*/
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.geom.AffineTransform;
+import java.awt.image.ImageObserver;
+import java.util.BitSet;
+import java.util.Hashtable;
+
import jalview.analysis.AAFrequency;
import jalview.analysis.CodingUtils;
import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
-import jalview.bin.Jalview;
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;
-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.geom.AffineTransform;
-import java.awt.image.ImageObserver;
-import java.util.BitSet;
-import java.util.Hashtable;
-
public class AnnotationRenderer
{
private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
private ProfilesI hconsensus;
- private Hashtable[] complementConsensus;
+ private Hashtable<String, Object>[] complementConsensus;
- private Hashtable[] hStrucConsensus;
+ private Hashtable<String, Object>[] hStrucConsensus;
private boolean av_ignoreGapsConsensus;
*/
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 iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
{
- // System.out.println(nonCanColor);
+ // jalview.bin.Console.outPrintln(nonCanColor);
g.setColor(nonCanColor);
int sCol = (lastSSX / charWidth)
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
|| !dc.equals(row_annotations[column].displayCharacter);
- // System.out.println("Column "+column+" diff up: "+diffupstream+"
+ // jalview.bin.Console.outPrintln("Column "+column+" diff up: "+diffupstream+"
// down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && Rna.isClosingParenthesis(dc))
useClip = false;
}
+ rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
updateFromAlignViewport(av);
}
boolean rna = false;
+ private AnnotationRendererFactoryI rendererFactoryI;
+
/**
* Render the annotation rows associated with an alignment.
*
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
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 = ' ';
if (x > -1)
{
- int nb_annot = x - temp;
- // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
+ // int nb_annot = x - temp;
+ // jalview.bin.Console.outPrintln("\t type :"+lastSS+"\t x :"+x+"\t nbre
// annot :"+nb_annot);
switch (lastSS)
{
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;
+ // temp = x;
break;
}
}
case 'y':
case 'Z':
case 'z':
- // System.out.println(lastSS);
+ // jalview.bin.Console.outPrintln(lastSS);
Color nonCanColor = getNotCanonicalColor(lastSS);
drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
x, y, iconOffset, startRes, column, validRes, validEnd);
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
+ {
+ jalview.bin.Console.errPrintln(
+ "rendered with " + renderer.getClass().toString());
+ }
+ }
+
+ }
}
}
else
{
if (clipst)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Start clip at : " + yfrom + " (index " + f_i + ")");
}
if (clipend)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"End clip at : " + yto + " (index " + f_to + ")");
}
}
;
- System.err.println("Annotation Rendering time:"
+ jalview.bin.Console.errPrintln("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,
break;
}
- if (aa_annotations[column] == null
- || aa_annotations[column - 1] == null)
+ if (aa_annotations[column] == null)
{
x++;
continue;
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);
+ g.drawLine(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)
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);
+ final double normaliseFactor = normaliseProfile ? _aa.graphHeight
+ : (y2 - y1);
/**
* Render a single base for a sequence profile, a base pair for
// 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);
- // System.out.println(asc + " " + dec + " " + (asc - lm.getAscent())
+ // jalview.bin.Console.outPrintln(asc + " " + dec + " " + (asc - lm.getAscent())
// + " " + (dec - lm.getDescent()));
double asc = fm.getAscent();
s = new String(dc);
}
// next profl[] position is profile % for the character(s)
-
- double newHeight = normaliseFactor * scale * profl[c++];
+
+ 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
// (int)(scl));
// g.setColor(profcolour.findColour(dc[0]).darker());
- double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
+ double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
double sy = newHeight / asc;
- double newAsc = asc * sy;
+ 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
// int hght = (int) (ht + (newAsc - newDec);
// - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
- if (Jalview.isJS())
+ if (Platform.isJS())
{
/*
* SwingJS does not implement font.deriveFont()
ht2 += newHeight;
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- /*
- * Java ('normal') method is to scale the font to fit
- */
+ // 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;
}
}
Graphics2D g2 = (Graphics2D) g;
g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ { 5f, 3f }, 0f));
y2 = (int) (y
- ((_aa.threshold.value - min) / range) * _aa.graphHeight);
return new Color(0, 80, 255);
default:
- System.out.println("This is not a interaction : " + lastss);
+ jalview.bin.Console.outPrintln("This is not a interaction : " + lastss);
return null;
}
git://source.jalview.org / jalview.git / blobdiff