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;
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;
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
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;
+ // 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,
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
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);
git://source.jalview.org / jalview.git / blobdiff