/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.RenderingHints;
import java.awt.Stroke;
import java.awt.geom.AffineTransform;
import java.awt.image.ImageObserver;
import java.util.BitSet;
import java.util.Hashtable;
import org.jfree.graphics2d.svg.SVGGraphics2D;
import org.jibble.epsgraphics.EpsGraphics2D;
import jalview.analysis.AAFrequency;
import jalview.analysis.CodingUtils;
import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.ProfilesI;
import jalview.renderer.api.AnnotationRendererFactoryI;
import jalview.renderer.api.AnnotationRowRendererI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
public class AnnotationRenderer
{
private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
private static final int CHAR_A = 'A'; // 65
private static final int CHAR_Z = 'Z'; // 90
/**
* flag indicating if timing and redraw parameter info should be output
*/
private final boolean debugRedraw;
private int charWidth, endRes, charHeight;
private boolean validCharWidth, hasHiddenColumns;
private FontMetrics fm;
private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS();
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
ResidueShaderI profcolour = null;
private ColumnSelection columnSelection;
private HiddenColumns hiddenColumns;
private ProfilesI hconsensus;
private Hashtable[] complementConsensus;
private Hashtable[] hStrucConsensus;
private boolean av_ignoreGapsConsensus;
private boolean renderingVectors = false;
private boolean glyphLineDrawn = false;
/**
* attributes set from AwtRenderPanelI
*/
/**
* old image used when data is currently being calculated and cannot be
* rendered
*/
private Image fadedImage;
/**
* panel being rendered into
*/
private ImageObserver annotationPanel;
/**
* width of image to render in panel
*/
private int imgWidth;
/**
* offset to beginning of visible area
*/
private int sOffset;
/**
* offset to end of visible area
*/
private int visHeight;
/**
* indicate if the renderer should only render the visible portion of the
* annotation given the current view settings
*/
private boolean useClip = true;
/**
* master flag indicating if renderer should ever try to clip. not enabled for
* jalview 2.8.1
*/
private boolean canClip = false;
public AnnotationRenderer()
{
this(false);
}
/**
* Create a new annotation Renderer
*
* @param debugRedraw
* flag indicating if timing and redraw parameter info should be
* output
*/
public AnnotationRenderer(boolean debugRedraw)
{
this.debugRedraw = debugRedraw;
}
/**
* Remove any references and resources when this object is no longer required
*/
public void dispose()
{
hiddenColumns = null;
hconsensus = null;
complementConsensus = null;
hStrucConsensus = null;
fadedImage = null;
annotationPanel = null;
rendererFactoryI = null;
}
void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
: row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
|| dc != row_annotations[sCol - 1].secondaryStructure
|| !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| dc != row_annotations[column].secondaryStructure;
if (diffupstream || diffdownstream)
{
// draw glyphline under arrow
drawGlyphLine(g, lastSSX, x, y, iconOffset);
}
g.setColor(STEM_COLOUR);
if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
/*
* if new annotation with a closing base pair half of the stem,
* display a backward arrow
*/
fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
{ y + iconOffset + 1, y + 13 + iconOffset,
y + 7 + iconOffset },
3);
x1 += 5;
}
if (diffdownstream)
{
x2 -= 1;
}
}
else
{
// display a forward arrow
if (diffdownstream)
{
/*
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
new int[]
{ y + iconOffset + 1, y + 13 + iconOffset,
y + 7 + iconOffset },
3);
x2 -= 5;
}
if (diffupstream)
{
x1 += 1;
}
}
// draw arrow body
unsetAntialias(g);
fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
Annotation[] row_annotations, int lastSSX, int x, int y,
int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
// Console.info(nonCanColor);
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
: row_annotations[column - 1].displayCharacter;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
|| !dc.equals(row_annotations[sCol - 1].displayCharacter)
|| !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
// Console.info("Column "+column+" diff up:
// "+diffupstream+"
// down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
if (diffupstream || diffdownstream)
{
// draw glyphline under arrow
drawGlyphLine(g, lastSSX, x, y, iconOffset);
}
g.setColor(nonCanColor);
if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
{
fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
new int[]
{ y + iconOffset + 1, y + 13 + iconOffset,
y + 7 + iconOffset },
3);
x1 += 5;
}
if (diffdownstream)
{
x2 -= 1;
}
}
else
{
// display a forward arrow
if (diffdownstream)
{
fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
new int[]
{ y + iconOffset + 1, y + 13 + iconOffset,
y + 7 + iconOffset },
3);
x2 -= 5;
}
if (diffupstream)
{
x1 += 1;
}
}
// draw arrow body
unsetAntialias(g);
fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
// av)
public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
AlignViewportI av)
{
fm = annotPanel.getFontMetrics();
annotationPanel = annotPanel;
fadedImage = annotPanel.getFadedImage();
imgWidth = annotPanel.getFadedImageWidth();
// visible area for rendering
int[] bounds = annotPanel.getVisibleVRange();
if (bounds != null)
{
sOffset = bounds[0];
visHeight = bounds[1];
if (visHeight == 0)
{
useClip = false;
}
else
{
useClip = canClip;
}
}
else
{
useClip = false;
}
rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
updateFromAlignViewport(av);
}
public void updateFromAlignViewport(AlignViewportI av)
{
charWidth = av.getCharWidth();
endRes = av.getRanges().getEndRes();
charHeight = av.getCharHeight();
hasHiddenColumns = av.hasHiddenColumns();
validCharWidth = av.isValidCharWidth();
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
av_normaliseProfile = av.isNormaliseSequenceLogo();
profcolour = av.getResidueShading();
if (profcolour == null || profcolour.getColourScheme() == null)
{
/*
* Use default colour for sequence logo if
* the alignment has no colourscheme set
* (would like to use user preference but n/a for applet)
*/
ColourSchemeI col = av.getAlignment().isNucleotide()
? new NucleotideColourScheme()
: new ZappoColourScheme();
profcolour = new ResidueShader(col);
}
columnSelection = av.getColumnSelection();
hiddenColumns = av.getAlignment().getHiddenColumns();
hconsensus = av.getSequenceConsensusHash();
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
}
/**
* Returns profile data; the first element is the profile type, the second is
* the number of distinct values, the third the total count, and the remainder
* depend on the profile type.
*
* @param aa
* @param column
* @return
*/
int[] getProfileFor(AlignmentAnnotation aa, int column)
{
// TODO : consider refactoring the global alignment calculation
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
if (aa.autoCalculated && (aa.label.startsWith("Consensus")
|| aa.label.startsWith("cDNA Consensus")))
{
boolean forComplement = aa.label.startsWith("cDNA Consensus");
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
aa.groupRef.consensusData.get(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)
{
if (forComplement)
{
return AAFrequency.extractCdnaProfile(complementConsensus[column],
av_ignoreGapsConsensus);
}
else
{
return AAFrequency.extractProfile(hconsensus.get(column),
av_ignoreGapsConsensus);
}
}
}
else
{
if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
{
// TODO implement group structure consensus
/*
* 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()); }
*/
// TODO extend annotation row to enable dynamic and static profile data
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
&& hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
av_ignoreGapsConsensus);
}
}
}
return null;
}
boolean rna = false;
private AnnotationRendererFactoryI rendererFactoryI;
/**
* Render the annotation rows associated with an alignment.
