/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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 java.awt.image.*;
import java.util.Hashtable;
import javax.swing.*;
-import com.stevesoft.pat.Regex;
-
import jalview.analysis.AAFrequency;
import jalview.analysis.StructureFrequency;
import jalview.datamodel.*;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class AnnotationPanel extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener, AdjustmentListener
+public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
+ MouseListener, MouseMotionListener, ActionListener,
+ AdjustmentListener
{
final String HELIX = "Helix";
final String COLOUR = "Colour";
- final Color HELIX_COLOUR = Color.red.darker();
+ public final Color HELIX_COLOUR = Color.red.darker();
- final Color SHEET_COLOUR = Color.green.darker().darker();
+ public final Color SHEET_COLOUR = Color.green.darker().darker();
- final Color STEM_COLOUR = Color.blue.darker();
+ public final Color STEM_COLOUR = Color.blue.darker();
/** DOCUMENT ME!! */
- AlignViewport av;
+ public AlignViewport av;
AlignmentPanel ap;
- int activeRow = -1;
+ public int activeRow = -1;
- BufferedImage image;
+ public BufferedImage image;
- BufferedImage fadedImage;
+ public BufferedImage fadedImage;
Graphics2D gg;
- FontMetrics fm;
+ public FontMetrics fm;
- int imgWidth = 0;
+ public int imgWidth = 0;
boolean fastPaint = false;
int cursorY = 0;
+ public final AnnotationRenderer renderer;
+
/**
* Creates a new AnnotationPanel object.
*
addMouseMotionListener(this);
ap.annotationScroller.getVerticalScrollBar()
.addAdjustmentListener(this);
+ renderer = new AnnotationRenderer();
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
+ renderer = new AnnotationRenderer();
}
/**
public int calcPanelHeight()
{
// setHeight of panels
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int height = 0;
if (aa != null)
*/
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
continue;
if (anot[index] == null)
anot[index].displayCharacter = label;
}
}
+ aa[activeRow].validateRangeAndDisplay();
adjustPanelHeight();
repaint();
{
String collatedInput = "";
String last = "";
+ // TODO: refactor and save av.getColumnSelection for efficiency
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))
+ if (!av.getColumnSelection().isVisible(index))
continue;
String tlabel = null;
if (anot[index] != null)
public void mousePressed(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
/*
* Just display the needed structure options
*/
- if (av.alignment.isNucleotide() == true)
+ if (av.getAlignment().isNucleotide() == true)
{
item = new JMenuItem(STEM);
item.addActionListener(this);
{
if (graphStretch > -1)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- evt.getY();
- if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
adjustPanelHeight();
*/
public void mouseMoved(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
{
if (activeRow != -1)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
AlignmentAnnotation anot = aa[activeRow];
if (anot.description.equals("secondary structure"))
{
if ((horizontal == 0) || gg == null
- || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1
- || av.updatingConsensus || av.updatingConservation)
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1
+ || av.isCalcInProgress())
{
repaint();
return;
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
- if (av.updatingConsensus || av.updatingConservation)
+ if (av.isCalcInProgress())
{
if (image == null)
{
fm = g.getFontMetrics();
}
- if ((av.alignment.getAlignmentAnnotation() == null)
- || (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
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;
- }
-
- // first pass sets up state for drawing continuation from left-hand column
- // of startRes
- x = (startRes == 0) ? 0 : -1;
- 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 (x > -1)
- {
- 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)
- {
- char ss = row.annotations[column].secondaryStructure;
- if (ss == 'S')
- {
- // distinguish between forward/backward base-pairing
- if (row.annotations[column].displayCharacter.indexOf(')') > -1)
- {
- ss = 's';
- }
- }
- if (!validRes || (ss != lastSS))
- {
- if (x > -1)
- {
- switch (lastSS)
- {
- case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- - lastSSX, 2);
-
- break;
- }
- }
- if (validRes)
- {
- lastSS = ss;
- }
- else
- {
- lastSS = ' ';
- }
- if (x > -1)
- {
- 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':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
- case 's':
- case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- break;
- default:
- drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
- 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;
- }
- }
- }
-
- private void drawStemAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(STEM_COLOUR);
