import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
// TODO Auto-generated constructor stub
}
- public void drawStemAnnot(Graphics g, AlignmentAnnotation row,
+ public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
int lastSSX, int x, int y, int iconOffset, int startRes,
int column, boolean validRes, boolean validEnd)
{
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
- String dc = (column == 0 || row.annotations[column - 1] == null) ? ""
- : row.annotations[column - 1].displayCharacter;
+ 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);
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || !dc.equals(row_annotations[sCol - 1].displayCharacter);
boolean diffdownstream = !validRes || !validEnd
- || row.annotations[column] == null
- || !dc.equals(row.annotations[column].displayCharacter);
+ || row_annotations[column] == null
+ || !dc.equals(row_annotations[column].displayCharacter);
// System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
if (column > 0 && closeparen.search(dc))
{
if (diffupstream)
- // if (validRes && column>1 && row.annotations[column-2]!=null &&
- // dc.equals(row.annotations[column-2].displayCharacter))
+ // 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[]
private FontMetrics fm;
- private boolean MAC = new jalview.util.Platform().isAMac();
+ private final boolean MAC = new jalview.util.Platform().isAMac();
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
}
/**
- * DOCUMENT ME!
+ * Render the annotation rows associated with an alignment.
*
- * @param annotationPanel
- * TODO
+ * @param annotPanel
+ * container frame
+ * @param av
+ * data and view settings to render
* @param g
- * DOCUMENT ME!
+ * destination for graphics
+ * @param activeRow
+ * row where a mouse event occured (or -1)
* @param startRes
- * DOCUMENT ME!
+ * first column that will be drawn
* @param endRes
- * DOCUMENT ME!
+ * last column that will be drawn
+ * @return true if the fadedImage was used for any alignment annotation rows
+ * currently being calculated
*/
- public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av,
- Graphics g, int activeRow, int startRes, int endRes)
+ public boolean drawComponent(AwtRenderPanelI annotPanel,
+ AlignViewportI av, Graphics g, int activeRow, int startRes,
+ int endRes)
{
+ boolean usedFaded = false;
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to
// AlignViewport
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
-
+ Annotation[] row_annotations = row.annotations;
if (!row.visible)
{
continue;
iconOffset = 0;
}
- if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
+ 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);
if (hasHiddenColumns)
{
column = columnSelection.adjustForHiddenColumns(startRes + x);
- if (column > row.annotations.length - 1)
+ if (column > row_annotations.length - 1)
{
break;
}
column = startRes + x;
}
- if ((row.annotations == null) || (row.annotations.length <= column)
- || (row.annotations[column] == null))
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
{
validRes = false;
}
}
if (validCharWidth
&& validRes
- && row.annotations[column].displayCharacter != null
- && (row.annotations[column].displayCharacter.length() > 0))
+ && row_annotations[column].displayCharacter != null
+ && (row_annotations[column].displayCharacter.length() > 0))
{
if (centreColLabels || scaleColLabel)
{
- fmWidth = (float) fm.charsWidth(
- row.annotations[column].displayCharacter
+ fmWidth = fm.charsWidth(
+ row_annotations[column].displayCharacter
.toCharArray(), 0,
- row.annotations[column].displayCharacter.length());
+ row_annotations[column].displayCharacter.length());
if (scaleColLabel)
{
}
else
{
- fmWidth = (float) fm
- .charWidth(row.annotations[column].displayCharacter
+ fmWidth = fm
+ .charWidth(row_annotations[column].displayCharacter
.charAt(0));
}
charOffset = (int) ((charWidth - fmWidth) / 2f);
- if (row.annotations[column].colour == null)
+ if (row_annotations[column].colour == null)
g.setColor(Color.black);
else
- g.setColor(row.annotations[column].colour);
+ g.setColor(row_annotations[column].colour);
if (column == 0 || row.graph > 0)
{
- g.drawString(row.annotations[column].displayCharacter,
+ g.drawString(row_annotations[column].displayCharacter,
(x * charWidth) + charOffset, y + iconOffset);
}
- else if (row.annotations[column - 1] == null
+ else if (row_annotations[column - 1] == null
|| (labelAllCols
- || !row.annotations[column].displayCharacter
- .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
- .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
+ || !row_annotations[column].displayCharacter
+ .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
+ .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row.annotations[column].displayCharacter, x
+ g.drawString(row_annotations[column].displayCharacter, x
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
}
if (row.hasIcons)
{
- char ss = validRes ? row.annotations[column].secondaryStructure
+ char ss = validRes ? row_annotations[column].secondaryStructure