*
* @param annotPanel
* container frame
* @param av
* data and view settings to render
* @param g
* destination for graphics
* @param activeRow
* row where a mouse event occured (or -1)
* @param startRes
* first column that will be drawn
* @param endRes
* last column that will be drawn
* @return true if the fadedImage was used for any alignment annotation rows
* currently being calculated
*/
public boolean drawComponent(AwtRenderPanelI annotPanel,
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D)
{
this.setVectorRendering(true);
}
Graphics2D g2d = (Graphics2D) g;
long stime = System.currentTimeMillis();
boolean usedFaded = false;
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to
// AlignViewport
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
// int temp = 0;
if (aa == null)
{
return false;
}
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;
// boolean centreColLabelsDef = av.isCentreColumnLabels();
boolean scaleColLabel = false;
final AlignmentAnnotation consensusAnnot = av
.getAlignmentConsensusAnnotation();
final AlignmentAnnotation structConsensusAnnot = av
.getAlignmentStrucConsensusAnnotation();
final AlignmentAnnotation complementConsensusAnnot = av
.getComplementConsensusAnnotation();
BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
// \u03B2 \u03B1
// debug ints
int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
boolean clipst = false, clipend = false;
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
boolean renderHistogram = true;
boolean renderProfile = false;
boolean normaliseProfile = false;
boolean isRNA = row.isRNA();
// check if this is a consensus annotation row and set the display
// settings appropriately
// TODO: generalise this to have render styles for consensus/profile
// data
if (row.groupRef != null && row == row.groupRef.getConsensus())
{
renderHistogram = row.groupRef.isShowConsensusHistogram();
renderProfile = row.groupRef.isShowSequenceLogo();
normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
}
else if (row == consensusAnnot || row == structConsensusAnnot
|| row == complementConsensusAnnot)
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
normaliseProfile = av_normaliseProfile;
}
Annotation[] row_annotations = row.annotations;
if (!row.visible)
{
continue;
}
// centreColLabels = row.centreColLabels || centreColLabelsDef;
labelAllCols = row.showAllColLabels;
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
if (!useClip || ((y - charHeight) < visHeight
&& (y + row.height + charHeight * 2) >= sOffset))
{// if_in_visible_region
if (!clipst)
{
clipst = true;
yfrom = y;
f_i = i;
}
yto = y;
f_to = i;
if (row.graph > 0)
{
if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
{
continue;
}
// this is so that we draw the characters below the graph
y += row.height;
if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
y -= charHeight;
}
}
else if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
}
else
{
iconOffset = 0;
}
if (row.autoCalculated && av.isCalculationInProgress(row))
{
y += charHeight;
usedFaded = true;
g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
y - row.height, imgWidth, y, annotationPanel);
g.setColor(Color.black);
// g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
continue;
}
/*
* else if (annotationPanel.av.updatingConservation &&
* aa[i].label.equals("Conservation")) {
*
* y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
* row.height, annotationPanel.imgWidth, y, 0, y - row.height,
* annotationPanel.imgWidth, y, annotationPanel);
*
* g.setColor(Color.black); //
* g.drawString("Calculating Conservation.....",20, y-row.height/2);
*
* continue; } else if (annotationPanel.av.updatingConservation &&
* aa[i].label.equals("Quality")) {
*
* y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
* row.height, annotationPanel.imgWidth, y, 0, y - row.height,
* annotationPanel.imgWidth, y, annotationPanel);
* 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
// flag used for vector rendition
this.glyphLineDrawn = false;
x = (startRes == 0) ? 0 : -1;
while (x < endRes - startRes)
{
if (hasHiddenColumns)
{
column = hiddenColumns.visibleToAbsoluteColumn(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;
}
final String displayChar = validRes
? row_annotations[column].displayCharacter
: null;
if (x > -1)
{
unsetAntialias(g);
if (activeRow == i)
{
g.setColor(Color.red);
if (columnSelection != null)
{
if (columnSelection.contains(column))
{
fillRect(g, x * charWidth, y, charWidth, charHeight);
}
}
}
if (row.getInvalidStrucPos() > x)
{
g.setColor(Color.orange);
fillRect(g, x * charWidth, y, charWidth, charHeight);
}
else if (row.getInvalidStrucPos() == x)
{
g.setColor(Color.orange.darker());
fillRect(g, x * charWidth, y, charWidth, charHeight);
}
if (validCharWidth && validRes && displayChar != null
&& (displayChar.length() > 0))
{
// Graphics2D gg = (g);
float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
displayChar.length());
/*
* shrink label width to fit in column, if that is
* both configured and necessary
*/
boolean scaledToFit = false;
float fmScaling = 1f;
if (scaleColLabel && fmWidth > charWidth)
{
scaledToFit = true;
fmScaling = charWidth;
fmScaling /= fmWidth;
// and update the label's width to reflect the scaling.
