -680,30 +707,45 @@ public class CalculationChooser extends JPanel
     if (doPCA)
     {
       openPcaPanel(modelName, params);
-       } else if (doPaSiMap) {
-               openPasimapPanel(modelName, params);
-       } else if (doPairwise) {
-               openPairwisePanel(modelName, params);
-       } else {
-               openTreePanel(modelName, params);
-       }
+    }
+    else if (doPaSiMap)
+    {
+      openPasimapPanel(modelName, params);
+    }
+    else if (doPairwise)
+    {
+      openPairwisePanel(modelName, params);
+    }
+    else
+    {
+      openTreePanel(modelName, params);
+    }
 
     closeFrame();
   }
 
   private void openPairwisePanel(String modelName, SimilarityParamsI params)
   {
-    ScoreModelI sm = ScoreModels.getInstance().getScoreModel(modelName, af.alignPanel);
-    if (sm==null || !(sm instanceof ScoreMatrix))
+    ScoreModelI sm = ScoreModels.getInstance().getScoreModel(modelName,
+            af.alignPanel);
+    if (sm == null || !(sm instanceof ScoreMatrix))
     {
       return;
     }
-    JInternalFrame frame = new JInternalFrame();
-    frame.setFrameIcon(null);
-    frame.setContentPane(new PairwiseAlignPanel(af.getViewport(),(ScoreMatrix)sm));
-    Desktop.addInternalFrame(frame,
-            MessageManager.getString("action.pairwise_alignment"), 600,
-            500);    
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        JInternalFrame frame = new JInternalFrame();
+        frame.setFrameIcon(null);
+        frame.setContentPane(
+                new PairwiseAlignPanel(af.getViewport(), (ScoreMatrix) sm));
+        Desktop.addInternalFrame(frame,
+                MessageManager.getString("action.pairwise_alignment"), 600,
+                500);
+      }
+    }).start();
   }
 
   /**
@@ -780,7 +822,8 @@ public class CalculationChooser extends JPanel
    * @param modelName
    * @param params
    */
-  protected void openPasimapPanel(String modelName, SimilarityParamsI params)
+  protected void openPasimapPanel(String modelName,
+          SimilarityParamsI params)
   {
     AlignViewport viewport = af.getViewport();
 
@@ -789,9 +832,11 @@ public class CalculationChooser extends JPanel
      * this check in in case this method gets exposed programmatically in future
      */
     if (((viewport.getSelectionGroup() != null)
-            && (viewport.getSelectionGroup().getSize() < MIN_PASIMAP_SELECTION)
+            && (viewport.getSelectionGroup()
+                    .getSize() < MIN_PASIMAP_SELECTION)
             && (viewport.getSelectionGroup().getSize() > 0))
-            || (viewport.getAlignment().getHeight() < MIN_PASIMAP_SELECTION))
+            || (viewport.getAlignment()
+                    .getHeight() < MIN_PASIMAP_SELECTION))
     {
       JvOptionPane.showInternalMessageDialog(this,
               MessageManager.formatMessage(

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index 3bf731d..702c4f4 100644 (file)
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -213,6 +213,9 @@ public class PaSiMapPanel extends GPaSiMapPanel
       
       PairwiseAlignPanel pap = new PairwiseAlignPanel(av, selGroup, true,
               GAP_OPEN_COST, GAP_EXTEND_COST, false, null);
+      pap.setDiscardAlignments(true);
+      pap.setQuiet(true);
+      
       System.out.println(pap != null);
       setPairwiseAlignPanel(pap);
       getPasimapModel().calculate(pap);
@@ -702,7 +705,11 @@ public class PaSiMapPanel extends GPaSiMapPanel
     pBar.repaint();
   }
 
