*/
package jalview.renderer;
-import jalview.analysis.AAFrequency;
-import jalview.analysis.CodingUtils;
-import jalview.analysis.Rna;
-import jalview.analysis.StructureFrequency;
-import jalview.api.AlignViewportI;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
-import java.awt.font.LineMetrics;
+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 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<String, Object>[] complementConsensus;
+
+ private Hashtable<String, Object>[] 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);
this.debugRedraw = debugRedraw;
}
- void drawStemAnnot(Graphics g, Annotation[] row_annotations,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ /**
+ * Remove any references and resources when this object is no longer required
+ */
+ public void dispose()
{
- g.setColor(STEM_COLOUR);
- int sCol = (lastSSX / charWidth) + startRes;
+ 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);
: row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || dc != row_annotations[sCol - 1].secondaryStructure;
+ || 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 new annotation with a closing base pair half of the stem,
* display a backward arrow
*/
- g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
- new int[] { y + iconOffset, y + 14 + iconOffset,
- y + 8 + iconOffset }, 3);
+ 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)
* if annotation ending with an opeing base pair half of the stem,
* display a forward arrow
*/
- g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
- y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ 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)
}
}
// draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ unsetAntialias(g);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
- private int charWidth, endRes, charHeight;
-
- private boolean validCharWidth, hasHiddenColumns;
-
- private FontMetrics fm;
-
- private final boolean MAC = jalview.util.Platform.isAMac();
-
- boolean av_renderHistogram = true, av_renderProfile = true,
- av_normaliseProfile = false;
-
- ColourSchemeI profcolour = null;
-
- private ColumnSelection columnSelection;
-
- private Hashtable[] hconsensus;
-
- private Hashtable[] complementConsensus;
-
- private Hashtable[] hStrucConsensus;
-
- private boolean av_ignoreGapsConsensus;
-
- /**
- * 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;
-
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)
{
- // System.out.println(nonCanColor);
+ // Console.info(nonCanColor);
- g.setColor(nonCanColor);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
: row_annotations[column - 1].displayCharacter;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter)
+ || !validEnd;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
- // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
+ // 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 (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);
+ 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)
// 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);
+ 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)
}
}
// draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ unsetAntialias(g);
+ fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
}
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
useClip = false;
}
+ rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
updateFromAlignViewport(av);
}
public void updateFromAlignViewport(AlignViewportI av)
{
charWidth = av.getCharWidth();
- endRes = av.getEndRes();
+ 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.getGlobalColourScheme();
- if (profcolour == null)
+ profcolour = av.getResidueShading();
+ if (profcolour == null || profcolour.getColourScheme() == null)
{
- // Set the default colour for sequence logo if the alignnent has no
- // colourscheme set
- profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
- : new jalview.schemes.ZappoColourScheme();
+ /*
+ * 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();
// 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")))
+ 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
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
- aa.groupRef.consensusData[column],
+ aa.groupRef.consensusData.get(column),
aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
{
if (forComplement)
{
- return AAFrequency.extractCdnaProfile(
- complementConsensus[column], av_ignoreGapsConsensus);
+ return AAFrequency.extractCdnaProfile(complementConsensus[column],
+ av_ignoreGapsConsensus);
}
else
{
- return AAFrequency.extractProfile(hconsensus[column],
+ return AAFrequency.extractProfile(hconsensus.get(column),
av_ignoreGapsConsensus);
}
}
boolean rna = false;
+ private AnnotationRendererFactoryI rendererFactoryI;
+
/**
* Render the annotation rows associated with an alignment.
