-package jalview.gui;\r
-\r
-import jalview.math.*;\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-\r
-\r
-public class RotatableCanvas extends JPanel implements MouseListener,\r
- MouseMotionListener,\r
- KeyListener\r
- //RubberbandListener,\r
- //SequenceSelectionListener\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
-\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
-// Controller controller;\r
-\r
-\r
- public RotatableCanvas(AlignViewport av,\r
- Vector points, int npoint) {\r
- this.points = points;\r
- this.npoint = npoint;\r
- this.av = av;\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- PaintRefresher.Register(this);\r
-//\r
- prefsize = getPreferredSize();\r
- orig = new float[npoint][3];\r
-\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- for (int j=0; j < 3; j++) {\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
- for (int j = 0; j < 3 ; j++) {\r
- if (i != j) {\r
- idmat.addElement(i,j,0);\r
- objmat.addElement(i,j,0);\r
- rotmat.addElement(i,j,0);\r
- } else {\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
- for (int i = 0; i < 3; i++) {\r
- for (int j=0; j < 3; j++) {\r
- if (i != j) {\r
- axes[i][j] = 0;\r
- } else {\r
- axes[i][j] = 1;\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void findWidth() {\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
- for (int j = 0; j < npoint; j++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(j);\r
- if (sp.coord[i] >= max[i]) {\r
- max[i] = sp.coord[i];\r
- }\r
- if (sp.coord[i] <= min[i]) {\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
- maxwidth = width[1];\r
- if (width[2] > width[1])\r
- maxwidth = width[2];\r
-\r
- //System.out.println("Maxwidth = " + maxwidth);\r
- }\r
-\r
- public float findScale() {\r
- int dim, width, height;\r
- if (getWidth() != 0) {\r
- width = getWidth();\r
- height = getHeight();\r
- } else {\r
- width = prefsize.width;\r
- height = prefsize.height;\r
- }\r
-\r
- if (width < height) {\r
- dim = width;\r
- } else {\r
- dim = height;\r
- }\r
-\r
- return (float)(dim*scalefactor/(2*maxwidth));\r
- }\r
-\r
- public void findCentre() {\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
- if (prefsize != null) {\r
- return prefsize;\r
- } else {\r
- return new Dimension(400,400);\r
- }\r
- }\r
-\r
- public Dimension getMinimumSize() {\r
- return getPreferredSize();\r
- }\r
-\r
- public void paintComponent(Graphics g) {\r
- //Only create the image at the beginning -\r
- if ((img == null) || (prefsize.width != getWidth()) || (prefsize.height != getHeight())) {\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
-\r
- drawBackground(ig,Color.black);\r
- drawScene(ig);\r
- if (drawAxes == true)\r
- {\r
- drawAxes(ig);\r
- }\r
-\r
-\r
- g.drawImage(img,0,0,this);\r
- }\r
-\r
- public void drawAxes(Graphics g) {\r
-\r
- g.setColor(Color.yellow);\r
- for (int i=0; i < 3 ; i++) {\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
- public void drawBackground(Graphics g, Color col) {\r
- g.setColor(col);\r
- g.fillRect(0,0,prefsize.width,prefsize.height);\r
- }\r
-\r
-\r
- public void drawScene(Graphics g) {\r
- boolean darker = false;\r
-\r
- int halfwidth = getWidth()/2;\r
- int halfheight = getHeight()/2;\r
-\r
- for (int i = 0; i < npoint; i++) {\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
-\r
-\r
-\r
- if (sp.sequence.getColor() == Color.black)\r
- g.setColor(Color.white);\r
- else\r
- g.setColor(sp.sequence.getColor());\r
-\r
-\r
- if (av != null)\r
- {\r
- if (av.getSelection().contains(((SequencePoint)points.elementAt(i)).sequence))\r
- g.setColor(Color.gray);\r
- }\r
- if (z < 0)\r
- g.setColor(g.getColor().darker());\r
-\r
-\r
- g.fillRect(x-3,y-3,6,6);\r
- g.setColor(Color.red);\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
- public Dimension minimumsize() {\r
- return prefsize;\r
- }\r
-\r
- public Dimension preferredsize() {\r
- return prefsize;\r
- }\r
-\r
- public void keyTyped(KeyEvent evt) { }\r
- public void keyReleased(KeyEvent evt) { }\r
-\r
- public void keyPressed(KeyEvent evt) {\r
- requestFocus();\r
- if (evt.getKeyCode() == KeyEvent.VK_UP) {\r
- scalefactor = (float)(scalefactor * 1.1);\r
- scale = findScale();\r
- } else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {\r
- scalefactor = (float)(scalefactor * 0.9);\r
- scale = findScale();\r
- } else if (evt.getKeyChar() == 's') {\r
- System.out.println("Rectangle selection");\r
- if (rectx2 != -1 && recty2 != -1) {\r
- rectSelect(rectx1,recty1,rectx2,recty2);\r
-\r
- }\r
- }\r
- repaint();\r
- }\r
-\r
- public void printPoints() {\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- Format.print(System.out,"%5d ", i);\r
- for (int j=0; j < 3;j++) {\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
- public void mouseEntered(MouseEvent evt) { }\r
- public void mouseExited(MouseEvent evt) { }\r
- public void mouseReleased(MouseEvent evt) { }\r
-\r
- public void mousePressed(MouseEvent evt) {\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
- if (av != null) {\r
-\r
- if (av.getSelection().contains(found)) {\r
- av.getSelection().removeElement(found);\r
- } else {\r
- av.getSelection().addElement(found);\r
- }\r
- PaintRefresher.Refresh(this);\r
- }\r
- }\r
- repaint();\r
- }\r
-\r
- // private void fireSequenceSelectionEvent(Selection sel) {\r
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
- //}\r
-\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- SequenceI found = findPoint(evt.getX(), evt.getY());\r
- if (found != null)\r
- this.setToolTipText(found.getName());\r
- else\r
- this.setToolTipText(null);\r
- }\r
-\r
- public void mouseDragged(MouseEvent evt) {\r
- mx = evt.getX();\r
- my = evt.getY();\r
- //Check if this is a rectangle drawing drag\r
- if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0) {\r
-// rectx2 = evt.getX();\r
-// recty2 = evt.getY();\r
- } else {\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
- 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
- axes[i] = rotmat.vectorMultiply(axes[i]);\r
- }\r
- omx = mx;\r
- omy = my;\r
-\r
- paint(this.getGraphics());\r
- }\r
-\r
- }\r
-\r
- public void rectSelect(int x1, int y1, int x2, int y2) {\r
- boolean changedSel = false;\r
- for (int i=0; i < npoint; i++) {\r
- SequencePoint sp = (SequencePoint)points.elementAt(i);\r
- int tmp1 = (int)((sp.coord[0] - centre[0])*scale + (float)getWidth()/2.0);\r
- int tmp2 = (int)((sp.coord[1] - centre[1])*scale + (float)getHeight()/2.0);\r
-\r
- if (tmp1 > x1 && tmp1 < x2 && tmp2 > y1 && tmp2 < y2) {\r
- if (av != null) {\r
- if (!av.getSelection().contains(sp.sequence)) {\r
- changedSel = true;\r
- av.getSelection().addElement(sp.sequence);\r
- }\r
- }\r
- }\r
- }\r
- // if (changedSel) {\r
- // fireSequenceSelectionEvent(av.getSelection());\r
- // }\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) + halfwidth;\r
