import jalview.analysis.AAFrequency;
import jalview.analysis.CodingUtils;
+import jalview.analysis.Rna;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
import java.awt.BasicStroke;
import java.awt.Color;
import java.util.BitSet;
import java.util.Hashtable;
-import com.stevesoft.pat.Regex;
-
public class AnnotationRenderer
{
- /**
- * flag indicating if timing and redraw parameter info should be output
- */
- private final boolean debugRedraw;
+ private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
- public AnnotationRenderer()
- {
- this(false);
- }
+ private static final int CHAR_A = 'A'; // 65
+
+ private static final int CHAR_Z = 'Z'; // 90
/**
- * Create a new annotation Renderer
- *
- * @param debugRedraw
- * flag indicating if timing and redraw parameter info should be
- * output
+ * flag indicating if timing and redraw parameter info should be output
*/
- public AnnotationRenderer(boolean debugRedraw)
- {
- this.debugRedraw = debugRedraw;
- }
-
- public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
- 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("(\\))");
-
- char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
- : row_annotations[column - 1].secondaryStructure;
-
- boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || dc != row_annotations[sCol - 1].secondaryStructure;
- boolean diffdownstream = !validRes || !validEnd
- || row_annotations[column] == null
- || dc != row_annotations[column].secondaryStructure;
- // 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 && ResidueProperties.isCloseParenRNA(dc))
- {
-
- if (diffupstream)
- // 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[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
- x1 += 5;
- }
- if (diffdownstream)
- {
- x2 -= 1;
- }
- }
- else
- {
-
- // display a forward arrow
- if (diffdownstream)
- {
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
- x2 -= 5;
- }
- if (diffupstream)
- {
- x1 += 1;
- }
- }
- // draw arrow body
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
- }
+ private final boolean debugRedraw;
private int charWidth, endRes, charHeight;
private FontMetrics fm;
- private final boolean MAC = jalview.util.Platform.isAMac();
+ private final boolean MAC = Platform.isAMac();
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
*/
private boolean canClip = false;
- public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+ public AnnotationRenderer()
+ {
+ this(false);
+ }
+
+ /**
+ * Create a new annotation Renderer
+ *
+ * @param debugRedraw
+ * flag indicating if timing and redraw parameter info should be
+ * output
+ */
+ public AnnotationRenderer(boolean debugRedraw)
+ {
+ this.debugRedraw = debugRedraw;
+ }
+
+ /**
+ * Remove any references and resources when this object is no longer required
+ */
+ public void dispose()
+ {
+ hconsensus = null;
+ complementConsensus = null;
+ hStrucConsensus = null;
+ fadedImage = null;
+ annotationPanel = null;
+ }
+
+ void drawStemAnnot(Graphics g, Annotation[] row_annotations, 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);
+
+ char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
+ : row_annotations[column - 1].secondaryStructure;
+
+ boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+ || dc != row_annotations[sCol - 1].secondaryStructure;
+ boolean diffdownstream = !validRes || !validEnd
+ || row_annotations[column] == null
+ || dc != row_annotations[column].secondaryStructure;
+
+ if (column > 0 && Rna.isClosingParenthesis(dc))
+ {
+ if (diffupstream)
+ // if (validRes && column>1 && row_annotations[column-2]!=null &&
+ // dc.equals(row_annotations[column-2].displayCharacter))
+ {
+ /*
+ * if new annotation with a closing base pair half of the stem,
+ * display a backward arrow
+ */
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[] { y + iconOffset, y + 14 + iconOffset,
+ y + 8 + iconOffset }, 3);
+ x1 += 5;
+ }
+ if (diffdownstream)
+ {
+ x2 -= 1;
+ }
+ }
+ else
+ {
+ // display a forward arrow
+ if (diffdownstream)
+ {
+ /*
+ * if annotation ending with an opeing base pair half of the stem,
+ * display a forward arrow
+ */
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x2 -= 5;
+ }
+ if (diffupstream)
+ {
+ x1 += 1;
+ }
+ }
+ // draw arrow body
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ }
+
+ void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
Annotation[] row_annotations, int lastSSX, int x, int y,
int iconOffset, int startRes, int column, boolean validRes,
