X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=615b4034e340caf928e8f338bb58db18994e4c99;hb=37651a9d177de05ff938276071c16ba95ac44c73;hp=fbbf269ea8948444d720b44ae3cf47a6144f1d0d;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index fbbf269..615b403 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,762 +1,799 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import jalview.math.*;
-
-import jalview.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import java.util.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class RotatableCanvas extends JPanel implements MouseListener,
- MouseMotionListener, KeyListener
-//RubberbandListener,
-//SequenceSelectionListener
-{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-
- //RubberbandRectangle rubberband;
- boolean drawAxes = true;
- int omx = 0;
- int mx = 0;
- int omy = 0;
- int my = 0;
- Image img;
- Graphics ig;
- Dimension prefsize;
- float[] centre = new float[3];
- float[] width = new float[3];
- float[] max = new float[3];
- float[] min = new float[3];
- float maxwidth;
- float scale;
- int npoint;
- Vector points;
- float[][] orig;
- float[][] axes;
- int startx;
- int starty;
- int lastx;
- int lasty;
- int rectx1;
- int recty1;
- int rectx2;
- int recty2;
- float scalefactor = 1;
- AlignViewport av;
-
- // Controller controller;
- public RotatableCanvas(AlignViewport av, Vector points, int npoint)
- {
- this.points = points;
- this.npoint = npoint;
- this.av = av;
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- PaintRefresher.Register(this, av.alignment);
-
- prefsize = getPreferredSize();
- orig = new float[npoint][3];
-
- 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);
- }
- }
- }
-
- axes = new float[3][3];
- initAxes();
-
- findCentre();
- findWidth();
-
- scale = findScale();
-
- // System.out.println("Scale factor = " + scale);
- addMouseListener(this);
- addKeyListener(this);
-
- // if (getParent() != null) {
- // getParent().addKeyListener(this);
- //}
- addMouseMotionListener(this);
-
- // Add rubberband
- // rubberband = new RubberbandRectangle(this);
- // rubberband.setActive(true);
- // rubberband.addListener(this);
- }
-
- /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {
- redrawneeded = true;
- repaint();
- return true;
- }
-
- public void removeNotify() {
- controller.removeListener(this);
- super.removeNotify();
- }*/
- public void initAxes()
- {
- 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;
- }
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void findWidth()
- {
- max = new float[3];
- min = new float[3];
-
- max[0] = (float) -1e30;
- max[1] = (float) -1e30;
- max[2] = (float) -1e30;
-
- min[0] = (float) 1e30;
- min[1] = (float) 1e30;
- min[2] = (float) 1e30;
-
- for (int i = 0; i < 3; i++)
- {
- 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];
- }
- }
- }
-
- // 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);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public float findScale()
- {
- int dim;
- int width;
- int height;
-
- if (getWidth() != 0)
- {
- width = getWidth();
- height = getHeight();
- }
- else
- {
- width = prefsize.width;
- height = prefsize.height;
- }
-
- if (width < height)
- {
- dim = width;
- }
- else
- {
- dim = height;
- }
-
- return (float) ((dim * scalefactor) / (2 * maxwidth));
- }
-
- /**
- * DOCUMENT ME!
- */
- public 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;
-
- // System.out.println("Centre x " + centre[0]);
- //System.out.println("Centre y " + centre[1]);
- //System.out.println("Centre z " + centre[2]);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension getPreferredSize()
- {
- if (prefsize != null)
- {
- return prefsize;
- }
- else
- {
- return new Dimension(400, 400);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension getMinimumSize()
- {
- return getPreferredSize();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
- {
- //Only create the image at the beginning -
- if ((img == null) || (prefsize.width != getWidth()) ||
- (prefsize.height != getHeight()))
- {
- prefsize.width = getWidth();
- prefsize.height = getHeight();
-
- scale = findScale();
-
- // System.out.println("New scale = " + scale);
- img = createImage(getWidth(), getHeight());
- ig = img.getGraphics();
- }
-
- drawBackground(ig, Color.black);
- drawScene(ig);
-
- if (drawAxes == true)
- {
- drawAxes(ig);
- }
-
- g.drawImage(img, 0, 0, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void drawAxes(Graphics g)
- {
- g.setColor(Color.yellow);
-
- for (int i = 0; i < 3; 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)));
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param col DOCUMENT ME!