fmWidth = charWidth;
}
charOffset = (int) ((charWidth - fmWidth) / 2f);
if (row_annotations[column].colour == null)
{
g2d.setColor(Color.black);
}
else
{
g2d.setColor(row_annotations[column].colour);
}
/*
* draw the label, unless it is the same secondary structure
* symbol (excluding RNA Helix) as the previous column
*/
final int xPos = (x * charWidth) + charOffset;
final int yPos = y + iconOffset;
/*
* translate to drawing position _before_ applying any scaling
*/
g2d.translate(xPos, yPos);
if (scaledToFit)
{
/*
* use a scaling transform to make the label narrower
* (JalviewJS doesn't have Font.deriveFont(AffineTransform))
*/
g2d.transform(
AffineTransform.getScaleInstance(fmScaling, 1.0));
}
setAntialias(g);
if (column == 0 || row.graph > 0)
{
g2d.drawString(displayChar, 0, 0);
}
else if (row_annotations[column - 1] == null || (labelAllCols
|| !displayChar.equals(
row_annotations[column - 1].displayCharacter)
|| (displayChar.length() < 2
&& row_annotations[column].secondaryStructure == ' ')))
{
g2d.drawString(displayChar, 0, 0);
}
if (scaledToFit)
{
/*
* undo scaling before translating back
* (restoring saved transform does NOT work in JS PDFGraphics!)
*/
g2d.transform(AffineTransform
.getScaleInstance(1D / fmScaling, 1.0));
}
g2d.translate(-xPos, -yPos);
}
}
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
: '-';
if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (displayChar.indexOf(')') > -1)
{
ss = ')';
}
}
if (ss == '[')
{
if ((displayChar.indexOf(']') > -1))
{
ss = ']';
}
}
if (ss == '{')
{
// distinguish between forward/backward base-pairing
if (displayChar.indexOf('}') > -1)
{
ss = '}';
}
}
if (ss == '<')
{
// distinguish between forward/backward base-pairing
if (displayChar.indexOf('<') > -1)
{
ss = '>';
}
}
if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
{
// distinguish between forward/backward base-pairing
int ssLowerCase = ss + UPPER_TO_LOWER;
// TODO would .equals() be safer here? or charAt(0)?
if (displayChar.indexOf(ssLowerCase) > -1)
{
ss = (char) ssLowerCase;
}
}
if (!validRes || (ss != lastSS))
{
if (x > -1)
{
// int nb_annot = x - temp;
// Console.info("\t type :"+lastSS+"\t x
// :"+x+"\t nbre
// annot :"+nb_annot);
switch (lastSS)
{
case '(': // Stem case for RNA secondary structure
case ')': // and opposite direction
drawStemAnnot(g, row_annotations, lastSSX, x, y,
iconOffset, startRes, column, validRes, validEnd);
// temp = x;
break;
case 'H':
if (!isRNA)
{
drawHelixAnnot(g, row_annotations, lastSSX, x, y,
iconOffset, startRes, column, validRes,
validEnd);
break;
}
// no break if isRNA - falls through to drawNotCanonicalAnnot!
case 'E':
if (!isRNA)
{
drawSheetAnnot(g, row_annotations, lastSSX, x, y,
iconOffset, startRes, column, validRes,
validEnd);
break;
}
// no break if isRNA - fall through to drawNotCanonicalAnnot!
case '{':
case '}':
case '[':
case ']':
case '>':
case '<':
case 'A':
case 'a':
case 'B':
case 'b':
case 'C':
case 'c':
case 'D':
case 'd':
case 'e':
case 'F':
case 'f':
case 'G':
case 'g':
case 'h':
case 'I':
case 'i':
case 'J':
case 'j':
case 'K':
case 'k':
case 'L':
case 'l':
case 'M':
case 'm':
case 'N':
case 'n':
case 'O':
case 'o':
case 'P':
case 'p':
case 'Q':
case 'q':
case 'R':
case 'r':
case 'S':
case 's':
case 'T':
case 't':
case 'U':
case 'u':
case 'V':
case 'v':
case 'W':
case 'w':
case 'X':
case 'x':
case 'Y':
case 'y':
case 'Z':
case 'z':
Color nonCanColor = getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
lastSSX, x, y, iconOffset, startRes, column,
validRes, validEnd);
// temp = x;
break;
default:
if (isVectorRendering())
{
// draw single full width glyphline
drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
// disable more glyph lines
this.glyphLineDrawn = true;
}
else
{
drawGlyphLine(g, lastSSX, x, y, iconOffset);
}
break;
}
}
if (validRes)
{
lastSS = ss;
}
else
{
lastSS = ' ';
}
if (x > -1)
{
lastSSX = (x * charWidth);
}
}
}
column++;
x++;
}
if (column >= row_annotations.length)
{
column = row_annotations.length - 1;
validEnd = false;
}
else
{
validEnd = true;
}
if ((row_annotations == null) || (row_annotations.length <= column)
|| (row_annotations[column] == null))
{
validRes = false;
}
else
{
validRes = true;
}
// x ++;
if (row.hasIcons)
{
switch (lastSS)
{
case 'H':
if (!isRNA)
{
drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
startRes, column, validRes, validEnd);
break;
}
// no break if isRNA - fall through to drawNotCanonicalAnnot!
