X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=1b58dbc7c8b04d31439cf2ee44c3229ae979c805;hb=8d2724b83aca38ef75d68787cc5939d950467e63;hp=d56ba54e41ba82a5770dd20c7f143e24187d69b5;hpb=a7f8fa9c06d82efbbdbc6a0bf1054bb21610b353;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index d56ba54..1b58dbc 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1,3 +1,21 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.renderer; import jalview.analysis.AAFrequency; @@ -18,23 +36,35 @@ import java.awt.Image; import java.awt.font.LineMetrics; import java.awt.geom.AffineTransform; import java.awt.image.ImageObserver; +import java.util.BitSet; import java.util.Hashtable; import com.stevesoft.pat.Regex; public class AnnotationRenderer { + /** + * flag indicating if timing and redraw parameter info should be output + */ + private final boolean debugRedraw; public AnnotationRenderer() { - // TODO Auto-generated constructor stub + this(false); + } + /** + * Create a new annotation Renderer + * @param debugRedraw flag indicating if timing and redraw parameter info should be output + */ + public AnnotationRenderer(boolean debugRedraw) + { + this.debugRedraw=debugRedraw; } public void drawStemAnnot(Graphics g, Annotation[] row_annotations, 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; @@ -127,18 +157,35 @@ public class AnnotationRenderer * width of image to render in panel */ private int imgWidth; + /** + * offset to beginning of visible area + */ + private int sOffset; + /** + * offset to end of visible area + */ + private int visHeight; + /** + * indicate if the renderer should only render the visible portion of the annotation given the current view settings + */ + private boolean useClip=true; + /** + * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1 + */ + private boolean canClip=false; - public void drawNotCanonicalAnnot(Graphics g, Annotation[] row_annotations, + public 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) { + //System.out.println(nonCanColor); - g.setColor(NOTCANONICAL_COLOUR); + g.setColor(nonCanColor); int sCol = (lastSSX / charWidth) + startRes; int x1 = lastSSX; int x2 = (x * charWidth); - Regex closeparen = new Regex("(}|]|a|b|c|d)"); + Regex closeparen = new Regex("}|]|<|[a-z]"); String dc = (column == 0 || row_annotations[column - 1] == null) ? "" : row_annotations[column - 1].displayCharacter; @@ -195,6 +242,22 @@ public class AnnotationRenderer annotationPanel = annotPanel; fadedImage = annotPanel.getFadedImage(); imgWidth = annotPanel.getFadedImageWidth(); + // visible area for rendering + int[] bounds=annotPanel.getVisibleVRange(); + if (bounds!=null) + { + sOffset = bounds[0]; + visHeight = bounds[1]; + if (visHeight==0) + { + useClip=false; + } else { + useClip=canClip; + } + } else { + useClip=false; + } + updateFromAlignViewport(av); } @@ -239,7 +302,7 @@ public class AnnotationRenderer } // 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) { return AAFrequency.extractProfile(hconsensus[column], av_ignoreGapsConsensus); @@ -261,7 +324,7 @@ public class AnnotationRenderer // to // be stored if (aa.groupRef == null && aa.sequenceRef == null - && av_renderProfile && hStrucConsensus != null + && hStrucConsensus != null && hStrucConsensus.length > column) { return StructureFrequency.extractProfile(hStrucConsensus[column], @@ -274,6 +337,7 @@ public class AnnotationRenderer /** * Render the annotation rows associated with an alignment. + * * @param annotPanel * container frame * @param av @@ -286,19 +350,26 @@ public class AnnotationRenderer * first column that will be drawn * @param endRes * last column that will be drawn - * @return true if the fadedImage was used for any alignment annotation rows currently being calculated + * @return true if the fadedImage was used for any alignment annotation rows + * currently being calculated */ - public boolean drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, - Graphics g, int activeRow, int startRes, int endRes) + public boolean drawComponent(AwtRenderPanelI annotPanel, + AlignViewportI av, Graphics g, int activeRow, int startRes, + int endRes) { - boolean usedFaded=false; + long stime=System.currentTimeMillis(); + boolean usedFaded = false; // NOTES: // AnnotationPanel needs to implement: ImageObserver, access to // AlignViewport updateFromAwtRenderPanel(annotPanel, av); fm = g.getFontMetrics(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - + int temp = 0; + if (aa==null) + { + return false; + } int x = 0, y = 0; int column = 0; char lastSS; @@ -310,16 +381,42 @@ public class AnnotationRenderer boolean centreColLabels, centreColLabelsDef = av .getCentreColumnLabels(); boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; + AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation(); + boolean renderHistogram = true, renderProfile = true, normaliseProfile = false; + + BitSet graphGroupDrawn = new BitSet(); int charOffset = 0; // offset for a label float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a // column. Font ofont = g.getFont(); // \u03B2 \u03B1 + // debug ints + int yfrom=0,f_i=0,yto=0,f_to=0; + boolean clipst=false,clipend=false; for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - Annotation[] row_annotations=row.annotations; + { + // 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) + { + 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 + } + } + Annotation[] row_annotations = row.annotations; if (!row.visible) { continue; @@ -329,10 +426,20 @@ public class AnnotationRenderer scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; + + if (!useClip || ((y-charHeight)=sOffset)) + {// if_in_visible_region + if (!clipst) + { + clipst=true; + yfrom=y; + f_i=i; + } + yto = y; + f_to=i; if (row.graph > 0) { - if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) - { + if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) { continue; } @@ -358,7 +465,7 @@ public class AnnotationRenderer if (row.autoCalculated && av.isCalculationInProgress(row)) { y += charHeight; - usedFaded=true; + usedFaded = true; g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - row.height, imgWidth, y, annotationPanel); g.setColor(Color.black); @@ -370,22 +477,22 @@ 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 @@ -492,7 +599,8 @@ public class AnnotationRenderer .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); @@ -501,56 +609,158 @@ public class AnnotationRenderer if (row.hasIcons) { char ss = validRes ? row_annotations[column].secondaryStructure - : ' '; - //System.out.println(ss); - if (ss == 'S') + : '-'; + + if (ss == '(') { // distinguish between forward/backward base-pairing if (row_annotations[column].displayCharacter.indexOf(')') > -1) { - ss = 's'; - System.out.println(ss); + + ss = ')'; + } } - if (ss == 'C') + if (ss == '[') { - if ((row_annotations[column].displayCharacter.indexOf(']') > -1) || (row_annotations[column].displayCharacter.indexOf('}') > -1)) + if ((row_annotations[column].displayCharacter.indexOf(']') > -1)) { - ss = 'c'; - System.out.println(ss); + ss = ']'; + + } } + if (ss == '{') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('}') > -1) + { + ss = '}'; + + + } + } + if (ss == '<') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('<') > -1) + { + ss = '>'; + + + } + } + if (ss >=65) + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf(ss+32) > -1) + { + + ss = (char) (ss+32); + + + } + } + + if (!validRes || (ss != lastSS)) - { + { + + if (x > -1) - { + { + + + int nb_annot=x-temp; + //System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot); switch (lastSS) - { - case 'H': + { + + case '$': drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; - case 'E': + case 'µ': drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; - case 'S': // Stem case for RNA secondary structure - case 's': // and opposite direction + case '(': // Stem case for RNA secondary structure + case ')': // and opposite direction drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); + temp=x; break; + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': case 'C': case 'c': - drawNotCanonicalAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + case 'D': + case 'd': + case 'E': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case 'H': + case 'h': + case 'I': + case 'i': + case 'J': + case 'j': + case 'K': + case 'k': + case 'L': + case 'l': + case 'M': + case 'm': + case 'N': + case 'n': + case 'O': + case 'o': + case 'P': + case 'p': + case 'Q': + case 'q': + case 'R': + case 'r': + case 'S': + case 's': + case 'T': + case 't': + case 'U': + case 'u': + case 'V': + case 'v': + case 'W': + case 'w': + case 'X': + case 'x': + case 'Y': + case 'y': + case 'Z': + case 'z': + + Color nonCanColor= getNotCanonicalColor(lastSS); + drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); + temp=x; break; default: g.setColor(Color.gray); g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2); - + temp=x; break; } } @@ -596,23 +806,81 @@ public class AnnotationRenderer { switch (lastSS) { - case 'H': + case '$': drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; - case 'E': + case 'µ': 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_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); + break; + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': + case 'C': case 'c': - case 'C': - drawNotCanonicalAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, + case 'D': + case 'd': + case 'E': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case 'H': + case 'h': + case 'I': + case 'i': + case 'J': + case 'j': + case 'K': + case 'k': + case 'L': + case 'l': + case 'M': + case 'm': + case 'N': + case 'n': + case 'O': + case 'o': + case 'P': + case 'p': + case 'Q': + case 'q': + case 'R': + case 'r': + case 'T': + case 't': + case 'U': + case 'u': + case 'V': + case 'v': + case 'W': + case 'w': + case 'X': + case 'x': + case 'Y': + case 'y': + case 'Z': + case 'z': + //System.out.println(lastSS); + Color nonCanColor = getNotCanonicalColor(lastSS); + drawNotCanonicalAnnot(g,nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; default: @@ -626,8 +894,9 @@ public class AnnotationRenderer { if (row.graph == AlignmentAnnotation.LINE_GRAPH) { - if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) + if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup)) { + // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels float groupmax = -999999, groupmin = 9999999; for (int gg = 0; gg < aa.length; gg++) { @@ -640,7 +909,6 @@ public class AnnotationRenderer { aa[gg].visible = false; } - if (aa[gg].graphMax > groupmax) { groupmax = aa[gg].graphMax; @@ -660,7 +928,7 @@ public class AnnotationRenderer } } - graphGroupDrawn[row.graphGroup] = true; + graphGroupDrawn.set(row.graphGroup); } else { @@ -670,11 +938,16 @@ public class AnnotationRenderer } else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { - drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin, - row.graphMax, y); + drawBarGraph(g, row, row_annotations, startRes, endRes, + row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile); } } - + } else { + if (clipst && !clipend) + { + clipend = true; + } + }// end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; @@ -685,6 +958,27 @@ public class AnnotationRenderer y += aa[i].height; } } + if (debugRedraw) + { + if (canClip) + { + if (clipst) + { + System.err.println("Start clip at : " + yfrom + " (index " + f_i + + ")"); + } + if (clipend) + { + System.err.println("End clip at : " + yto + " (index " + f_to + + ")"); + } + } + ; + System.err.println("Annotation Rendering time:" + + (System.currentTimeMillis() - stime)); + } + ; + return !usedFaded; } @@ -696,7 +990,7 @@ public class AnnotationRenderer private final Color STEM_COLOUR = Color.blue; - private final Color NOTCANONICAL_COLOUR = Color.red; + private Color sdNOTCANONICAL_COLOUR; public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x, int y, int iconOffset, int startRes, @@ -713,7 +1007,7 @@ public class AnnotationRenderer { g.setColor(SHEET_COLOUR); - if (!validEnd || !validRes || row==null || row[column] == null + if (!validEnd || !validRes || row == null || row[column] == null || row[column].secondaryStructure != 'E') { g.fillRect(lastSSX, y + 4 + iconOffset, @@ -732,9 +1026,9 @@ public class AnnotationRenderer } - public void drawHelixAnnot(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, + int x, int y, int iconOffset, int startRes, int column, + boolean validRes, boolean validEnd) { g.setColor(HELIX_COLOUR); @@ -792,8 +1086,9 @@ public class AnnotationRenderer g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } - public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, - int eRes, int y, float min, float max, int graphHeight) + 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) { @@ -881,8 +1176,9 @@ public class AnnotationRenderer } } - public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, - int eRes, float min, float max, int y) + public 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) { if (sRes > aa_annotations.length) { @@ -906,23 +1202,6 @@ public class AnnotationRenderer int column; 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) - { - renderHistogram = _aa.groupRef.isShowConsensusHistogram(); - renderProfile = _aa.groupRef.isShowSequenceLogo(); - normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo(); - } - else - { - renderHistogram = av_renderHistogram; - renderProfile = av_renderProfile; - normaliseProfile = av_normaliseProfile; - } - } while (x < eRes - sRes) { column = sRes + x; @@ -1018,7 +1297,7 @@ public class AnnotationRenderer // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, // (int)(scl)); // g.setColor(profcolour.findColour(dc[0]).darker()); - g.setColor(profcolour.findColour(dc[0], column,null)); + g.setColor(profcolour.findColour(dc[0], column, null)); hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm .getBaselineIndex()])); @@ -1039,15 +1318,16 @@ public class AnnotationRenderer 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, Annotation[] aa_annotations, int width, - int y, int sRes, int eRes) + 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); g.setColor(Color.white); @@ -1076,4 +1356,135 @@ public class AnnotationRenderer x += charWidth; } } + + + Color getNotCanonicalColor(char lastss) + { + switch (lastss) + { + case '{': + case '}': + return new Color(255,125,5); + + case '[': + case ']': + return new Color(245,115,10); + + case '>': + case '<': + return new Color(235,135,15); + + case 'A': + case 'a': + return new Color(225,105,20); + + case 'B': + case 'b': + return new Color(215,145,30); + + case 'C': + case 'c': + return new Color(205,95,35); + + case 'D': + case 'd': + return new Color(195,155,45); + + case 'E': + case 'e': + return new Color(185,85,55); + + case 'F': + case 'f': + return new Color(175,165,65); + + case 'G': + case 'g': + return new Color(170,75,75); + + case 'H': + case 'h': + return new Color(160,175,85); + + case 'I': + case 'i': + return new Color(150,65,95); + + case 'J': + case 'j': + return new Color(140,185,105); + + case 'K': + case 'k': + return new Color(130,55,110); + + case 'L': + case 'l': + return new Color(120,195,120); + + case 'M': + case 'm': + return new Color(110,45,130); + + case 'N': + case 'n': + return new Color(100,205,140); + + case 'O': + case 'o': + return new Color(90,35,150); + + case 'P': + case 'p': + return new Color(85,215,160); + + case 'Q': + case 'q': + return new Color(75,25,170); + + case 'R': + case 'r': + return new Color(65,225,180); + + case 'S': + case 's': + return new Color(55,15,185); + + case 'T': + case 't': + return new Color(45,235,195); + + case 'U': + case 'u': + return new Color(35,5,205); + + case 'V': + case 'v': + return new Color(25,245,215); + + case 'W': + case 'w': + return new Color(15,0,225); + + case 'X': + case 'x': + return new Color(10,255,235); + + case 'Y': + case 'y': + return new Color(5,150,245); + + case 'Z': + case 'z': + return new Color(0,80,255); + + default : + System.out.println("This is not a interaction : "+lastss); + return null; + + } + } } + + +