/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* 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 .
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
import java.awt.font.LineMetrics;
import java.awt.geom.AffineTransform;
import java.awt.image.*;
import java.util.Hashtable;
import javax.swing.*;
import jalview.analysis.AAFrequency;
import jalview.datamodel.*;
import jalview.schemes.ColourSchemeI;
/**
* 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;
BufferedImage image;
BufferedImage fadedImage;
Graphics2D gg;
FontMetrics fm;
int imgWidth = 0;
boolean fastPaint = false;
// Used For mouse Dragging and resizing graphs
int graphStretch = -1;
int graphStretchY = -1;
int min; // used by mouseDragged to see if user
int max; // used by mouseDragged to see if user
boolean mouseDragging = false;
boolean MAC = false;
/**
* Creates a new AnnotationPanel object.
*
* @param ap
* DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
MAC = new jalview.util.Platform().isAMac();
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());
}
/**
* Calculates the height of the annotation displayed in the annotation panel.
* Callers should normally call the ap.adjustAnnotationHeight method to ensure
* all annotation associated components are updated correctly.
*
*/
public int adjustPanelHeight()
{
// setHeight of panels
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int height = 0;
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
if (aa[i] == null)
{
System.err.println("Null annotation row: ignoring.");
continue;
}
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));
if (ap != null)
{
// revalidate only when the alignment panel is fully constructed
ap.validate();
}
return height;
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if (aa==null)
{
return;
}
Annotation[] anot = aa[activeRow].annotations;
if (anot.length < av.getColumnSelection().getMax())
{
Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
System.arraycopy(anot, 0, temp, 0, anot.length);
anot = temp;
aa[activeRow].annotations = anot;
}
if (evt.getActionCommand().equals(REMOVE))
{
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
anot[av.getColumnSelection().columnAt(i)] = null;
}
}
else if (evt.getActionCommand().equals(LABEL))
{
String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
String label = JOptionPane.showInputDialog(this, "Enter label",
exMesg);
if (label == null)
{
return;
}
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
// null exceptions
// aren't raised
// elsewhere.
}
else
{
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 < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.colSel.isVisible(index))
continue;
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 < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
anot[index].secondaryStructure = type;
anot[index].displayCharacter = label;
}
}
adjustPanelHeight();
repaint();
return;
}
private String collectAnnotVals(Annotation[] anot,
ColumnSelection columnSelection, String label2)
{
String collatedInput = "";
String last = "";
for (int i = 0; i < columnSelection.size(); i++)
{
int index = columnSelection.columnAt(i);
// always check for current display state - just in case
if (!av.colSel.isVisible(index))
continue;
String tlabel = null;
if (anot[index] != null)
{
if (label2.equals(HELIX) || label2.equals(SHEET)
|| label2.equals(LABEL))
{
tlabel = anot[index].description;
if (tlabel == null || tlabel.length() < 1)
{
if (label2.equals(HELIX) || label2.equals(SHEET))
{
tlabel = "" + anot[index].secondaryStructure;
}
else
{
tlabel = "" + anot[index].displayCharacter;
}
}
}
if (tlabel != null && !tlabel.equals(last))
{
if (last.length() > 0)
{
collatedInput += " ";
}
collatedInput += tlabel;
}
}
}
return collatedInput;
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if (aa == null)
{
return;
}
int height = 0;
activeRow = -1;
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)
{
// Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
break;
}
}
if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)
{
if (av.getColumnSelection() == 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;
}
ap.scalePanel.mousePressed(evt);
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
ap.scalePanel.mouseReleased(evt);
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
ap.scalePanel.mouseEntered(evt);
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(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 < 0)
{
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
adjustPanelHeight();
ap.paintAlignment(true);
}
else
{
ap.scalePanel.mouseDragged(evt);
}
}
/**
* DOCUMENT ME!
*
* @param evt
* DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
if (aa == null)
{
this.setToolTipText(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;
}
}
if (row == -1)
{
this.setToolTipText(null);
return;
}
int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
if (av.hasHiddenColumns)
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
if (row > -1 && aa[row].annotations != null
&& res < (int) aa[row].annotations.length)
{
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 + "
");
}
}
if (tip.length() != 6)
{
tip.setLength(tip.length() - 4);
this.setToolTipText(tip.toString() + "");
}
}
else if (aa[row].annotations[res] != null
&& aa[row].annotations[res].description != null
&& aa[row].annotations[res].description.length() > 0)
{
this.setToolTipText(aa[row].annotations[res].description);
}
else
{
// clear the tooltip.
