X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FRotatableCanvas.java;h=34f8ea5ab173bf3f7789968234e02b532ceac4e2;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=82207a22a0589bfa1fdf21ac295216776e256292;hpb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;p=jalview.git
diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 82207a2..34f8ea5 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,640 +1,679 @@
-/*
- * 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.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.math.*;
-import jalview.util.*;
-
-public class RotatableCanvas
- extends Panel 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;
- boolean showLabels = false;
-
- public RotatableCanvas(AlignViewport av)
- {
- this.av = av;
- }
-
- public void showLabels(boolean b)
- {
- showLabels = b;
- repaint();
- }
-
- public void setPoints(Vector points, int npoint)
- {
- this.points = points;
- this.npoint = npoint;
- this.av = av;
- 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;
- }
- }
- }
- }
-
- 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);
- }
-
- public float findScale()
- {
- int dim, width, height;
- if (getSize().width != 0)
- {
- width = getSize().width;
- height = getSize().height;
- }
- else
- {
- width = prefsize.width;
- height = prefsize.height;
- }
-
- if (width < height)
- {
- dim = width;
- }
- else
- {
- dim = height;
- }
-
- return (float) (dim * scalefactor / (2 * maxwidth));
- }
-
- 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]);
- }
-
- public Dimension getPreferredSize()
- {
- if (prefsize != null)
- {
- return prefsize;
- }
- else
- {
- return new Dimension(400, 400);
- }
- }
-
- public Dimension getMinimumSize()
- {
- return getPreferredSize();
- }
-
- public void paint(Graphics g)
- {
- if (points == null)
- {
- g.setFont(new Font("Verdana", Font.PLAIN, 18));
- g.drawString("Calculating PCA....", 20, getSize().height / 2);
- }
- else
- {
-
- //Only create the image at the beginning -
- if ( (img == null) || (prefsize.width != getSize().width) ||
- (prefsize.height != getSize().height))
- {
- prefsize.width = getSize().width;
- prefsize.height = getSize().height;
-
- scale = findScale();
-
- // System.out.println("New scale = " + scale);
- img = createImage(getSize().width, getSize().height);
- ig = img.getGraphics();
-
- }
-
- drawBackground(ig, Color.black);
- drawScene(ig);
- if (drawAxes == true)
- {
- drawAxes(ig);
- }
-
- g.drawImage(img, 0, 0, this);
- }
- }
-
- public void drawAxes(Graphics g)
- {
-
- g.setColor(Color.yellow);
- for (int i = 0; i < 3; i++)
- {
- g.drawLine(getSize().width / 2, getSize().height / 2,
- (int) (axes[i][0] * scale * max[0] + getSize().width / 2),
- (int) (axes[i][1] * scale * max[1] + getSize().height / 2));
- }
- }
-
- public void drawBackground(Graphics g, Color col)
- {
- g.setColor(col);
- g.fillRect(0, 0, prefsize.width, prefsize.height);
- }
-
- public void drawScene(Graphics g)
- {
- boolean darker = false;
-
- int halfwidth = getSize().width / 2;
- int halfheight = getSize().height / 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);
- 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);
-// }
- }
-
- public Dimension minimumsize()
- {
- return prefsize;
- }
-
- public Dimension preferredsize()
- {
- return prefsize;
- }
-
- public void keyTyped(KeyEvent evt)
- {}
-
- public void keyReleased(KeyEvent evt)
- {}
-
- 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();
- }
-
- 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();
- }
- }
-
- public void mouseClicked(MouseEvent evt)
- {}
-
- public void mouseEntered(MouseEvent evt)
- {}
-
- public void mouseExited(MouseEvent evt)
- {}
-
- public void mouseReleased(MouseEvent evt)
- {}
-
- 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);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
- PaintRefresher.Refresh(this, av.alignment);
- }
- else
- {
- av.setSelectionGroup(new SequenceGroup());
- av.getSelectionGroup().addOrRemove(found, true);
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
-
- }
- }
- repaint();