: ' ';
if (ss == 'S')
{
// distinguish between forward/backward base-pairing
- if (row.annotations[column].displayCharacter.indexOf(')') > -1)
+ if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
ss = 's';
}
switch (lastSS)
{
case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
break;
case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
break;
case 'S': // Stem case for RNA secondary structure
case 's': // and opposite direction
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawStemAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
break;
default:
column++;
x++;
}
- if (column >= row.annotations.length)
+ if (column >= row_annotations.length)
{
- column = row.annotations.length - 1;
+ column = row_annotations.length - 1;
validEnd = false;
}
else
{
validEnd = true;
}
- if ((row.annotations == null) || (row.annotations.length <= column)
- || (row.annotations[column] == null))
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
{
validRes = false;
}
switch (lastSS)
{
case 'H':
- drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
break;
case 'E':
- drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
break;
case 's':
case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
break;
default:
- drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
- column, validRes, validEnd);
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
break;
}
}
{
aa[gg].visible = false;
}
-
if (aa[gg].graphMax > groupmax)
{
groupmax = aa[gg].graphMax;
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
- groupmax, row.graphHeight);
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
+ endRes, y, groupmin, groupmax, row.graphHeight);
}
}
}
else
{
- drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
- row.graphMax, row.graphHeight);
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y,
+ row.graphMin, row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawBarGraph(g, row, startRes, endRes, row.graphMin,
- row.graphMax, y);
+ drawBarGraph(g, row, row_annotations, startRes, endRes,
+ row.graphMin, row.graphMax, y);
}
}
y += aa[i].height;
}
}
+ return !usedFaded;
}
- private Color GLYPHLINE_COLOR = Color.gray;
+ private final Color GLYPHLINE_COLOR = Color.gray;
- private Color SHEET_COLOUR = Color.green;
+ private final Color SHEET_COLOUR = Color.green;
- private Color HELIX_COLOUR = Color.red;
+ private final Color HELIX_COLOUR = Color.red;
- private Color STEM_COLOUR = Color.blue;
+ private final Color STEM_COLOUR = Color.blue;
- public void drawGlyphLine(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
+ int x, int y, int iconOffset, int startRes, int column,
+ boolean validRes, boolean validEnd)
{
g.setColor(GLYPHLINE_COLOR);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
- public void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ public void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX,
+ int x, int y, int iconOffset, int startRes, int column,
+ boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
- if (!validEnd || !validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'E')
+ if (!validEnd || !validRes || row == null || row[column] == null
+ || row[column].secondaryStructure != 'E')
{
g.fillRect(lastSSX, y + 4 + iconOffset,
(x * charWidth) - lastSSX - 4, 7);
}
- public void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
- int lastSSX, int x, int y, int iconOffset, int startRes,
- int column, boolean validRes, boolean validEnd)
+ public 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);
// 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);
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
+ if (sCol == 0 || row[sCol - 1] == null
+ || row[sCol - 1].secondaryStructure != 'H')
{
}
else
g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
0, 0);
}
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
+ if (!validRes || row[column] == null
+ || row[column].secondaryStructure != 'H')
{
}
return;
}
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
+ if (sCol == 0 || row[sCol - 1] == null
+ || row[sCol - 1].secondaryStructure != 'H')
{
g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
x1 += charWidth / 2;
}
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
+ if (!validRes || row[column] == null
+ || row[column].secondaryStructure != 'H')
{
g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
8, 270, 180);
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, int y, float min, float max, int graphHeight)
+ public 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)
+ if (sRes > aa_annotations.length)
{
return;
}
eRes++;
}
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
if (sRes == 0)
{
g.setColor(Color.gray);
g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
int column;
- int aaMax = aa.annotations.length - 1;
+ int aaMax = aa_annotations.length - 1;
while (x < eRes - sRes)
{
break;
}
- if (aa.annotations[column] == null
- || aa.annotations[column - 1] == null)
+ if (aa_annotations[column] == null
+ || aa_annotations[column - 1] == null)
{
x++;