- */
- public void drawBackground(Graphics g, Color col)
- {
- g.setColor(col);
- g.fillRect(0, 0, prefsize.width, prefsize.height);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void drawScene(Graphics g)
- {
- boolean darker = false;
-
- 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 (sp.sequence.getColor() == Color.black)
- {
- g.setColor(Color.white);
- }
- else
- {
- g.setColor(sp.sequence.getColor());
- }
-
- if (av.getSelectionGroup() != null)
- {
- if (av.getSelectionGroup().sequences.contains(
- ((SequencePoint) points.elementAt(i)).sequence))
- {
- g.setColor(Color.gray);
- }
- }
-
- if (z < 0)
- {
- g.setColor(g.getColor().darker());
- }
-
- g.fillRect(x - 3, y - 3, 6, 6);
- g.setColor(Color.red);
- }
-
- // //Now the rectangle
- // if (rectx2 != -1 && recty2 != -1) {
- // g.setColor(Color.white);
- //
- // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
- // }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void keyTyped(KeyEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void keyReleased(KeyEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void keyPressed(KeyEvent evt)
- {
- requestFocus();
-
- if (evt.getKeyCode() == KeyEvent.VK_UP)
- {
- scalefactor = (float) (scalefactor * 1.1);
- scale = findScale();
- }
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
- {
- scalefactor = (float) (scalefactor * 0.9);
- scale = findScale();
- }
- else if (evt.getKeyChar() == 's')
- {
- System.err.println("DEBUG: Rectangle selection"); // log.debug
-
- if ((rectx2 != -1) && (recty2 != -1))
- {
- rectSelect(rectx1, recty1, rectx2, recty2);
- }
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- */
- public void printPoints()
- {
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- Format.print(System.out, "%5d ", i);
-
- for (int j = 0; j < 3; j++)
- {
- Format.print(System.out, "%13.3f ", sp.coord[j]);
- }
-
- System.out.println();
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
- {
- int x = evt.getX();
- int y = evt.getY();
-
- mx = x;
- my = y;
-
- omx = mx;
- omy = my;
-
- startx = x;
- starty = y;
-
- rectx1 = x;
- recty1 = y;
-
- rectx2 = -1;
- recty2 = -1;
-
- SequenceI found = findPoint(x, y);
-
- if (found != null)
- {
- if (av.getSelectionGroup() != null)
- {
- av.getSelectionGroup().addOrRemove(found, true);
- PaintRefresher.Refresh(this, av.alignment);
- }
- else
- {
- av.setSelectionGroup(new SequenceGroup());
- av.getSelectionGroup().addOrRemove(found, true);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth());
- }
- }
-
- repaint();
- }
-
- // private void fireSequenceSelectionEvent(Selection sel) {
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
- //}
- public void mouseMoved(MouseEvent evt)
- {
- SequenceI found = findPoint(evt.getX(), evt.getY());
-
- if (found != null)
- {
- this.setToolTipText(found.getName());
- }
- else
- {
- this.setToolTipText(null);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
- {
- mx = evt.getX();
- my = evt.getY();
-
- //Check if this is a rectangle drawing drag
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
- {
- // rectx2 = evt.getX();
- // recty2 = evt.getY();
- }
- else
- {
- rotmat.setIdentity();
-
- rotmat.rotate((float) (my - omy), 'x');
- rotmat.rotate((float) (mx - omx), 'y');
-
- 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];
-
- //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];
- }
-
- for (int i = 0; i < 3; i++)
- {
- axes[i] = rotmat.vectorMultiply(axes[i]);
- }
-
- omx = mx;
- omy = my;
-
- paint(this.getGraphics());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @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)
- {
- boolean changedSel = false;
-
- 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));
-
- if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
- {
- if (av != null)
- {
- if (!av.getSelectionGroup().sequences.contains(sp.sequence))
- {
- changedSel = true;
- av.getSelectionGroup().addSequence(sp.sequence, true);
- }
- }
- }
- }
-
- // if (changedSel) {
- // fireSequenceSelectionEvent(av.getSelection());
- // }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceI findPoint(int x, int y)
- {
- int halfwidth = getWidth() / 2;
- int halfheight = getHeight() / 2;
-
- int found = -1;
-
- for (int i = 0; i < npoint; i++)
- {
- SequencePoint sp = (SequencePoint) points.elementAt(i);
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) +
- halfwidth;
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) +
- halfheight;
-
- if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
- {
- found = i;
- }
- }
-
- if (found != -1)
- {
- return ((SequencePoint) points.elementAt(found)).sequence;
- }
- else
- {
- return null;
- }
- }
-
- /* public boolean handleRubberbandEvent(RubberbandEvent evt) {
- System.out.println("Rubberband handler called in RotatableCanvas with " +
- evt.getBounds());
-
- Rubberband rb = (Rubberband)evt.getSource();
-
- // Clear the current selection (instance variable)
- //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {
- // clearSelection();
- //}
-
- if (rb.getComponent() == this) {
- Rectangle bounds = evt.getBounds();
- rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);
- }
-
- redrawneeded = true;
- paint(this.getGraphics());
-
- return true;
- }*/
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.RotatableCanvasI;
+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;
+
+/**
+ * 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
+{
+ private static final int DIMS = 3;
+
+ // RubberbandRectangle rubberband;
+ boolean drawAxes = true;
+
+ int mouseX = 0;
+
+ int mouseY = 0;
+
+ Image img;
+
+ Graphics ig;
+
+ Dimension prefsize;
+
+ Point centre;
+
+ float[] width = new float[DIMS];
+
+ float[] max = new float[DIMS];
+
+ float[] min = new float[DIMS];
+
+ float maxwidth;
+
+ float scale;
+
+ int npoint;
+
+ Vector points;
+
+ Point[] orig;
+
+ Point[] axisEndPoints;
+
+ int startx;
+
+ int starty;
+
+ int lastx;
+
+ int lasty;
+
+ int rectx1;
+
+ int recty1;
+
+ int rectx2;
+
+ int recty2;
+
+ float scalefactor = 1;
+
+ AlignmentViewport av;
+
+ AlignmentPanel ap;
+
+ boolean showLabels = false;
+
+ Color bgColour = Color.black;
+
+ boolean applyToAllViews = false;
+
+ boolean first = true;
+
+ /**
+ * Constructor
+ *
+ * @param panel
+ */
+ public RotatableCanvas(AlignmentPanel panel)
+ {
+ this.av = panel.av;
+ this.ap = panel;
+ axisEndPoints = new Point[DIMS];
+
+ addMouseWheelListener(new MouseWheelListener()
+ {
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ /*
+ * zoom in
+ */
+ scale = (float) (scale * 1.1);
+ repaint();
+ }
+ else if (wheelRotation < 0)
+ {
+ /*
+ * zoom out
+ */
+ scale = (float) (scale * 0.9);
+ repaint();
+ }
+ }
+ });
+
+ }
+
+ /**
+ * Refreshes the display with labels shown (or not)
+ *
+ * @param show
+ */
+ public void showLabels(boolean show)
+ {
+ showLabels = show;
+ repaint();
+ }
+
+ @Override
+ public void setPoints(Vector points, int npoint)
+ {
+ this.points = points;
+ this.npoint = npoint;
+ if (first)
+ {
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ }
+ prefsize = getPreferredSize();
+ orig = new Point[npoint];
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.elementAt(i);
+ orig[i] = sp.coord;
+ }
+
+ resetAxes();
+
+ findCentre();
+ findWidth();
+
+ scale = findScale();
+ if (first)
+ {
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ }
+ first = false;
+ }
+
+ /**
+ * 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()
+ {
+ axisEndPoints[0] = new Point(1f, 0f, 0f);
+ axisEndPoints[1] = new Point(0f, 1f, 0f);
+ axisEndPoints[2] = new Point(0f, 0f, 1f);
+ }
+
+ /**
+ * 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
+ */
+ protected void findWidth()
+ {
+ max = new float[DIMS];
+ min = new float[DIMS];
+
+ max[0] = Float.MIN_VALUE;
+ max[1] = Float.MIN_VALUE;
+ max[2] = Float.MIN_VALUE;
+
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
+
+ for (SequencePoint sp : points)
+ {
+ 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);
+ }
+
+ 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 = Math.max(width[0], Math.max(width[1], width[2]));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ protected float findScale()
+ {
+ int dim;
+ int w;
+ int height;
+
+ if (getWidth() != 0)
+ {
+ w = getWidth();
+ height = getHeight();
+ }
+ else
+ {
+ w = prefsize.width;
+ height = prefsize.height;
+ }
+
+ if (w < height)
+ {
+ dim = w;
+ }
+ else
+ {
+ dim = height;
+ }
+
+ return (dim * scalefactor) / (2 * maxwidth);
+ }
+
+ /**
+ * Computes and saves the position of the centre of the view
+ */
+ protected void findCentre()
+ {
+ findWidth();
+
+ float x = (max[0] + min[0]) / 2;
+ float y = (max[1] + min[1]) / 2;
+ float z = (max[2] + min[2]) / 2;
+
+ centre = new Point(x, y, z);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Dimension getPreferredSize()
+ {
+ if (prefsize != null)
+ {
+ return prefsize;
+ }
+ else
+ {
+ return new Dimension(400, 400);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public Dimension getMinimumSize()
+ {
+ return getPreferredSize();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g1)
+ {
+
+ Graphics2D g = (Graphics2D) g1;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ if (points == null)
+ {
+ g.setFont(new Font("Verdana", Font.PLAIN, 18));
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getHeight() / 2);
+ }
+ else
+ {
+ // Only create the image at the beginning -
+ if ((img == null) || (prefsize.width != getWidth())
+ || (prefsize.height != getHeight()))
+ {
+ prefsize.width = getWidth();
+ prefsize.height = getHeight();
+
+ scale = findScale();
+
+ // System.out.println("New scale = " + scale);
+ img = createImage(getWidth(), getHeight());
+ ig = img.getGraphics();
+ }
+
+ drawBackground(ig, bgColour);
+ drawScene(ig);
+
+ if (drawAxes)
+ {
+ drawAxes(ig);
+ }
+
+ g.drawImage(img, 0, 0, this);
+ }
+ }
+
+ /**
+ * Resets the view to initial state (no rotation)
+ */
+ public void resetView()
+ {
+ img = null;
+ resetAxes();
+ }
+
+ /**
+ * Draws lines for the x, y, z axes
+ *
+ * @param g
+ */
+ public void drawAxes(Graphics g)
+ {
+
+ g.setColor(Color.yellow);
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ g.drawLine(getWidth() / 2, getHeight() / 2,
+ (int) ((axisEndPoints[i].x * scale * max[0]) + (getWidth() / 2)),
+ (int) ((axisEndPoints[i].y * scale * max[1]) + (getHeight() / 2)));
+ }
+ }
+
+ /**
+ * Fills the background with the specified colour
+ *
+ * @param g
+ * @param col
+ */
+ public void drawBackground(Graphics g, Color col)
+ {
+ g.setColor(col);
+ g.fillRect(0, 0, prefsize.width, prefsize.height);
+ }
+
+ /**
+ * 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
+ */
+ public void drawScene(Graphics g1)
+ {
+ Graphics2D g = (Graphics2D) g1;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ for (int i = 0; i < npoint; i++)
+ {
+ /*
+ * 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(sp.getSequence().getName(), x - 3, y - 4);
+ }
+ }
+
+ // //Now the rectangle
+ // if (rectx2 != -1 && recty2 != -1) {
+ // g.setColor(Color.white);
+ //
+ // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+ // }
+ }
+
+ /**
+ * 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.
+ *
+ * @param sp
+ * @return
+ */
+ protected Color getSequencePointColour(SequencePoint sp)
+ {
+ 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;
+ }
+ }
+
+ /*
+ * graduate from front (brighter) to back (darker)
+ */
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, min[2],
+ max[2], sequenceColour);
+
+ return sequenceColour;
+ }
+
+ @Override
+ public void keyTyped(KeyEvent evt)
+ {
+ }
+
+ @Override
+ public void keyReleased(KeyEvent evt)
+ {
+ }
+
+ /**
+ * Responds to up or down arrow key by zooming in or out, respectively
+ *
+ * @param evt
+ */
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_UP)
+ {
+ scalefactor = (float) (scalefactor * 1.1);
+ scale = findScale();
+ }
+ else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ {
+ scalefactor = (float) (scalefactor * 0.9);
+ scale = findScale();
+ }
+ else if (evt.getKeyChar() == 's')
+ {
+ // 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();
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ }
+
+ /**
+ * 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();
+
+ mouseX = x;
+ mouseY = y;
+
+ startx = x;
+ starty = y;
+
+ rectx1 = x;
+ recty1 = y;
+
+ rectx2 = -1;
+ recty2 = -1;
+
+ SequenceI found = findSequenceAtPoint(x, y);
+
+ if (found != null)
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+
+ for (int a = 0; a < aps.length; a++)
+ {
+ if (aps[a].av.getSelectionGroup() != null)
+ {
+ aps[a].av.getSelectionGroup().addOrRemove(found, true);
+ }
+ else
+ {
+ aps[a].av.setSelectionGroup(new SequenceGroup());
+ aps[a].av.getSelectionGroup().addOrRemove(found, true);
+ aps[a].av.getSelectionGroup()
+ .setEndRes(aps[a].av.getAlignment().getWidth() - 1);
+ }
+ }
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // canonical selection is sent to other listeners
+ av.sendSelection();
+ }
+
+ repaint();
+ }
+
+ /**
+ * 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 = findSequenceAtPoint(evt.getX(), evt.getY());
+
+ this.setToolTipText(found == null ? null : found.getName());
+ }
+
+ /**
+ * 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
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ 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)
+ {
+ // rectx2 = evt.getX();
+ // recty2 = evt.getY();
+ }
+ else
+ {
+ /*
+ * 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);
+ }
+
+ /*
+ * 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 = points.elementAt(i);
+ sp.translateBack(centre);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre);
+ }
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
+ }
+
+ mouseX = xPos;
+ mouseY = yPos;
+
+ paint(this.getGraphics());
+ }
+ }
+
+ /**
+ * 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 y1
+ * @param x2
+ * @param y2
+ */
+ protected void rectSelect(int x1, int y1, int x2, int y2)
+ {
+ for (int i = 0; i < npoint; i++)
+ {
+ 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(sequence))
+ {
+ av.getSelectionGroup().addSequence(sequence, true);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 y
+ *
+ * @return
+ */
+ protected SequenceI findSequenceAtPoint(int x, int y)
+ {
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+
+ int found = -1;
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.elementAt(i);
+ int px = (int) ((sp.coord.x - centre.x) * scale)
+ + halfwidth;
+ 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 points.elementAt(found).getSequence();
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ /**
+ * 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)
+ {
+ return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+ }
+ else
+ {
+ return new AlignmentPanel[] { ap };
+ }
+ }
+}