JAL-2962 code tidying/documentation (non-functional) changes

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index d11d322..6f02b71 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -214,7 +214,7 @@ public class PCA implements Runnable
   }
 
   /**
-   * Returns a PrintStream that wraps (sends its output to) the given
+   * Returns a PrintStream that wraps (appends its output to) the given
    * StringBuilder
    * 
    * @param sb

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index afb4e95..c5ae339 100755 (executable)
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -87,7 +87,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
   int npoint;
 
-  Vector points;
+  Vector<SequencePoint> points;
 
   float[][] orig;
 
@@ -126,6 +126,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void setPoints(Vector points, int npoint)
   {
     this.points = points;
@@ -230,7 +231,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     {
       for (int j = 0; j < npoint; j++)
       {
-        SequencePoint sp = (SequencePoint) points.elementAt(j);
+        SequencePoint sp = points.elementAt(j);
         if (sp.coord[i] >= max[i])
         {
           max[i] = sp.coord[i];
@@ -287,7 +288,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
       dim = height;
     }
 
-    return (float) (dim * scalefactor / (2 * maxwidth));
+    return dim * scalefactor / (2 * maxwidth);
   }
 
   public void findCentre()
@@ -304,6 +305,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     // System.out.println("Centre z " + centre[2]);
   }
 
+  @Override
   public Dimension getPreferredSize()
   {
     if (prefsize != null)
@@ -316,16 +318,19 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public Dimension getMinimumSize()
   {
     return getPreferredSize();
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     if (points == null)
@@ -397,25 +402,26 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
-      int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      SequencePoint sp = points.elementAt(i);
+      int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
+      int y = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
       float z = sp.coord[1] - centre[2];
 
-      if (av.getSequenceColour(sp.sequence) == Color.black)
+      SequenceI sequence = sp.getSequence();
+      if (av.getSequenceColour(sequence) == Color.black)
       {
         g.setColor(Color.white);
       }
       else
       {
-        g.setColor(av.getSequenceColour(sp.sequence));
+        g.setColor(av.getSequenceColour(sequence));
       }
 
       if (av.getSelectionGroup() != null)
       {
         if (av.getSelectionGroup().getSequences(null)
-                .contains(((SequencePoint) points.elementAt(i)).sequence))
+                .contains(sequence))
         {
           g.setColor(Color.gray);
         }
@@ -429,9 +435,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
       if (showLabels)
       {
         g.setColor(Color.red);
-        g.drawString(
-                ((SequencePoint) points.elementAt(i)).sequence.getName(),
-                x - 3, y - 4);
+        g.drawString(sequence.getName(), x - 3, y - 4);
       }
     }
   }
@@ -446,14 +450,17 @@ public class RotatableCanvas extends Panel implements MouseListener,
     return prefsize;
   }
 
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
 
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_UP)
@@ -482,7 +489,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
   {
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       Format.print(System.out, "%5d ", i);
       for (int j = 0; j < 3; j++)
       {
@@ -492,22 +499,27 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     int x = evt.getX();
@@ -552,6 +564,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     SequenceI found = findPoint(evt.getX(), evt.getY());
@@ -568,6 +581,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     mx = evt.getX();
@@ -575,12 +589,12 @@ public class RotatableCanvas extends Panel implements MouseListener,
 
     rotmat.setIdentity();
 
-    rotmat.rotate((float) (my - omy), 'x');
-    rotmat.rotate((float) (mx - omx), 'y');
+    rotmat.rotate(my - omy, 'x');
+    rotmat.rotate(mx - omx, 'y');
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       sp.coord[0] -= centre[0];
       sp.coord[1] -= centre[1];
       sp.coord[2] -= centre[2];
@@ -609,20 +623,21 @@ public class RotatableCanvas extends Panel implements MouseListener,
     // boolean changedSel = false;
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       int tmp1 = (int) ((sp.coord[0] - centre[0]) * scale
-              + (float) getSize().width / 2.0);
+              + getSize().width / 2.0);
       int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale
-              + (float) getSize().height / 2.0);
+              + getSize().height / 2.0);
 
+      SequenceI sequence = sp.getSequence();
       if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
       {
         if (av != null)
         {
           if (!av.getSelectionGroup().getSequences(null)
-                  .contains(sp.sequence))
+                  .contains(sequence))
           {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
+            av.getSelectionGroup().addSequence(sequence, true);
           }
         }
       }
@@ -640,10 +655,10 @@ public class RotatableCanvas extends Panel implements MouseListener,
     for (int i = 0; i < npoint; i++)
     {
 
