X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRotatableCanvas.java;h=ef0b2aa0453802f9957457a8d19d31045391f783;hp=be1d3f5774280188fcd62696a6502d3a4d5025dc;hb=e3e0829f9fb59144a1ce6e3ae99f25dc2641ecb2;hpb=291f2e12795d442d6b0bf9e4fb9570b258194925
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index be1d3f5..ef0b2aa 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -1,771 +1,944 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 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
-{
- 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;
- AlignmentPanel ap;
- boolean showLabels = false;
- Color bgColour = Color.black;
- boolean applyToAllViews = false;
-
- // Controller controller;
- public RotatableCanvas(AlignmentPanel ap)
- {
- this.av = ap.av;
- this.ap = ap;
-
- addMouseWheelListener(new MouseWheelListener()
- {
- public void mouseWheelMoved(MouseWheelEvent e)
- {
- if (e.getWheelRotation() > 0)
- {
- scale = (float) (scale * 1.1);
- repaint();
- }
-
- else
- {
- scale = (float) (scale * 0.9);
- repaint();
- }
- }
- });
-
- }
-
- public void showLabels(boolean b)
- {
- showLabels = b;
- repaint();
- }
-
- public void setPoints(Vector points, int npoint)
- {
- this.points = points;
- this.npoint = npoint;
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
-
- 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();
-
- addMouseListener(this);
-
- addMouseMotionListener(this);
-
- }
-
- 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 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("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 == 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 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(false).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);
- if(showLabels)
- {
- g.setColor(Color.red);
- g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.
- 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);
- // }
- }
-
- /**
- * 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)
- {
- 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!
- *
- * @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)
- {
- 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.alignment.getWidth() - 1);
- }
- }
-
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- }
-
- 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)
- {
- 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().getSequences(false).contains(sp.sequence))
- {
- 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;
- }
- }
-
- AlignmentPanel[] getAssociatedPanels()
- {
- if (applyToAllViews)
- {
- return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
- }
- else
- return new AlignmentPanel[]
- { ap };
- }
-}
+/*
+ * 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 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.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
+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;
+
+/**
+ * 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, MouseWheelListener
+{
+ private static final float ZOOM_OUT = 0.9f;
+
+ private static final float ZOOM_IN = 1.1f;
+
+ /*
+ * pixels distance within which tooltip shows sequence name
+ */
+ private static final int NEARBY = 3;
+
+ private static final List AXES = Arrays.asList("x", "y", "z");
+
+ private static final Color AXIS_COLOUR = Color.yellow;
+
+ private static final int DIMS = 3;
+
+ boolean drawAxes = true;
+
+ int mouseX;
+
+ int mouseY;
+
+ Image img;
+
+ Graphics ig;
+
+ Dimension prefSize;
+
+ /*
+ * the min-max [x, y, z] values of sequence points when the points
+ * were set on the object, or when the view is reset;
+ * x and y ranges are not recomputed as points are rotated, as this
+ * would make scaling (zoom) unstable, but z ranges are (for correct
+ * graduated colour brightness based on z-coordinate)
+ */
+ float[] seqMin;
+
+ float[] seqMax;
+
+ /*
+ * a scale factor used in drawing; when equal to 1, the points span
+ * half the available width or height (whichever is less); increase this
