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JAL-2962 code tidying/documentation (non-functional) changes
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 26 Apr 2018 11:38:58 +0000
(12:38 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 26 Apr 2018 11:38:58 +0000
(12:38 +0100)
src/jalview/analysis/PCA.java
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src/jalview/appletgui/RotatableCanvas.java
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src/jalview/datamodel/SequencePoint.java
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src/jalview/gui/RotatableCanvas.java
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src/jalview/viewmodel/PCAModel.java
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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
* 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;
int npoint;
- Vector points;
+ Vector<SequencePoint> points;
float[][] orig;
float[][] orig;
@@
-126,6
+126,7
@@
public class RotatableCanvas extends Panel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void setPoints(Vector points, int npoint)
{
this.points = points;
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++)
{
{
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];
if (sp.coord[i] >= max[i])
{
max[i] = sp.coord[i];
@@
-287,7
+288,7
@@
public class RotatableCanvas extends Panel implements MouseListener,
dim = height;
}
dim = height;
}
- return (float) (dim * scalefactor / (2 * maxwidth));
+ return dim * scalefactor / (2 * maxwidth);
}
public void findCentre()
}
public void findCentre()
@@
-304,6
+305,7
@@
public class RotatableCanvas extends Panel implements MouseListener,
// System.out.println("Centre z " + centre[2]);
}
// System.out.println("Centre z " + centre[2]);
}
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
public Dimension getPreferredSize()
{
if (prefsize != null)
@@
-316,16
+318,19
@@
public class RotatableCanvas extends Panel implements MouseListener,
}
}
}
}
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
}
public Dimension getMinimumSize()
{
return getPreferredSize();
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (points == null)
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++)
{
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];
+ 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(Color.white);
}
else
{
- g.setColor(av.getSequenceColour(sp.sequence));
+ g.setColor(av.getSequenceColour(sequence));
}
if (av.getSelectionGroup() != null)
{
if (av.getSelectionGroup().getSequences(null)
}
if (av.getSelectionGroup() != null)
{
if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
+ .contains(sequence))
{
g.setColor(Color.gray);
}
{
g.setColor(Color.gray);
}
@@
-429,9
+435,7
@@
public class RotatableCanvas extends Panel implements MouseListener,
if (showLabels)
{
g.setColor(Color.red);
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;
}
return prefsize;
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
public void keyReleased(KeyEvent evt)
{
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_UP)
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++)
{
{
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++)
{
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)
{
}
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
}
public void mouseReleased(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
public void mousePressed(MouseEvent evt)
{
int x = evt.getX();
@@
-552,6
+564,7
@@
public class RotatableCanvas extends Panel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
SequenceI found = findPoint(evt.getX(), evt.getY());
public void mouseMoved(MouseEvent evt)
{
SequenceI found = findPoint(evt.getX(), evt.getY());
@@
-568,6
+581,7
@@
public class RotatableCanvas extends Panel implements MouseListener,
repaint();
}
repaint();
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
mx = evt.getX();
public void mouseDragged(MouseEvent evt)
{
mx = evt.getX();
@@
-575,12
+589,12
@@
public class RotatableCanvas extends Panel implements MouseListener,
rotmat.setIdentity();
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++)
{
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];
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++)
{
// 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
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
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)
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++)
{
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;
+ 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)
+ 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)
{
}
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.elementAt(found).getSequence();
}
else
{
}
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;
/**
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
{
*/
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 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;
package jalview.gui;
import jalview.api.RotatableCanvasI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
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;
int npoint;
- Vector points;
+ Vector<SequencePoint> points;
float[][] orig;
float[][] orig;
@@
-128,6
+129,8
@@
public class RotatableCanvas extends JPanel implements MouseListener,
boolean applyToAllViews = false;
boolean applyToAllViews = false;
+ boolean first = true;
+
public RotatableCanvas(AlignmentPanel ap)
{
this.av = ap.av;
public RotatableCanvas(AlignmentPanel ap)
{
this.av = ap.av;
@@
-166,10
+169,8
@@
public class RotatableCanvas extends JPanel implements MouseListener,
repaint();
}
repaint();
}
- boolean first = true;
-
@Override
@Override
- public void setPoints(Vector points, int npoint)
+ public void setPoints(Vector<SequencePoint> points, int npoint)
{
this.points = points;
this.npoint = 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++)
{
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++)
{
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++)
{
{
for (int j = 0; j < npoint; j++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(j);
+ SequencePoint sp = points.elementAt(j);
if (sp.coord[i] >= max[i])
{
if (sp.coord[i] >= max[i])
{
@@
-311,23
+312,23
@@
public class RotatableCanvas extends JPanel implements MouseListener,
public float findScale()
{
int dim;
public float findScale()
{
int dim;
- int width;
+ int w;
int height;
if (getWidth() != 0)
{
int height;
if (getWidth() != 0)
{
- width = getWidth();
+ w = getWidth();
height = getHeight();
}
else
{
height = getHeight();
}
else
{
- width = prefsize.width;
+ w = prefsize.width;
height = prefsize.height;
}
height = prefsize.height;
}
- if (width < height)
+ if (w < height)
{
{
- dim = width;
+ dim = w;
}
else
{
}
else
{
@@
-423,7
+424,7
@@
public class RotatableCanvas extends JPanel implements MouseListener,
drawBackground(ig, bgColour);
drawScene(ig);
drawBackground(ig, bgColour);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
{
drawAxes(ig);
}
@@
-484,25
+485,26
@@
public class RotatableCanvas extends JPanel implements MouseListener,
for (int i = 0; i < npoint; i++)
{
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];
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(Color.white);
}
else
{
- g.setColor(av.getSequenceColour(sp.sequence));
+ g.setColor(av.getSequenceColour(sequence));
}
if (av.getSelectionGroup() != null)
{
if (av.getSelectionGroup().getSequences(null)
}
if (av.getSelectionGroup() != null)
{
if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
+ .contains(sequence))
{
g.setColor(Color.gray);
}
{
g.setColor(Color.gray);
}
@@
-517,9
+519,7
@@
public class RotatableCanvas extends JPanel implements MouseListener,
if (showLabels)
{
g.setColor(Color.red);
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')
{
}
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);
if ((rectx2 != -1) && (recty2 != -1))
{
rectSelect(rectx1, recty1, rectx2, recty2);
@@
-605,55
+606,31
@@
public class RotatableCanvas extends JPanel implements MouseListener,
repaint();
}
repaint();
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseClicked(MouseEvent evt)
{
}
@Override
public void mouseClicked(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseEntered(MouseEvent evt)
{
}
@Override
public void mouseEntered(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseExited(MouseEvent evt)
{
}
@Override
public void mouseExited(MouseEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
@Override
public void mouseReleased(MouseEvent evt)
{
}
/**
@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)
*/
@Override
public void mousePressed(MouseEvent evt)
@@
-676,7
+653,7
@@
public class RotatableCanvas extends JPanel implements MouseListener,
rectx2 = -1;
recty2 = -1;
rectx2 = -1;
recty2 = -1;
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
if (found != null)
{
@@
-704,23
+681,16
@@
public class RotatableCanvas extends JPanel implements MouseListener,
repaint();
}
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)
{
@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++)
{
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];
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
*
* @param x1
- * DOCUMENT ME!
* @param y1
* @param y1
- * DOCUMENT ME!
* @param x2
* @param x2
- * DOCUMENT ME!
* @param y2
* @param y2
- * DOCUMENT ME!
*/
public void rectSelect(int x1, int y1, int x2, int y2)
{
for (int i = 0; i < npoint; i++)
{
*/
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)
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)
{
{
if (av != null)
{
+ SequenceI sequence = sp.getSequence();
if (!av.getSelectionGroup().getSequences(null)
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
*
* @param x
- * DOCUMENT ME!
* @param y
* @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;
{
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++)
{
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)
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)
{
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.elementAt(found).getSequence();
}
else
{
}
else
{
@@
-876,8
+840,8
@@
public class RotatableCanvas extends JPanel implements MouseListener,
*/
public double[] getPointPosition(int s)
{
*/
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];
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
*/
/*
* outputs
*/
- private volatile PCA pca;
+ private PCA pca;
int top;
int top;
@@
-77,10
+77,14
@@
public class PCAModel
similarityParams = params;
}
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);
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;
// Now find the component coordinates
int ii = 0;