-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.math.*;\r
-import jalview.util.*;\r
-\r
-public class RotatableCanvas\r
- extends Panel implements MouseListener,\r
- MouseMotionListener,\r
- KeyListener\r
-{\r
- RotatableMatrix idmat = new RotatableMatrix(3, 3);\r
- RotatableMatrix objmat = new RotatableMatrix(3, 3);\r
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);\r
- String tooltip;\r
- int toolx, tooly;\r
-\r
- //RubberbandRectangle rubberband;\r
-\r
- boolean drawAxes = true;\r
-\r
- int omx = 0;\r
- int mx = 0;\r
- int omy = 0;\r
- int my = 0;\r
-\r
- Image img;\r
- Graphics ig;\r
-\r
- Dimension prefsize;\r
-\r
- float centre[] = new float[3];\r
- float width[] = new float[3];\r
-\r
- float max[] = new float[3];\r
- float min[] = new float[3];\r
-\r
- float maxwidth;\r
- float scale;\r
-\r
- int npoint;\r
-\r
- Vector points;\r
- float[][] orig;\r
- float[][] axes;\r
-\r
- int startx;\r
- int starty;\r
-\r
- int lastx;\r
- int lasty;\r
-\r
- int rectx1;\r
- int recty1;\r
- int rectx2;\r
- int recty2;\r
-\r
- float scalefactor = 1;\r
-\r
- AlignViewport av;\r
- boolean showLabels = false;\r
-\r
- public RotatableCanvas(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void showLabels(boolean b)\r
- {\r
- showLabels = b;\r
- repaint();\r
- }\r
-\r
- public void setPoints(Vector points, int npoint)\r
- {\r
- this.points = points;\r
- this.npoint = npoint;\r
- PaintRefresher.Register(this, av.getSequenceSetId());\r
-\r
- prefsize = getPreferredSize();\r
- orig = new float[npoint][3];\r
-\r
- for (int i = 0; i < npoint; i++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- for (int j = 0; j < 3; j++)\r
- {\r
- orig[i][j] = sp.coord[j];\r
- }\r
- }\r
- //Initialize the matrices to identity\r
-\r
- for (int i = 0; i < 3; i++)\r
- {\r
- for (int j = 0; j < 3; j++)\r
- {\r
- if (i != j)\r
- {\r
- idmat.addElement(i, j, 0);\r
- objmat.addElement(i, j, 0);\r
- rotmat.addElement(i, j, 0);\r
- }\r
- else\r
- {\r
- idmat.addElement(i, j, 0);\r
- objmat.addElement(i, j, 0);\r
- rotmat.addElement(i, j, 0);\r
- }\r
- }\r
- }\r
-\r
- axes = new float[3][3];\r
- initAxes();\r
-\r
- findCentre();\r
- findWidth();\r
-\r
- scale = findScale();\r
-\r
- // System.out.println("Scale factor = " + scale);\r
-\r
- addMouseListener(this);\r
- addKeyListener(this);\r
- // if (getParent() != null) {\r
- // getParent().addKeyListener(this);\r
- //}\r
- addMouseMotionListener(this);\r
-\r
- // Add rubberband\r
- // rubberband = new RubberbandRectangle(this);\r
- // rubberband.setActive(true);\r
- // rubberband.addListener(this);\r
- }\r
-\r
- /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {\r
- redrawneeded = true;\r
- repaint();\r
- return true;\r
- }\r
-\r
- public void removeNotify() {\r
- controller.removeListener(this);\r
- super.removeNotify();\r
- }*/\r
-\r
- public void initAxes()\r
- {\r
- for (int i = 0; i < 3; i++)\r
- {\r
- for (int j = 0; j < 3; j++)\r
- {\r
- if (i != j)\r
- {\r
- axes[i][j] = 0;\r
- }\r
- else\r
- {\r
- axes[i][j] = 1;\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void findWidth()\r
- {\r
- max = new float[3];\r
- min = new float[3];\r
-\r
- max[0] = (float) - 1e30;\r
- max[1] = (float) - 1e30;\r
- max[2] = (float) - 1e30;\r
-\r
- min[0] = (float) 1e30;\r
- min[1] = (float) 1e30;\r
- min[2] = (float) 1e30;\r
-\r
- for (int i = 0; i < 3; i++)\r
- {\r
- for (int j = 0; j < npoint; j++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(j);\r
- if (sp.coord[i] >= max[i])\r
- {\r
- max[i] = sp.coord[i];\r
- }\r
- if (sp.coord[i] <= min[i])\r
- {\r
- min[i] = sp.coord[i];\r
- }\r
- }\r
- }\r
-\r
- // System.out.println("xmax " + max[0] + " min " + min[0]);\r
- //System.out.println("ymax " + max[1] + " min " + min[1]);\r
- //System.out.println("zmax " + max[2] + " min " + min[2]);\r
-\r
- width[0] = Math.abs(max[0] - min[0]);\r
- width[1] = Math.abs(max[1] - min[1]);\r
- width[2] = Math.abs(max[2] - min[2]);\r
-\r
- maxwidth = width[0];\r
-\r
- if (width[1] > width[0])\r
- {\r
- maxwidth = width[1];\r
- }\r
- if (width[2] > width[1])\r
- {\r
- maxwidth = width[2];\r
- }\r
