/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.*;
import java.awt.event.*;
+import java.awt.font.LineMetrics;
+import java.awt.geom.AffineTransform;
+
+import jalview.analysis.AAFrequency;
import jalview.datamodel.*;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
import jalview.schemes.ColourSchemeI;
-public class AnnotationPanel extends Panel implements AdjustmentListener,
+public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener,
ActionListener, MouseListener, MouseMotionListener
{
AlignViewport av;
boolean MAC = false;
+ public final AnnotationRenderer renderer;
+
public AnnotationPanel(AlignmentPanel ap)
{
MAC = new jalview.util.Platform().isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
- adjustPanelHeight();
+ int height = adjustPanelHeight();
+ ap.apvscroll.setValues(0, getSize().height, 0, height);
addMouseMotionListener(this);
addMouseListener(this);
// ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+ renderer = new AnnotationRenderer();
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
+ renderer = new AnnotationRenderer();
}
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset(-evt.getValue());
}
/**
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if (aa==null)
+ if (aa == null)
{
return;
}
return;
}
- int height = 0;
+ int height = -scrollOffset;
activeRow = -1;
for (int i = 0; i < aa.length; i++)
if (needValidating)
{
ap.validate();
- needValidating=false;
+ needValidating = false;
}
ap.scalePanel.mouseReleased(evt);
}
public void mouseClicked(MouseEvent evt)
{
}
- boolean needValidating=false;
+
+ boolean needValidating = false;
+
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
- adjustPanelHeight();
- needValidating=true;
+ calcPanelHeight();
+ needValidating = true;
ap.paintAlignment(true);
}
else
}
int row = -1;
- int height = 0;
+ int height = -scrollOffset;
for (int i = 0; i < aa.length; i++)
{
public int adjustPanelHeight()
{
+ return adjustPanelHeight(true);
+ }
+
+ public int adjustPanelHeight(boolean repaint)
+ {
+ int height = calcPanelHeight();
+ this.setSize(new Dimension(getSize().width, height));
+ if (repaint)
+ {
+ repaint();
+ }
+ return height;
+ }
+ /**
+ * calculate the height for visible annotation, revalidating bounds where necessary
+ * ABSTRACT GUI METHOD
+ * @return total height of annotation
+ */
+ public int calcPanelHeight()
+ {
// setHeight of panels
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int height = 0;
height += aa[i].height;
}
}
- if (height==0)
+ if (height == 0)
{
height = 20;
}
- this.setSize(getSize().width, height);
- repaint();
return height;
public void paint(Graphics g)
{
-
- imgWidth = getSize().width;
+ Dimension d = getSize();
+ imgWidth = d.width;
// (av.endRes - av.startRes + 1) * av.charWidth;
-
- if (image == null || imgWidth != image.getWidth(this))
+ if (imgWidth<1 || d.height<1)
{
- image = createImage(imgWidth, ap.annotationPanel.getSize().height);
+ return;
+ }
+ if (image == null || imgWidth != image.getWidth(this) || d.height != image.getHeight(this))
+ {
+ image = createImage(imgWidth, d.height);
gg = image.getGraphics();
gg.setFont(av.getFont());
fm = gg.getFontMetrics();
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;
- }
- }
+ g.translate(0, -scrollOffset);
+ renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
+ g.translate(0, +scrollOffset);
}
+
+ int scrollOffset = 0;
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, int y, float min, float max, int graphHeight)
+ public void setScrollOffset(int value)
{
- 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);
- }
+ scrollOffset = value;
+ repaint();
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, float min, float max, int y)
+ @Override
+ public FontMetrics getFontMetrics()
{
- 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 && c<profl[0];) { dc[0] = (char) profl[c++];
- * wdth = av.charWidth; wdth/=(float) fm .charsWidth(dc,0,1);
- *
- * if (c>2) { 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);
- }
+ return fm;
}
- /*
- * 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)
+ @Override
+ public Image getFadedImage()
{
- 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);
+ return image;
+ }
- 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;
- }
+ @Override
+ public int getFadedImageWidth()
+ {
+ return imgWidth;
}
}