-  //&!
+  /**
+   * adds a listener for a pairwise alignment panel's progress
+   * TODO: generalise for anything that can report progress ?
+   * @param pap
+   */
   public void setPairwiseAlignPanel(PairwiseAlignPanel pap)
   {
     pap.addPropertyChangeListener(new PropertyChangeListener()
@@ -710,12 +717,14 @@ public class PaSiMapPanel extends GPaSiMapPanel
       @Override
       public void propertyChange(PropertyChangeEvent pcEvent)
       {
-       if (PairwiseAlignPanel.PROGRESS.equals(pcEvent.getPropertyName()))
-       {
-         updateProgressBar((int) pcEvent.getNewValue());
-       } else if (PairwiseAlignPanel.TOTAL.equals(pcEvent.getPropertyName())) {
-         updateProgressBar((int) pcEvent.getNewValue(), 0);
-       }
+        if (PairwiseAlignPanel.PROGRESS.equals(pcEvent.getPropertyName()))
+        {
+          updateProgressBar((int) pcEvent.getNewValue());
+        }
+        else if (PairwiseAlignPanel.TOTAL.equals(pcEvent.getPropertyName()))
+        {
+          updateProgressBar((int) pcEvent.getNewValue(), 0);
+        }
       }
     });
   }

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index e8b130e..3e8fb02 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -22,8 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignSeq;
 import jalview.analysis.scoremodels.ScoreMatrix;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
@@ -33,10 +31,8 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.math.MiscMath;
 
-import java.beans.PropertyChangeListener;
 import java.awt.event.ActionEvent;
 import java.util.Vector;
-import javax.swing.event.SwingPropertyChangeSupport;
 
 /**
  * DOCUMENT ME!
@@ -63,7 +59,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private String alignmentOutput;
 
-  private boolean suppressTextbox;
+  private boolean quiet;
  
   private boolean discardAlignments;
 
@@ -77,13 +73,15 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
   private int total;
 
   private int progress;
-
+  
   private SequenceGroup selection;
   /**
    * input sequences
    */
   private SequenceI[] seqs=null;
 
+  private ScoreMatrix scoreMatrix;
+
   /**
    * Creates a new PairwiseAlignPanel object.
    * 
@@ -124,17 +122,15 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     this.endGaps = endGaps;
     this.selection = selection;
     this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2);
-    
+    this.scoreMatrix = scoreMatrix;
     if (run) {
-      calculate(scoreMatrix);
+      calculate();
     }
-    
-    System.out.println("Creating pap");
   }
   
   public void calculate()
   {
-    calculate(null);
+    calculate(scoreMatrix);
   }
   public void calculate (ScoreMatrix sm)
   {
@@ -181,8 +177,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     float[][] alignmentScores = new float[seqs.length][seqs.length];
     double totscore = 0D;
     int count = seqs.length;
-    suppressTextbox = count>10;
-    discardAlignments = count>15;
+    
     boolean first = true;
 
     progress = 0;
@@ -217,7 +212,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         }
         as.scoreAlignment();
 
-        if (!first && !suppressTextbox)
+        if (!first && !quiet)
         {
           jalview.bin.Console.outPrintln(DASHES);
           textarea.append(DASHES);
@@ -230,7 +225,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         scores[i][j] = as.getMaxScore() / as.getASeq1().length;
         alignmentScores[i][j] = as.getAlignmentScore();
         totscore = totscore + scores[i][j];
-        if (!suppressTextbox)
+        if (!quiet)
         {
           textarea.append(as.getOutput());
           sb.append(as.getOutput());
@@ -248,7 +243,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     this.scores = scores;
     this.alignmentScores = alignmentScores;
 
-    if (count > 2)
+    if (count > 2 && !quiet) 
     {
       printScoreMatrix(seqs, scores, totscore);
     }
@@ -353,4 +348,20 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
   {
     return seqs;
   }
+  /**
+   * Set to true to suppress output of progress to Console.stdout or GUI 
+   * @param quiet 
+   */
+  public void setQuiet(boolean quiet)
+  {
+    this.quiet=quiet;    
+  }
+  /**
+   * set this if you are only interested in final alignment scores
+   * @param discard
+   */
+  public void setDiscardAlignments(boolean discard)
+  {
+    discardAlignments=discard;
+  }
 }