-\r
- //System.out.println("Maxwidth = " + maxwidth);\r
- }\r
-\r
- public float findScale()\r
- {\r
- int dim, width, height;\r
- if (getSize().width != 0)\r
- {\r
- width = getSize().width;\r
- height = getSize().height;\r
- }\r
- else\r
- {\r
- width = prefsize.width;\r
- height = prefsize.height;\r
- }\r
-\r
- if (width < height)\r
- {\r
- dim = width;\r
- }\r
- else\r
- {\r
- dim = height;\r
- }\r
-\r
- return (float) (dim * scalefactor / (2 * maxwidth));\r
- }\r
-\r
- public void findCentre()\r
- {\r
- //Find centre coordinate\r
- findWidth();\r
-\r
- centre[0] = (max[0] + min[0]) / 2;\r
- centre[1] = (max[1] + min[1]) / 2;\r
- centre[2] = (max[2] + min[2]) / 2;\r
-\r
- // System.out.println("Centre x " + centre[0]);\r
- //System.out.println("Centre y " + centre[1]);\r
- //System.out.println("Centre z " + centre[2]);\r
- }\r
-\r
- public Dimension getPreferredSize()\r
- {\r
- if (prefsize != null)\r
- {\r
- return prefsize;\r
- }\r
- else\r
- {\r
- return new Dimension(400, 400);\r
- }\r
- }\r
-\r
- public Dimension getMinimumSize()\r
- {\r
- return getPreferredSize();\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
- public void paint(Graphics g)\r
- {\r
- if (points == null)\r
- {\r
- g.setFont(new Font("Verdana", Font.PLAIN, 18));\r
- g.drawString("Calculating PCA....", 20, getSize().height / 2);\r
- }\r
- else\r
- {\r
-\r
- //Only create the image at the beginning -\r
- if ( (img == null) || (prefsize.width != getSize().width) ||\r
- (prefsize.height != getSize().height))\r
- {\r
- prefsize.width = getSize().width;\r
- prefsize.height = getSize().height;\r
-\r
- scale = findScale();\r
-\r
- // System.out.println("New scale = " + scale);\r
- img = createImage(getSize().width, getSize().height);\r
- ig = img.getGraphics();\r
-\r
- }\r
-\r
- drawBackground(ig, Color.black);\r
- drawScene(ig);\r
- if (drawAxes == true)\r
- {\r
- drawAxes(ig);\r
- }\r
-\r
- if(tooltip!=null)\r
- {\r
- ig.setColor(Color.red);\r
- ig.drawString(tooltip, toolx, tooly);\r
- }\r
-\r
- g.drawImage(img, 0, 0, this);\r
- }\r
- }\r
-\r
- public void drawAxes(Graphics g)\r
- {\r
-\r
- g.setColor(Color.yellow);\r
- for (int i = 0; i < 3; i++)\r
- {\r
- g.drawLine(getSize().width / 2, getSize().height / 2,\r
- (int) (axes[i][0] * scale * max[0] + getSize().width / 2),\r
- (int) (axes[i][1] * scale * max[1] + getSize().height / 2));\r
- }\r
- }\r
-\r
- public void drawBackground(Graphics g, Color col)\r
- {\r
- g.setColor(col);\r
- g.fillRect(0, 0, prefsize.width, prefsize.height);\r
- }\r
-\r
- public void drawScene(Graphics g)\r
- {\r
- //boolean darker = false;\r
-\r
- int halfwidth = getSize().width / 2;\r
- int halfheight = getSize().height / 2;\r
-\r
- for (int i = 0; i < npoint; i++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- int x = (int) ( (float) (sp.coord[0] - centre[0]) * scale) + halfwidth;\r
- int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;\r
- float z = sp.coord[1] - centre[2];\r
-\r
- if (av.getSequenceColour(sp.sequence) == Color.black)\r
- {\r
- g.setColor(Color.white);\r
- }\r
- else\r
- {\r
- g.setColor(av.getSequenceColour(sp.sequence));\r
- }\r
-\r
- if (av.getSelectionGroup() != null)\r
- {\r
- if (av.getSelectionGroup().getSequences(false).contains( ( (SequencePoint) points.\r
- elementAt(i)).sequence))\r
- {\r
- g.setColor(Color.gray);\r
- }\r
- }\r
- if (z < 0)\r
- {\r
- g.setColor(g.getColor().darker());\r
- }\r
-\r
- g.fillRect(x - 3, y - 3, 6, 6);\r
- if (showLabels)\r
- {\r
- g.setColor(Color.red);\r
- g.drawString( ( (SequencePoint) points.elementAt(i)).sequence.\r
- getName(),\r
- x - 3, y - 4);\r
- }\r
- }\r
- }\r
-\r
- public Dimension minimumsize()\r
- {\r
- return prefsize;\r
- }\r
-\r
- public Dimension preferredsize()\r
- {\r
- return prefsize;\r
- }\r
-\r
- public void keyTyped(KeyEvent evt)\r
- {}\r
-\r
- public void keyReleased(KeyEvent evt)\r
- {}\r
-\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- if (evt.getKeyCode() == KeyEvent.VK_UP)\r
- {\r
- scalefactor = (float) (scalefactor * 1.1);\r
- scale = findScale();\r
- }\r
- else if (evt.getKeyCode() == KeyEvent.VK_DOWN)\r
