X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=e527c100d60fa9a82519c59dc903230164836679;hb=6d981e3a3cac0e7f487d2b3d40e45cfd6ca8435c;hp=36550df3047e726d3d9cba81c689d0584281861f;hpb=acf1fd1686b151d14c0d73c91869b9e41726822d;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 36550df..e527c10 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -4,6 +4,7 @@ import jalview.analysis.AAFrequency; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.schemes.ColourSchemeI; @@ -29,7 +30,7 @@ public class AnnotationRenderer // 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) { @@ -39,21 +40,21 @@ public class AnnotationRenderer 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[] @@ -90,7 +91,7 @@ public class AnnotationRenderer 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; @@ -211,20 +212,25 @@ public class AnnotationRenderer } /** - * DOCUMENT ME! - * - * @param annotationPanel - * TODO + * Render the annotation rows associated with an alignment. + * @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, + 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 @@ -252,7 +258,7 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - + Annotation[] row_annotations=row.annotations; if (!row.visible) { continue; @@ -288,10 +294,10 @@ public class AnnotationRenderer 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); @@ -303,22 +309,22 @@ public class AnnotationRenderer /* * 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 @@ -329,7 +335,7 @@ public class AnnotationRenderer if (hasHiddenColumns) { column = columnSelection.adjustForHiddenColumns(startRes + x); - if (column > row.annotations.length - 1) + if (column > row_annotations.length - 1) { break; } @@ -339,8 +345,8 @@ public class AnnotationRenderer 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; } @@ -375,16 +381,16 @@ public class AnnotationRenderer } 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) { @@ -403,29 +409,29 @@ public class AnnotationRenderer } 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); @@ -433,12 +439,12 @@ public class AnnotationRenderer } 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'; } @@ -450,18 +456,18 @@ public class AnnotationRenderer switch (lastSS) { case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + 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, + drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; @@ -490,17 +496,17 @@ public class AnnotationRenderer 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; } @@ -516,21 +522,21 @@ public class AnnotationRenderer switch (lastSS) { case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + 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, + drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; default: - drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, + drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; } @@ -554,7 +560,6 @@ public class AnnotationRenderer { aa[gg].visible = false; } - if (aa[gg].graphMax > groupmax) { groupmax = aa[gg].graphMax; @@ -569,7 +574,7 @@ public class AnnotationRenderer { if (aa[gg].graphGroup == row.graphGroup) { - drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, + drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin, groupmax, row.graphHeight); } } @@ -578,13 +583,13 @@ public class AnnotationRenderer } else { - drawLineGraph(g, row, startRes, endRes, y, row.graphMin, + 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, + drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin, row.graphMax, y); } } @@ -599,17 +604,18 @@ public class AnnotationRenderer 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, + public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { @@ -617,14 +623,14 @@ public class AnnotationRenderer g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); } - public void drawSheetAnnot(Graphics g, AlignmentAnnotation row, + 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); @@ -642,7 +648,7 @@ public class AnnotationRenderer } - public void drawHelixAnnot(Graphics g, AlignmentAnnotation row, + public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) { @@ -658,8 +664,8 @@ public class AnnotationRenderer // 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 @@ -668,8 +674,8 @@ public class AnnotationRenderer 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') { } @@ -684,15 +690,15 @@ public class AnnotationRenderer 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); @@ -702,10 +708,10 @@ public class AnnotationRenderer g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, + 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; } @@ -718,7 +724,7 @@ public class AnnotationRenderer eRes++; } - eRes = Math.min(eRes, aa.annotations.length); + eRes = Math.min(eRes, aa_annotations.length); if (sRes == 0) { @@ -737,10 +743,10 @@ public class AnnotationRenderer 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) { @@ -755,51 +761,51 @@ public class AnnotationRenderer 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, + 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; @@ -807,7 +813,7 @@ public class AnnotationRenderer if (min < 0) { - y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); + y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight); } g.setColor(Color.gray); @@ -815,16 +821,16 @@ public class AnnotationRenderer 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 { @@ -846,18 +852,18 @@ public class AnnotationRenderer 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) { @@ -871,15 +877,15 @@ public class AnnotationRenderer } } // 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; @@ -906,17 +912,17 @@ public class AnnotationRenderer { 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( @@ -941,25 +947,25 @@ public class AnnotationRenderer } 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, + 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)); @@ -968,14 +974,14 @@ public class AnnotationRenderer 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;