- int py = (int)((float)(sp.coord[1] - centre[1])*scale) + halfheight;\r
-\r
-\r
- if (Math.abs(px-x)<3 && Math.abs(py - y) < 3 ) {\r
- found = i;\r
- }\r
- }\r
- if (found != -1) {\r
- return ((SequencePoint)points.elementAt(found)).sequence;\r
- } else {\r
- return null;\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
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.gui;
+
+import jalview.api.RotatableCanvasI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequencePoint;
+import jalview.math.RotatableMatrix;
+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.Graphics2D;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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);
+
+ // 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;
+
+ AlignmentPanel ap;
+
+ boolean showLabels = false;
+
+ Color bgColour = Color.black;
+
+ boolean applyToAllViews = false;
+
+ // Controller controller;
+ public RotatableCanvas(AlignmentPanel ap)
+ {
+ this.av = ap.av;
+ this.ap = ap;
+
+ addMouseWheelListener(new MouseWheelListener()
+ {
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ if (e.getWheelRotation() > 0)
+ {
+ scale = (float) (scale * 1.1);
+ repaint();
+ }
+
+ else
+ {
+ scale = (float) (scale * 0.9);
+ repaint();
+ }
+ }
+ });
+
+ }
+
+ public void showLabels(boolean b)
+ {
+ showLabels = b;
+ repaint();
+ }
+
+ boolean first = true;
+
+ public void setPoints(Vector points, int npoint)
+ {
+ this.points = points;
+ this.npoint = npoint;
+ if (first)
+ {
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ }
+ prefsize = getPreferredSize();
+ orig = new float[npoint][3];
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = (SequencePoint) points.elementAt(i);
+
+ for (int j = 0; j < 3; j++)
+ {
+ orig[i][j] = sp.coord[j];
+ }
+ }
+
+ // Initialize the matrices to identity
+ for (int i = 0; i < 3; i++)
+ {
+ for (int j = 0; j < 3; j++)
+ {
+ if (i != j)
+ {
+ idmat.addElement(i, j, 0);
+ objmat.addElement(i, j, 0);
+ rotmat.addElement(i, j, 0);
+ }
+ else
+ {
+ idmat.addElement(i, j, 0);
+ objmat.addElement(i, j, 0);
+ rotmat.addElement(i, j, 0);
+ }
+ }
+ }
+
+ axes = new float[3][3];
+ initAxes();
+
+ findCentre();
+ findWidth();
+
+ scale = findScale();
+ if (first)
+ {
+
+ addMouseListener(this);
+
+ addMouseMotionListener(this);
+ }
+ first = false;
+ }
+
+ 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(MessageManager.getString("label.calculating_pca")
+ + "....", 20, getHeight() / 2);
+ }
+ else
+ {
+ // Only create the image at the beginning -
+ if ((img == null) || (prefsize.width != getWidth())
+ || (prefsize.height != getHeight()))
+ {
+ prefsize.width = getWidth();
+ prefsize.height = getHeight();
+
+ scale = findScale();
+
+ // System.out.println("New scale = " + scale);
+ img = createImage(getWidth(), getHeight());
+ ig = img.getGraphics();
+ }
+
+ drawBackground(ig, bgColour);
+ drawScene(ig);
+
+ if (drawAxes == true)
+ {
+ drawAxes(ig);
+ }
+
+ g.drawImage(img, 0, 0, this);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void drawAxes(Graphics g)
+ {
+
+ g.setColor(Color.yellow);
+
+ for (int i = 0; i < 3; i++)
+ {
+ g.drawLine(getWidth() / 2, getHeight() / 2, (int) ((axes[i][0]
+ * scale * max[0]) + (getWidth() / 2)), (int) ((axes[i][1]
+ * scale * max[1]) + (getHeight() / 2)));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param col
+ * DOCUMENT ME!
+ */
+ public void drawBackground(Graphics g, Color col)
+ {
+ g.setColor(col);
+ g.fillRect(0, 0, prefsize.width, prefsize.height);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ public void drawScene(Graphics g1)
+ {
+
+ Graphics2D g = (Graphics2D) g1;
+
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = (SequencePoint) points.elementAt(i);
+ int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
+ int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ + halfheight;
+ float z = sp.coord[1] - centre[2];
+
+ if (av.getSequenceColour(sp.sequence) == Color.black)
+ {
+ g.setColor(Color.white);
+ }
+ else
+ {
+ g.setColor(av.getSequenceColour(sp.sequence));
+ }
+
+ if (av.getSelectionGroup() != null)
+ {
+ if (av.getSelectionGroup().getSequences(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);
+ }
+ }
+
+ // //Now the rectangle
+ // if (rectx2 != -1 && recty2 != -1) {
+ // g.setColor(Color.white);
+ //
+ // g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
+ // }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension minimumsize()
+ {
+ return prefsize;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Dimension preferredsize()
+ {
+ return prefsize;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void keyTyped(KeyEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void keyReleased(KeyEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void keyPressed(KeyEvent evt)
+ {
+ if (evt.getKeyCode() == KeyEvent.VK_UP)
+ {
+ scalefactor = (float) (scalefactor * 1.1);
+ scale = findScale();
+ }
+ else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
+ {
+ scalefactor = (float) (scalefactor * 0.9);
+ scale = findScale();
+ }
+ else if (evt.getKeyChar() == 's')
+ {
+ System.err.println("DEBUG: Rectangle selection"); // log.debug
+
+ if ((rectx2 != -1) && (recty2 != -1))
+ {
+ rectSelect(rectx1, recty1, rectx2, recty2);
+ }
+ }
+
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent evt)
+ {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+ int x = evt.getX();
+ int y = evt.getY();
+
+ mx = x;
+ my = y;
+
+ omx = mx;
+ omy = my;
+
+ startx = x;
+ starty = y;
+
+ rectx1 = x;
+ recty1 = y;
+
+ rectx2 = -1;
+ recty2 = -1;
+
+ SequenceI found = findPoint(x, y);
+
+ if (found != null)
+ {
+ AlignmentPanel[] aps = getAssociatedPanels();
+
+ for (int a = 0; a < aps.length; a++)
+ {
+ if (aps[a].av.getSelectionGroup() != null)
+ {
+ aps[a].av.getSelectionGroup().addOrRemove(found, true);
+ }
+ else
+ {
+ aps[a].av.setSelectionGroup(new SequenceGroup());
+ aps[a].av.getSelectionGroup().addOrRemove(found, true);
+ aps[a].av.getSelectionGroup().setEndRes(
+ aps[a].av.getAlignment().getWidth() - 1);
+ }
+ }
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // canonical selection is sent to other listeners
+ av.sendSelection();
+ }
+
+ 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(null)
+ .contains(sp.sequence))
+ {
+ av.getSelectionGroup().addSequence(sp.sequence, true);
+ }
+ }
+ }
+ }
+
+ // if (changedSel) {
+ // fireSequenceSelectionEvent(av.getSelection());
+ // }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param x
+ * DOCUMENT ME!
+ * @param y
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceI findPoint(int x, int y)
+ {
+ int halfwidth = getWidth() / 2;
+ int halfheight = getHeight() / 2;
+
+ int found = -1;
+
+ for (int i = 0; i < npoint; i++)
+ {
+ SequencePoint sp = (SequencePoint) points.elementAt(i);
+ int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+ + halfwidth;
+ int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+ + halfheight;
+
+ if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
+ {
+ found = i;
+ }
+ }
+
+ if (found != -1)
+ {
+ return ((SequencePoint) points.elementAt(found)).sequence;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ AlignmentPanel[] getAssociatedPanels()
+ {
+ if (applyToAllViews)
+ {
+ return PaintRefresher.getAssociatedPanels(av.getSequenceSetId());
+ }
+ else
+ {
+ return new AlignmentPanel[] { ap };
+ }
+ }
+
+ /**
+ *
+ * @return x,y,z positions of point s (index into points) under current
+ * transform.
+ */
+ public double[] getPointPosition(int s)
+ {
+ double pts[] = new double[3];
+ float[] p = ((SequencePoint) points.elementAt(s)).coord;
+ pts[0] = p[0];
+ pts[1] = p[1];
+ pts[2] = p[2];
+ return pts;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff