-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.math.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class RotatableCanvas extends JPanel implements MouseListener,\r
- MouseMotionListener, KeyListener\r
-{\r
- RotatableMatrix idmat = new RotatableMatrix(3, 3);\r
- RotatableMatrix objmat = new RotatableMatrix(3, 3);\r
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);\r
-\r
- //RubberbandRectangle rubberband;\r
- boolean drawAxes = true;\r
- int omx = 0;\r
- int mx = 0;\r
- int omy = 0;\r
- int my = 0;\r
- Image img;\r
- Graphics ig;\r
- Dimension prefsize;\r
- float[] centre = new float[3];\r
- float[] width = new float[3];\r
- float[] max = new float[3];\r
- float[] min = new float[3];\r
- float maxwidth;\r
- float scale;\r
- int npoint;\r
- Vector points;\r
- float[][] orig;\r
- float[][] axes;\r
- int startx;\r
- int starty;\r
- int lastx;\r
- int lasty;\r
- int rectx1;\r
- int recty1;\r
- int rectx2;\r
- int recty2;\r
- float scalefactor = 1;\r
- AlignViewport av;\r
- boolean showLabels = false;\r
- Color bgColour = Color.black;\r
-\r
- // Controller controller;\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
- ToolTipManager.sharedInstance().registerComponent(this);\r
- ToolTipManager.sharedInstance().setInitialDelay(0);\r
- ToolTipManager.sharedInstance().setDismissDelay(10000);\r
- PaintRefresher.Register(this, av.alignment);\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
-\r
- for (int j = 0; j < 3; j++)\r
- {\r
- orig[i][j] = sp.coord[j];\r
- }\r
- }\r
-\r
- //Initialize the matrices to identity\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
- addMouseListener(this);\r
- addKeyListener(this);\r
-\r
- addMouseMotionListener(this);\r
-\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
- /**\r
- * DOCUMENT ME!\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
-\r
- if (sp.coord[i] >= max[i])\r
- {\r
- max[i] = sp.coord[i];\r
- }\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
- 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
-\r
- if (width[2] > width[1])\r
- {\r
- maxwidth = width[2];\r
- }\r
-\r
- //System.out.println("Maxwidth = " + maxwidth);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float findScale()\r
- {\r
- int dim;\r
- int width;\r
- int height;\r
-\r
- if (getWidth() != 0)\r
- {\r
- width = getWidth();\r
- height = getHeight();\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
- /**\r
- * DOCUMENT ME!\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Dimension getMinimumSize()\r
- {\r
- return getPreferredSize();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g1)\r
- {\r
-\r
- Graphics2D g = (Graphics2D) g1;\r
-\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- if(points==null)\r
- {\r
- g.setFont(new Font("Verdana", Font.PLAIN, 18));\r
- g.drawString("Calculating PCA....", 20, getHeight()/2);\r
- }\r
- else\r
- {\r
- //Only create the image at the beginning -\r
- if ( (img == null) || (prefsize.width != getWidth()) ||\r
- (prefsize.height != getHeight()))\r
- {\r
- prefsize.width = getWidth();\r
- prefsize.height = getHeight();\r
-\r
- scale = findScale();\r
-\r
- // System.out.println("New scale = " + scale);\r
- img = createImage(getWidth(), getHeight());\r
- ig = img.getGraphics();\r
- }\r
-\r
-\r
- drawBackground(ig, bgColour);\r
- drawScene(ig);\r
-\r
- if (drawAxes == true)\r
- {\r
- drawAxes(ig);\r
- }\r
-\r
- g.drawImage(img, 0, 0, this);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void drawAxes(Graphics g)\r
- {\r
-\r
- g.setColor(Color.yellow);\r
-\r
- for (int i = 0; i < 3; i++)\r
- {\r
- g.drawLine(getWidth() / 2, getHeight() / 2,\r
- (int) ((axes[i][0] * scale * max[0]) + (getWidth() / 2)),\r
- (int) ((axes[i][1] * scale * max[1]) + (getHeight() / 2)));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param col DOCUMENT ME!\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void drawScene(Graphics g1)\r
- {\r
-\r
- Graphics2D g = (Graphics2D) g1;\r
-\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
-\r
- int halfwidth = getWidth() / 2;\r
- int halfheight = getHeight() / 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) +\r
- halfwidth;\r
- int y = (int) ((float) (sp.coord[1] - centre[1]) * scale) +\r
- halfheight;\r
- float z = sp.coord[1] - centre[2];\r
-\r
- if (sp.sequence.getColor() == Color.black)\r
- {\r
- g.setColor(Color.white);\r
- }\r
- else\r
- {\r
- g.setColor(sp.sequence.getColor());\r
- }\r
-\r
- if (av.getSelectionGroup() != null)\r
- {\r
- if (av.getSelectionGroup().sequences.contains(\r
- ((SequencePoint) points.elementAt(i)).sequence))\r
- {\r
- g.setColor(Color.gray);\r
- }\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
- // //Now the rectangle\r
- // if (rectx2 != -1 && recty2 != -1) {\r
- // g.setColor(Color.white);\r
- //\r
- // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);\r
