// TODO Auto-generated constructor stub
}
- public void drawStemAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
+ public void drawStemAnnot(Graphics g, AlignmentAnnotation row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
g.setColor(STEM_COLOUR);
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
-
- String dc = (column == 0 || row.annotations[column-1]==null) ? ""
+
+ 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 diffdownstream = !validRes || !validEnd
// draw arrow body
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
}
- private int charWidth,endRes,charHeight;
+
+ private int charWidth, endRes, charHeight;
+
private boolean validCharWidth, hasHiddenColumns;
+
private FontMetrics fm;
- private boolean MAC=new jalview.util.Platform().isAMac();
- boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile=false;
- ColourSchemeI profcolour=null;
+
+ private boolean MAC = new 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[] hStrucConsensus;
+
private boolean av_ignoreGapsConsensus;
-
+
/**
* attributes set from AwtRenderPanelI
*/
/**
- * old image used when data is currently being calculated and cannot be rendered
+ * 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;
-
- // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI av)
- public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, AlignViewportI av)
+ private int imgWidth;
+
+ // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
+ // av)
+ public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
+ AlignViewportI av)
{
fm = annotPanel.getFontMetrics();
annotationPanel = annotPanel;
- fadedImage=annotPanel.getFadedImage();
- imgWidth=annotPanel.getFadedImageWidth();
+ fadedImage = annotPanel.getFadedImage();
+ imgWidth = annotPanel.getFadedImageWidth();
updateFromAlignViewport(av);
}
+
public void updateFromAlignViewport(AlignViewportI av)
{
charWidth = av.getCharWidth();
validCharWidth = av.isValidCharWidth();
av_renderHistogram = av.isShowConsensusHistogram();
av_renderProfile = av.isShowSequenceLogo();
- av_normaliseProfile= av.isNormaliseSequenceLogo();
+ av_normaliseProfile = av.isNormaliseSequenceLogo();
profcolour = av.getGlobalColourScheme();
if (profcolour == 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();
+ // 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();
}
columnSelection = av.getColumnSelection();
- hconsensus = av.getSequenceConsensusHash();//hconsensus;
- hStrucConsensus = av.getRnaStructureConsensusHash(); //hStrucConsensus;
- av_ignoreGapsConsensus=av.getIgnoreGapsConsensus();
+ hconsensus = av.getSequenceConsensusHash();// hconsensus;
+ hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
+ av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
}
+
public int[] getProfileFor(AlignmentAnnotation aa, int column)
{
- // TODO : consider refactoring the global alignment calculation properties/rendering attributes as a global 'alignment group' which holds all vis settings for the alignment as a whole rather than a subset
- //
+ // TODO : consider refactoring the global alignment calculation
+ // 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"))
{
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
return AAFrequency.extractProfile(
- aa.groupRef.consensusData[column], aa.groupRef
- .getIgnoreGapsConsensus());
+ aa.groupRef.consensusData[column],
+ aa.groupRef.getIgnoreGapsConsensus());
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
- if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile)
+ if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
{
- return AAFrequency.extractProfile(hconsensus[column], av_ignoreGapsConsensus);
+ return AAFrequency.extractProfile(hconsensus[column],
+ av_ignoreGapsConsensus);
}
}
else
if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
{
// TODO implement group structure consensus
- /* if (aa.groupRef != null && aa.groupRef.consensusData != null
- && aa.groupRef.isShowSequenceLogo())
- {
- //TODO check what happens for group selections
- return StructureFrequency.extractProfile(
- aa.groupRef.consensusData[column], aa.groupRef
- .getIgnoreGapsConsensus());
- }
- */
+ /*
+ * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
+ * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
+ * group selections return StructureFrequency.extractProfile(
+ * aa.groupRef.consensusData[column], aa.groupRef
+ * .getIgnoreGapsConsensus()); }
+ */
// TODO extend annotation row to enable dynamic and static profile data
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile && hStrucConsensus!=null && hStrucConsensus.length>column)
+ && av_renderProfile && hStrucConsensus != null
+ && hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
av_ignoreGapsConsensus);
}
return null;
}
-
+
/**
* DOCUMENT ME!
*
- * @param annotationPanel TODO
+ * @param annotationPanel
+ * TODO
* @param g
* DOCUMENT ME!
* @param startRes
* @param endRes
* DOCUMENT ME!
*/
- public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes)
+ public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av,
+ Graphics g, int activeRow, int startRes, int endRes)
{
// NOTES:
- // AnnotationPanel needs to implement: ImageObserver, access to AlignViewport
+ // AnnotationPanel needs to implement: ImageObserver, access to
+ // AlignViewport
updateFromAwtRenderPanel(annotPanel, av);
- fm = g.getFontMetrics();
+ fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-
+
int x = 0, y = 0;
int column = 0;
char lastSS;
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
-
+
if (!row.visible)
{
continue;
{
continue;
}
-
+
// this is so that we draw the characters below the graph
y += row.height;
-
+
if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
else if (row.hasText)
{
iconOffset = charHeight - fm.getDescent();
-
+
}
else
{
iconOffset = 0;
}
-
+
if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
{
y += charHeight;
-
+
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;
- }
-
-/* else if (annotationPanel.av.updatingConservation
- && aa[i].label.equals("Conservation"))
- {
-
- y += charHeight;
- g.drawImage(annotationPanel.fadedImage, 0, y - row.height, annotationPanel.imgWidth, y, 0, y
- - row.height, annotationPanel.imgWidth, y, annotationPanel);
-
- g.setColor(Color.black);
- // g.drawString("Calculating Conservation.....",20, y-row.height/2);
-
- continue;
- }
- else if (annotationPanel.av.updatingConservation && aa[i].label.equals("Quality"))
- {
-
- y += charHeight;
- g.drawImage(annotationPanel.fadedImage, 0, y - row.height, annotationPanel.imgWidth, y, 0, y
- - row.height, annotationPanel.imgWidth, y, annotationPanel);
- g.setColor(Color.black);
- // / g.drawString("Calculating Quality....",20, y-row.height/2);
-
+
continue;
}
- */
+
+ /*
+ * else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Conservation")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ *
+ * g.setColor(Color.black); //
+ * g.drawString("Calculating Conservation.....",20, y-row.height/2);
+ *
+ * continue; } else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Quality")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel); g.setColor(Color.black);
+ * // / g.drawString("Calculating Quality....",20, y-row.height/2);
+ *
+ * continue; }
+ */
// first pass sets up state for drawing continuation from left-hand column
// of startRes
x = (startRes == 0) ? 0 : -1;
{
if (hasHiddenColumns)
{
- column = columnSelection.adjustForHiddenColumns(
- startRes + x);
+ column = columnSelection.adjustForHiddenColumns(startRes + x);
if (column > row.annotations.length - 1)
{
break;
{
column = startRes + x;
}
-
+
if ((row.annotations == null) || (row.annotations.length <= column)
|| (row.annotations[column] == null))
{
if (activeRow == i)
{
g.setColor(Color.red);
-
+
if (columnSelection != null)
{
for (int n = 0; n < columnSelection.size(); n++)
{
int v = columnSelection.columnAt(n);
-
+
if (v == column)
{
- g.fillRect(x * charWidth, y, charWidth,
- charHeight);
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
}
}
if (!row.isValidStruc())
{
g.setColor(Color.orange);
- g.fillRect((int)row.getInvalidStrucPos()*charWidth, y, charWidth, charHeight);
+ g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
+ charWidth, charHeight);
}
if (validCharWidth
&& validRes
&& row.annotations[column].displayCharacter != null
&& (row.annotations[column].displayCharacter.length() > 0))
{
-
+
if (centreColLabels || scaleColLabel)
{
fmWidth = (float) fm.charsWidth(
row.annotations[column].displayCharacter
.toCharArray(), 0,
row.annotations[column].displayCharacter.length());
-
+
if (scaleColLabel)
{
// justify the label and scale to fit in column
.charAt(0));
}
charOffset = (int) ((charWidth - fmWidth) / 2f);
-
+
if (row.annotations[column].colour == null)
g.setColor(Color.black);
else
g.setColor(row.annotations[column].colour);
-
+
if (column == 0 || row.graph > 0)
{
g.drawString(row.annotations[column].displayCharacter,
drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
-
+
case 'E':
drawSheetAnnot(g, row, 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);
break;
-
+
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- lastSSX, 2);
-
+
break;
}
}
{
validRes = true;
}
-
+
// x ++;
-
+
if (row.hasIcons)
{
switch (lastSS)
drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
-
+
case 'E':
drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
column, validRes, validEnd);
break;
}
}
-
+
if (row.graph > 0 && row.graphHeight > 0)
{
if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
continue;
}
-
+
if (aa[gg] != row)
{
aa[gg].visible = false;
}
-
+
if (aa[gg].graphMax > groupmax)
{
groupmax = aa[gg].graphMax;
groupmin = aa[gg].graphMin;
}
}
-
+
for (int gg = 0; gg < aa.length; gg++)
{
if (aa[gg].graphGroup == row.graphGroup)
groupmax, row.graphHeight);
}
}
-
+
graphGroupDrawn[row.graphGroup] = true;
}
else
{
- drawLineGraph( g, row, startRes, endRes, y, row.graphMin,
+ drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
row.graphMax, row.graphHeight);
}
}
row.graphMax, y);
}
}
-
+
if (row.graph > 0 && row.hasText)
{
y += charHeight;
}
-
+
if (row.graph == 0)
{
y += aa[i].height;
}
}
- private Color GLYPHLINE_COLOR=Color.gray;
- private Color SHEET_COLOUR=Color.green;
- private Color HELIX_COLOUR=Color.red;
- private 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)
+ private Color GLYPHLINE_COLOR = Color.gray;
+
+ private Color SHEET_COLOUR = Color.green;
+
+ private Color HELIX_COLOUR = Color.red;
+
+ private 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)
{
g.setColor(GLYPHLINE_COLOR);
- g
- .fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
+ 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, AlignmentAnnotation 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')
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX
- - 4, 7);
- g.fillPolygon(
+ 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[]
- { (x * charWidth) - 4, (x * charWidth) - 4,
- (x * charWidth) }, new int[]
{ y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
3);
}
else
{
- g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth
- - lastSSX, 7);
+ g.fillRect(lastSSX, y + 4 + iconOffset,
+ (x + 1) * charWidth - lastSSX, 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, AlignmentAnnotation 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 x1 = lastSSX;
int x2 = (x * charWidth);
-
+
if (MAC)
{
int ofs = charWidth / 2;
if (!validRes || row.annotations[column] == null
|| row.annotations[column].secondaryStructure != 'H')
{
-
+
}
else
{
// g.setColor(Color.magenta);
g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
+ 1, 8, 0, 0);
-
+
}
-
+
return;
}
-
+
if (sCol == 0 || row.annotations[sCol - 1] == null
|| row.annotations[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')
{
- g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset,
- charWidth, 8, 270, 180);
+ g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
+ 8, 270, 180);
x2 -= charWidth / 2;
}
-
+
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, int sRes,
+ int eRes, int y, float min, float max, int graphHeight)
{
if (sRes > aa.annotations.length)
{
return;
}
-
+
int x = 0;
-
+
// Adjustment for fastpaint to left
if (eRes < endRes)
{
eRes++;
}
-
+
eRes = Math.min(eRes, aa.annotations.length);
-
+
if (sRes == 0)
{
x++;
}
-
+
int y1 = y, y2 = y;
float range = max - min;
-
+
// //Draw origin
if (min < 0)
{
y2 = y - (int) ((0 - min / range) * graphHeight);
}
-
+
g.setColor(Color.gray);
g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
-
+
eRes = Math.min(eRes, aa.annotations.length);
-
+
int column;
int aaMax = aa.annotations.length - 1;
-
+
while (x < eRes - sRes)
{
column = sRes + x;
{
column = columnSelection.adjustForHiddenColumns(column);
}
-
+
if (column > aaMax)
{
break;
}
-
+
if (aa.annotations[column] == null
|| aa.annotations[column - 1] == null)
{
x++;
continue;
}
-
+
if (aa.annotations[column].colour == null)
g.setColor(Color.black);
else
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);
-
+
g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
+ charWidth / 2, y2);
x++;
}
-
+
if (aa.threshold != null)
{
g.setColor(aa.threshold.colour);
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);
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, int sRes,
+ int eRes, float min, float max, int y)
{
if (sRes > aa.annotations.length)
{
}
Font ofont = g.getFont();
eRes = Math.min(eRes, aa.annotations.length);
-
+
int x = 0, y1 = y, y2 = y;
-
+