case 'E':
if (!isRNA)
{
drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
startRes, column, validRes, validEnd);
break;
}
// no break if isRNA - fall through to drawNotCanonicalAnnot!
case '(':
case ')': // Stem case for RNA secondary structure
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
startRes, column, validRes, validEnd);
break;
case '{':
case '}':
case '[':
case ']':
case '>':
case '<':
case 'A':
case 'a':
case 'B':
case 'b':
case 'C':
case 'c':
case 'D':
case 'd':
case 'e':
case 'F':
case 'f':
case 'G':
case 'g':
case 'h':
case 'I':
case 'i':
case 'J':
case 'j':
case 'K':
case 'k':
case 'L':
case 'l':
case 'M':
case 'm':
case 'N':
case 'n':
case 'O':
case 'o':
case 'P':
case 'p':
case 'Q':
case 'q':
case 'R':
case 'r':
case 'T':
case 't':
case 'U':
case 'u':
case 'V':
case 'v':
case 'W':
case 'w':
case 'X':
case 'x':
case 'Y':
case 'y':
case 'Z':
case 'z':
// Console.info(lastSS);
Color nonCanColor = getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
x, y, iconOffset, startRes, column, validRes, validEnd);
break;
default:
if (isVectorRendering())
{
// draw single full width glyphline
drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
// disable more glyph lines
this.glyphLineDrawn = true;
}
else
{
drawGlyphLine(g, lastSSX, x, y, iconOffset);
}
break;
}
}
if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
{
// TODO: JAL-1291 revise rendering model so the graphGroup map is
// computed efficiently for all visible labels
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], aa[gg].annotations, startRes,
endRes, y, groupmin, groupmax, row.graphHeight);
}
}
graphGroupDrawn.set(row.graphGroup);
}
else
{
drawLineGraph(g, row, row_annotations, startRes, endRes, y,
row.graphMin, row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
drawBarGraph(g, row, row_annotations, startRes, endRes,
row.graphMin, row.graphMax, y, renderHistogram,
renderProfile, normaliseProfile);
}
else
{
AnnotationRowRendererI renderer = rendererFactoryI
.getRendererFor(row);
if (renderer != null)
{
renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns,
av, hiddenColumns, columnSelection, row,
row_annotations, startRes, endRes, row.graphMin,
row.graphMax, y);
}
if (debugRedraw)
{
if (renderer == null)
{
System.err
.println("No renderer found for " + row.toString());
}
else
{
Console.warn(
"rendered with " + renderer.getClass().toString());
}
}
}
}
}
else
{
if (clipst && !clipend)
{
clipend = true;
}
} // end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
}
if (row.graph == 0)
{
y += aa[i].height;
}
}
if (debugRedraw)
{
if (canClip)
{
if (clipst)
{
Console.warn("Start clip at : " + yfrom + " (index " + f_i + ")");
}
if (clipend)
{
Console.warn("End clip at : " + yto + " (index " + f_to + ")");
}
}
;
Console.warn("Annotation Rendering time:"
+ (System.currentTimeMillis() - stime));
}
;
return !usedFaded;
}
public static final Color GLYPHLINE_COLOR = Color.gray;
public static final Color SHEET_COLOUR = Color.green;
public static final Color HELIX_COLOUR = Color.red;
public static final Color STEM_COLOUR = Color.blue;
// private Color sdNOTCANONICAL_COLOUR;
void drawGlyphLine(Graphics g, int lastSSX, int x, int y, int iconOffset)
{
if (glyphLineDrawn)
{
// if we've drawn a single long glyphline for an export, don't draw the
// bits
return;
}
unsetAntialias(g);
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
void drawSheetAnnot(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
