X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=ace94f4e28c0aad34a13f38bd65b76dc8a0004eb;hb=ef23315db576f5451de0fcb850f645c5db222b20;hp=c3d4ef5bc46eda4a8be7ba2f801396a801cc1bc0;hpb=57c960648b550f10c7db40e39c7bb6a761d732b1;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index c3d4ef5..ace94f4 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -29,17 +29,19 @@ public class AnnotationRenderer // 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 ? "" + + 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 @@ -81,42 +83,59 @@ public class AnnotationRenderer // 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(); @@ -126,56 +145,62 @@ public class AnnotationRenderer 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")) { - 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 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()); } + */ // TODO extend annotation row to enable dynamic and static profile data // to // be stored if (aa.groupRef == null && aa.sequenceRef == null - && av_renderProfile) + && av_renderProfile && hStrucConsensus != null + && hStrucConsensus.length > column) { return StructureFrequency.extractProfile(hStrucConsensus[column], av_ignoreGapsConsensus); @@ -184,11 +209,12 @@ public class AnnotationRenderer } return null; } - + /** * DOCUMENT ME! * - * @param annotationPanel TODO + * @param annotationPanel + * TODO * @param g * DOCUMENT ME! * @param startRes @@ -196,13 +222,16 @@ public class AnnotationRenderer * @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(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - + int x = 0, y = 0; int column = 0; char lastSS; @@ -223,7 +252,7 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - + if (!row.visible) { continue; @@ -239,10 +268,10 @@ public class AnnotationRenderer { continue; } - + // this is so that we draw the characters below the graph y += row.height; - + if (row.hasText) { iconOffset = charHeight - fm.getDescent(); @@ -252,50 +281,46 @@ public class AnnotationRenderer 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; @@ -303,8 +328,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns( - startRes + x); + column = columnSelection.adjustForHiddenColumns(startRes + x); if (column > row.annotations.length - 1) { break; @@ -314,7 +338,7 @@ public class AnnotationRenderer { column = startRes + x; } - + if ((row.annotations == null) || (row.annotations.length <= column) || (row.annotations[column] == null)) { @@ -329,35 +353,39 @@ public class AnnotationRenderer 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); + } 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 @@ -380,12 +408,12 @@ public class AnnotationRenderer .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, @@ -425,23 +453,23 @@ public class AnnotationRenderer 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; } } @@ -471,9 +499,18 @@ public class AnnotationRenderer { validEnd = true; } - + if ((row.annotations == null) || (row.annotations.length <= column) + || (row.annotations[column] == null)) + { + validRes = false; + } + else + { + validRes = true; + } + // x ++; - + if (row.hasIcons) { switch (lastSS) @@ -482,7 +519,7 @@ public class AnnotationRenderer 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); @@ -498,7 +535,7 @@ public class AnnotationRenderer break; } } - + if (row.graph > 0 && row.graphHeight > 0) { if (row.graph == AlignmentAnnotation.LINE_GRAPH) @@ -512,12 +549,12 @@ public class AnnotationRenderer { continue; } - + if (aa[gg] != row) { aa[gg].visible = false; } - + if (aa[gg].graphMax > groupmax) { groupmax = aa[gg].graphMax; @@ -527,7 +564,7 @@ public class AnnotationRenderer groupmin = aa[gg].graphMin; } } - + for (int gg = 0; gg < aa.length; gg++) { if (aa[gg].graphGroup == row.graphGroup) @@ -536,12 +573,12 @@ public class AnnotationRenderer 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); } } @@ -551,12 +588,12 @@ public class AnnotationRenderer row.graphMax, y); } } - + if (row.graph > 0 && row.hasText) { y += charHeight; } - + if (row.graph == 0) { y += aa[i].height; @@ -564,52 +601,57 @@ public class AnnotationRenderer } } - 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; @@ -629,76 +671,77 @@ public class AnnotationRenderer 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; @@ -706,34 +749,34 @@ public class AnnotationRenderer { 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); @@ -741,14 +784,15 @@ public class AnnotationRenderer 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) { @@ -756,37 +800,37 @@ public class AnnotationRenderer } 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) @@ -796,12 +840,12 @@ public class AnnotationRenderer { column = columnSelection.adjustForHiddenColumns(column); } - + if (column > aaMax) { break; } - + if (aa.annotations[column] == null) { x++; @@ -811,10 +855,10 @@ public class AnnotationRenderer 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) @@ -827,27 +871,26 @@ public class AnnotationRenderer } } // draw profile if available - if (renderProfile && aa.annotations[column].value != 0) + if (renderProfile) { - + 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]; } @@ -855,52 +898,42 @@ public class AnnotationRenderer { 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,null)); + + hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm + .getBaselineIndex()])); + + g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); } } g.setFont(ofont); @@ -915,12 +948,13 @@ public class AnnotationRenderer 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)