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 java.util.BitSet;
import java.util.Hashtable;
-import com.stevesoft.pat.Regex;
-
public class AnnotationRenderer
{
private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
this.debugRedraw = debugRedraw;
}
- public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
+ void drawStemAnnot(Graphics g, 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("(\\))");
char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
: row_annotations[column - 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 (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);
}
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;
*/
private boolean canClip = false;
- public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+ 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.charAt(0)))
{
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)
{
- if (columnSelection.isSelected(column))
+ if (columnSelection.contains(column))
{
g.fillRect(x * charWidth, y, charWidth, charHeight);
}
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,
+ void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
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)
}
- public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
+ void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
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)
{
}
}
- 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
git://source.jalview.org / jalview.git / blobdiff