if (!validEnd || !validRes || row == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
// draw the glyphline underneath
drawGlyphLine(g, lastSSX, x, y, iconOffset);
g.setColor(SHEET_COLOUR);
fillRect(g, lastSSX, y + 4 + iconOffset,
(x * charWidth) - lastSSX - 4, 6);
fillPolygon(g,
new int[]
{ (x * charWidth) - 6, (x * charWidth) - 6,
(x * charWidth - 1) },
new int[]
{ y + iconOffset + 1, y + 13 + iconOffset,
y + 7 + iconOffset },
3);
}
else
{
g.setColor(SHEET_COLOUR);
fillRect(g, lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX,
6);
}
}
void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
int y, int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
int sCol = (lastSSX / charWidth)
+ hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
if (USE_FILL_ROUND_RECT || isVectorRendering())
{
// draw glyph line behind helix (visible in EPS or SVG output)
drawGlyphLine(g, lastSSX, x, y, iconOffset);
g.setColor(HELIX_COLOUR);
setAntialias(g);
int ofs = charWidth / 2;
// Off by 1 offset when drawing rects and ovals
// to offscreen image on the MAC
fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - 1, 8, 8, 8);
if (sCol == 0 || row[sCol - 1] == null
|| row[sCol - 1].secondaryStructure != 'H')
{
}
else
{
fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
0);
}
if (!validRes || row[column] == null
|| row[column].secondaryStructure != 'H')
{
}
else
{
fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
8, 0, 0);
}
return;
}
boolean leftEnd = sCol == 0 || row[sCol - 1] == null
|| row[sCol - 1].secondaryStructure != 'H';
boolean rightEnd = !validRes || row[column] == null
|| row[column].secondaryStructure != 'H';
if (leftEnd || rightEnd)
{
drawGlyphLine(g, lastSSX, x, y, iconOffset);
}
g.setColor(HELIX_COLOUR);
if (leftEnd)
{
fillArc(g, lastSSX, y + 3 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
if (rightEnd)
{
fillArc(g, ((x - 1) * charWidth), y + 3 + iconOffset, charWidth, 8,
270, 180);
x2 -= charWidth / 2;
}
fillRect(g, x1, y + 3 + iconOffset, x2 - x1, 8);
}
void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
float max, int graphHeight)
{
if (sRes > aa_annotations.length)
{
return;
}
Stroke roundStroke = new BasicStroke(1, BasicStroke.CAP_ROUND,
BasicStroke.JOIN_ROUND);
Stroke squareStroke = new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_MITER);
Graphics2D g2d = (Graphics2D) g;
Stroke prevStroke = g2d.getStroke();
g2d.setStroke(roundStroke);
int x = 0;
// Adjustment for fastpaint to left
if (eRes < 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);
drawLine(g, squareStroke, x * charWidth - charWidth, y2,
(eRes - sRes) * 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 (hasHiddenColumns)
{
column = hiddenColumns.visibleToAbsoluteColumn(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);
}
if (aa_annotations[column - 1] == null
&& aa_annotations.length > column + 1
&& aa_annotations[column + 1] == null)
{
// standalone value
y1 = y - (int) (((aa_annotations[column].value - min) / range)
* graphHeight);
drawLine(g, x * charWidth + charWidth / 4, y1,
x * charWidth + 3 * charWidth / 4, y1);
x++;
continue;
}
if (aa_annotations[column - 1] == null)
{
x++;
continue;
}
y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
* graphHeight);
y2 = y - (int) (((aa_annotations[column].value - min) / range)
* graphHeight);
drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
x * charWidth + charWidth / 2, y2);
x++;
}
if (_aa.threshold != null)
