X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=7730210dcfebf1de737da9c2ad195e4e96128891;hb=ba1f9fee25b87bdac0c535019252b787939a8f80;hp=efb204ea2a54bb97291949818e07bf131977599f;hpb=cee29c9fa89ed1d1df7b3af9f97055d8cd6eb77e;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index efb204e..7730210 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -25,7 +25,7 @@ import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -48,8 +48,8 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 
-public class PCAPanel extends EmbmenuFrame implements Runnable,
-        ActionListener, ItemListener
+public class PCAPanel extends EmbmenuFrame
+        implements Runnable, ActionListener, ItemListener
 {
   RotatableCanvas rc;
 
@@ -88,7 +88,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     }
     else
     {
-      seqs = viewport.getSelectionGroup().getSequencesInOrder(viewport.getAlignment());
+      seqs = viewport.getSelectionGroup()
+              .getSequencesInOrder(viewport.getAlignment());
     }
     SeqCigar sq[] = seqstrings.getSequences();
     int length = sq[0].getWidth();
@@ -103,10 +104,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       }
     }
 
-    ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
-            !nucleotide);
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
- scoreModel,
+    ScoreModelI scoreModel = ScoreModels.getInstance()
+            .getDefaultModel(!nucleotide);
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             SimilarityParams.SeqSpace);
 
     rc = new RotatableCanvas(viewport);
@@ -134,7 +134,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     {
       nuclSetting.setState(pcaModel.isNucleotide());
       protSetting.setState(!pcaModel.isNucleotide());
-      pcaModel.run();
+      pcaModel.calculate();
       // ////////////////
       xCombobox.select(0);
       yCombobox.select(1);
@@ -145,7 +145,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       top = pcaModel.getTop();
     } catch (OutOfMemoryError x)
     {
-      System.err.println("Out of memory when calculating PCA.");
+      jalview.bin.Console.errPrintln("Out of memory when calculating PCA.");
       return;
     }
     calcSettings.setEnabled(true);
@@ -167,9 +167,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     int dim2 = top - yCombobox.getSelectedIndex();
     int dim3 = top - zCombobox.getSelectedIndex();
     pcaModel.updateRcView(dim1, dim2, dim3);
-    rc.img = null;
-    rc.rotmat.setIdentity();
-    rc.initAxes();
+    rc.resetView();
     rc.paint(rc.getGraphics());
   }
 
@@ -217,6 +215,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (!pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(true);
+        ScoreModelI scoreModel = ScoreModels.getInstance()
+                .getDefaultModel(false);
+        pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
     }
@@ -225,6 +226,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(false);
+        ScoreModelI scoreModel = ScoreModels.getInstance()
+                .getDefaultModel(true);
+        pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
     }
@@ -275,16 +279,17 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     {
     }
     ;
-    Object[] alAndColsel = pcaModel.getSeqtrings()
-            .getAlignmentAndColumnSelection(gc);
+    Object[] alAndColsel = pcaModel.getInputData()
+            .getAlignmentAndHiddenColumns(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {
       Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-      AlignFrame af = new AlignFrame(al, av.applet,
-              "Original Data for PCA", false);
+      AlignFrame af = new AlignFrame(al, av.applet, "Original Data for PCA",
+              false);
 
-      af.viewport.setHiddenColumns((ColumnSelection) alAndColsel[1]);
+      af.viewport.getAlignment()
+              .setHiddenColumns((HiddenColumns) alAndColsel[1]);
     }
   }
 
@@ -360,8 +365,8 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     values.setLabel(MessageManager.getString("label.output_values"));
     values.addActionListener(this);
     inputData.setLabel(MessageManager.getString("label.input_data"));
-    nuclSetting.setLabel(MessageManager
-            .getString("label.nucleotide_matrix"));
+    nuclSetting
+            .setLabel(MessageManager.getString("label.nucleotide_matrix"));
     nuclSetting.addItemListener(this);
     protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
     protSetting.addItemListener(this);