-/*
- * 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.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.SequencePoint;
-import jalview.math.RotatableMatrix;
-import jalview.util.Format;
-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 javax.swing.JPanel;
-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.Vector;
-
-public class RotatableCanvas extends JPanel implements MouseListener,
- MouseMotionListener, KeyListener, RotatableCanvasI
-{
- RotatableMatrix idmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix objmat = new RotatableMatrix(3, 3);
-
- RotatableMatrix rotmat = new RotatableMatrix(3, 3);
-
- String tooltip;
-
- int toolx, tooly;
-
- // 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;
-
- AlignmentViewport av;
-
- boolean showLabels = false;
-
- public RotatableCanvas(AlignmentViewport 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;
- PaintRefresher.Register(this, av.getSequenceSetId());
-
- 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 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 update(Graphics g)
- {
- paint(g);
- }
-
- 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 == true)
- {
- 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) (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) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
- int y = (int) ((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(null)
- .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);
- }
- }
- }
-
- 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)
- {
- 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.printLong(System.out, "%5d ", i);
- for (int j = 0; j < 3; j++)
- {
- Format.printDouble(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)
- {
- // 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();
- }
-
- public void mouseMoved(MouseEvent evt)
- {
- SequenceI found = findPoint(evt.getX(), evt.getY());
- if (found == null)
- {
- tooltip = null;
- }
- else
- {
- tooltip = found.getName();
- toolx = evt.getX();
- tooly = evt.getY();
- }
- repaint();
- }
-
- public void mouseDragged(MouseEvent evt)
- {
- mx = evt.getX();
- my = evt.getY();
-
- rotmat.setIdentity();
-
- rotmat.rotate(my - omy, 'x');
- rotmat.rotate(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 + getSize().width / 2.0);
- int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + getSize().height / 2.0);
-
- if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2)
- {
- if (av != null)
- {
- if (!av.getSelectionGroup().getSequences(null)
- .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) ((sp.coord[0] - centre[0]) * scale)
- + halfwidth;
- int py = (int) ((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;
- }
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.api.RotatableCanvasI;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.datamodel.SequencePoint;\r
+import jalview.math.RotatableMatrix;\r
+import jalview.util.Format;\r
+import jalview.util.MessageManager;\r
+import jalview.viewmodel.AlignmentViewport;\r
+\r
+import java.awt.Color;\r
+import java.awt.Dimension;\r
+import java.awt.Font;\r
+import java.awt.Graphics;\r
+import java.awt.Image;\r
+import javax.swing.JPanel;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.KeyListener;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.awt.event.MouseMotionListener;\r
+import java.util.Vector;\r
+\r
+public class RotatableCanvas extends JPanel implements MouseListener,\r
+ MouseMotionListener, KeyListener, RotatableCanvasI\r
+{\r
+ RotatableMatrix idmat = new RotatableMatrix(3, 3);\r
+\r
+ RotatableMatrix objmat = new RotatableMatrix(3, 3);\r
+\r
+ RotatableMatrix rotmat = new RotatableMatrix(3, 3);\r
+\r
+ String tooltip;\r
+\r
+ int toolx, tooly;\r
+\r
+ // RubberbandRectangle rubberband;\r
+\r
+ boolean drawAxes = true;\r
+\r
+ int omx = 0;\r
+\r
+ int mx = 0;\r
+\r
+ int omy = 0;\r
+\r
+ int my = 0;\r
+\r
+ Image img;\r
+\r
+ Graphics ig;\r
+\r
+ Dimension prefsize;\r
+\r
+ float centre[] = new float[3];\r
+\r
+ float width[] = new float[3];\r
+\r
+ float max[] = new float[3];\r
+\r
+ float min[] = new float[3];\r
+\r
+ float maxwidth;\r
+\r
+ float scale;\r
+\r
+ int npoint;\r
+\r
+ Vector points;\r
+\r
+ float[][] orig;\r
+\r
+ float[][] axes;\r
+\r
+ int startx;\r
+\r
+ int starty;\r
+\r
+ int lastx;\r
+\r
+ int lasty;\r
+\r
+ int rectx1;\r
+\r
+ int recty1;\r
+\r
+ int rectx2;\r
+\r
+ int recty2;\r
+\r
+ float scalefactor = 1;\r
+\r
+ AlignmentViewport av;\r
+\r
+ boolean showLabels = false;\r
+\r
+ public RotatableCanvas(AlignmentViewport 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
+ /*\r
+ * public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) {\r
+ * redrawneeded = true; repaint(); return true; }\r
+ * \r
+ * public void removeNotify() { 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 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
+\r
+ public void paint(Graphics g)\r
+ {\r
+ if (points == null)\r
+ {\r
+ g.setFont(new Font("Verdana", Font.PLAIN, 18));\r
+ g.drawString(MessageManager.getString("label.calculating_pca")\r
+ + "....", 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) ((sp.coord[0] - centre[0]) * scale) + halfwidth;\r
+ int y = (int) ((sp.coord[1] - centre[1]) * scale)\r
+ + 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(null)\r
+ .contains(((SequencePoint) points.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(\r
+ ((SequencePoint) points.elementAt(i)).sequence.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
+\r
+ public void keyReleased(KeyEvent evt)\r
+ {\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.printLong(System.out, "%5d ", i);\r
+ for (int j = 0; j < 3; j++)\r
+ {\r
+ Format.printDouble(System.out, "%13.3f ", sp.coord[j]);\r
+ }\r
+ System.out.println();\r
+ }\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\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
+ // TODO: applet PCA is not associatable with multi-panels - only parent\r
+ // view\r
+ if (av.getSelectionGroup() != null)\r
+ {\r
+ av.getSelectionGroup().addOrRemove(found, true);\r
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);\r
+ }\r
+ else\r
+ {\r
+ av.setSelectionGroup(new SequenceGroup());\r
+ av.getSelectionGroup().addOrRemove(found, true);\r
+ av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);\r
+\r
+ }\r
+ PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+ av.sendSelection();\r
+ }\r
+ repaint();\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ SequenceI found = findPoint(evt.getX(), evt.getY());\r
+ if (found == null)\r
+ {\r
+ tooltip = null;\r
+ }\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(my - omy, 'x');\r
+ rotmat.rotate(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 + getSize().width / 2.0);\r
+ int tmp2 = (int) ((sp.coord[1] - centre[1]) * scale + 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(null)\r
+ .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) ((sp.coord[0] - centre[0]) * scale)\r
+ + halfwidth;\r
+ int py = (int) ((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
+ if (found != -1)\r
+ {\r
+ return ((SequencePoint) points.elementAt(found)).sequence;\r
+ }\r
+ else\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff