/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
package jalview.gui;
import jalview.datamodel.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.image.*;
import java.util.*;
import javax.swing.*;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class AnnotationPanel extends JPanel implements MouseListener,
MouseMotionListener, ActionListener, AdjustmentListener
{
final String HELIX = "Helix";
final String SHEET = "Sheet";
final String LABEL = "Label";
final String REMOVE = "Remove Annotation";
final String COLOUR = "Colour";
final Color HELIX_COLOUR = Color.red.darker();
final Color SHEET_COLOUR = Color.green.darker().darker();
/** DOCUMENT ME!! */
AlignViewport av;
AlignmentPanel ap;
int activeRow = -1;
Vector activeRes;
BufferedImage image;
Graphics2D gg;
FontMetrics fm;
int imgWidth = 0;
boolean fastPaint = false;
//Used For mouse Dragging and resizing graphs
int graphStretch = -1;
int graphStretchY = -1;
/**
* Creates a new AnnotationPanel object.
*
* @param ap DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
this.ap = ap;
av = ap.av;
this.setLayout(null);
addMouseListener(this);
addMouseMotionListener(this);
ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
}
/**
* DOCUMENT ME!
*
* @param evt DOCUMENT ME!
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
ap.alabels.setScrollOffset(-evt.getValue());
}
/**
* DOCUMENT ME!
*/
public int adjustPanelHeight()
{
// setHeight of panels
image = null;
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int height = 0;
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
if (!aa[i].visible)
{
continue;
}
aa[i].height = 0;
if (aa[i].hasText)
{
aa[i].height += av.charHeight;
}
if (aa[i].hasIcons)
{
aa[i].height += 16;
}
if (aa[i].graph>0)
{
aa[i].height += aa[i].graphHeight;
}
if (aa[i].height == 0)
{
aa[i].height = 20;
}
height += aa[i].height;
}
}
else
{
height = 20;
}
this.setPreferredSize(new Dimension(1, height));
return height;
}
/**
* DOCUMENT ME!
*
* @param col DOCUMENT ME!
*/
public void removeEditableColumn(int col)
{
if (activeRow == -1)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if(aa==null)
return;
for (int j = 0; j < aa.length; j++)
{
if (aa[j].editable)
{
activeRow = j;
break;
}
}
}
if ((activeRes != null) && activeRes.contains(String.valueOf(col)))
{
activeRes.removeElement(String.valueOf(col));
}
repaint();
}
/**
* DOCUMENT ME!
*
* @param col DOCUMENT ME!
*/
public void addEditableColumn(int col)
{
if (activeRow == -1)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if(aa==null)
return;
for (int j = 0; j < aa.length; j++)
{
if (aa[j].editable)
{
activeRow = j;
break;
}
}
}
if (activeRes == null)
{
activeRes = new Vector();
}
if (!activeRes.contains(String.valueOf(col)))
{
activeRes.addElement(String.valueOf(col));
}
repaint();
}
/**
* DOCUMENT ME!
*
* @param evt DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
Annotation[] anot = aa[activeRow].annotations;
if (evt.getActionCommand().equals(REMOVE))
{
for (int i = 0; i < activeRes.size(); i++)
{
anot[Integer.parseInt(activeRes.get(i).toString())] = null;
anot[Integer.parseInt(activeRes.get(i).toString())] = null;
}
}
else if (evt.getActionCommand().equals(LABEL))
{
String label = JOptionPane.showInputDialog(this, "Enter Label ",
"Enter label", JOptionPane.QUESTION_MESSAGE);
if (label == null)
{
return;
}
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
for (int i = 0; i < activeRes.size(); i++)
{
int index = Integer.parseInt(activeRes.get(i).toString());
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", ' ', 0);
}
anot[index].displayCharacter = label;
}
}
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
"Choose foreground colour", Color.black);
for (int i = 0; i < activeRes.size(); i++)
{
int index = Integer.parseInt(activeRes.get(i).toString());
if (anot[index] == null)
{
anot[index] = new Annotation("", "", ' ', 0);
}
anot[index].colour = col;
}
}
else // HELIX OR SHEET
{
char type = 0;
String symbol = "\u03B1";
if (evt.getActionCommand().equals(HELIX))
{
type = 'H';
}
else if (evt.getActionCommand().equals(SHEET))
{
type = 'E';
symbol = "\u03B2";
}
if (!aa[activeRow].hasIcons)
{
aa[activeRow].hasIcons = true;
}
String label = JOptionPane.showInputDialog("Enter a label for the structure?",
symbol);
if (label == null)
{
return;
}
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
for (int i = 0; i < activeRes.size(); i++)
{
int index = Integer.parseInt(activeRes.get(i).toString());
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
anot[index].secondaryStructure = type;
anot[index].displayCharacter = label;
}
}
adjustPanelHeight();
activeRes = null;
repaint();
return;
}
/**
* DOCUMENT ME!