continue;
}
- if (aa.annotations[column].colour == null)
+ if (aa_annotations[column].colour == null)
g.setColor(Color.black);
else
- g.setColor(aa.annotations[column].colour);
+ g.setColor(aa_annotations[column].colour);
y1 = y
- - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
+ - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
y2 = y
- - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
+ - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
+ charWidth / 2, y2);
x++;
}
- if (aa.threshold != null)
+ if (_aa.threshold != null)
{
- g.setColor(aa.threshold.colour);
+ 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));
- y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
+ y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, float min, float max, int y)
+ public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
+ Annotation[] aa_annotations, int sRes, int eRes, float min,
+ float max, int y)
{
- if (sRes > aa.annotations.length)
+ if (sRes > aa_annotations.length)
{
return;
}
Font ofont = g.getFont();
- eRes = Math.min(eRes, aa.annotations.length);
+ eRes = Math.min(eRes, aa_annotations.length);
int x = 0, y1 = y, y2 = y;
if (min < 0)
{
- y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
+ y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
}
g.setColor(Color.gray);
g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
int column;
- int aaMax = aa.annotations.length - 1;
+ int aaMax = aa_annotations.length - 1;
boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
// if (aa.autoCalculated && aa.label.startsWith("Consensus"))
{
// TODO: generalise this to have render styles for consensus/profile data
- if (aa.groupRef != null)
+ if (_aa.groupRef != null)
{
- renderHistogram = aa.groupRef.isShowConsensusHistogram();
- renderProfile = aa.groupRef.isShowSequenceLogo();
- normaliseProfile = aa.groupRef.isNormaliseSequenceLogo();
+ renderHistogram = _aa.groupRef.isShowConsensusHistogram();
+ renderProfile = _aa.groupRef.isShowSequenceLogo();
+ normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
}
else
{
break;
}
- if (aa.annotations[column] == null)
+ if (aa_annotations[column] == null)
{
x++;
continue;
}
- if (aa.annotations[column].colour == null)
+ if (aa_annotations[column].colour == null)
g.setColor(Color.black);
else
- g.setColor(aa.annotations[column].colour);
+ g.setColor(aa_annotations[column].colour);
y1 = y
- - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+ - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
if (renderHistogram)
{
}
}
// draw profile if available
- if (renderProfile && aa.annotations[column].value != 0)
+ if (renderProfile)
{
- int profl[] = getProfileFor(aa, column);
+ int profl[] = getProfileFor(_aa, column);
// just try to draw the logo if profl is not null
if (profl != null && profl[1] != 0)
{
- float ht = normaliseProfile ? y - aa.graphHeight : y1;
- double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
+ float ht = normaliseProfile ? y - _aa.graphHeight : y1;
+ double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
double hght;
float wdth;
double ht2 = 0;
{
dc[0] = (char) profl[c++];
- if (aa.label.startsWith("StrucConsensus"))
+ if (_aa.label.startsWith("StrucConsensus"))
{
dc[1] = (char) profl[c++];
}
wdth = charWidth;
- wdth /= (float) fm.charsWidth(dc, 0, dc.length);
+ wdth /= fm.charsWidth(dc, 0, dc.length);
ht += scl;
{
- scl = ((double) htn) * scale * ((double) profl[c++]);
+ scl = htn * scale * profl[c++];
lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
.getFontRenderContext());
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
// g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
// (int)(scl));
// g.setColor(profcolour.findColour(dc[0]).darker());
- g.setColor(profcolour.findColour(dc[0], column));
+ g.setColor(profcolour.findColour(dc[0], column, null));
hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
.getBaselineIndex()]));
}
x++;
}
- if (aa.threshold != null)
+ if (_aa.threshold != null)
{
- g.setColor(aa.threshold.colour);
+ 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));
- y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
+ y2 = (int) (y - ((_aa.threshold.value - min) / range)
+ * _aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
// used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
- int y, int sRes, int eRes)
+ 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);
+ eRes = Math.min(eRes, aa_annotations.length);
g.setColor(Color.white);
g.fillRect(0, 0, width, y);
g.setColor(new Color(0, 0, 180));
for (int j = sRes; j < eRes; j++)
{
- if (aa.annotations[j] != null)
+ if (aa_annotations[j] != null)
{
- if (aa.annotations[j].colour == null)
+ if (aa_annotations[j].colour == null)
g.setColor(Color.black);
else
- g.setColor(aa.annotations[j].colour);
+ g.setColor(aa_annotations[j].colour);
- height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
+ height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
if (height > y)
{
height = y;
git://source.jalview.org / jalview.git / blobdiff