+ * factor to zoom in, decrease it to zoom out
+ */
+ private float scaleFactor;
+
+ int npoint;
+
+ /*
+ * sequences and their (x, y, z) PCA dimension values
+ */
+ List sequencePoints;
+
+ /*
+ * x, y, z axis end points (PCA dimension values)
+ */
+ private Point[] axisEndPoints;
+
+ // fields for 'select rectangle' (JAL-1124)
+ // int rectx1;
+ // int recty1;
+ // int rectx2;
+ // int recty2;
+
+ AlignmentViewport av;
+
+ AlignmentPanel ap;
+
+ private boolean showLabels;
+
+ private Color bgColour;
+
+ private boolean applyToAllViews;
+
+ /**
+ * Constructor
+ *
+ * @param panel
+ */
+ public RotatableCanvas(AlignmentPanel panel)
+ {
+ this.av = panel.av;
+ this.ap = panel;
+ setAxisEndPoints(new Point[DIMS]);
+ setShowLabels(false);
+ setApplyToAllViews(false);
+ setBgColour(Color.BLACK);
+ resetAxes();
+
+ ToolTipManager.sharedInstance().registerComponent(this);
+
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(this);
+ }
+
+ /**
+ * Refreshes the display with labels shown (or not)
+ *
+ * @param show
+ */
+ public void showLabels(boolean show)
+ {
+ setShowLabels(show);
+ repaint();
+ }
+
+ @Override
+ public void setPoints(List points, int np)
+ {
+ this.sequencePoints = points;
+ this.npoint = np;
+ prefSize = getPreferredSize();
+
+ findWidths();
+
+ setScaleFactor(1f);
+ }
+
+ /**
+ * 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()
+ {
+ getAxisEndPoints()[0] = new Point(1f, 0f, 0f);
+ getAxisEndPoints()[1] = new Point(0f, 1f, 0f);
+ getAxisEndPoints()[2] = new Point(0f, 0f, 1f);
+ }
+
+ /**
+ * Computes and saves the min-max ranges of x/y/z positions of the sequence
+ * points
+ */
+ protected void findWidths()
+ {
+ float[] max = new float[DIMS];
+ float[] min = new float[DIMS];
+
+ max[0] = -Float.MAX_VALUE;
+ max[1] = -Float.MAX_VALUE;
+ max[2] = -Float.MAX_VALUE;
+
+ min[0] = Float.MAX_VALUE;
+ min[1] = Float.MAX_VALUE;
+ min[2] = Float.MAX_VALUE;
+
+ for (SequencePoint sp : sequencePoints)
+ {
+ 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);
+ }
+
+ seqMin = min;
+ seqMax = max;
+ }
+
+ /**
+ * Answers the preferred size if it has been set, else 400 x 400
+ *
+ * @return
+ */
+ @Override
+ public Dimension getPreferredSize()
+ {
+ if (prefSize != null)
+ {
+ return prefSize;
+ }
+ else
+ {
+ return new Dimension(400, 400);
+ }
+ }
+
+ /**
+ * Answers the preferred size
+ *
+ * @return
+ * @see RotatableCanvas#getPreferredSize()
+ */
+ @Override
+ public Dimension getMinimumSize()
+ {
+ return getPreferredSize();
+ }
+
+ /**
+ * Repaints the panel
+ *
+ * @param g
+ */
+ @Override
+ public void paintComponent(Graphics g1)
+ {
+
+ Graphics2D g = (Graphics2D) g1;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ if (sequencePoints == null)
+ {
+ g.setFont(new Font("Verdana", Font.PLAIN, 18));
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getHeight() / 2);
+ }
+ else
+ {
+ /*
+ * create the image at the beginning or after a resize
+ */
+ boolean resized = prefSize.width != getWidth()
+ || prefSize.height != getHeight();
+ if (img == null || resized)
+ {
+ prefSize.width = getWidth();
+ prefSize.height = getHeight();
+
+ img = createImage(getWidth(), getHeight());
+ ig = img.getGraphics();
+ }
+
+ drawBackground(ig);
+ drawScene(ig);
+
+ if (drawAxes)
+ {
+ drawAxes(ig);
+ }
+
+ g.drawImage(img, 0, 0, this);
+ }
+ }
+
+ /**
+ * Resets the rotation and choice of axes to the initial state (without change
+ * of scale factor)
+ */
+ public void resetView()
+ {
+ img = null;
+ findWidths();
+ resetAxes();
+ repaint();
+ }
+
+ /**
+ * Draws lines for the x, y, z axes
+ *
+ * @param g
+ */
+ public void drawAxes(Graphics g)
+ {
+ g.setColor(AXIS_COLOUR);
+
+ int midX = getWidth() / 2;
+ int midY = getHeight() / 2;
+ // float maxWidth = Math.max(Math.abs(seqMax[0] - seqMin[0]),
+ // Math.abs(seqMax[1] - seqMin[1]));
+ int pix = Math.min(getWidth(), getHeight());
+ float scaleBy = pix * getScaleFactor() / (2f);
+
+ for (int i = 0; i < DIMS; i++)
+ {
+ g.drawLine(midX, midY,
+ midX + (int) (getAxisEndPoints()[i].x * scaleBy * 0.25),