*
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:
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- int temp = 0;
+ // int temp = 0;
if (aa == null)
{
return false;
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
- boolean centreColLabels;
- boolean centreColLabelsDef = av.isCentreColumnLabels();
+ // boolean centreColLabels;
+ // boolean centreColLabelsDef = av.isCentreColumnLabels();
boolean scaleColLabel = false;
final AlignmentAnnotation consensusAnnot = av
.getAlignmentConsensusAnnotation();
.getAlignmentStrucConsensusAnnotation();
final AlignmentAnnotation complementConsensusAnnot = av
.getComplementConsensusAnnotation();
- boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
BitSet graphGroupDrawn = new BitSet();
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
// debug ints
int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
- isRNA = row.isRNA();
+ 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())
{
- // 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;
- }
- else
- {
- renderHistogram = true;
- // don't need to set render/normaliseProfile since they are not
- // currently used in any other annotation track renderer
- }
+ 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;
+ // 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 (!useClip || ((y - charHeight) < visHeight
+ && (y + row.height + charHeight * 2) >= sOffset))
{// if_in_visible_region
if (!clipst)
{
{
y += charHeight;
usedFaded = true;
- g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- - row.height, imgWidth, y, annotationPanel);
+ 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; }
*/
+
// 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 = columnSelection.adjustForHiddenColumns(startRes + x);
+ column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
if (column > row_annotations.length - 1)
{
break;
{
validRes = true;
}
- final String displayChar = validRes ? row_annotations[column].displayCharacter
+ final String displayChar = validRes
+ ? row_annotations[column].displayCharacter
: null;
if (x > -1)
{
+ unsetAntialias(g);
if (activeRow == i)
{
g.setColor(Color.red);
{
if (columnSelection.contains(column))
{
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
}
}
if (row.getInvalidStrucPos() > x)
{
g.setColor(Color.orange);
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
else if (row.getInvalidStrucPos() == x)
{
g.setColor(Color.orange.darker());
- g.fillRect(x * charWidth, y, charWidth, charHeight);
+ fillRect(g, x * charWidth, y, charWidth, charHeight);
}
if (validCharWidth && validRes && displayChar != null
&& (displayChar.length() > 0))
{
-
- fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ // Graphics2D gg = (g);
+ float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
displayChar.length());
- if (/* centreColLabels || */scaleColLabel)
+
+ /*
+ * shrink label width to fit in column, if that is
+ * both configured and necessary
+ */
+ boolean scaledToFit = false;
+ float fmScaling = 1f;
+ if (scaleColLabel && fmWidth > charWidth)
{
- // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
- // displayChar.length());
- //
- // if (scaleColLabel)
- // {
- // justify the label and scale to fit in column
- if (fmWidth > charWidth)
- {
- // scale only if the current font isn't already small enough
- fmScaling = charWidth;
- fmScaling /= fmWidth;
- g.setFont(ofont.deriveFont(AffineTransform
- .getScaleInstance(fmScaling, 1.0)));
- // and update the label's width to reflect the scaling.
- fmWidth = charWidth;
- }
- // }
+ scaledToFit = true;
+ fmScaling = charWidth;
+ fmScaling /= fmWidth;
+ // and update the label's width to reflect the scaling.
+ fmWidth = charWidth;
}
- // TODO is it ok to use width of / show all characters here?
- // else
- // {
- // fmWidth = fm.charWidth(displayChar.charAt(0));
- // }
+
charOffset = (int) ((charWidth - fmWidth) / 2f);
if (row_annotations[column].colour == null)
{
- g.setColor(Color.black);
+ g2d.setColor(Color.black);
}
else
{
- g.setColor(row_annotations[column].colour);
+ 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)
{
- g.drawString(displayChar, (x * charWidth) + charOffset, y
- + iconOffset);
+ 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 == ' ')))
+ else if (row_annotations[column - 1] == null || (labelAllCols
+ || !displayChar.equals(
+ row_annotations[column - 1].displayCharacter)
+ || (displayChar.length() < 2
+ && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(displayChar, x * charWidth + charOffset, y
- + iconOffset);
+ g2d.drawString(displayChar, 0, 0);
}
- g.setFont(ofont);
+ 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)
if (x > -1)
{
- int nb_annot = x - temp;
- // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
+ // 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;
+ // temp = x;
break;
case 'H':
drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
lastSSX, x, y, iconOffset, startRes, column,
validRes, validEnd);
- temp = x;
+ // temp = x;
break;
default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
- temp = x;
+ 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;
}
}
case 'y':
case 'Z':
case 'z':
- // System.out.println(lastSS);
+ // Console.info(lastSS);
Color nonCanColor = getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
x, y, iconOffset, startRes, column, validRes, validEnd);
break;
default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ 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;
}
}
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
{
clipend = true;
}
- }// end if_in_visible_region
+ } // end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
{
if (clipst)
{
- System.err.println("Start clip at : " + yfrom + " (index " + f_i
- + ")");
+ Console.warn("Start clip at : " + yfrom + " (index " + f_i + ")");
}
if (clipend)
{
- System.err.println("End clip at : " + yto + " (index " + f_to
- + ")");
+ Console.warn("End clip at : " + yto + " (index " + f_to + ")");
}
}
;
- System.err.println("Annotation Rendering time:"
+ Console.warn("Annotation Rendering time:"
+ (System.currentTimeMillis() - stime));
}
;
public static final Color STEM_COLOUR = Color.blue;
- private Color sdNOTCANONICAL_COLOUR;
+ // private Color sdNOTCANONICAL_COLOUR;
- void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
- boolean validRes, boolean validEnd)
+ 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)
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
- g.setColor(SHEET_COLOUR);
-
if (!validEnd || !validRes || row == null || row[column] == null
|| row[column].secondaryStructure != 'E')
{
- g.fillRect(lastSSX, y + 4 + iconOffset,
- (x * charWidth) - lastSSX - 4, 7);
- g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
- (x * charWidth) }, new int[] { y + iconOffset,
- y + 14 + iconOffset, y + 7 + iconOffset }, 3);
+ // 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.fillRect(lastSSX, y + 4 + iconOffset,
- (x + 1) * charWidth - lastSSX, 7);
+ 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)
+ void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
+ int y, int iconOffset, int startRes, int column, boolean validRes,
+ boolean validEnd)
{
- g.setColor(HELIX_COLOUR);
-
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
- if (MAC)
+ 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
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
+ 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
{
- // g.setColor(Color.orange);
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
- 0, 0);
+ fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
+ 0);
}
if (!validRes || row[column] == null
|| row[column].secondaryStructure != 'H')
}
else
{
- // g.setColor(Color.magenta);
- g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
- + 1, 8, 0, 0);
-
+ fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
+ 8, 0, 0);
}
return;
}
- if (sCol == 0 || row[sCol - 1] == null
- || row[sCol - 1].secondaryStructure != 'H')
+ 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)
{
- g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
+ 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 (!validRes || row[column] == null
- || row[column].secondaryStructure != 'H')
+ if (rightEnd)
{
- g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
- 8, 270, 180);
+ fillArc(g, ((x - 1) * charWidth), y + 3 + iconOffset, charWidth, 8,
+ 270, 180);
x2 -= charWidth / 2;
}
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+ 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)
+ 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;
}
g.setColor(Color.gray);
- g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
+ drawLine(g, squareStroke, x * charWidth - charWidth, y2,
+ (eRes - sRes) * charWidth, y2);
eRes = Math.min(eRes, aa_annotations.length);
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
}
if (column > aaMax)
break;
}
- if (aa_annotations[column] == null
- || aa_annotations[column - 1] == null)
+ if (aa_annotations[column] == null)
{
x++;
continue;
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);
+ 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);
- g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
- + charWidth / 2, y2);
+ drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
+ x * charWidth + charWidth / 2, y2);
x++;
}
{
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));
+ 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);
- g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- g2.setStroke(new BasicStroke());
+ 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,
g.setColor(Color.gray);
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+ drawLine(g, x, y2, (eRes - sRes) * charWidth, y2);
int column;
int aaMax = aa_annotations.length - 1;
column = sRes + x;
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
}
if (column > aaMax)
g.setColor(aa_annotations[column].colour);
}
- y1 = y
- - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
+ y1 = y - (int) (((aa_annotations[column].value - min) / (range))
+ * _aa.graphHeight);
if (renderHistogram)
{
if (y1 - y2 > 0)
{
- g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
+ fillRect(g, x * charWidth, y2, charWidth, y1 - y2);
}
else
{
- g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
+ fillRect(g, x * charWidth, y1, charWidth, y2 - y1);
}
}
// draw profile if available
boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
- double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
- double hght;
- float wdth;
- double ht2 = 0;
- char[] dc;
+ 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
*/
- dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
+ 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();
- LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
double scale = 1f / (normaliseProfile ? profl[2] : 100f);
- float ofontHeight = 1f / lm.getAscent();// magnify to fill box
- double scl = 0.0;
+ // float ofontHeight = 1f / fm.getAscent();// magnify to fill box
/*
* Traverse the character(s)/percentage data in the array
*/
- int c = 3;
- int valuesProcessed = 0;
+
+ float ht2 = ht;
+
// profl[1] is the number of values in the profile
- while (valuesProcessed < profl[1])
+ 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)
{
- dc = CodingUtils.decodeCodon(profl[c++]);
+ CodingUtils.decodeCodon2(profl[c++], dc);
+ s = new String(dc);
}
else
{
dc[0] = (char) profl[c++];
+ s = new String(dc);
}
-
- wdth = charWidth;
- wdth /= fm.charsWidth(dc, 0, dc.length);
-
- ht += scl;
// next profl[] position is profile % for the character(s)
- scl = htn * scale * profl[c++];
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
- .getFontRenderContext());
- Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent()));
- g.setFont(font);
- lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
- // 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());
+ 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
if (isCdnaProfile)
{
final String codonTranslation = ResidueProperties
- .codonTranslate(new String(dc));
+ .codonTranslate(s);
colour = profcolour.findColour(codonTranslation.charAt(0),
column, null);
}
}
g.setColor(colour == Color.white ? Color.lightGray : colour);
- hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
- .getBaselineIndex()]));
+ // 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);
- g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
- valuesProcessed++;
+ ht += newHeight;
+ }
}
- 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));
+ 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);
- g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
- g2.setStroke(new BasicStroke());
+ y2 = (int) (y
+ - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
+ drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
}
}
{
eRes = Math.min(eRes, aa_annotations.length);
g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
+ fillRect(g, 0, 0, width, y);
g.setColor(new Color(0, 0, 180));
int x = 0, height;
height = y;
}
- g.fillRect(x, y - height, charWidth, height);
+ fillRect(g, x, y - height, charWidth, height);
}
x += charWidth;
}
return new Color(0, 80, 255);
default:
- System.out.println("This is not a interaction : " + lastss);
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff