/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
import jalview.api.RotatableCanvasI;
-import jalview.datamodel.*;
-import jalview.math.*;
+import jalview.datamodel.Point;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+import jalview.math.RotatableMatrix.Axis;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Models a Panel on which a set of points, and optionally x/y/z axes, can be
+ * drawn, and rotated or zoomed with the mouse
*/
public class RotatableCanvas extends JPanel implements MouseListener,
MouseMotionListener, KeyListener, RotatableCanvasI
{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
+ private static final int DIMS = 3;
// RubberbandRectangle rubberband;
boolean drawAxes = true;
- int omx = 0;
-
- int mx = 0;
+ int mouseX = 0;
- int omy = 0;
-
- int my = 0;
+ int mouseY = 0;
Image img;
Dimension prefsize;
- float[] centre = new float[3];
+ Point centre;
- float[] width = new float[3];
+ float[] width = new float[DIMS];
- float[] max = new float[3];
+ float[] max = new float[DIMS];
- float[] min = new float[3];
+ float[] min = new float[DIMS];
float maxwidth;
int npoint;
- Vector points;
+ Vector<SequencePoint> points;
- float[][] orig;
+ Point[] orig;
- float[][] axes;
+ Point[] axisEndPoints;
int startx;
float scalefactor = 1;
- AlignViewport av;
+ AlignmentViewport av;
AlignmentPanel ap;
boolean applyToAllViews = false;
- // Controller controller;
- public RotatableCanvas(AlignmentPanel ap)
+ boolean first = true;
+
+ /**
+ * Constructor
+ *
+ * @param panel
+ */
+ public RotatableCanvas(AlignmentPanel panel)
{
- this.av = ap.av;
- this.ap = ap;
+ this.av = panel.av;
+ this.ap = panel;
+ axisEndPoints = new Point[DIMS];
addMouseWheelListener(new MouseWheelListener()
{
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
- if (e.getWheelRotation() > 0)
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
{
+ /*
+ * zoom in
+ */
scale = (float) (scale * 1.1);
repaint();
}
-
- else
+ else if (wheelRotation < 0)
{
+ /*
+ * zoom out
+ */
scale = (float) (scale * 0.9);
repaint();
}
}
- public void showLabels(boolean b)
+ /**
+ * Refreshes the display with labels shown (or not)
+ *
+ * @param show
+ */
+ public void showLabels(boolean show)
{
- showLabels = b;
+ showLabels = show;
repaint();
}
- boolean first = true;
-
- public void setPoints(Vector points, int npoint)
+ @Override
+ public void setPoints(Vector<SequencePoint> points, int npoint)
{
this.points = points;
this.npoint = npoint;
ToolTipManager.sharedInstance().setDismissDelay(10000);
}
prefsize = getPreferredSize();
- orig = new float[npoint][3];
+ orig = new Point[npoint];
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
-
- for (int j = 0; j < 3; j++)
- {
- orig[i][j] = sp.coord[j];
- }
- }
-
- // Initialize the matrices to identity
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- else
- {
- idmat.addElement(i, j, 0);
- objmat.addElement(i, j, 0);
- rotmat.addElement(i, j, 0);
- }
- }
+ SequencePoint sp = points.elementAt(i);
+ orig[i] = sp.coord;
}
- axes = new float[3][3];
- initAxes();
+ resetAxes();
findCentre();
findWidth();
scale = findScale();
if (first)
{
-
addMouseListener(this);
-
addMouseMotionListener(this);
}
first = false;
}
- public void initAxes()
+ /**
+ * Resets axes to the initial state: x-axis to the right, y-axis up, z-axis to
+ * back (so obscured in a 2-D display)
+ */
+ protected void resetAxes()
{
- for (int i = 0; i < 3; i++)
- {
- for (int j = 0; j < 3; j++)
- {
- if (i != j)
- {
- axes[i][j] = 0;
- }
- else
- {
- axes[i][j] = 1;
- }
- }
- }
+ axisEndPoints[0] = new Point(1f, 0f, 0f);
+ axisEndPoints[1] = new Point(0f, 1f, 0f);
+ axisEndPoints[2] = new Point(0f, 0f, 1f);
}
/**
- * DOCUMENT ME!
+ * Computes and saves the maximum and minimum (x, y, z) positions of any
+ * sequence point, and also the min-max range (width) for each dimension, and
+ * the maximum width for all dimensions
*/
- public void findWidth()
+ protected void findWidth()
{
- max = new float[3];
- min = new float[3];
+ max = new float[DIMS];
+ min = new float[DIMS];
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
+ max[0] = Float.MIN_VALUE;
+ max[1] = Float.MIN_VALUE;
+ max[2] = Float.MIN_VALUE;
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
- for (int i = 0; i < 3; i++)
+ for (SequencePoint sp : points)
{
- for (int j = 0; j < npoint; j++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(j);
-
- if (sp.coord[i] >= max[i])
- {
- max[i] = sp.coord[i];
- }
-
- if (sp.coord[i] <= min[i])
- {
- min[i] = sp.coord[i];
- }
- }
+ max[0] = Math.max(max[0], sp.coord.x);
+ max[1] = Math.max(max[1], sp.coord.y);
+ max[2] = Math.max(max[2], sp.coord.z);
+ min[0] = Math.min(min[0], sp.coord.x);
+ min[1] = Math.min(min[1], sp.coord.y);
+ min[2] = Math.min(min[2], sp.coord.z);
}
- // System.out.println("xmax " + max[0] + " min " + min[0]);
- // System.out.println("ymax " + max[1] + " min " + min[1]);
- // System.out.println("zmax " + max[2] + " min " + min[2]);
width[0] = Math.abs(max[0] - min[0]);
width[1] = Math.abs(max[1] - min[1]);
width[2] = Math.abs(max[2] - min[2]);
- maxwidth = width[0];
-
- if (width[1] > width[0])
- {
- maxwidth = width[1];
- }
-
- if (width[2] > width[1])
- {
- maxwidth = width[2];
- }
-
- // System.out.println("Maxwidth = " + maxwidth);
+ maxwidth = Math.max(width[0], Math.max(width[1], width[2]));
}
/**
*
* @return DOCUMENT ME!
*/
- public float findScale()
+ protected 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
{
dim = height;
}
- return (float) ((dim * scalefactor) / (2 * maxwidth));
+ return (dim * scalefactor) / (2 * maxwidth);
}
/**
- * DOCUMENT ME!
+ * Computes and saves the position of the centre of the view
*/
- public void findCentre()
+ protected void findCentre()
{
- // Find centre coordinate
findWidth();
- centre[0] = (max[0] + min[0]) / 2;
- centre[1] = (max[1] + min[1]) / 2;
- centre[2] = (max[2] + min[2]) / 2;
+ float x = (max[0] + min[0]) / 2;
+ float y = (max[1] + min[1]) / 2;
+ float z = (max[2] + min[2]) / 2;
- // System.out.println("Centre x " + centre[0]);
- // System.out.println("Centre y " + centre[1]);
- // System.out.println("Centre z " + centre[2]);
+ centre = new Point(x, y, z);
}
/**
*
* @return DOCUMENT ME!
*/
+ @Override
public Dimension getPreferredSize()
{
if (prefsize != null)
*
* @return DOCUMENT ME!
*/
+ @Override
public Dimension getMinimumSize()
{
return getPreferredSize();
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g1)
{
if (points == null)
{
g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString("Calculating PCA....", 20, getHeight() / 2);
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getHeight() / 2);
}
else
{
drawBackground(ig, bgColour);
drawScene(ig);
- if (drawAxes == true)
+ if (drawAxes)
{
drawAxes(ig);
}
}
/**
- * DOCUMENT ME!
+ * Resets the view to initial state (no rotation)
+ */
+ public void resetView()
+ {
+ img = null;
+ resetAxes();
+ }
+
+ /**
+ * Draws lines for the x, y, z axes
*
* @param g
- * DOCUMENT ME!
*/
public void drawAxes(Graphics g)
{
g.setColor(Color.yellow);
- for (int i = 0; i < 3; i++)
+ for (int i = 0; i < DIMS; i++)
{
- g.drawLine(getWidth() / 2, getHeight() / 2, (int) ((axes[i][0]
- * scale * max[0]) + (getWidth() / 2)), (int) ((axes[i][1]
- * scale * max[1]) + (getHeight() / 2)));
+ g.drawLine(getWidth() / 2, getHeight() / 2,
+ (int) ((axisEndPoints[i].x * scale * max[0]) + (getWidth() / 2)),
+ (int) ((axisEndPoints[i].y * scale * max[1]) + (getHeight() / 2)));
}
}
/**
- * DOCUMENT ME!
+ * Fills the background with the specified colour
*
* @param g
- * DOCUMENT ME!
* @param col
- * DOCUMENT ME!
*/
public void drawBackground(Graphics g, Color col)
{
}
/**
- * DOCUMENT ME!
+ * Draws points (6x6 squares) for the sequences of the PCA, and labels
+ * (sequence names) if configured to do so. The sequence points colours are
+ * taken from the sequence ids in the alignment (converting black to white).
+ * Sequences 'at the back' (z-coordinate is negative) are shaded slightly
+ * darker to help give a 3-D sensation.
*
* @param g
- * DOCUMENT ME!
*/
public void drawScene(Graphics g1)
{
-
Graphics2D g = (Graphics2D) g1;
g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
- int halfwidth = getWidth() / 2;
- int halfheight = getHeight() / 2;
-
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)
- + halfheight;
- float z = sp.coord[1] - centre[2];
-
- if (av.getSequenceColour(sp.sequence) == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(av.getSequenceColour(sp.sequence));
- }
-
- if (av.getSelectionGroup() != null)
- {
- if (av.getSelectionGroup().getSequences(null)
- .contains(((SequencePoint) points.elementAt(i)).sequence))
- {
- g.setColor(Color.gray);
- }
- }
-
- if (z < 0)
- {
- g.setColor(g.getColor().darker());
- }
-
+ /*
+ * sequence point colour as sequence id, but
+ * gray if sequence is currently selected
+ */
+ SequencePoint sp = points.elementAt(i);
+ Color sequenceColour = getSequencePointColour(sp);
+ g.setColor(sequenceColour);
+
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+ int x = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+ int y = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
g.fillRect(x - 3, y - 3, 6, 6);
+
if (showLabels)
{
g.setColor(Color.red);
- g.drawString(
- ((SequencePoint) points.elementAt(i)).sequence.getName(),
- x - 3, y - 4);
+ g.drawString(sp.getSequence().getName(), x - 3, y - 4);
}
}
}
/**
- * DOCUMENT ME!
+ * Determines the colour to use when drawing a sequence point. The colour is
+ * taken from the sequence id, with black converted to white, and then
+ * graduated from darker (at the back) to brighter (at the front) based on the
+ * z-axis coordinate of the point.
*
- * @return DOCUMENT ME!
+ * @param sp
+ * @return
*/
- public Dimension minimumsize()
+ protected Color getSequencePointColour(SequencePoint sp)
{
- return prefsize;
- }
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ if (sequenceColour == Color.black)
+ {
+ sequenceColour = Color.white;
+ }
+ if (av.getSelectionGroup() != null)
+ {
+ if (av.getSelectionGroup().getSequences(null).contains(sequence))
+ {
+ sequenceColour = Color.gray;
+ }
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension preferredsize()
- {
- return prefsize;
+ /*
+ * graduate from front (brighter) to back (darker)
+ */
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, min[2],
+ max[2], sequenceColour);
+
+ return sequenceColour;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void keyTyped(KeyEvent evt)
{
}
- /**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
- */
+ @Override
public void keyReleased(KeyEvent evt)
{
}
/**
- * DOCUMENT ME!
+ * Responds to up or down arrow key by zooming in or out, respectively
*
* @param evt
- * DOCUMENT ME!
