JAL-2944 open selected structures in existing or a new view, and by default offer...
[jalview.git] / src / jalview / gui / PCAPanel.java
index 3f0c37f..9f52d26 100644 (file)
 package jalview.gui;
 
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
-import jalview.bin.Cache;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPCAPanel;
 import jalview.util.MessageManager;
@@ -37,6 +36,7 @@ import jalview.viewmodel.PCAModel;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -59,8 +59,8 @@ import javax.swing.event.InternalFrameEvent;
  * @author $author$
  * @version $Revision$
  */
-public class PCAPanel extends GPCAPanel implements Runnable,
-        IProgressIndicator
+public class PCAPanel extends GPCAPanel
+        implements Runnable, IProgressIndicator
 {
 
   private IProgressIndicator progressBar;
@@ -73,29 +73,59 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   PCAModel pcaModel;
 
+  private static final int MIN_WIDTH = 470;
+
+  private static final int MIN_HEIGHT = 250;
+
   int top = 0;
 
+  private boolean working;
+
   /**
-   * Creates a new PCAPanel object.
+   * Creates a new PCAPanel object using default score model and parameters
    * 
-   * @param av
-   *          DOCUMENT ME!
-   * @param s
-   *          DOCUMENT ME!
+   * @param alignPanel
+   */
+  public PCAPanel(AlignmentPanel alignPanel)
+  {
+    this(alignPanel,
+            ScoreModels.getInstance()
+                    .getDefaultModel(
+                            !alignPanel.av.getAlignment().isNucleotide())
+                    .getName(),
+            SimilarityParams.SeqSpace);
+  }
+
+  /**
+   * Constructor given sequence data, a similarity (or distance) score model
+   * name, and score calculation parameters
+   * 
+   * @param alignPanel
+   * @param modelName
+   * @param params
    */
-  public PCAPanel(AlignmentPanel ap)
+  public PCAPanel(AlignmentPanel alignPanel, String modelName,
+          SimilarityParamsI params)
   {
     super();
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alignPanel.av;
+    this.ap = alignPanel;
+    boolean nucleotide = av.getAlignment().isNucleotide();
 
     progressBar = new ProgressBar(statusPanel, statusBar);
 
-    boolean sameLength = true;
+    addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(InternalFrameEvent e)
+      {
+        close_actionPerformed();
+      }
+    });
+
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
     AlignmentView seqstrings = av.getAlignmentView(selected);
-    boolean nucleotide = av.getAlignment().isNucleotide();
     SequenceI[] seqs;
     if (!selected)
     {
@@ -105,41 +135,14 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     {
       seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
-    SeqCigar sq[] = seqstrings.getSequences();
-    int length = sq[0].getWidth();
-
-    for (int i = 0; i < seqs.length; i++)
-    {
-      if (sq[i].getWidth() != length)
-      {
-        sameLength = false;
-        break;
-      }
-    }
-
-    if (!sameLength)
-    {
-      JvOptionPane.showMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.pca_sequences_not_aligned"),
-              MessageManager.getString("label.sequences_not_aligned"),
-              JvOptionPane.WARNING_MESSAGE);
-
-      return;
-    }
-
-    addInternalFrameListener(new InternalFrameAdapter()
-    {
-      @Override
-      public void internalFrameClosed(InternalFrameEvent e)
-      {
-        close_actionPerformed();
-      }
-    });
 
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
+    ScoreModelI scoreModel = ScoreModels.getInstance()
+            .getScoreModel(modelName, ap);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
+            params);
     PaintRefresher.Register(this, av.getSequenceSetId());
 
-    rc = new RotatableCanvas(ap);
+    rc = new RotatableCanvas(alignPanel);
     this.getContentPane().add(rc, BorderLayout.CENTER);
     Thread worker = new Thread(this);
     worker.start();
@@ -167,10 +170,19 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     for (final ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
       final String name = sm.getName();
-      // create an entry for this score matrix for use in PCA
-      JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
-      jm.setText(MessageManager.getStringOrReturn("label.score_model_",
-              name));
+      JCheckBoxMenuItem jm = new JCheckBoxMenuItem(name);
+
+      /*
+       * if the score model doesn't provide a description, try to look one
+       * up in the text bundle, falling back on its name
+       */
+      String tooltip = sm.getDescription();
+      if (tooltip == null)
+      {
+        tooltip = MessageManager.getStringOrReturn("label.score_model_",
+                name);
+      }
+      jm.setToolTipText(tooltip);
       jm.setSelected(pcaModel.getScoreModelName().equals(name));
       if ((pcaModel.isNucleotide() && sm.isDNA())
               || (!pcaModel.isNucleotide() && sm.isProtein()))
@@ -182,7 +194,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
           {
             if (!pcaModel.getScoreModelName().equals(name))
             {
-              ScoreModelI sm2 = configureScoreModel(sm);
+              ScoreModelI sm2 = ScoreModels.getInstance()
+                      .getScoreModel(name, ap);
               pcaModel.setScoreModel(sm2);
               Thread worker = new Thread(PCAPanel.this);
               worker.start();
@@ -223,6 +236,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       message = MessageManager.getString("label.pca_calculating");
     }
     progress.setProgressBar(message, progId);
+    working = true;
     try
     {
       calcSettings.setEnabled(false);
@@ -236,12 +250,12 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       // rc.invalidate();
       nuclSetting.setSelected(pcaModel.isNucleotide());
       protSetting.setSelected(!pcaModel.isNucleotide());
-      jvVersionSetting.setSelected(pcaModel.isJvCalcMode());
       top = pcaModel.getTop();
 
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("calculating PCA", er);
+      working = false;
       return;
     } finally
     {
@@ -254,7 +268,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       addKeyListener(rc);
       Desktop.addInternalFrame(this, MessageManager
               .getString("label.principal_component_analysis"), 475, 450);
+      this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
+    working = false;
   }
 
   @Override
@@ -263,8 +279,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (!pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(true);
-      pcaModel.setScoreModel(ScoreModels.getInstance().getDefaultModel(
-              false));
+      pcaModel.setScoreModel(
+              ScoreModels.getInstance().getDefaultModel(false));
       Thread worker = new Thread(this);
       worker.start();
     }
@@ -278,21 +294,13 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     if (pcaModel.isNucleotide())
     {
       pcaModel.setNucleotide(false);
-      pcaModel.setScoreModel(ScoreModels.getInstance()
-              .getDefaultModel(true));
+      pcaModel.setScoreModel(
+              ScoreModels.getInstance().getDefaultModel(true));
       Thread worker = new Thread(this);
       worker.start();
     }
   }
 
-  @Override
-  protected void jvVersionSetting_actionPerfomed(ActionEvent arg0)
-  {
-    pcaModel.setJvCalcMode(jvVersionSetting.isSelected());
-    Thread worker = new Thread(this);
-    worker.start();
-  }
-
   /**
    * DOCUMENT ME!
    */
@@ -385,8 +393,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     // make this an abstract function of all jalview analysis windows
     if (pcaModel.getSeqtrings() == null)
     {
-      jalview.bin.Cache.log
-              .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      jalview.bin.Cache.log.info(
+              "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
     // decide if av alignment is sufficiently different to original data to
@@ -406,15 +414,16 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
     ;
     Object[] alAndColsel = pcaModel.getSeqtrings()
-            .getAlignmentAndColumnSelection(gc);
+            .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
       AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
-      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
-              .getAlignment().getDataset() : null;
+      AlignmentI dataset = (av != null && av.getAlignment() != null)
+              ? av.getAlignment().getDataset()
+              : null;
       if (dataset != null)
       {
         al.setDataset(dataset);
@@ -423,9 +432,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       if (true)
       {
         // make a new frame!
-        AlignFrame af = new AlignFrame(al,
-                (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
+        AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
         // >>>This is a fix for the moment, until a better solution is
         // found!!<<<
@@ -435,8 +443,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params",
-                new String[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params", new String[]
+                { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -567,8 +575,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   void buildAssociatedViewMenu()
   {
-    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
-            .getSequenceSetId());
+    AlignmentPanel[] aps = PaintRefresher
+            .getAssociatedPanels(av.getSequenceSetId());
     if (aps.length == 1 && rc.av == aps[0].av)
     {
       associateViewsMenu.setVisible(false);
@@ -577,7 +585,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
     associateViewsMenu.setVisible(true);
 
-    if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    if ((viewMenu
+            .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
     {
       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
     }
@@ -608,7 +617,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       associateViewsMenu.add(item);
     }
 
-    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+    final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+            "All Views");
 
     buttonGroup.add(itemf);
 
@@ -641,9 +651,9 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.setText(pcaModel.getPointsasCsv(false,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
-      Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.points_for_params", new String[] { this.getTitle() }),
-              500, 500);
+      Desktop.addInternalFrame(cap, MessageManager
+              .formatMessage("label.points_for_params", new String[]
+              { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting PCA points", oom);
@@ -668,8 +678,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
               xCombobox.getSelectedIndex(), yCombobox.getSelectedIndex(),
               zCombobox.getSelectedIndex()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-              "label.transformed_points_for_params",
-              new String[] { this.getTitle() }), 500, 500);
+              "label.transformed_points_for_params", new String[]
+              { this.getTitle() }), 500, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning("exporting transformed PCA points", oom);
@@ -785,26 +795,12 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   }
 
   /**
-   * If the score model is one that requires to get state data from the current
-   * view, allow it to do so
+   * Answers true if PCA calculation is in progress, else false
    * 
-   * @param sm
    * @return
    */
-  protected ScoreModelI configureScoreModel(ScoreModelI sm)
+  public boolean isWorking()
   {
-    if (sm instanceof ViewBasedAnalysisI)
-    {
-      try
-      {
-        sm = sm.getClass().newInstance();
-        ((ViewBasedAnalysisI) sm).configureFromAlignmentView(ap);
-      } catch (Exception q)
-      {
-        Cache.log.error("Couldn't create a scoremodel instance for "
-                + sm.getName());
-      }
-    }
-    return sm;
+    return working;
   }
 }