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+      SequencePoint sp = points.elementAt(i);
+      int px = (int) ((sp.coord[0] - centre[0]) * scale)
               + halfwidth;
-      int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      int py = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
 
       if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
@@ -653,7 +668,7 @@ public class RotatableCanvas extends Panel implements MouseListener,
     }
     if (found != -1)
     {
-      return ((SequencePoint) points.elementAt(found)).sequence;
+      return points.elementAt(found).getSequence();
     }
     else
     {

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index a6b967e..28db278 100755 (executable)
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -21,33 +21,35 @@
 package jalview.datamodel;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A bean that models a point with (x, y, z) coordinates and a reference to a
+ * sequence
  */
 public class SequencePoint
 {
-  // SMJS PUBLIC
-  /**
-   * for points with no real physical association with an alignment sequence
+  /*
+   * Associated alignment sequence, or dummy sequence object
    */
-  public boolean isPlaceholder = false;
+  private final SequenceI sequence;
 
-  /**
-   * Associated alignment sequence, or dummy sequence object.
+  /*
+   * array of coordinates in embedded sequence space
    */
-  public SequenceI sequence;
+  public float[] coord;
 
   /**
-   * array of coordinates in embedded sequence space.
+   * Constructor
+   * 
+   * @param sequence
+   * @param coord
    */
-  public float[] coord;
-
-  // SMJS ENDPUBLIC
   public SequencePoint(SequenceI sequence, float[] coord)
   {
     this.sequence = sequence;
     this.coord = coord;
   }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
 }

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 02368df..dc33b36 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.RotatableCanvasI;
+import jalview.bin.Cache;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequencePoint;
@@ -94,7 +95,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   int npoint;
 
-  Vector points;
+  Vector<SequencePoint> points;
 
   float[][] orig;
 
@@ -128,6 +129,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   boolean applyToAllViews = false;
 
+  boolean first = true;
+
   public RotatableCanvas(AlignmentPanel ap)
   {
     this.av = ap.av;
@@ -166,10 +169,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
-  boolean first = true;
-
   @Override
-  public void setPoints(Vector points, int npoint)
+  public void setPoints(Vector<SequencePoint> points, int npoint)
   {
     this.points = points;
     this.npoint = npoint;
@@ -184,7 +185,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
 
       for (int j = 0; j < 3; j++)
       {
@@ -267,7 +268,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     {
       for (int j = 0; j < npoint; j++)
       {
-        SequencePoint sp = (SequencePoint) points.elementAt(j);
+        SequencePoint sp = points.elementAt(j);
 
         if (sp.coord[i] >= max[i])
         {
@@ -311,23 +312,23 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   public float findScale()
   {
     int dim;
-    int width;
+    int w;
     int height;
 
     if (getWidth() != 0)
     {
-      width = getWidth();
+      w = getWidth();
       height = getHeight();
     }
     else
     {
-      width = prefsize.width;
+      w = prefsize.width;
       height = prefsize.height;
     }
 
-    if (width < height)
+    if (w < height)
     {
-      dim = width;
+      dim = w;
     }
     else
     {
@@ -423,7 +424,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       drawBackground(ig, bgColour);
       drawScene(ig);
 
-      if (drawAxes == true)
+      if (drawAxes)
       {
         drawAxes(ig);
       }
@@ -484,25 +485,26 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
       int y = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
       float z = sp.coord[1] - centre[2];
 
-      if (av.getSequenceColour(sp.sequence) == Color.black)
+      SequenceI sequence = sp.getSequence();
+      if (av.getSequenceColour(sequence) == Color.black)
       {
         g.setColor(Color.white);
       }
       else
       {
-        g.setColor(av.getSequenceColour(sp.sequence));
+        g.setColor(av.getSequenceColour(sequence));
       }
 
       if (av.getSelectionGroup() != null)
       {
         if (av.getSelectionGroup().getSequences(null)
-                .contains(((SequencePoint) points.elementAt(i)).sequence))
+                .contains(sequence))
         {
           g.setColor(Color.gray);
         }
@@ -517,9 +519,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       if (showLabels)
       {
         g.setColor(Color.red);
-        g.drawString(
-                ((SequencePoint) points.elementAt(i)).sequence.getName(),
-                x - 3, y - 4);
+        g.drawString(sequence.getName(), x - 3, y - 4);
       }
     }
 
@@ -594,8 +594,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     }
     else if (evt.getKeyChar() == 's')
     {
-      System.err.println("DEBUG: Rectangle selection"); // log.debug
-
+      Cache.log.warn("DEBUG: Rectangle selection");
+      // todo not yet enabled as rectx2, recty2 are always -1
+      // need to set them in mouseDragged
       if ((rectx2 != -1) && (recty2 != -1))
       {
         rectSelect(rectx1, recty1, rectx2, recty2);
@@ -605,55 +606,31 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
   @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
   @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
   @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
   @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
+   * If the mouse press is at (within 2 pixels of) a sequence point, toggles
+   * (adds or removes) the corresponding sequence as a member of the viewport
+   * selection group. This supports configuring a group in the alignment by
+   * clicking on points in the PCA display.
    */
   @Override
   public void mousePressed(MouseEvent evt)
@@ -676,7 +653,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     rectx2 = -1;
     recty2 = -1;
 
-    SequenceI found = findPoint(x, y);
+    SequenceI found = findSequenceAtPoint(x, y);
 
     if (found != null)
     {
@@ -704,23 +681,16 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
-  // private void fireSequenceSelectionEvent(Selection sel) {
-  // controller.handleSequenceSelectionEvent(new
-  // SequenceSelectionEvent(this,sel));
-  // }
+  /**
+   * Sets the tooltip to the name of the sequence within 2 pixels of the mouse
+   * position, or clears the tooltip if none found
+   */
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    SequenceI found = findPoint(evt.getX(), evt.getY());
+    SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
 
-    if (found != null)
-    {
-      this.setToolTipText(found.getName());
-    }
-    else
-    {
-      this.setToolTipText(null);
-    }
+    this.setToolTipText(found == null ? null : found.getName());
   }
 
   /**
@@ -750,7 +720,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
       for (int i = 0; i < npoint; i++)
       {
-        SequencePoint sp = (SequencePoint) points.elementAt(i);
+        SequencePoint sp = points.elementAt(i);
         sp.coord[0] -= centre[0];
         sp.coord[1] -= centre[1];
         sp.coord[2] -= centre[2];
@@ -777,22 +747,20 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Adds any sequences whose displayed points are within the given rectangle to
+   * the viewport's current selection. Intended for key 's' after dragging to
+   * select a region of the PCA.
    * 
    * @param x1
-   *          DOCUMENT ME!
    * @param y1
-   *          DOCUMENT ME!
    * @param x2
-   *          DOCUMENT ME!
    * @param y2
-   *          DOCUMENT ME!
    */
   public void rectSelect(int x1, int y1, int x2, int y2)
   {
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
               + (getWidth() / 2.0));
       int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
@@ -802,31 +770,27 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       {
         if (av != null)
         {
+          SequenceI sequence = sp.getSequence();
           if (!av.getSelectionGroup().getSequences(null)
-                  .contains(sp.sequence))
+                  .contains(sequence))
           {
-            av.getSelectionGroup().addSequence(sp.sequence, true);
+            av.getSelectionGroup().addSequence(sequence, true);
           }
         }
       }
     }
-
-    // if (changedSel) {
-    // fireSequenceSelectionEvent(av.getSelection());
-    // }
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the first sequence found whose point on the display is within 2
+   * pixels of the given coordinates, or null if none is found
    * 
    * @param x
-   *          DOCUMENT ME!
    * @param y
-   *          DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
-  public SequenceI findPoint(int x, int y)
+  public SequenceI findSequenceAtPoint(int x, int y)
   {
     int halfwidth = getWidth() / 2;
     int halfheight = getHeight() / 2;
@@ -835,7 +799,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     for (int i = 0; i < npoint; i++)
     {
-      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      SequencePoint sp = points.elementAt(i);
       int px = (int) ((sp.coord[0] - centre[0]) * scale)
               + halfwidth;
       int py = (int) ((sp.coord[1] - centre[1]) * scale)
@@ -849,7 +813,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     if (found != -1)
     {
-      return ((SequencePoint) points.elementAt(found)).sequence;
+      return points.elementAt(found).getSequence();
     }
     else
     {
@@ -876,8 +840,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    */
   public double[] getPointPosition(int s)
   {
-    double pts[] = new double[3];
-    float[] p = ((SequencePoint) points.elementAt(s)).coord;
+    double[] pts = new double[3];
+    float[] p = points.elementAt(s).coord;
     pts[0] = p[0];
     pts[1] = p[1];
     pts[2] = p[2];

diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 0dcdbca..db0f4dd 100644 (file)
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -51,7 +51,7 @@ public class PCAModel
   /*
    * outputs
    */
-  private volatile PCA pca;
+  private PCA pca;
 
   int top;
 
@@ -77,10 +77,14 @@ public class PCAModel
     similarityParams = params;
   }
 
+  /**
+   * Performs the PCA calculation (in the same thread) and extracts result data
+   * needed for visualisation by PCAPanel
+   */
   public void run()
   {
     pca = new PCA(seqstrings, scoreModel, similarityParams);
-    pca.run();
+    pca.run(); // executes in same thread, wait for completion
 
     // Now find the component coordinates
     int ii = 0;