X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=deb2b6f3c383d15004c94cd3818942a21b03e0ff;hb=5571d7868cad5493b52c9fc421c88c025e7c2d35;hp=ed266ae0ccbc3782e4ea866d235ea55976ce9f87;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index ed266ae..deb2b6f 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -80,9 +80,9 @@ public class AnnotationRenderer private ProfilesI hconsensus; - private Hashtable[] complementConsensus; + private Hashtable[] complementConsensus; - private Hashtable[] hStrucConsensus; + private Hashtable[] hStrucConsensus; private boolean av_ignoreGapsConsensus; @@ -149,6 +149,7 @@ public class AnnotationRenderer */ public void dispose() { + hiddenColumns = null; hconsensus = null; complementConsensus = null; hStrucConsensus = null; @@ -416,8 +417,6 @@ public class AnnotationRenderer return null; } - boolean rna = false; - /** * Render the annotation rows associated with an alignment. * @@ -448,7 +447,7 @@ public class AnnotationRenderer updateFromAwtRenderPanel(annotPanel, av); fm = g.getFontMetrics(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - int temp = 0; + // int temp = 0; if (aa == null) { return false; @@ -461,8 +460,8 @@ public class AnnotationRenderer boolean validRes = false; boolean validEnd = false; boolean labelAllCols = false; - boolean centreColLabels; - boolean centreColLabelsDef = av.isCentreColumnLabels(); +// boolean centreColLabels; +// boolean centreColLabelsDef = av.isCentreColumnLabels(); boolean scaleColLabel = false; final AlignmentAnnotation consensusAnnot = av .getAlignmentConsensusAnnotation(); @@ -470,8 +469,6 @@ public class AnnotationRenderer .getAlignmentStrucConsensusAnnotation(); final AlignmentAnnotation complementConsensusAnnot = av .getComplementConsensusAnnotation(); - boolean renderHistogram = true, renderProfile = true, - normaliseProfile = false, isRNA = rna; BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label @@ -482,38 +479,35 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - isRNA = row.isRNA(); + boolean renderHistogram = true; + boolean renderProfile = false; + boolean normaliseProfile = false; + boolean isRNA = row.isRNA(); + + // check if this is a consensus annotation row and set the display + // settings appropriately + // TODO: generalise this to have render styles for consensus/profile + // data + if (row.groupRef != null && row == row.groupRef.getConsensus()) { - // check if this is a consensus annotation row and set the display - // settings appropriately - // TODO: generalise this to have render styles for consensus/profile - // data - if (row.groupRef != null && row == row.groupRef.getConsensus()) - { - renderHistogram = row.groupRef.isShowConsensusHistogram(); - renderProfile = row.groupRef.isShowSequenceLogo(); - normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); - } - else if (row == consensusAnnot || row == structConsensusAnnot - || row == complementConsensusAnnot) - { - renderHistogram = av_renderHistogram; - renderProfile = av_renderProfile; - normaliseProfile = av_normaliseProfile; - } - else - { - renderHistogram = true; - // don't need to set render/normaliseProfile since they are not - // currently used in any other annotation track renderer - } + renderHistogram = row.groupRef.isShowConsensusHistogram(); + renderProfile = row.groupRef.isShowSequenceLogo(); + normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); + } + else if (row == consensusAnnot || row == structConsensusAnnot + || row == complementConsensusAnnot) + { + renderHistogram = av_renderHistogram; + renderProfile = av_renderProfile; + normaliseProfile = av_normaliseProfile; } + Annotation[] row_annotations = row.annotations; if (!row.visible) { continue; } - centreColLabels = row.centreColLabels || centreColLabelsDef; +// centreColLabels = row.centreColLabels || centreColLabelsDef; labelAllCols = row.showAllColLabels; scaleColLabel = row.scaleColLabel; lastSS = ' '; @@ -781,7 +775,7 @@ public class AnnotationRenderer if (x > -1) { - int nb_annot = x - temp; + // int nb_annot = x - temp; // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre // annot :"+nb_annot); switch (lastSS) @@ -790,7 +784,7 @@ public class AnnotationRenderer case ')': // and opposite direction drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); - temp = x; + // temp = x; break; case 'H': @@ -873,13 +867,13 @@ public class AnnotationRenderer drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); - temp = x; + // temp = x; break; default: g.setColor(Color.gray); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); - temp = x; + // temp = x; break; } } @@ -1120,7 +1114,7 @@ public class AnnotationRenderer public static final Color STEM_COLOUR = Color.blue; - private Color sdNOTCANONICAL_COLOUR; + // private Color sdNOTCANONICAL_COLOUR; void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, @@ -1396,7 +1390,8 @@ public class AnnotationRenderer boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE; boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE; float ht = normaliseProfile ? y - _aa.graphHeight : y1; - final double normaliseFactor = normaliseProfile ? _aa.graphHeight : (y2 - y1); + final double normaliseFactor = normaliseProfile ? _aa.graphHeight + : (y2 - y1); /** * Render a single base for a sequence profile, a base pair for @@ -1447,8 +1442,14 @@ public class AnnotationRenderer s = new String(dc); } // next profl[] position is profile % for the character(s) - - double newHeight = normaliseFactor * scale * profl[c++]; + + int percent = profl[c++]; + if (percent == 0) + { + // failsafe in case a count rounds down to 0% + continue; + } + double newHeight = normaliseFactor * scale * percent; /* * Set character colour as per alignment colour scheme; use the @@ -1474,9 +1475,9 @@ public class AnnotationRenderer // (int)(scl)); // g.setColor(profcolour.findColour(dc[0]).darker()); - double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length); + double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length); double sy = newHeight / asc; - double newAsc = asc * sy; + double newAsc = asc * sy; double newDec = dec * sy; // it is not necessary to recalculate lm for the new font. // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0 @@ -1502,15 +1503,21 @@ public class AnnotationRenderer ht2 += newHeight; } else + /** + * Java only + * + * @j2sIgnore + */ { - /* - * Java ('normal') method is to scale the font to fit - */ + // Java ('normal') method is to scale the font to fit + final int hght = (int) (ht + (newAsc - newDec)); Font font = ofont .deriveFont(AffineTransform.getScaleInstance(sx, sy)); g.setFont(font); g.drawChars(dc, 0, dc.length, x * charWidth, hght); + g.setFont(ofont); + ht += newHeight; } } @@ -1524,7 +1531,7 @@ public class AnnotationRenderer Graphics2D g2 = (Graphics2D) g; g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); + { 5f, 3f }, 0f)); y2 = (int) (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight);