import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.ProfilesI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
+import jalview.workers.InformationThread;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
-import java.awt.font.LineMetrics;
import java.awt.geom.AffineTransform;
import java.awt.image.ImageObserver;
import java.util.BitSet;
private FontMetrics fm;
- private final boolean MAC = Platform.isAMac();
+ private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS();
- boolean av_renderHistogram = true, av_renderProfile = true,
- av_normaliseProfile = false;
+ // todo remove these flags, read from group/viewport where needed
+ boolean av_renderHistogram = true;
+
+ boolean av_renderProfile = true;
+
+ boolean av_normaliseProfile = false;
+
+ boolean av_infoHeight = false;
ResidueShaderI profcolour = null;
private ProfilesI hconsensus;
- private Hashtable[] complementConsensus;
+ private Hashtable<String, Object>[] complementConsensus;
- private Hashtable[] hStrucConsensus;
+ private Hashtable<String, Object>[] hStrucConsensus;
private boolean av_ignoreGapsConsensus;
+ private boolean av_ignoreBelowBackground;
+
/**
* attributes set from AwtRenderPanelI
*/
*/
public void dispose()
{
+ hiddenColumns = null;
hconsensus = null;
complementConsensus = null;
hStrucConsensus = null;
complementConsensus = av.getComplementConsensusHash();
hStrucConsensus = av.getRnaStructureConsensusHash();
av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+ av_ignoreBelowBackground = av.isIgnoreBelowBackground();
+ av_infoHeight = av.isInfoLetterHeight();
}
+
+
/**
* 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
// 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 (InformationThread.HMM_CALC_ID.equals(aa.getCalcId()))
+ {
+ HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
+ return AAFrequency.extractHMMProfile(hmm, column,
+ av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
+ // pipeline
+ }
+ 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
+ if (aa.groupRef != null && aa.groupRef.getConsensusData() != null
&& aa.groupRef.isShowSequenceLogo())
{
// TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
- aa.groupRef.consensusData.get(column),
- aa.groupRef.getIgnoreGapsConsensus());
+ aa.groupRef.getConsensusData().get(column),
+ aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
return null;
}
- boolean rna = false;
-
/**
* 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
- 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 = 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 if (InformationThread.HMM_CALC_ID.equals(row.getCalcId()))
+ {
+ if (row.groupRef != null)
{
- renderHistogram = av_renderHistogram;
- renderProfile = av_renderProfile;
- normaliseProfile = av_normaliseProfile;
+ renderHistogram = row.groupRef.isShowInformationHistogram();
+ renderProfile = row.groupRef.isShowHMMSequenceLogo();
+ normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo();
}
else
{
- renderHistogram = true;
- // don't need to set render/normaliseProfile since they are not
- // currently used in any other annotation track renderer
+ renderHistogram = av.isShowInformationHistogram();
+ renderProfile = av.isShowHMMSequenceLogo();
+ normaliseProfile = av.isNormaliseHMMSequenceLogo();
}
}
+ 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 (validCharWidth && validRes && displayChar != null
&& (displayChar.length() > 0))
{
-
- fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ Graphics2D gg = ((Graphics2D) 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);
+ gg.setColor(Color.black);
}
else
{
- g.setColor(row_annotations[column].colour);
+ gg.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
+ */
+ gg.translate(xPos, yPos);
+ if (scaledToFit)
+ {
+ /*
+ * use a scaling transform to make the label narrower
+ * (JalviewJS doesn't have Font.deriveFont(AffineTransform))
+ */
+ gg.transform(
+ AffineTransform.getScaleInstance(fmScaling, 1.0));
+ }
if (column == 0 || row.graph > 0)
{
- g.drawString(displayChar, (x * charWidth) + charOffset,
- y + iconOffset);
+ gg.drawString(displayChar, 0, 0);
}
else if (row_annotations[column - 1] == null || (labelAllCols
|| !displayChar.equals(
|| (displayChar.length() < 2
&& row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(displayChar, x * charWidth + charOffset,
- y + iconOffset);
+ gg.drawString(displayChar, 0, 0);
}
- g.setFont(ofont);
+ if (scaledToFit)
+ {
+ /*
+ * undo scaling before translating back
+ * (restoring saved transform does NOT work in JS PDFGraphics!)
+ */
+ gg.transform(AffineTransform
+ .getScaleInstance(1D / fmScaling, 1.0));
+ }
+ gg.translate(-xPos, -yPos);
}
}
if (row.hasIcons)
if (x > -1)
{
- int nb_annot = x - temp;
+ // int nb_annot = x - temp;
// System.out.println("\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;
}
}
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,
int x1 = lastSSX;
int x2 = (x * charWidth);
- if (MAC)
+ if (USE_FILL_ROUND_RECT)
{
int ofs = charWidth / 2;
// Off by 1 offset when drawing rects and ovals
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;
+ final double normaliseFactor = normaliseProfile ? _aa.graphHeight
+ : (y2 - y1);
/**
* Render a single base for a sequence profile, a base pair for
s = new String(dc);
}
// next profl[] position is profile % for the character(s)
-
- double newHeight = htn * 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 recalculated lm for the new font.
+ // 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()]));
-
- // original:
-
- if (/** @j2sNative false && */ true) {
- int hght = (int) (ht + (newAsc - newDec)); // Q: why " - newDec " ? (0,0) is on the font baseline, I think
- Font font = ofont.deriveFont(AffineTransform.getScaleInstance(sx, sy));
- g.setFont(font);
- g.drawChars(dc, 0, dc.length, x * charWidth, hght);
- ht += newHeight;
- } else {
- // SwingJS does not implement font.deriveFont()
- // this is off by a very small amount.
- int hght2 = (int) (ht2 + newAsc);
- Graphics2D gg = (Graphics2D) g.create();
- gg.setFont(ofont);
+ // 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));
- //System.out.println("sx " + sx + " sy " + sy + " " + hght + " " + lm.getDescent() + " " + dec + " " + newDec + " " + lm.getAscent() + " " + asc + " " + newAsc);
- gg.drawString(s, (int) (x * charWidth / sx),
- (int) (hght2 / sy));
- gg.dispose();
+ 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;
+ }
}
- g.setFont(ofont);
}
}
x++;
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);
git://source.jalview.org / jalview.git / blobdiff