X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=94015de4325c6bc04b515eb0094817faf862f857;hb=0ca96db9937136626dcd867e122d1762b28e15bd;hp=2ba7aff98d562611520cd95375b42dee3891f3eb;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 2ba7aff..94015de 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -22,6 +22,7 @@ package jalview.renderer; import jalview.analysis.AAFrequency; import jalview.analysis.CodingUtils; +import jalview.analysis.Rna; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; @@ -43,10 +44,14 @@ import java.awt.image.ImageObserver; 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 + + private static final int CHAR_A = 'A'; // 65 + + private static final int CHAR_Z = 'Z'; // 90 + /** * flag indicating if timing and redraw parameter info should be output */ @@ -69,7 +74,7 @@ public class AnnotationRenderer 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) { @@ -77,7 +82,6 @@ public class AnnotationRenderer 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; @@ -87,18 +91,20 @@ public class AnnotationRenderer 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)) { - g.fillPolygon(new int[] - { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3); + /* + * 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) @@ -108,13 +114,15 @@ public class AnnotationRenderer } 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); + /* + * 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) @@ -132,7 +140,7 @@ public class AnnotationRenderer private FontMetrics fm; - private final boolean MAC = new jalview.util.Platform().isAMac(); + private final boolean MAC = jalview.util.Platform.isAMac(); boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile = false; @@ -190,7 +198,7 @@ public class AnnotationRenderer */ 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) @@ -201,7 +209,6 @@ public class AnnotationRenderer 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; @@ -213,17 +220,16 @@ public class AnnotationRenderer || !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) // 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) @@ -237,9 +243,8 @@ public class AnnotationRenderer // 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) @@ -317,7 +322,7 @@ public class AnnotationRenderer * @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 @@ -594,14 +599,9 @@ public class AnnotationRenderer 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); } } } @@ -628,17 +628,17 @@ public class AnnotationRenderer // // 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? @@ -715,14 +715,14 @@ public class AnnotationRenderer } } - 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; } } @@ -751,7 +751,7 @@ public class AnnotationRenderer validEnd); break; } - + // no break if isRNA - falls through to drawNotCanonicalAnnot! case 'E': if (!isRNA) { @@ -760,6 +760,7 @@ public class AnnotationRenderer validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '{': case '}': @@ -867,7 +868,6 @@ public class AnnotationRenderer { validRes = true; } - // x ++; if (row.hasIcons) @@ -882,6 +882,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case 'E': if (!isRNA) @@ -890,6 +891,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '(': case ')': // Stem case for RNA secondary structure @@ -1070,7 +1072,7 @@ public class AnnotationRenderer 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) { @@ -1078,7 +1080,7 @@ public class AnnotationRenderer 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) @@ -1090,11 +1092,9 @@ public class AnnotationRenderer { 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 { @@ -1104,7 +1104,7 @@ public class AnnotationRenderer } - 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) { @@ -1164,7 +1164,7 @@ public class AnnotationRenderer 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) { @@ -1249,8 +1249,7 @@ public class AnnotationRenderer 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); @@ -1258,7 +1257,7 @@ public class AnnotationRenderer } } - 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) @@ -1389,8 +1388,9 @@ public class AnnotationRenderer 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 @@ -1433,8 +1433,7 @@ public class AnnotationRenderer 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);