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
- Regex closeparen = new Regex("(\\))");
-
- String dc = column == 0 ? ""
- : row.annotations[column - 1].displayCharacter;
-
- boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null
- || !dc.equals(row.annotations[sCol - 1].displayCharacter);
- boolean diffdownstream = !validRes || !validEnd
- || row.annotations[column] == null
- || !dc.equals(row.annotations[column].displayCharacter);
- // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
- // If a closing base pair half of the stem, display a backward arrow
- if (column > 0 && closeparen.search(dc))
- {
- if (diffupstream)
- // if (validRes && column>1 && row.annotations[column-2]!=null &&
- // dc.equals(row.annotations[column-2].displayCharacter))
- {
- g.fillPolygon(new int[]
- { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
- x1 += 5;
- }
- if (diffdownstream)
- {
- x2 -= 1;
- }
- }
- else
- {
- // display a forward arrow
- if (diffdownstream)
- {
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
- x2 -= 5;
- }
- if (diffupstream)
- {
- x1 += 1;
- }
- }
- // draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
- }
-
- private void drawGlyphLine(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(Color.gray);
- g
- .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- - lastSSX, 2);
- }
-
- private void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(SHEET_COLOUR);
-
- if (!validEnd || !validRes || row.annotations[column] == null
- || row.annotations[column].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);
- }
-
- }
-
- private void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
- {
- g.setColor(HELIX_COLOUR);
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (MAC)
- {
- int ofs = av.charWidth / 2;
- // Off by 1 offset when drawing rects and ovals
- // to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- }
- else
- {
- // g.setColor(Color.orange);
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
- 0, 0);
- }
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
- {
-
- }
- else
- {
- // g.setColor(Color.magenta);
- g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
- + 1, 8, 0, 0);
-
- }
-
- return;
- }
-
- 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);
+ renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, int y, float min, float max, int graphHeight)
+ @Override
+ public FontMetrics getFontMetrics()
{
- 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());
- }
+ return fm;
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, float min, float max, int y)
+ @Override
+ public Image getFadedImage()
{
- 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 (renderProfile && aa.annotations[column].value != 0)
- {
-
- int profl[] = getProfileFor(aa, column);
- // just try to draw the logo if profl is not null
- if (profl != null)
- {
-
- /*
- * if (profl != null) {
- *
- * for (int i = 0; i < profl.length; i++) { System.out.print(profl[i]
- * + ","); }
- *
- * }
- */
- int ht = y1, htn = y2 - y1;// aa.graphHeight;
- float wdth;
- double ht2 = 0;
- char[] dc;
-
- /**
- * profl.length == 11 indicates that the profile of a secondary
- * structure conservation row was accesed.
- * Therefore dc gets length 2, to have space for a basepair instead of
- * just a single nucleotide
- */
- if (profl.length == 22)
- {
- dc = new char[2];
- }
- else
- {
- dc = new char[1];
- }
-
- LineMetrics lm;
- for (int c = 1; profl != null && c < profl[0];)
- {
- dc[0] = (char) profl[c++];
-
- if (aa.label.startsWith("StrucConsensus"))
- {
- dc[1] = 'A';
- }
-
- wdth = av.charWidth;
- wdth /= (float) fm.charsWidth(dc, 0, dc.length);
-
- 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));
- // System.out.println(dc[0]);
-
- g.drawChars(dc, 0, dc.length, 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());
- }
- }
- else
- {
- if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
- {
- if (aa.groupRef != null && aa.groupRef.consensusData != null
- && aa.groupRef.isShowSequenceLogo())
- {
- //TODO check what happens for group selections
- return StructureFrequency.extractProfile(
- aa.groupRef.consensusData[column], aa.groupRef
- .getIgnoreGapsConsensus(),column);
- }
- // TODO extend annotation row to enable dynamic and static profile data
- // to
- // be stored
- if (aa.groupRef == null && aa.sequenceRef == null
- && av.isShowSequenceLogo())
- {
- return StructureFrequency.extractProfile(av.hStrucConsensus[column],
- av.getIgnoreGapsConsensus(),column);
- }
- }
-
- }
- return null;
+ return fadedImage;
}
- // used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
- int y, int sRes, int eRes)
+ @Override
+ public int getFadedImageWidth()
{
- 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;
- }
+ return imgWidth;
}
-
}
git://source.jalview.org / jalview.git / blobdiff