this.setToolTipText(null);
}
if (aa[row].annotations[res] != null)
{
StringBuffer text = new StringBuffer("Sequence position "
+ (res + 1));
if (aa[row].annotations[res].description != null)
{
text.append(" " + aa[row].annotations[res].description);
}
ap.alignFrame.statusBar.setText(text.toString());
}
}
else
{
this.setToolTipText(null);
}
}
/**
* 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 (imgWidth < 1)
return;
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();
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, image.getHeight());
}
drawComponent(gg, av.startRes, av.endRes + 1);
g.drawImage(image, 0, 0, this);
}
/**
* non-Thread safe repaint
*
* @param horizontal
* repaint with horizontal shift in alignment
*/
public void fastPaint(int horizontal)
{
if ((horizontal == 0) || gg == null
|| av.alignment.getAlignmentAnnotation() == null
|| av.alignment.getAlignmentAnnotation().length < 1
|| av.updatingConsensus || av.updatingConservation)
{
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)
{
if (av.updatingConsensus || av.updatingConservation)
{
if (image == null)
{
return;
}
// We'll keep a record of the old image,
// and draw a faded image until the calculation
// has completed
if (fadedImage == null || fadedImage.getWidth() != imgWidth
|| fadedImage.getHeight() != image.getHeight())
{
fadedImage = new BufferedImage(imgWidth, image.getHeight(),
BufferedImage.TYPE_INT_RGB);
Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
fadedG.setColor(Color.white);
fadedG.fillRect(0, 0, imgWidth, image.getHeight());
fadedG.setComposite(AlphaComposite.getInstance(
AlphaComposite.SRC_OVER, .3f));
fadedG.drawImage(image, 0, 0, this);
}
}
else
{
fadedImage = null;
}
g.setColor(Color.white);
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
g.setFont(av.getFont());
if (fm == null)
{
fm = g.getFontMetrics();
}
if ((av.alignment.getAlignmentAnnotation() == null)
|| (av.alignment.getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
g.setColor(Color.black);
if (av.validCharWidth)
{
g.drawString("Alignment has no annotations", 20, 15);
}
return;
}
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int x = 0, y = 0;
int column = 0;
char lastSS;
int lastSSX;
int iconOffset = 0;
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
boolean[] graphGroupDrawn = new boolean[aa.length];
int charOffset = 0; // offset for a label
float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
// column.
Font ofont = g.getFont();
// \u03B2 \u03B1
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
if (!row.visible)
{
continue;
}
centreColLabels = row.centreColLabels || centreColLabelsDef;
labelAllCols = row.showAllColLabels;
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
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)
{
iconOffset = av.charHeight - fm.getDescent();
y -= av.charHeight;
}
}
else if (row.hasText)
{
iconOffset = av.charHeight - fm.getDescent();
}
else
{
iconOffset = 0;
}
if (av.updatingConsensus && aa[i] == av.consensus)
{
y += av.charHeight;
g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- row.height, imgWidth, y, this);
g.setColor(Color.black);
// g.drawString("Calculating Consensus....",20, y-row.height/2);
continue;
}
else if (av.updatingConservation
&& aa[i].label.equals("Conservation"))
{
y += av.charHeight;
g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- row.height, imgWidth, y, this);
g.setColor(Color.black);
// g.drawString("Calculating Conservation.....",20, y-row.height/2);
continue;
}
else if (av.updatingConservation && aa[i].label.equals("Quality"))
{
y += av.charHeight;
g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- row.height, imgWidth, y, this);
g.setColor(Color.black);
// / g.drawString("Calculating Quality....",20, y-row.height/2);
continue;
}
x = 0;
while (x < endRes - startRes)
{
if (av.hasHiddenColumns)
{
column = av.getColumnSelection().adjustForHiddenColumns(
startRes + x);
if (column > row.annotations.length - 1)
{
break;
}
}
else
{
column = startRes + x;
}
if ((row.annotations == null) || (row.annotations.length <= column)
|| (row.annotations[column] == null))
{
validRes = false;
}
else
{
validRes = true;
}
if (activeRow == i)
{
g.setColor(Color.red);
if (av.getColumnSelection() != null)
{
for (int n = 0; n < av.getColumnSelection().size(); n++)
{
int v = av.getColumnSelection().columnAt(n);
if (v == column)
{
g
.fillRect(x * av.charWidth, y, av.charWidth,
av.charHeight);
}
}
}
}
if (av.validCharWidth && validRes
&& row.annotations[column].displayCharacter != null
&& (row.annotations[column].displayCharacter.length() > 0))
{
if (centreColLabels || scaleColLabel)
{
fmWidth = (float) fm.charsWidth(
row.annotations[column].displayCharacter.toCharArray(),
0, row.annotations[column].displayCharacter.length());
if (scaleColLabel)
{
// justify the label and scale to fit in column
if (fmWidth > av.charWidth)
{
// scale only if the current font isn't already small enough
fmScaling = av.charWidth;
fmScaling /= fmWidth;
g.setFont(ofont.deriveFont(AffineTransform
.getScaleInstance(fmScaling, 1.0)));
// and update the label's width to reflect the scaling.
fmWidth = av.charWidth;
}
}
}
else
{
fmWidth = (float) fm
.charWidth(row.annotations[column].displayCharacter
.charAt(0));
}
charOffset = (int) ((av.charWidth - fmWidth) / 2f);
if (row.annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(row.annotations[column].colour);
if (column == 0 || row.graph > 0)
{
g.drawString(row.annotations[column].displayCharacter,
(x * av.charWidth) + charOffset, y + iconOffset);
}
else if (row.annotations[column - 1] == null
|| (labelAllCols
|| !row.annotations[column].displayCharacter
.equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
.length() < 2 && row.annotations[column].secondaryStructure == ' ')))
{
g.drawString(row.annotations[column].displayCharacter, x
* av.charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
}
if (row.hasIcons)
{
if (!validRes
|| (row.annotations[column].secondaryStructure != lastSS))
{
switch (lastSS)
{
case 'H':
g.setColor(HELIX_COLOUR);
if (MAC)
{
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
g.fillRoundRect(lastSSX, y + 4 + iconOffset,
(x * av.charWidth) - lastSSX, 7, 8, 8);
break;
}
int sCol = (lastSSX / av.charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * av.charWidth);
if (sCol == 0
|| row.annotations[sCol - 1] == null
|| row.annotations[sCol - 1].secondaryStructure != 'H')
{
g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
180);
x1 += av.charWidth / 2;
}
if (!validRes || row.annotations[column] == null
|| row.annotations[column].secondaryStructure != 'H')
{
g.fillArc((x * av.charWidth) - av.charWidth, y + 4
+ iconOffset, av.charWidth, 8, 270, 180);
x2 -= av.charWidth / 2;
}
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
break;
case 'E':
g.setColor(SHEET_COLOUR);
g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
- lastSSX - 4, 7);
g.fillPolygon(new int[]
{ (x * av.charWidth) - 4, (x * av.charWidth) - 4,
(x * av.charWidth) }, new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
3);
break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- lastSSX, 2);
break;
}
if (validRes)
{
lastSS = row.annotations[column].secondaryStructure;
}
else
{
lastSS = ' ';
}
lastSSX = (x * av.charWidth);
}
}
column++;
x++;
}
if (column >= row.annotations.length)
{
column = row.annotations.length - 1;
validEnd = false;
}
else
{
validEnd = true;
}
// x ++;
if (row.hasIcons)
{
switch (lastSS)
{
case 'H':
g.setColor(HELIX_COLOUR);
if (MAC)
{
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
- lastSSX, 7, 8, 8);
break;
}
int sCol = (lastSSX / av.charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * av.charWidth);
if (sCol == 0 || row.annotations[sCol - 1] == null
|| row.annotations[sCol - 1].secondaryStructure != 'H')
{
g
.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
90, 180);
x1 += av.charWidth / 2;
}
if (row.annotations[column] == null
|| row.annotations[column].secondaryStructure != 'H')
{
g.fillArc((x * av.charWidth) - av.charWidth,
y + 4 + iconOffset, av.charWidth, 8, 270, 180);
x2 -= av.charWidth / 2;
}
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
break;
case 'E':
g.setColor(SHEET_COLOUR);
if (!validEnd || row.annotations[endRes] == null
|| row.annotations[endRes].secondaryStructure != 'E')
{
g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
- lastSSX - 4, 7);
g.fillPolygon(new int[]
{ (x * av.charWidth) - 4, (x * av.charWidth) - 4,
(x * av.charWidth) }, new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
}
else
{
g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth
- lastSSX, 7);
}
break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- lastSSX, 2);
break;
}
}
if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
{
float groupmax = -999999, groupmin = 9999999;
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup != row.graphGroup)
{
continue;
}
if (aa[gg] != row)
{
aa[gg].visible = false;
}
if (aa[gg].graphMax > groupmax)
{
groupmax = aa[gg].graphMax;
}
if (aa[gg].graphMin < groupmin)
{
groupmin = aa[gg].graphMin;
}
}
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == row.graphGroup)
{
drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
groupmax, row.graphHeight);
}
}
graphGroupDrawn[row.graphGroup] = true;
}
else
{
drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
drawBarGraph(g, row, startRes, endRes, row.graphMin,
row.graphMax, y);
}
}
if (row.graph > 0 && 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 (eRes < av.endRes)
{
eRes++;
}
eRes = Math.min(eRes, aa.annotations.length);
if (sRes == 0)
{
x++;
}
int y1 = y, y2 = y;
float range = max - min;
// //Draw origin
if (min < 0)
{
y2 = y - (int) ((0 - min / range) * graphHeight);
}
g.setColor(Color.gray);
g.drawLine(x - av.charWidth, y2, (eRes - sRes + 1) * av.charWidth, y2);
eRes = Math.min(eRes, aa.annotations.length);
int column;
int aaMax = aa.annotations.length - 1;
while (x < eRes - sRes)
{
column = sRes + x;
if (av.hasHiddenColumns)
{
column = av.getColumnSelection().adjustForHiddenColumns(column);
}
if (column > aaMax)
{
break;
}
if (aa.annotations[column] == null
|| aa.annotations[column - 1] == null)
{
x++;
continue;
}
if (aa.annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(aa.annotations[column].colour);
y1 = y
- (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
y2 = y
- (int) (((aa.annotations[column].value - min) / range) * graphHeight);
g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+ av.charWidth / 2, y2);
x++;
}
if (aa.threshold != null)
{
g.setColor(aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
{ 5f, 3f }, 0f));
y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
int eRes, float min, float max, int y)
{
ColourSchemeI profcolour = av.getGlobalColourScheme();
if (profcolour == null)
{
profcolour = new jalview.schemes.ZappoColourScheme();
}
if (sRes > aa.annotations.length)
{
return;
}
Font ofont = g.getFont();
eRes = Math.min(eRes, aa.annotations.length);
int x = 0, y1 = y, y2 = y;
float range = max - min;
if (min < 0)
{
y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
}
g.setColor(Color.gray);
g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
int column;
int aaMax = aa.annotations.length - 1;
boolean renderHistogram = true, renderProfile = true;
if (aa.autoCalculated && aa.label.startsWith("Consensus"))
{
// TODO: generalise this to have render styles for consensus/profile data
if (aa.groupRef != null)
{
renderHistogram = aa.groupRef.isShowConsensusHistogram();
renderProfile = aa.groupRef.isShowSequenceLogo();
}
else
{
renderHistogram = av.isShowConsensusHistogram();
renderProfile = av.isShowSequenceLogo();
}
}
while (x < eRes - sRes)
{
column = sRes + x;
if (av.hasHiddenColumns)
{
column = av.getColumnSelection().adjustForHiddenColumns(column);
}
if (column > aaMax)
{
break;
}
if (aa.annotations[column] == null)
{
x++;
continue;
}
if (aa.annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(aa.annotations[column].colour);
y1 = y
- (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
if (renderHistogram)
{
if (y1 - y2 > 0)
{
g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
}
else
{
g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
}
}
// draw profile if available
if (aa.annotations[column].value != 0 && renderProfile)
{
int profl[] = getProfileFor(aa, column);
int ht = y1, htn = y2 - y1;// aa.graphHeight;
float wdth;
double ht2 = 0;
char[] dc = new char[1];
LineMetrics lm;
for (int c = 1; profl != null && c < profl[0];)
{
dc[0] = (char) profl[c++];
wdth = av.charWidth;
wdth /= (float) fm.charsWidth(dc, 0, 1);
if (c > 2)
{
ht += (int) ht2;
}
{
// if (aa.annotations[column].value==0) {
// g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
// (ht2=(aa.graphHeight*0.1/av.charHeight)))));
// ht = y2-(int)ht2;
// } else {
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
/ av.charHeight)));
lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
// htn -=ht2;
// }
g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null)
// ? );// try to get a
// colourscheme for the
// group(aa.groupRef.cs==null)
// ? av.textColour2 :
// cs.findColour(dc));
g.drawChars(dc, 0, 1, x * av.charWidth, (int) (ht + lm
.getHeight()));
// ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
}
}
g.setFont(ofont);
}
x++;
}
if (aa.threshold != null)
{
g.setColor(aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
{ 5f, 3f }, 0f));
y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
private int[] getProfileFor(AlignmentAnnotation aa, int column)
{
if (aa.autoCalculated && aa.label.startsWith("Consensus"))
{
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
return AAFrequency.extractProfile(
aa.groupRef.consensusData[column], aa.groupRef
.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
&& av.isShowSequenceLogo())
{
return AAFrequency.extractProfile(av.hconsensus[column], av
.getIgnoreGapsConsensus());
}
}
return null;
}
// used by overview window
public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
int y, int sRes, int eRes)
{
eRes = Math.min(eRes, aa.annotations.length);
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++)
{
if (aa.annotations[j] != null)
{
if (aa.annotations[j].colour == null)
g.setColor(Color.black);
else
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;
}
}
}