/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* 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.appletgui;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import jalview.datamodel.*;
import jalview.schemes.ColourSchemeI;
public class AnnotationPanel extends Panel implements AdjustmentListener,
ActionListener, MouseListener, MouseMotionListener
{
AlignViewport av;
AlignmentPanel ap;
int activeRow = -1;
Vector activeRes;
static String HELIX = "Helix";
static String SHEET = "Sheet";
static String LABEL = "Label";
static String REMOVE = "Remove Annotation";
static String COLOUR = "Colour";
static Color HELIX_COLOUR = Color.red.darker();
static Color SHEET_COLOUR = Color.green.darker().darker();
Image image;
Graphics gg;
FontMetrics fm;
int imgWidth = 0;
boolean fastPaint = false;
// Used For mouse Dragging and resizing graphs
int graphStretch = -1;
int graphStretchY = -1;
boolean mouseDragging = false;
public static int GRAPH_HEIGHT = 40;
boolean MAC = false;
public AnnotationPanel(AlignmentPanel ap)
{
MAC = new jalview.util.Platform().isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
adjustPanelHeight();
addMouseMotionListener(this);
addMouseListener(this);
// ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
}
public void adjustmentValueChanged(AdjustmentEvent evt)
{
ap.alabels.setScrollOffset(-evt.getValue());
}
/**
* 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;
}
String label = "";
if (av.colSel != null && av.colSel.size() > 0
&& anot[av.colSel.getMin()] != null)
label = anot[av.getColumnSelection().getMin()].displayCharacter;
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))
{
label = enterLabel(label, "Enter Label");
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);
}
anot[index].displayCharacter = label;
}
}
else if (evt.getActionCommand().equals(COLOUR))
{
UserDefinedColours udc = new UserDefinedColours(this, Color.black,
ap.alignFrame);
Color col = udc.getColor();
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;
}
label = enterLabel(symbol, "Enter Label");
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;
}
String enterLabel(String text, String label)
{
EditNameDialog dialog = new EditNameDialog(text, null, label, null,
ap.alignFrame, "Enter Label", 400, 200, true);
if (dialog.accept)
return dialog.getName();
else
return null;
}
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 ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
&& activeRow != -1)
{
if (av.getColumnSelection() == null)
{
return;
}
PopupMenu pop = new PopupMenu("Structure type");
MenuItem item = new MenuItem(HELIX);
item.addActionListener(this);
pop.add(item);
item = new MenuItem(SHEET);
item.addActionListener(this);
pop.add(item);
item = new MenuItem(LABEL);
item.addActionListener(this);
pop.add(item);
item = new MenuItem(COLOUR);
item.addActionListener(this);
pop.add(item);
item = new MenuItem(REMOVE);
item.addActionListener(this);
pop.add(item);
ap.alignFrame.add(pop);
pop.show(this, evt.getX(), evt.getY());
return;
}
if (aa == null)
{
return;
}
ap.scalePanel.mousePressed(evt);
}
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
if (needValidating)
{
ap.validate();
needValidating = false;
}
ap.scalePanel.mouseReleased(evt);
}
public void mouseClicked(MouseEvent evt)
{
}
boolean needValidating = false;
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();
needValidating = true;
ap.paintAlignment(true);
}
else
{
ap.scalePanel.mouseDragged(evt);
}
}
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 (av.hasHiddenColumns)
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
if (row > -1 && res < aa[row].annotations.length
&& 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());
}
}
public void mouseEntered(MouseEvent evt)
{
ap.scalePanel.mouseEntered(evt);
}
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(evt);
}
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].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;
}
}
if (height == 0)
{
height = 20;
}
this.setSize(getSize().width, height);
repaint();
return height;
}
public void addEditableColumn(int i)
{
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();
activeRes.addElement(String.valueOf(i));
return;
}
activeRes.addElement(String.valueOf(i));
}
public void update(Graphics g)
{
paint(g);
}
public void paint(Graphics g)
{
imgWidth = getSize().width;
// (av.endRes - av.startRes + 1) * av.charWidth;
if (image == null || imgWidth != image.getWidth(this))
{
image = createImage(imgWidth, ap.annotationPanel.getSize().height);
gg = image.getGraphics();
gg.setFont(av.getFont());
fm = gg.getFontMetrics();
fastPaint = false;
}
if (fastPaint)
{
g.drawImage(image, 0, 0, this);
fastPaint = false;
return;
}
gg.setColor(Color.white);
gg.fillRect(0, 0, getSize().width, getSize().height);
drawComponent(gg, av.startRes, av.endRes + 1);
g.drawImage(image, 0, 0, this);
}
public void fastPaint(int horizontal)
{
if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null
|| av.alignment.getAlignmentAnnotation().length < 1)
{
repaint();
return;
}
gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
* av.charWidth, 0);
int sr = av.startRes, er = av.endRes + 1, 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)
{
Font ofont = av.getFont();
g.setFont(ofont);
g.setColor(Color.white);
g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
if (fm == null)
{
fm = g.getFontMetrics();
}
if ((av.alignment.getAlignmentAnnotation() == null)
|| (av.alignment.getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
if (av.validCharWidth)
{
g.drawString("Alignment has no annotations", 20, 15);
}
return;
}
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int x = 0;
int y = 0;
int column = 0;
char lastSS;
int lastSSX;
int iconOffset = av.charHeight / 2;
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.
// \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;
}
}
// TODO: else is the logic used in application, applet had no 'else'
else if (row.hasText)
{
iconOffset = av.charHeight - fm.getDescent();
}
else
{
iconOffset = 0;
}
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.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;
// not 1.1 // g.setFont(new
// Font(ofont,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 + 3); // +
// 3?
}
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 + 3); // +3?
}
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 * av.charWidth
- lastSSX, 7);
}
break;
default:
g.setColor(Color.gray);
if (!av.wrapAlignment || endRes == av.endRes)
{
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);
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) * 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) // || coaa.annotations[column - 1] ==
// null)
{
x++;
continue;
}
if (aa.annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(aa.annotations[column].colour);
if (column == 0 || aa.annotations[column - 1] == null)
{
y1 = y
- (int) (((aa.annotations[column].value - min) / range) * graphHeight);
}
else
{
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);
y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
}
}
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 = false;
/*
* Logos are disabled for 2.5 release : Bug # 0060064 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
// Disabled for 2.5 release: see bug #0060064
/**
* 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 && c2) { ht+=(int)ht2; } { // not java 1.1 compatible: Bug # 0060064
* g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
* (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight))); lm =
* g.getFontMetrics().getLineMetrics(dc,0,1, g);
* g.setColor(profcolour.findColour(dc[0]));
* g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight())); } }
* g.setFont(ofont); }
**/
x++;
}
if (aa.threshold != null)
{
g.setColor(aa.threshold.colour);
y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
}
}
/*
* Disabled for 2.5 release - see bug #0060064 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].colour == null)
g.setColor(Color.black);
else
g.setColor(aa.annotations[j].colour);
height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
if (height > y)
{
height = y;
}
g.fillRect(x, y - height, av.charWidth, height);
x += av.charWidth;
}
}
}