- {\r
- scalefactor = (float) (scalefactor * 0.9);\r
- scale = findScale();\r
- }\r
- else if (evt.getKeyChar() == 's')\r
- {\r
- System.err.println("DEBUG: Rectangle selection"); // log.debug\r
- if (rectx2 != -1 && recty2 != -1)\r
- {\r
- rectSelect(rectx1, recty1, rectx2, recty2);\r
-\r
- }\r
- }\r
- repaint();\r
- }\r
-\r
- public void printPoints()\r
- {\r
- for (int i = 0; i < npoint; i++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- Format.print(System.out, "%5d ", i);\r
- for (int j = 0; j < 3; j++)\r
- {\r
- Format.print(System.out, "%13.3f ", sp.coord[j]);\r
- }\r
- System.out.println();\r
- }\r
- }\r
-\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
-\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {}\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- int x = evt.getX();\r
- int y = evt.getY();\r
-\r
- mx = x;\r
- my = y;\r
-\r
- omx = mx;\r
- omy = my;\r
-\r
- startx = x;\r
- starty = y;\r
-\r
- rectx1 = x;\r
- recty1 = y;\r
-\r
- rectx2 = -1;\r
- recty2 = -1;\r
-\r
- SequenceI found = findPoint(x, y);\r
-\r
- if (found != null)\r
- {\r
- if (av.getSelectionGroup() != null)\r
- {\r
- av.getSelectionGroup().addOrRemove(found, true);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
- PaintRefresher.Refresh(this, av.getSequenceSetId());\r
- }\r
- else\r
- {\r
- av.setSelectionGroup(new SequenceGroup());\r
- av.getSelectionGroup().addOrRemove(found, true);\r
- av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);\r
-\r
- }\r
- }\r
- repaint();\r
- }\r
-\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- SequenceI found = findPoint(evt.getX(), evt.getY());\r
- if(found==null)\r
- tooltip = null;\r
- else\r
- {\r
- tooltip = found.getName();\r
- toolx = evt.getX();\r
- tooly = evt.getY();\r
- }\r
- repaint();\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- mx = evt.getX();\r
- my = evt.getY();\r
-\r
- rotmat.setIdentity();\r
-\r
- rotmat.rotate( (float) (my - omy), 'x');\r
- rotmat.rotate( (float) (mx - omx), 'y');\r
-\r
- for (int i = 0; i < npoint; i++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- sp.coord[0] -= centre[0];\r
- sp.coord[1] -= centre[1];\r
- sp.coord[2] -= centre[2];\r
-\r
- //Now apply the rotation matrix\r
- sp.coord = rotmat.vectorMultiply(sp.coord);\r
-\r
- //Now translate back again\r
- sp.coord[0] += centre[0];\r
- sp.coord[1] += centre[1];\r
- sp.coord[2] += centre[2];\r
- }\r
-\r
- for (int i = 0; i < 3; i++)\r
- {\r
- axes[i] = rotmat.vectorMultiply(axes[i]);\r
- }\r
- omx = mx;\r
- omy = my;\r
-\r
- paint(this.getGraphics());\r
- }\r
-\r
- public void rectSelect(int x1, int y1, int x2, int y2)\r
- {\r
- //boolean changedSel = false;\r
- for (int i = 0; i < npoint; i++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- int tmp1 = (int) ( (sp.coord[0] - centre[0]) * scale +\r
- (float) getSize().width / 2.0);\r
- int tmp2 = (int) ( (sp.coord[1] - centre[1]) * scale +\r
- (float) getSize().height / 2.0);\r
-\r
- if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)\r
- {\r
- if (av != null)\r
- {\r
- if (!av.getSelectionGroup().getSequences(false).contains(sp.sequence))\r
- {\r
- av.getSelectionGroup().addSequence(sp.sequence, true);\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- public SequenceI findPoint(int x, int y)\r
- {\r
-\r
- int halfwidth = getSize().width / 2;\r
- int halfheight = getSize().height / 2;\r
-\r
- int found = -1;\r
-\r
- for (int i = 0; i < npoint; i++)\r
- {\r
-\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- int px = (int) ( (float) (sp.coord[0] - centre[0]) * scale) + halfwidth;\r
- int py = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;\r
-\r
- if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)\r
- {\r
- found = i;\r
- }\r
- }\r
- if (found != -1)\r
- {\r
- return ( (SequencePoint) points.elementAt(found)).sequence;\r
- }\r
- else\r
- {\r
- return null;\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<SequencePoint> 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<SequencePoint> 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]);
+ }
+ }
+
+}