{
g.setColor(_aa.threshold.colour);
Graphics2D g2 = (Graphics2D) g;
Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
{ 5f, 3f }, 0f);
y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
g2d.setStroke(prevStroke);
}
@SuppressWarnings("unused")
void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
float max, int y, boolean renderHistogram, boolean renderProfile,
boolean normaliseProfile)
{
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);
drawLine(g, x, y2, (eRes - sRes) * charWidth, y2);
int column;
int aaMax = aa_annotations.length - 1;
while (x < eRes - sRes)
{
column = sRes + x;
if (hasHiddenColumns)
{
column = hiddenColumns.visibleToAbsoluteColumn(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)
{
fillRect(g, x * charWidth, y2, charWidth, y1 - y2);
}
else
{
fillRect(g, x * charWidth, y1, charWidth, y2 - y1);
}
}
// draw profile if available
if (renderProfile)
{
/*
* {profile type, #values, total count, char1, pct1, char2, pct2...}
*/
int profl[] = getProfileFor(_aa, column);
// just try to draw the logo if profl is not null
if (profl != null && profl[2] != 0)
{
boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
final double normaliseFactor = normaliseProfile ? _aa.graphHeight
: (y2 - y1);
/**
* Render a single base for a sequence profile, a base pair for
* structure profile, and a triplet for a cdna profile
*/
char[] dc = new char[isStructureProfile ? 2
: (isCdnaProfile ? 3 : 1)];
// lm is not necessary - we can just use fm - could be off by no more
// than 0.5 px
// LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
// Console.info(asc + " " + dec + " " + (asc -
// lm.getAscent())
// + " " + (dec - lm.getDescent()));
double asc = fm.getAscent();
double dec = fm.getDescent();
double fht = fm.getHeight();
double scale = 1f / (normaliseProfile ? profl[2] : 100f);
// float ofontHeight = 1f / fm.getAscent();// magnify to fill box
/*
* Traverse the character(s)/percentage data in the array
*/
float ht2 = ht;
// profl[1] is the number of values in the profile
for (int i = 0, c = 3, last = profl[1]; i < last; i++)
{
String s;
if (isStructureProfile)
{
// todo can we encode a structure pair as an int, like codons?
dc[0] = (char) profl[c++];
dc[1] = (char) profl[c++];
s = new String(dc);
}
else if (isCdnaProfile)
{
CodingUtils.decodeCodon2(profl[c++], dc);
s = new String(dc);
}
else
{
dc[0] = (char) profl[c++];
s = new String(dc);
}
// next profl[] position is profile % for the character(s)
int percent = profl[c++];
if (percent == 0)
{
// failsafe in case a count rounds down to 0%
continue;
}
double newHeight = normaliseFactor * scale * percent;
/*
* Set character colour as per alignment colour scheme; use the
* codon translation if a cDNA profile
*/
Color colour = null;
if (isCdnaProfile)
{
final String codonTranslation = ResidueProperties
.codonTranslate(s);
colour = profcolour.findColour(codonTranslation.charAt(0),
column, null);
}
else
{
colour = profcolour.findColour(dc[0], column, null);
}
g.setColor(colour == Color.white ? Color.lightGray : colour);
// Debug - render boxes around characters
// g.setColor(Color.red);
// g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
// (int)(scl));
// g.setColor(profcolour.findColour(dc[0]).darker());
double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
double sy = newHeight / asc;
double newAsc = asc * sy;
double newDec = dec * sy;
// it is not necessary to recalculate lm for the new font.
// note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
// by definition. Was:
// int hght = (int) (ht + (newAsc - newDec);
// - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
if (Platform.isJS())
{
/*
* SwingJS does not implement font.deriveFont()
* so use a scaling transform to draw instead,
* this is off by a very small amount
*/
final int hght = (int) (ht2 + (newAsc - newDec));
Graphics2D gg = (Graphics2D) g;
int xShift = (int) Math.round(x * charWidth / sx);
int yShift = (int) Math.round(hght / sy);
gg.transform(AffineTransform.getScaleInstance(sx, sy));
gg.drawString(s, xShift, yShift);
gg.transform(
AffineTransform.getScaleInstance(1D / sx, 1D / sy));
ht2 += newHeight;
}
else
/**
* Java only
*
* @j2sIgnore
*/
{
// Java ('normal') method is to scale the font to fit
final int hght = (int) (ht + (newAsc - newDec));
Font font = ofont
.deriveFont(AffineTransform.getScaleInstance(sx, sy));
g.setFont(font);
g.drawChars(dc, 0, dc.length, x * charWidth, hght);
g.setFont(ofont);
ht += newHeight;
}
}
}
}
x++;
}
if (_aa.threshold != null)
{
g.setColor(_aa.threshold.colour);
Stroke s = 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);
drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
}
// used by overview window
public void drawGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
{
eRes = Math.min(eRes, aa_annotations.length);
g.setColor(Color.white);
fillRect(g, 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;
}
fillRect(g, x, y - height, charWidth, height);
}
x += charWidth;
}
}
Color getNotCanonicalColor(char lastss)
{
switch (lastss)
{
case '{':
case '}':
return new Color(255, 125, 5);
case '[':
case ']':
return new Color(245, 115, 10);
case '>':
case '<':
return new Color(235, 135, 15);
case 'A':
case 'a':
return new Color(225, 105, 20);
case 'B':
case 'b':
return new Color(215, 145, 30);
case 'C':
case 'c':
return new Color(205, 95, 35);
case 'D':
case 'd':
return new Color(195, 155, 45);
case 'E':
case 'e':
return new Color(185, 85, 55);
case 'F':
case 'f':
return new Color(175, 165, 65);
case 'G':
case 'g':
return new Color(170, 75, 75);
case 'H':
case 'h':
return new Color(160, 175, 85);
case 'I':
case 'i':
return new Color(150, 65, 95);
case 'J':
case 'j':
return new Color(140, 185, 105);
case 'K':
case 'k':
return new Color(130, 55, 110);
case 'L':
case 'l':
return new Color(120, 195, 120);
case 'M':
case 'm':
return new Color(110, 45, 130);
case 'N':
case 'n':
return new Color(100, 205, 140);
case 'O':
case 'o':
return new Color(90, 35, 150);
case 'P':
case 'p':
return new Color(85, 215, 160);
case 'Q':
case 'q':
return new Color(75, 25, 170);
case 'R':
case 'r':
return new Color(65, 225, 180);
case 'S':
case 's':
return new Color(55, 15, 185);
case 'T':
case 't':
return new Color(45, 235, 195);
case 'U':
case 'u':
return new Color(35, 5, 205);
case 'V':
case 'v':
return new Color(25, 245, 215);
case 'W':
case 'w':
return new Color(15, 0, 225);
case 'X':
case 'x':
return new Color(10, 255, 235);
case 'Y':
case 'y':
return new Color(5, 150, 245);
case 'Z':
case 'z':
return new Color(0, 80, 255);
default:
Console.info("This is not a interaction : " + lastss);
return null;
}
}
private void fillPolygon(Graphics g, int[] xpoints, int[] ypoints, int n)
{
setAntialias(g);
g.fillPolygon(xpoints, ypoints, n);
}
/*
private void fillRect(Graphics g, int a, int b, int c, int d)
{
fillRect(g, false, a, b, c, d);
}*/
private void fillRect(Graphics g, int a, int b, int c, int d)
{
unsetAntialias(g);
g.fillRect(a, b, c, d);
}
private void fillRoundRect(Graphics g, int a, int b, int c, int d, int e,
int f)
{
setAntialias(g);
g.fillRoundRect(a, b, c, d, e, f);
}
private void fillArc(Graphics g, int a, int b, int c, int d, int e, int f)
{
setAntialias(g);
g.fillArc(a, b, c, d, e, f);
}
private void drawLine(Graphics g, Stroke s, int a, int b, int c, int d)
{
Graphics2D g2d = (Graphics2D) g;
Stroke p = g2d.getStroke();
g2d.setStroke(s);
drawLine(g, a, b, c, d);
g2d.setStroke(p);
}
private void drawLine(Graphics g, int a, int b, int c, int d)
{
setAntialias(g);
g.drawLine(a, b, c, d);
}
private void setAntialias(Graphics g)
{
if (isVectorRendering())
{
// no need to antialias vector drawings
return;
}
if (Cache.getDefault("ANTI_ALIAS", true))
{
Graphics2D g2d = (Graphics2D) g;
g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
}
}
private void unsetAntialias(Graphics g)
{
if (isVectorRendering())
{
// no need to antialias vector drawings
return;
}
Graphics2D g2d = (Graphics2D) g;
g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_OFF);
}
public void setVectorRendering(boolean b)
{
renderingVectors = b;
}
public boolean isVectorRendering()
{
return renderingVectors;
}
}