- }
-
- // private void fireSequenceSelectionEvent(Selection sel) {
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));
- //}
-
- public void mouseMoved(MouseEvent evt)
- {
- // SequenceI found = findPoint(evt.getX(), evt.getY());
- }
-
- 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());
- }
-
- }
-
- 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) getSize().width / 2.0);
- int tmp2 = (int) ( (sp.coord[1] - centre[1]) * scale +
- (float) getSize().height / 2.0);
-
- if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
- {
- if (av != null)
- {
- if (!av.getSelectionGroup().sequences.contains(sp.sequence))
- {
- av.getSelectionGroup().addSequence(sp.sequence, true);
- }
- }
- }
- }
- }
-
- public SequenceI findPoint(int x, int y)
- {
-
- int halfwidth = getSize().width / 2;
- int halfheight = getSize().height / 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.appletgui;
+
+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.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+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.util.List;
+
+public class RotatableCanvas extends Panel implements MouseListener,
+ MouseMotionListener, KeyListener, RotatableCanvasI
+{
+ private static final int DIMS = 3;
+
+ String tooltip;
+
+ int toolx;
+
+ int tooly;
+
+ // 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;
+
+ List 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;
+
+ boolean showLabels = false;
+
+ public RotatableCanvas(AlignmentViewport viewport)
+ {
+ this.av = viewport;
+ axisEndPoints = new Point[DIMS];
+ }
+
+ public void showLabels(boolean b)
+ {
+ showLabels = b;
+ repaint();
+ }
+
+ @Override
+ public void setPoints(List points, int npoint)
+ {
+ this.points = points;
+ this.npoint = npoint;
+ PaintRefresher.Register(this, av.getSequenceSetId());
+
+ prefsize = getPreferredSize();
+ orig = new Point[npoint];
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ orig[i] = sp.coord;
+ }
+
+ resetAxes();
+
+ 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(); }
+ */
+
+ /**
+ * 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)
+ */
+ public 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
+ */
+ public void findWidth()
+ {
+ max = new float[3];
+ min = new float[3];
+
+ 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]));
+ }
+
+ public float findScale()
+ {
+ int dim, w, height;
+ if (getSize().width != 0)
+ {
+ w = getSize().width;
+ height = getSize().height;
+ }
+ 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
+ */
+ public 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);
+ }
+
+ @Override
+ public Dimension getPreferredSize()
+ {
+ if (prefsize != null)
+ {
+ return prefsize;
+ }
+ else
+ {
+ return new Dimension(400, 400);
+ }
+ }
+
+ @Override
+ public Dimension getMinimumSize()
+ {
+ return getPreferredSize();
+ }
+
+ @Override
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ if (points == null)
+ {
+ g.setFont(new Font("Verdana", Font.PLAIN, 18));
+ g.drawString(
+ MessageManager.getString("label.calculating_pca") + "....",
+ 20, getSize().height / 2);
+ }
+ else
+ {
+
+ // Only create the image at the beginning -
+ if ((img == null) || (prefsize.width != getSize().width)
+ || (prefsize.height != getSize().height))
+ {
+ prefsize.width = getSize().width;
+ prefsize.height = getSize().height;
+
+ scale = findScale();
+
+ // System.out.println("New scale = " + scale);
+ img = createImage(getSize().width, getSize().height);
+ ig = img.getGraphics();
+
+ }
+
+ drawBackground(ig, Color.black);
+ drawScene(ig);
+ if (drawAxes)
+ {
+ drawAxes(ig);
+ }
+
+ if (tooltip != null)
+ {
+ ig.setColor(Color.red);
+ ig.drawString(tooltip, toolx, tooly);
+ }
+
+ g.drawImage(img, 0, 0, this);
+ }
+ }
+
+ public void drawAxes(Graphics g)
+ {
+
+ g.setColor(Color.yellow);
+ for (int i = 0; i < 3; i++)
+ {
+ g.drawLine(getSize().width / 2, getSize().height / 2,
+ (int) (axisEndPoints[i].x * scale * max[0] + getSize().width / 2),
+ (int) (axisEndPoints[i].y * scale * max[1] + getSize().height / 2));
+ }
+ }
+