*/
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_UP)
}
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);
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)
{
int x = evt.getX();
int y = evt.getY();
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
+ mouseX = x;
+ mouseY = y;
startx = x;
starty = y;
rectx2 = -1;
recty2 = -1;
- SequenceI found = findPoint(x, y);
+ SequenceI found = findSequenceAtPoint(x, y);
if (found != null)
{
{
aps[a].av.setSelectionGroup(new SequenceGroup());
aps[a].av.getSelectionGroup().addOrRemove(found, true);
- aps[a].av.getSelectionGroup().setEndRes(
- aps[a].av.getAlignment().getWidth() - 1);
+ aps[a].av.getSelectionGroup()
+ .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
}
}
PaintRefresher.Refresh(this, av.getSequenceSetId());
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());
}
/**
- * DOCUMENT ME!
+ * Action handler for a mouse drag. Rotates the display around the X axis (for
+ * up/down mouse movement) and/or the Y axis (for left/right mouse movement).
*
* @param evt
- * DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
- mx = evt.getX();
- my = evt.getY();
+ int xPos = evt.getX();
+ int yPos = evt.getY();
+
+ if (xPos == mouseX && yPos == mouseY)
+ {
+ return;
+ }
// Check if this is a rectangle drawing drag
if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
}
else
{
- rotmat.setIdentity();
+ /*
+ * get the identity transformation...
+ */
+ RotatableMatrix rotmat = new RotatableMatrix();
+
+ /*
+ * rotate around the X axis for change in Y
+ * (mouse movement up/down); note we are equating a
+ * number of pixels with degrees of rotation here!
+ */
+ if (yPos != mouseY)
+ {
+ rotmat.rotate(yPos - mouseY, Axis.X);
+ }
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (xPos != mouseX)
+ {
+ rotmat.rotate(xPos - mouseX, Axis.Y);
+ }
+ /*
+ * apply the composite transformation to sequence points
+ */
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- sp.coord[0] -= centre[0];
- sp.coord[1] -= centre[1];
- sp.coord[2] -= centre[2];
+ SequencePoint sp = points.elementAt(i);
+ sp.translateBack(centre);
// Now apply the rotation matrix
sp.coord = rotmat.vectorMultiply(sp.coord);
// Now translate back again
- sp.coord[0] += centre[0];
- sp.coord[1] += centre[1];
- sp.coord[2] += centre[2];
+ sp.translate(centre);
}
- for (int i = 0; i < 3; i++)
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
{
- axes[i] = rotmat.vectorMultiply(axes[i]);
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
}
- omx = mx;
- omy = my;
+ mouseX = xPos;
+ mouseY = yPos;
paint(this.getGraphics());
}
}
/**
- * 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)
+ protected void rectSelect(int x1, int y1, int x2, int y2)
{
for (int i = 0; i < npoint; i++)
{
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale) + ((float) getWidth() / 2.0));
- int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) + ((float) getHeight() / 2.0));
+ SequencePoint sp = points.elementAt(i);
+ int tmp1 = (int) (((sp.coord.x - centre.x) * scale)
+ + (getWidth() / 2.0));
+ int tmp2 = (int) (((sp.coord.y - centre.y) * scale)
+ + (getHeight() / 2.0));
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
{
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)
+ protected SequenceI findSequenceAtPoint(int x, int y)
{
int halfwidth = getWidth() / 2;
int halfheight = getHeight() / 2;
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.x - centre.x) * scale)
+ halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ int py = (int) ((sp.coord.y - centre.y) * scale)
+ halfheight;
if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
{
found = i;
+ break;
}
}
if (found != -1)
{
- return ((SequencePoint) points.elementAt(found)).sequence;
+ return points.elementAt(found).getSequence();
}
else
{
}
}
+ /**
+ * Answers the panel the PCA is associated with (all panels for this alignment
+ * if 'associate with all panels' is selected).
+ *
+ * @return
+ */
AlignmentPanel[] getAssociatedPanels()
{
if (applyToAllViews)
}
else
{
- return new AlignmentPanel[]
- { ap };
+ return new AlignmentPanel[] { ap };
}
}
-
- /**
- *
- * @return x,y,z positions of point s (index into points) under current
- * transform.
- */
- public double[] getPointPosition(int s)
- {
- double pts[] = new double[3];
- float[] p = ((SequencePoint) points.elementAt(s)).coord;
- pts[0] = p[0];
- pts[1] = p[1];
- pts[2] = p[2];
- return pts;
- }
-
}
git://source.jalview.org / jalview.git / blobdiff