*
* @param evt DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
int height = 0;
activeRow = -1;
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if(aa==null)
return;
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
{
height += aa[i].height;
}
if (evt.getY() < height)
{
if (aa[i].editable)
{
activeRow = i;
}
else if(aa[i].graph>0)
{
if(SwingUtilities.isRightMouseButton(evt)
&& aa[i].graphLines!=null
&& aa[i].graphLines.size()>0)
{
SliderPanel sp = new SliderPanel(aa[i], ap);
return;
}
else
{
//Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
activeRes = null;
}
}
else
{
activeRes = null;
}
break;
}
}
if (SwingUtilities.isRightMouseButton(evt))
{
if (activeRes == null)
{
return;
}
JPopupMenu pop = new JPopupMenu("Structure type");
JMenuItem item = new JMenuItem(HELIX);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(SHEET);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(LABEL);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(COLOUR);
item.addActionListener(this);
pop.add(item);
item = new JMenuItem(REMOVE);
item.addActionListener(this);
pop.add(item);
pop.show(this, evt.getX(), evt.getY());
return;
}
if (aa == null)
{
return;
}
int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if (evt.isControlDown() || evt.isAltDown())
{
addEditableColumn(res);
}
else if (evt.isShiftDown())
{
if (activeRes == null)
{
activeRes = new Vector();
}
else
{
int start = Integer.parseInt(activeRes.get(activeRes.size() -
1).toString());
int end = res;
if (end < start)
{
int temp = end;
end = start;
start = temp;
}
for (int n = start; n <= end; n++)
{
addEditableColumn(n);
}
}
}
else
{
activeRes = new Vector();
activeRes.addElement(String.valueOf(res));
}
}
/**
* DOCUMENT ME!
*
* @param evt DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
graphStretchY = -1;
}
/**
* 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 mouseDragged(MouseEvent evt)
{
if(graphStretch>-1)
{
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();
if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;
graphStretchY = evt.getY();
adjustPanelHeight();
ap.repaint();
}
}
/**
* DOCUMENT ME!
*
* @param evt DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if (aa == null)
{
return;
}
int row = -1;
int height = 0;
for (int i = 0; i < aa.length; i++)
{
if (aa[i].visible)
{
height += aa[i].height;
}
if (evt.getY() < height)
{
row = i;
break;
}
}
int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if ((row > -1) && (res < aa[row].annotations.length) &&
(aa[row].annotations[res] != null))
{
if(aa[row].graphGroup>-1)
{
StringBuffer tip = new StringBuffer("");
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)
tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"
" );
}
tip.setLength(tip.length()-4);
this.setToolTipText(tip.toString()+"");
}
else
this.setToolTipText(aa[row].annotations[res].description);
StringBuffer text = new StringBuffer("Sequence position " +
(res + 1) + " " + aa[row].annotations[res].description);
ap.alignFrame.statusBar.setText(text.toString());
}
}
/**
* DOCUMENT ME!
*
* @param evt DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
}
/**
* DOCUMENT ME!
*
* @param g DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
if(image!=null)
{if (fastPaint
|| (getVisibleRect().width != g.getClipBounds().width)
|| (getVisibleRect().height != g.getClipBounds().height))
{
g.drawImage(image, 0, 0, this);
fastPaint = false;
return;
}
}
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
if (image == null || imgWidth != image.getWidth()
|| image.getHeight(this) != getHeight())
{
image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
BufferedImage.TYPE_INT_RGB);
gg = (Graphics2D) image.getGraphics();
if(av.antiAlias)
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
gg.setFont(av.getFont());
fm = gg.getFontMetrics();
}
drawComponent(gg, av.startRes, av.endRes + 1);
g.drawImage(image, 0, 0, this);
}
/**
* DOCUMENT ME!
*
* @param horizontal DOCUMENT ME!
*/
public void fastPaint(int horizontal)
{
if ((horizontal == 0) || gg==null ||
(av.alignment.getAlignmentAnnotation() == null) ||
(av.alignment.getAlignmentAnnotation().length < 1))
{
repaint();
return;
}
gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
int sr = av.startRes;
int er = av.endRes + 1;
int transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
transX = (er - sr - horizontal) * av.charWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
{
er = sr - horizontal;
}
gg.translate(transX, 0);
drawComponent(gg, sr, er);
gg.translate(-transX, 0);
fastPaint = true;
repaint();
}
/**
* DOCUMENT ME!
*
* @param g DOCUMENT ME!
* @param startRes DOCUMENT ME!