+ public void drawBackground(Graphics g, Color col)
+ {
+ g.setColor(col);
+ g.fillRect(0, 0, prefsize.width, prefsize.height);
+ }
+
+ public void drawScene(Graphics g)
+ {
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ SequenceI sequence = sp.getSequence();
+ Color sequenceColour = av.getSequenceColour(sequence);
+ g.setColor(
+ sequenceColour == Color.black ? Color.white : sequenceColour);
+ if (av.getSelectionGroup() != null)
+ {
+ if (av.getSelectionGroup().getSequences(null)
+ .contains(sequence))
+ {
+ g.setColor(Color.gray);
+ }
+ }
+
+ if (sp.coord.z < centre.z)
+ {
+ g.setColor(g.getColor().darker());
+ }
+
+ int halfwidth = getSize().width / 2;
+ int halfheight = getSize().height / 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(sequence.getName(), x - 3, y - 4);
+ }
+ }
+ }
+
+ @Override
+ public void keyTyped(KeyEvent evt)
+ {
+ }
+
+ @Override
+ public void keyReleased(KeyEvent evt)
+ {
+ }
+
+ @Override
+ public void keyPressed(KeyEvent evt)
+ {
+ boolean shiftDown = evt.isShiftDown();
+ int keyCode = evt.getKeyCode();
+ if (keyCode == KeyEvent.VK_UP)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, -1f);
+ }
+ else
+ {
+ zoom(1.1f);
+ }
+ }
+ else if (keyCode == KeyEvent.VK_DOWN)
+ {
+ if (shiftDown)
+ {
+ rotate(0f, 1f);
+ }
+ else
+ {
+ zoom(0.9f);
+ }
+ }
+ 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')
+ {
+ System.err.println("DEBUG: Rectangle selection"); // log.debug
+ 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)
+ {
+ }
+
+ @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)
+ {
+ // TODO: applet PCA is not associatable with multi-panels - only parent
+ // view
+ if (av.getSelectionGroup() != null)
+ {
+ av.getSelectionGroup().addOrRemove(found, true);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
+ }
+ else
+ {
+ av.setSelectionGroup(new SequenceGroup());
+ av.getSelectionGroup().addOrRemove(found, true);
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
+
+ }
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ av.sendSelection();
+ }
+ repaint();
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ SequenceI found = findSequenceAtPoint(evt.getX(), evt.getY());
+ if (found == null)
+ {
+ tooltip = null;
+ }
+ else
+ {
+ tooltip = found.getName();
+ toolx = evt.getX();
+ tooly = evt.getY();
+ }
+ repaint();
+ }
+
+ @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;
+
+ rotate(xDelta, yDelta);
+ repaint();
+ }
+
+ public void rectSelect(int x1, int y1, int x2, int y2)
+ {
+ // boolean changedSel = false;
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ int tmp1 = (int) ((sp.coord.x - centre.x) * scale
+ + getSize().width / 2.0);
+ int tmp2 = (int) ((sp.coord.y - centre.y) * scale
+ + getSize().height / 2.0);
+
+ SequenceI sequence = sp.getSequence();
+ if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
+ {
+ if (av != null)
+ {
+ if (!av.getSelectionGroup().getSequences(null)
+ .contains(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
+ */
+ public SequenceI findSequenceAtPoint(int x, int y)
+ {
+ int halfwidth = getSize().width / 2;
+ int halfheight = getSize().height / 2;
+
+ int found = -1;
+
+ for (int i = 0; i < npoint; i++)
+ {
+
+ SequencePoint sp = points.get(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.get(found).getSequence();
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Resets the view to initial state (no rotation)
+ */
+ public void resetView()
+ {
+ img = null;
+ resetAxes();
+ }
+
+ @Override
+ public void zoom(float factor)
+ {
+ if (factor > 0f)
+ {
+ scalefactor *= factor;
+ }
+ scale = findScale();
+ }
+
+ @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
+ */
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = points.get(i);
+ sp.translate(-centre.x, -centre.y, -centre.z);
+
+ // Now apply the rotation matrix
+ sp.coord = rotmat.vectorMultiply(sp.coord);
+
+ // Now translate back again
+ sp.translate(centre.x, centre.y, centre.z);
+ }
+
+ /*
+ * rotate the x/y/z axis positions
+ */
+ for (int i = 0; i < DIMS; i++)
+ {
+ axisEndPoints[i] = rotmat.vectorMultiply(axisEndPoints[i]);
+ }
+ }
+
+}