JAL-2959 no Print dialog shown if Page Format is Cancelled

[jalview.git] / src / jalview / gui / PCAPanel.java

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 0675cdf..7ceceee 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -27,7 +27,7 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPCAPanel;
 import jalview.util.MessageManager;
@@ -36,6 +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;
@@ -58,8 +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;
@@ -72,8 +73,14 @@ 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 using default score model and parameters
    * 
@@ -81,9 +88,12 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public PCAPanel(AlignmentPanel alignPanel)
   {
-    this(alignPanel, ScoreModels.getInstance()
-            .getDefaultModel(!alignPanel.av.getAlignment().isNucleotide())
-            .getName(), SimilarityParams.SeqSpace);
+    this(alignPanel,
+            ScoreModels.getInstance()
+                    .getDefaultModel(
+                            !alignPanel.av.getAlignment().isNucleotide())
+                    .getName(),
+            SimilarityParams.SeqSpace);
   }
 
   /**
@@ -126,8 +136,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
 
-    ScoreModelI scoreModel = ScoreModels.getInstance().getScoreModel(
-            modelName, ap);
+    ScoreModelI scoreModel = ScoreModels.getInstance()
+            .getScoreModel(modelName, ap);
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             params);
     PaintRefresher.Register(this, av.getSequenceSetId());
@@ -184,8 +194,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
           {
             if (!pcaModel.getScoreModelName().equals(name))
             {
-              ScoreModelI sm2 = ScoreModels.getInstance().getScoreModel(
-                      name, ap);
+              ScoreModelI sm2 = ScoreModels.getInstance()
+                      .getScoreModel(name, ap);
               pcaModel.setScoreModel(sm2);
               Thread worker = new Thread(PCAPanel.this);
               worker.start();
@@ -226,6 +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);
@@ -244,6 +255,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     } catch (OutOfMemoryError er)
     {
       new OOMWarning("calculating PCA", er);
+      working = false;
       return;
     } finally
     {
@@ -256,7 +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
@@ -265,8 +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();
     }
@@ -280,8 +294,8 @@ 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();
     }
@@ -379,8 +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
@@ -400,15 +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);
@@ -417,9 +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!!<<<
@@ -429,8 +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);
       }
     }
@@ -450,7 +464,16 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     public void run()
     {
       PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      PageFormat defaultPage = printJob.defaultPage();
+      PageFormat pf = printJob.pageDialog(defaultPage);
+
+      if (defaultPage == pf)
+      {
+        /*
+         * user cancelled
+         */
+        return;
+      }
 
       printJob.setPrintable(this, pf);
 
@@ -561,8 +584,8 @@ 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);
@@ -571,7 +594,8 @@ 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);
     }
@@ -602,7 +626,8 @@ 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);
 
@@ -635,9 +660,9 @@ 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);
@@ -662,8 +687,8 @@ 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);
@@ -777,4 +802,14 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     top = t;
     zCombobox.setSelectedIndex(2);
   }
+
+  /**
+   * Answers true if PCA calculation is in progress, else false
+   * 
+   * @return
+   */
+  public boolean isWorking()
+  {
+    return working;
+  }
 }