* @param endRes DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
g.setFont(av.getFont());
if (fm == null)
fm = g.getFontMetrics();
g.setColor(Color.white);
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
if ((av.alignment.getAlignmentAnnotation() == null) ||
(av.alignment.getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
g.setColor(Color.black);
g.drawString("Alignment has no annotations", 20, 15);
return;
}
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int j;
int x = 0;
int y = 0;
char[] lastSS = new char[aa.length];
int[] lastSSX = new int[aa.length];
int iconOffset = av.charHeight / 2;
boolean validRes = false;
boolean [] graphGroupDrawn = new boolean[aa.length];
//\u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
if (!row.visible)
{
continue;
}
if (row.graph>0)
{
if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
continue;
// this is so that we draw the characters below the graph
y += row.height;
if (row.hasText)
{
y -= av.charHeight;
}
}
if (row.hasText)
{
iconOffset = av.charHeight / 2;
}
else
{
iconOffset = 0;
}
for (j = startRes; j < endRes; j++)
{
if ((row.annotations.length <= j) ||
(row.annotations[j] == null))
{
validRes = false;
}
else
{
validRes = true;
}
x = (j - startRes) * av.charWidth;
if (activeRow == i)
{
g.setColor(Color.red);
if (activeRes != null)
{
for (int n = 0; n < activeRes.size(); n++)
{
int v = Integer.parseInt(activeRes.get(n).toString());
if (v == j)
{
g.fillRect((j - startRes) * av.charWidth, y,
av.charWidth, row.height);
}
}
}
}
if (validRes &&
(row.annotations[j].displayCharacter.length() > 0))
{
int charOffset = (av.charWidth -
fm.charWidth(row.annotations[j].displayCharacter.charAt(
0))) / 2;
g.setColor(row.annotations[j].colour);
if (j == 0 || row.graph>0)
{
g.drawString(row.annotations[j].displayCharacter, x+charOffset,
y + iconOffset + 3);
}
else if (((row.annotations[j - 1] == null) ||
(row.annotations[j].displayCharacter != row.annotations[j -
1].displayCharacter)))
{
g.drawString(row.annotations[j].displayCharacter, x+charOffset,
y + iconOffset + 3);
}
}
if (row.hasIcons)
{
if (!validRes ||
(row.annotations[j].secondaryStructure != lastSS[i]))
{
switch (lastSS[i])
{
case 'H':
g.setColor(HELIX_COLOUR);
g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
x - lastSSX[i], 7, 8, 8);
break;
case 'E':
g.setColor(SHEET_COLOUR);
g.fillRect(lastSSX[i], y + 4 + iconOffset,
x - lastSSX[i] - 4, 7);
g.fillPolygon(new int[] { x - 4, x - 4, x },
new int[]
{
y + iconOffset, y + 14 + iconOffset,
y + 8 + iconOffset
}, 3);
break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX[i], y + 6 + iconOffset,
x - lastSSX[i], 2);
break;
}
if (validRes)
{
lastSS[i] = row.annotations[j].secondaryStructure;
}
else
{
lastSS[i] = ' ';
}
lastSSX[i] = x;
}
}
}
x += av.charWidth;
if (row.hasIcons)
{
switch (lastSS[i])
{
case 'H':
g.setColor(HELIX_COLOUR);
g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
x - lastSSX[i], 7, 8, 8);
break;
case 'E':
g.setColor(SHEET_COLOUR);
if (row.annotations[endRes].secondaryStructure != 'E')
{
g.fillRect(lastSSX[i], y + 4 + iconOffset,
x - lastSSX[i] - 4, 7);
g.fillPolygon(new int[]
{x - 4, x - 4, x},
new int[]
{
y + iconOffset, y + 14 + iconOffset,
y + 7 + iconOffset
}, 3);
}
else
g.fillRect(lastSSX[i], y + 4 + iconOffset,
x - lastSSX[i], 7);
break;
case 'C':
break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
break;
}
}
if (row.graph>0)
{
if(row.graph == AlignmentAnnotation.LINE_GRAPH )
{
if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
{
float groupmax=-999999, groupmin=9999999;
for(int gg=0; gggroupmax)
groupmax = aa[gg].graphMax;
if(aa[gg].graphMin0 && row.hasText)
{
y += av.charHeight;
}
if (row.graph==0)
{
y += aa[i].height;
}
}
}
public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
int sRes, int eRes,
int y,
float min, float max,
int graphHeight)
{
if(sRes>aa.annotations.length)
return;
int x = 0;
//Adjustment for fastpaint to left
if(eResaa.annotations.length)
return;
int x=0, y1, y2;
float range = max - min;
if(aa.graphLines!=null)
{
for(int l=0; l0)
g.fillRect(x, y2, av.charWidth, y1-y2 );
else
g.fillRect(x, y1, av.charWidth, y2-y1 );
x += av.charWidth;
}
}
// used by overview window
public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
{
g.setColor(Color.white);
g.fillRect(0, 0, width, y);
g.setColor(new Color(0, 0, 180));
int x = 0, height;
for (int j = sRes; j < eRes; j++)
{
g.setColor(aa.annotations[j].colour);
height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
if(height>y)
height = y;
g.fillRect(x, y - height, av.charWidth, height);
x += av.charWidth;
}
}
}