- // }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Dimension minimumsize()\r
- {\r
- return prefsize;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Dimension preferredsize()\r
- {\r
- return prefsize;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void keyTyped(KeyEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void keyReleased(KeyEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\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
-\r
- if ((rectx2 != -1) && (recty2 != -1))\r
- {\r
- rectSelect(rectx1, recty1, rectx2, recty2);\r
- }\r
- }\r
-\r
- repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\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
-\r
- for (int j = 0; j < 3; j++)\r
- {\r
- Format.print(System.out, "%13.3f ", sp.coord[j]);\r
- }\r
-\r
- System.out.println();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseClicked(MouseEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\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
- PaintRefresher.Refresh(this, av.alignment);\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
- // private void fireSequenceSelectionEvent(Selection sel) {\r
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
- //}\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- SequenceI found = findPoint(evt.getX(), evt.getY());\r
-\r
- if (found != null)\r
- {\r
- this.setToolTipText(found.getName());\r
- }\r
- else\r
- {\r
- this.setToolTipText(null);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- mx = evt.getX();\r
- my = evt.getY();\r
-\r
- //Check if this is a rectangle drawing drag\r
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)\r
- {\r
- // rectx2 = evt.getX();\r
- // recty2 = evt.getY();\r
- }\r
- else\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
-\r
- omx = mx;\r
- omy = my;\r
-\r
- paint(this.getGraphics());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param x2 DOCUMENT ME!\r
- * @param y2 DOCUMENT ME!\r
- */\r
- public void rectSelect(int x1, int y1, int x2, int y2)\r
- {\r
- boolean changedSel = false;\r
-\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) getWidth() / 2.0));\r
- int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale) +\r
- ((float) getHeight() / 2.0));\r
-\r
- if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))\r
- {\r
- if (av != null)\r
- {\r
- if (!av.getSelectionGroup().sequences.contains(sp.sequence))\r
- {\r
- changedSel = true;\r
- av.getSelectionGroup().addSequence(sp.sequence, true);\r
- }\r
- }\r
- }\r
- }\r
-\r
- // if (changedSel) {\r
- // fireSequenceSelectionEvent(av.getSelection());\r
- // }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param x DOCUMENT ME!\r
- * @param y DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI findPoint(int x, int y)\r
- {\r
- int halfwidth = getWidth() / 2;\r
- int halfheight = getHeight() / 2;\r
-\r
- int found = -1;\r
-\r
- for (int i = 0; i < npoint; i++)\r
- {\r
- SequencePoint sp = (SequencePoint) points.elementAt(i);\r
- int px = (int) ((float) (sp.coord[0] - centre[0]) * scale) +\r
- halfwidth;\r
- int py = (int) ((float) (sp.coord[1] - centre[1]) * scale) +\r
- halfheight;\r
-\r
- if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))\r
- {\r
- found = i;\r
- }\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
- /* public boolean handleRubberbandEvent(RubberbandEvent evt) {\r
- System.out.println("Rubberband handler called in RotatableCanvas with " +\r
- evt.getBounds());\r
-\r
- Rubberband rb = (Rubberband)evt.getSource();\r
-\r
- // Clear the current selection (instance variable)\r
- //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {\r
- // clearSelection();\r
- //}\r
-\r
- if (rb.getComponent() == this) {\r
- Rectangle bounds = evt.getBounds();\r
- rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);\r
- }\r
-\r
- redrawneeded = true;\r
- paint(this.getGraphics());\r
-\r
- return true;\r
- }*/\r
-}\r
+/*
+ * 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;
+ boolean showLabels = false;
+ Color bgColour = Color.black;
+
+ // Controller controller;
+ 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;
+ 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();
+
+ addMouseListener(this);
+ addKeyListener(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 (sp.sequence.getColor() == Color.black)
+ {
+ g.setColor(Color.white);
+ }
+ else
+ {
+ g.setColor(sp.sequence.getColor());
+ }
+
+ 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)
+ {
+ 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()-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());
+
+ 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;
+ }
+ }
+
+ /* 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;
+ }*/
+}
git://source.jalview.org / jalview.git / blobdiff