+ midY + (int) (getAxisEndPoints()[i].y * scaleBy * 0.25));
+ }
+ }
+
+ /**
+ * Fills the background with the currently configured background colour
+ *
+ * @param g
+ */
+ public void drawBackground(Graphics g)
+ {
+ g.setColor(getBgColour());
+ 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);
+ int pix = Math.min(getWidth(), getHeight());
+ float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+ float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+ float maxWidth = Math.max(xWidth, yWidth);
+ float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
+
+ float[] centre = getCentre();
+
+ for (int i = 0; i < npoint; i++)
+ {
+ /*
+ * sequence point colour as sequence id, but
+ * gray if sequence is currently selected
+ */
+ SequencePoint sp = sequencePoints.get(i);
+ Color sequenceColour = getSequencePointColour(sp);
+ g.setColor(sequenceColour);
+
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+ int x = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
+ int y = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
+ g.fillRect(x - 3, y - 3, 6, 6);
+
+ if (isShowLabels())
+ {
+ g.setColor(Color.red);
+ g.drawString(sp.getSequence().getName(), x - 3, y - 4);
+ }
+ }
+ if (isShowLabels())
+ {
+ g.setColor(AXIS_COLOUR);
+ int midX = getWidth() / 2;
+ int midY = getHeight() / 2;
+ Iterator axes = AXES.iterator();
+ for (Point p : getAxisEndPoints())
+ {
+ int x = midX + (int) (p.x * scaleBy * seqMax[0]);
+ int y = midY + (int) (p.y * scaleBy * seqMax[1]);
+ g.drawString(axes.next(), 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 brighter for point in front of centre, darker if behind centre
+ */
+ float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+ if (sp.coord.z > zCentre)
+ {
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, 0,
+ sequenceColour, seqMax[2], sequenceColour.brighter());
+ }
+ else if (sp.coord.z < zCentre)
+ {
+ sequenceColour = ColorUtils.getGraduatedColour(sp.coord.z, seqMin[2],
+ sequenceColour.darker(), 0, 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)
+ {
+ int keyCode = evt.getKeyCode();
+ boolean shiftDown = evt.isShiftDown();
+
+ if (keyCode == KeyEvent.VK_UP)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(ZOOM_IN);
+ }
+ }
+ else if (keyCode == KeyEvent.VK_DOWN)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(ZOOM_OUT);
+ }
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_LEFT)
+ {
+ rotate(1f, 0f);
+ }
+ else if (shiftDown && keyCode == KeyEvent.VK_RIGHT)
+ {
+ rotate(-1f, 0f);
+ }
+ else if (evt.getKeyChar() == 's')
+ {
+ // Cache.warn("DEBUG: Rectangle selection");
+ // todo not yet enabled as rectx2, recty2 are always -1
+ // need to set them in mouseDragged; JAL-1124
+ // if ((rectx2 != -1) && (recty2 != -1))
+ // {
+ // rectSelect(rectx1, recty1, rectx2, recty2);
+ // }
+ }
+
+ repaint();
+ }
+
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ setScaleFactor(getScaleFactor() * factor);
+ }
+ }
+
+ @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;
+
+ // 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;
+ }
+
+ int xDelta = xPos - mouseX;
+ int yDelta = yPos - mouseY;
+
+ // Check if this is a rectangle drawing drag
+ if ((evt.getModifiersEx() & InputEvent.BUTTON2_DOWN_MASK) != 0)
+ {
+ // rectx2 = evt.getX();
+ // recty2 = evt.getY();
+ }
+ else
+ {
+ rotate(xDelta, yDelta);
+
+ mouseX = xPos;
+ mouseY = yPos;
+
+ // findWidths();
+
+ repaint();
+ }
+ }
+
+ @Override
+ public void rotate(float x, float y)
+ {
+ if (x == 0f && y == 0f)
+ {
+ return;
+ }
+
+ /*
+ * 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 (y != 0)
+ {
+ rotmat.rotate(y, Axis.X);
+ }
+
+ /*
+ * rotate around the Y axis for change in X
+ * (mouse movement left/right)
+ */
+ if (x != 0)
+ {
+ rotmat.rotate(x, Axis.Y);
+ }
+
+ /*
+ * apply the composite transformation to sequence points;
+ * update z min-max range (affects colour graduation), but not
+ * x or y min-max (as this would affect axis scaling)
+ */
+ float[] centre = getCentre();
+ float zMin = Float.MAX_VALUE;
+ float zMax = -Float.MAX_VALUE;
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = sequencePoints.get(i);
+ sp.translate(-centre[0], -centre[1], -centre[2]);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre[0], centre[1], centre[2]);
+
+ zMin = Math.min(zMin, sp.coord.z);
+ zMax = Math.max(zMax, sp.coord.z);
+ }
+
+ seqMin[2] = zMin;
+ seqMax[2] = zMax;
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ getAxisEndPoints()[i] = rotmat.vectorMultiply(getAxisEndPoints()[i]);
+ }
+ }
+
+ /**
+ * Answers the x/y/z coordinates that are midway between the maximum and
+ * minimum sequence point values
+ *
+ * @return
+ */
+ private float[] getCentre()
+ {
+ float xCentre = (seqMin[0] + seqMax[0]) / 2f;
+ float yCentre = (seqMin[1] + seqMax[1]) / 2f;
+ float zCentre = (seqMin[2] + seqMax[2]) / 2f;
+
+ return new float[] { xCentre, yCentre, zCentre };
+ }
+
+ /**
+ * 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)
+ {
+ float[] centre = getCentre();
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = sequencePoints.get(i);
+ int tmp1 = (int) (((sp.coord.x - centre[0]) * getScaleFactor())
+ + (getWidth() / 2.0));
+ int tmp2 = (int) (((sp.coord.y - centre[1]) * getScaleFactor())
+ + (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;
+ int pix = Math.min(getWidth(), getHeight());
+ float xWidth = Math.abs(seqMax[0] - seqMin[0]);
+ float yWidth = Math.abs(seqMax[1] - seqMin[1]);
+ float maxWidth = Math.max(xWidth, yWidth);
+ float scaleBy = pix * getScaleFactor() / (2f * maxWidth);
+
+ float[] centre = getCentre();
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = sequencePoints.get(i);
+ int px = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
+ int py = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
+
+ if ((Math.abs(px - x) < NEARBY) && (Math.abs(py - y) < NEARBY))
+ {
+ found = i;
+ break;
+ }
+ }
+
+ if (found != -1)
+ {
+ return sequencePoints.get(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 (isApplyToAllViews())
+ {
+ return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+ }
+ else
+ {
+ return new AlignmentPanel[] { ap };
+ }
+ }
+
+ public Color getBackgroundColour()
+ {
+ return getBgColour();
+ }
+
+ /**
+ * Zooms in or out in response to mouse wheel movement
+ */
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ zoom(ZOOM_IN);
+ repaint();
+ }
+ else if (wheelRotation < 0)
+ {
+ zoom(ZOOM_OUT);
+ repaint();
+ }
+ }
+
+ /**
+ * Answers the sequence point minimum [x, y, z] values. Note these are derived
+ * when sequence points are set, but x and y values are not updated on
+ * rotation (because this would result in changes to scaling).
+ *
+ * @return
+ */
+ public float[] getSeqMin()
+ {
+ return seqMin;
+ }
+
+ /**
+ * Answers the sequence point maximum [x, y, z] values. Note these are derived
+ * when sequence points are set, but x and y values are not updated on
+ * rotation (because this would result in changes to scaling).
+ *
+ * @return
+ */
+ public float[] getSeqMax()
+ {
+ return seqMax;
+ }
+
+ /**
+ * Sets the minimum and maximum [x, y, z] positions for sequence points. For
+ * use when restoring a saved PCA from state data.
+ *
+ * @param min
+ * @param max
+ */
+ public void setSeqMinMax(float[] min, float[] max)
+ {
+ seqMin = min;
+ seqMax = max;
+ }
+
+ public float getScaleFactor()
+ {
+ return scaleFactor;
+ }
+
+ public void setScaleFactor(float scaleFactor)
+ {
+ this.scaleFactor = scaleFactor;
+ }
+
+ public boolean isShowLabels()
+ {
+ return showLabels;
+ }
+
+ public void setShowLabels(boolean showLabels)
+ {
+ this.showLabels = showLabels;
+ }
+
+ public boolean isApplyToAllViews()
+ {
+ return applyToAllViews;
+ }
+
+ public void setApplyToAllViews(boolean applyToAllViews)
+ {
+ this.applyToAllViews = applyToAllViews;
+ }
+
+ public Point[] getAxisEndPoints()
+ {
+ return axisEndPoints;
+ }
+
+ public void setAxisEndPoints(Point[] axisEndPoints)
+ {
+ this.axisEndPoints = axisEndPoints;
+ }
+
+ public Color getBgColour()
+ {
+ return bgColour;
+ }
+
+ public void setBgColour(Color bgColour)
+ {
+ this.bgColour = bgColour;
+ }
+}