boolean validEnd)
int sCol = (lastSSX / charWidth) + startRes;
int x1 = lastSSX;
int x2 = (x * charWidth);
- Regex closeparen = new Regex("}|]|<|[a-z]");
String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
: row_annotations[column - 1].displayCharacter;
|| !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))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
- // )
+ if (column > 0 && Rna.isClosingParenthesis(dc))
{
if (diffupstream)
// 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[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
+ new int[] { y + iconOffset, y + 14 + iconOffset,
+ y + 8 + iconOffset }, 3);
x1 += 5;
}
if (diffdownstream)
// display a forward arrow
if (diffdownstream)
{
- g.fillPolygon(new int[]
- { x2 - 5, x2 - 5, x2 }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
+ y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
x2 -= 5;
}
if (diffupstream)
* @param column
* @return
*/
- public int[] getProfileFor(AlignmentAnnotation aa, int column)
+ int[] getProfileFor(AlignmentAnnotation aa, int column)
{
// TODO : consider refactoring the global alignment calculation
// properties/rendering attributes as a global 'alignment group' which holds
if (columnSelection != null)
{
- for (int n = 0; n < columnSelection.size(); n++)
+ if (columnSelection.contains(column))
{
- int v = columnSelection.columnAt(n);
-
- if (v == column)
- {
- g.fillRect(x * charWidth, y, charWidth, charHeight);
- }
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
}
}
//
// 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;
- }
+ // 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;
+ }
// }
}
// TODO is it ok to use width of / show all characters here?
}
}
- if (ss >= 65)
+ if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
{
// distinguish between forward/backward base-pairing
- if (displayChar.indexOf(ss + 32) > -1)
+ int ssLowerCase = ss + UPPER_TO_LOWER;
+ // TODO would .equals() be safer here? or charAt(0)?
+ if (displayChar.indexOf(ssLowerCase) > -1)
{
-
- ss = (char) (ss + 32);
-
+ ss = (char) ssLowerCase;
}
}
validEnd);
break;
}
-
+ // no break if isRNA - falls through to drawNotCanonicalAnnot!
case 'E':
if (!isRNA)
{
validEnd);
break;
}
+ // no break if isRNA - fall through to drawNotCanonicalAnnot!
case '{':
case '}':
{
validRes = true;
}
-
// x ++;
if (row.hasIcons)
startRes, column, validRes, validEnd);
break;
}
+ // no break if isRNA - fall through to drawNotCanonicalAnnot!
case 'E':
if (!isRNA)
startRes, column, validRes, validEnd);
break;
}
+ // no break if isRNA - fall through to drawNotCanonicalAnnot!
case '(':
case ')': // Stem case for RNA secondary structure
private Color sdNOTCANONICAL_COLOUR;
- public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
+ 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, Annotation[] row,
+ void drawSheetAnnot(Graphics g, Annotation[] row,
int lastSSX, int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
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[]
- { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
- 3);
+ g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
+ (x * charWidth) }, new int[] { y + iconOffset,
+ y + 14 + iconOffset, y + 7 + iconOffset }, 3);
}
else
{
}
- public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
+ 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);
g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
+ void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, int y,
float min, float max, int graphHeight)
{
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));
+ 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);
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
+ void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
float max, int y, boolean renderHistogram, boolean renderProfile,
boolean normaliseProfile)
scl = htn * scale * profl[c++];
lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
.getFontRenderContext());
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent())));
+ Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, scl / lm.getAscent()));
+ g.setFont(font);
lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
// Debug - render boxes around characters
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));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
y2 = (int) (y - ((_aa.threshold.value - min) / range)
* _aa.graphHeight);
git://source.jalview.org / jalview.git / blobdiff