float range = max - min;
-
+
if (min < 0)
{
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;
- boolean renderHistogram = true, renderProfile = true, normaliseProfile=false;
- // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ 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)
{
renderHistogram = aa.groupRef.isShowConsensusHistogram();
renderProfile = aa.groupRef.isShowSequenceLogo();
- normaliseProfile= aa.groupRef.isNormaliseSequenceLogo();
+ normaliseProfile = aa.groupRef.isNormaliseSequenceLogo();
}
else
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
- normaliseProfile= av_normaliseProfile;
+ normaliseProfile = av_normaliseProfile;
}
}
while (x < eRes - sRes)
{
column = columnSelection.adjustForHiddenColumns(column);
}
-
+
if (column > aaMax)
{
break;
}
-
+
if (aa.annotations[column] == null)
{
x++;
g.setColor(Color.black);
else
g.setColor(aa.annotations[column].colour);
-
+
y1 = y
- (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
-
+
if (renderHistogram)
{
if (y1 - y2 > 0)
// draw profile if available
if (renderProfile && aa.annotations[column].value != 0)
{
-
+
int profl[] = getProfileFor(aa, column);
// just try to draw the logo if profl is not null
- if (profl != null)
+ if (profl != null && profl[1] != 0)
{
-
- float ht = normaliseProfile ? y-aa.graphHeight : y1;
+ 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;
-
+
/**
- * profl.length == 52 indicates that the profile of a secondary
- * structure conservation row was accesed.
- * Therefore dc gets length 2, to have space for a basepair instead of
- * just a single nucleotide
+ * profl.length == 74 indicates that the profile of a secondary
+ * structure conservation row was accesed. Therefore dc gets length 2,
+ * to have space for a basepair instead of just a single nucleotide
*/
- if (profl.length == 52)
+ if (profl.length == 74)
{
dc = new char[2];
}
{
dc = new char[1];
}
- LineMetrics lm=g.getFontMetrics(ofont).getLineMetrics("Q", g);
- double scale = 1f/(normaliseProfile ? profl[1] : 100f);
- float ofontHeight = 1f/lm.getAscent();// magnify to fill box
- double scl=0.0;
- for (int c = 2; profl != null && c < profl[0];)
+ LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
+ double scale = 1f / (normaliseProfile ? profl[1] : 100f);
+ float ofontHeight = 1f / lm.getAscent();// magnify to fill box
+ double scl = 0.0;
+ for (int c = 2; c < profl[0];)
{
dc[0] = (char) profl[c++];
-
+
if (aa.label.startsWith("StrucConsensus"))
{
dc[1] = (char) profl[c++];
}
-
+
wdth = charWidth;
wdth /= (float) fm.charsWidth(dc, 0, dc.length);
-
- ht += scl;
+
+ ht += scl;
{
- // if (aa.annotations[column].value==0) {
- // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
- // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
- // ht = y2-(int)ht2;
- // } else {
- scl=((double)htn)*scale* ((double) profl[c++]);
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics().getFontRenderContext());
+ scl = ((double) htn) * scale * ((double) profl[c++]);
+ lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
+ .getFontRenderContext());
g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl/lm.getAscent())));
+ wdth, scl / lm.getAscent())));
lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-
- // htn -=ht2;
- // }
- // ? );// try to get a
- // colourscheme for the
- // group(aa.groupRef.cs==null)
- // ? av.textColour2 :
- // cs.findColour(dc));
- // System.out.println(dc[0]);
+
// Debug - render boxes around characters
// g.setColor(Color.red);
- // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, (int)(scl));
+ // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
+ // (int)(scl));
// g.setColor(profcolour.findColour(dc[0]).darker());
- g.setColor(profcolour.findColour(dc[0]));
- // (av.globalColourScheme!=null)
- g.drawChars(dc, 0, dc.length, x * charWidth,
- (int) (ht + (scl-lm.getDescent()-lm.getBaselineOffsets()[lm.getBaselineIndex()])));
- // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+ g.setColor(profcolour.findColour(dc[0], column));
+
+ hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
+ .getBaselineIndex()]));
+
+ g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
}
}
g.setFont(ofont);
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);
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)