X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=671bf6b799c8d58e305fc558015e51a307b90cb4;hb=f6d3b491c392914981b65fee21df51b530ee80f7;hp=0d7d4ca463dd7ea60438dbce7f4121fe6ea0751c;hpb=f51ad53a1437086e6deea02e4f8930078b92bfcc;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 0d7d4ca..671bf6b 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1,11 +1,40 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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; +import jalview.analysis.CodingUtils; +import jalview.analysis.Rna; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.ProfilesI; import jalview.schemes.ColourSchemeI; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.ZappoColourScheme; +import jalview.util.Platform; import java.awt.BasicStroke; import java.awt.Color; @@ -17,45 +46,217 @@ 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 { + 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 + */ + private final boolean debugRedraw; + + private int charWidth, endRes, charHeight; + + private boolean validCharWidth, hasHiddenColumns; + + private FontMetrics fm; + + private final boolean MAC = Platform.isAMac(); + + boolean av_renderHistogram = true, av_renderProfile = true, + av_normaliseProfile = false; + + ResidueShaderI profcolour = null; + + private ColumnSelection columnSelection; + + private HiddenColumns hiddenColumns; + + private ProfilesI hconsensus; + + private Hashtable[] complementConsensus; + + private Hashtable[] hStrucConsensus; + + private boolean av_ignoreGapsConsensus; + + /** + * attributes set from AwtRenderPanelI + */ + /** + * 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; + + /** + * 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 AnnotationRenderer() { - // TODO Auto-generated constructor stub + this(false); } - public void drawStemAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) + /** + * 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; + } + + /** + * Remove any references and resources when this object is no longer required + */ + public void dispose() + { + hiddenColumns = null; + hconsensus = null; + complementConsensus = null; + hStrucConsensus = null; + fadedImage = null; + annotationPanel = null; + } + + 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 sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); + int x1 = lastSSX; + int x2 = (x * charWidth); + + char dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' + : row_annotations[column - 1].secondaryStructure; + + boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null + || dc != row_annotations[sCol - 1].secondaryStructure; + boolean diffdownstream = !validRes || !validEnd + || row_annotations[column] == null + || dc != row_annotations[column].secondaryStructure; + + if (column > 0 && Rna.isClosingParenthesis(dc)) + { + if (diffupstream) + // if (validRes && column>1 && row_annotations[column-2]!=null && + // dc.equals(row_annotations[column-2].displayCharacter)) + { + /* + * 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) + { + x2 -= 1; + } + } + else + { + // display a forward arrow + if (diffdownstream) + { + /* + * 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) + { + x1 += 1; + } + } + // draw arrow body + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); + } + + 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(nonCanColor); + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); - Regex closeparen = new Regex("(\\))"); - - 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); + + 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 - || row.annotations[column] == null - || !dc.equals(row.annotations[column].displayCharacter); - // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); + || 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 (column > 0 && Rna.isClosingParenthesis(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[] - { 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) @@ -65,12 +266,14 @@ 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); + g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, + new int[] + { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, + 3); x2 -= 5; } if (diffupstream) @@ -81,82 +284,111 @@ public class AnnotationRenderer // draw arrow body g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); } - 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 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 - */ - 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) + + // 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(); + // 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); } + public void updateFromAlignViewport(AlignViewportI av) { charWidth = av.getCharWidth(); - endRes = av.getEndRes(); + endRes = av.getRanges().getEndRes(); charHeight = av.getCharHeight(); hasHiddenColumns = av.hasHiddenColumns(); validCharWidth = av.isValidCharWidth(); av_renderHistogram = av.isShowConsensusHistogram(); av_renderProfile = av.isShowSequenceLogo(); - av_normaliseProfile= av.isNormaliseSequenceLogo(); - profcolour = av.getGlobalColourScheme(); - if (profcolour == null) + av_normaliseProfile = av.isNormaliseSequenceLogo(); + profcolour = av.getResidueShading(); + if (profcolour == null || profcolour.getColourScheme() == 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(); + /* + * Use default colour for sequence logo if + * the alignment has no colourscheme set + * (would like to use user preference but n/a for applet) + */ + ColourSchemeI col = av.getAlignment().isNucleotide() + ? new NucleotideColourScheme() + : new ZappoColourScheme(); + profcolour = new ResidueShader(col); } columnSelection = av.getColumnSelection(); - hconsensus = av.getSequenceConsensusHash();//hconsensus; - hStrucConsensus = av.getRnaStructureConsensusHash(); //hStrucConsensus; - av_ignoreGapsConsensus=av.getIgnoreGapsConsensus(); + hiddenColumns = av.getAlignment().getHiddenColumns(); + hconsensus = av.getSequenceConsensusHash(); + complementConsensus = av.getComplementConsensusHash(); + hStrucConsensus = av.getRnaStructureConsensusHash(); + av_ignoreGapsConsensus = av.isIgnoreGapsConsensus(); } - public int[] getProfileFor(AlignmentAnnotation aa, int column) + + /** + * Returns profile data; the first element is the profile type, the second is + * the number of distinct values, the third the total count, and the remainder + * depend on the profile type. + * + * @param aa + * @param column + * @return + */ + 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 - // - if (aa.autoCalculated && aa.label.startsWith("Consensus")) + // 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") + || aa.label.startsWith("cDNA Consensus"))) { + boolean forComplement = aa.label.startsWith("cDNA Consensus"); if (aa.groupRef != null && aa.groupRef.consensusData != null && aa.groupRef.isShowSequenceLogo()) { + // TODO? group consensus for cDNA complement return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], aa.groupRef - .getIgnoreGapsConsensus()); + aa.groupRef.consensusData.get(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) { - return AAFrequency.extractProfile(hconsensus[column], av_ignoreGapsConsensus); + if (forComplement) + { + return AAFrequency.extractCdnaProfile(complementConsensus[column], + av_ignoreGapsConsensus); + } + else + { + return AAFrequency.extractProfile(hconsensus.get(column), + av_ignoreGapsConsensus); + } } } else @@ -164,20 +396,19 @@ public class AnnotationRenderer if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) { // 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()); - } - */ + /* + * 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 && hStrucConsensus!=null && hStrucConsensus.length>column) + && hStrucConsensus != null + && hStrucConsensus.length > column) { return StructureFrequency.extractProfile(hStrucConsensus[column], av_ignoreGapsConsensus); @@ -186,25 +417,44 @@ public class AnnotationRenderer } return null; } - + + boolean rna = false; + /** - * DOCUMENT ME! + * Render the annotation rows associated with an alignment. * - * @param annotationPanel TODO + * @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, Graphics g, int activeRow, int startRes, int endRes) + public boolean drawComponent(AwtRenderPanelI annotPanel, + AlignViewportI av, Graphics g, int activeRow, int startRes, + int endRes) { + long stime = System.currentTimeMillis(); + boolean usedFaded = false; // 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 temp = 0; + if (aa == null) + { + return false; + } int x = 0, y = 0; int column = 0; char lastSS; @@ -213,19 +463,57 @@ public class AnnotationRenderer boolean validRes = false; boolean validEnd = false; boolean labelAllCols = false; - boolean centreColLabels, centreColLabelsDef = av - .getCentreColumnLabels(); + boolean centreColLabels; + boolean centreColLabelsDef = av.isCentreColumnLabels(); boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; + final AlignmentAnnotation consensusAnnot = av + .getAlignmentConsensusAnnotation(); + final AlignmentAnnotation structConsensusAnnot = av + .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 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]; - + 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()) + { + 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 + } + } + Annotation[] row_annotations = row.annotations; if (!row.visible) { continue; @@ -235,137 +523,147 @@ public class AnnotationRenderer scaleColLabel = row.scaleColLabel; lastSS = ' '; lastSSX = 0; - if (row.graph > 0) - { - if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) + + if (!useClip || ((y - charHeight) < visHeight + && (y + row.height + charHeight * 2) >= sOffset)) + {// if_in_visible_region + if (!clipst) { - continue; + clipst = true; + yfrom = y; + f_i = i; } - - // this is so that we draw the characters below the graph - y += row.height; - - if (row.hasText) + yto = y; + f_to = i; + if (row.graph > 0) { - iconOffset = charHeight - fm.getDescent(); - y -= charHeight; - } - } - 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; - } - */ - // first pass sets up state for drawing continuation from left-hand column - // of startRes - x = (startRes == 0) ? 0 : -1; - while (x < endRes - startRes) - { - if (hasHiddenColumns) - { - column = columnSelection.adjustForHiddenColumns( - startRes + x); - if (column > row.annotations.length - 1) + if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) { - break; + continue; + } + + // this is so that we draw the characters below the graph + y += row.height; + + if (row.hasText) + { + iconOffset = charHeight - fm.getDescent(); + y -= charHeight; } } - else + else if (row.hasText) { - column = startRes + x; + iconOffset = charHeight - fm.getDescent(); + } - - if ((row.annotations == null) || (row.annotations.length <= column) - || (row.annotations[column] == null)) + else { - validRes = false; + iconOffset = 0; } - else + + if (row.autoCalculated && av.isCalculationInProgress(row)) { - validRes = true; + y += charHeight; + usedFaded = true; + 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; } - if (x > -1) + + /* + * 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; + while (x < endRes - startRes) { - if (activeRow == i) + if (hasHiddenColumns) { - g.setColor(Color.red); - - if (columnSelection != null) + column = hiddenColumns.visibleToAbsoluteColumn(startRes + x); + if (column > row_annotations.length - 1) { - for (int n = 0; n < columnSelection.size(); n++) - { - int v = columnSelection.columnAt(n); - - if (v == column) - { - g.fillRect(x * charWidth, y, charWidth, - charHeight); - } - } + break; } } - if (!row.isValidStruc()) + else + { + column = startRes + x; + } + + if ((row_annotations == null) + || (row_annotations.length <= column) + || (row_annotations[column] == null)) + { + validRes = false; + } + else { - g.setColor(Color.orange); - g.fillRect((int)row.getInvalidStrucPos()*charWidth, y, charWidth, charHeight); + validRes = true; } - if (validCharWidth - && validRes - && row.annotations[column].displayCharacter != null - && (row.annotations[column].displayCharacter.length() > 0)) + final String displayChar = validRes + ? row_annotations[column].displayCharacter + : null; + if (x > -1) { - - if (centreColLabels || scaleColLabel) + if (activeRow == i) { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter - .toCharArray(), 0, - row.annotations[column].displayCharacter.length()); - - if (scaleColLabel) + g.setColor(Color.red); + + if (columnSelection != null) { + if (columnSelection.contains(column)) + { + g.fillRect(x * charWidth, y, charWidth, charHeight); + } + } + } + if (row.getInvalidStrucPos() > x) + { + g.setColor(Color.orange); + g.fillRect(x * charWidth, y, charWidth, charHeight); + } + else if (row.getInvalidStrucPos() == x) + { + g.setColor(Color.orange.darker()); + g.fillRect(x * charWidth, y, charWidth, charHeight); + } + if (validCharWidth && validRes && displayChar != null + && (displayChar.length() > 0)) + { + + fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, + displayChar.length()); + if (/* centreColLabels || */scaleColLabel) + { + // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0, + // displayChar.length()); + // + // if (scaleColLabel) + // { // justify the label and scale to fit in column if (fmWidth > charWidth) { @@ -377,262 +675,494 @@ public class AnnotationRenderer // and update the label's width to reflect the scaling. fmWidth = charWidth; } + // } + } + // TODO is it ok to use width of / show all characters here? + // else + // { + // fmWidth = fm.charWidth(displayChar.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(displayChar, (x * charWidth) + charOffset, + y + iconOffset); } + else if (row_annotations[column - 1] == null || (labelAllCols + || !displayChar.equals( + row_annotations[column - 1].displayCharacter) + || (displayChar.length() < 2 + && row_annotations[column].secondaryStructure == ' '))) + { + g.drawString(displayChar, x * charWidth + charOffset, + y + iconOffset); + } + g.setFont(ofont); } - else + } + if (row.hasIcons) + { + char ss = validRes ? row_annotations[column].secondaryStructure + : '-'; + + if (ss == '(') { - fmWidth = (float) fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0)); + // distinguish between forward/backward base-pairing + if (displayChar.indexOf(')') > -1) + { + + ss = ')'; + + } } - 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) + if (ss == '[') { - g.drawString(row.annotations[column].displayCharacter, - (x * charWidth) + charOffset, y + iconOffset); + if ((displayChar.indexOf(']') > -1)) + { + ss = ']'; + + } } - 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 == ' '))) + if (ss == '{') { - g.drawString(row.annotations[column].displayCharacter, x - * charWidth + charOffset, y + iconOffset); + // distinguish between forward/backward base-pairing + if (displayChar.indexOf('}') > -1) + { + ss = '}'; + + } } - g.setFont(ofont); - } - } - if (row.hasIcons) - { - char ss = validRes ? row.annotations[column].secondaryStructure - : ' '; - if (ss == 'S') - { - // distinguish between forward/backward base-pairing - if (row.annotations[column].displayCharacter.indexOf(')') > -1) + if (ss == '<') { - ss = 's'; + // distinguish between forward/backward base-pairing + if (displayChar.indexOf('<') > -1) + { + ss = '>'; + + } } - } - if (!validRes || (ss != lastSS)) - { - if (x > -1) + if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z)) { - switch (lastSS) + // distinguish between forward/backward base-pairing + int ssLowerCase = ss + UPPER_TO_LOWER; + // TODO would .equals() be safer here? or charAt(0)? + if (displayChar.indexOf(ssLowerCase) > -1) { - case 'H': - 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; + ss = (char) ssLowerCase; } } - if (validRes) + + if (!validRes || (ss != lastSS)) { - lastSS = ss; + + 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 '(': // 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 'H': + if (!isRNA) + { + drawHelixAnnot(g, row_annotations, lastSSX, x, y, + iconOffset, startRes, column, validRes, + validEnd); + break; + } + // no break if isRNA - falls through to drawNotCanonicalAnnot! + case 'E': + if (!isRNA) + { + drawSheetAnnot(g, row_annotations, lastSSX, x, y, + iconOffset, startRes, column, validRes, + validEnd); + break; + } + // no break if isRNA - fall through to drawNotCanonicalAnnot! + + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': + case 'C': + case 'c': + case 'D': + case 'd': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + 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; + } + } + if (validRes) + { + lastSS = ss; + } + else + { + lastSS = ' '; + } + if (x > -1) + { + lastSSX = (x * charWidth); + } } - else + } + column++; + x++; + } + if (column >= row_annotations.length) + { + column = row_annotations.length - 1; + validEnd = false; + } + else + { + 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) + { + + case 'H': + if (!isRNA) { - lastSS = ' '; + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); + break; } - if (x > -1) + // no break if isRNA - fall through to drawNotCanonicalAnnot! + + case 'E': + if (!isRNA) { - lastSSX = (x * charWidth); + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); + break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! + + case '(': + case ')': // 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 'D': + case 'd': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + 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: + drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, + startRes, column, validRes, validEnd); + break; } } - column++; - x++; - } - if (column >= row.annotations.length) - { - column = row.annotations.length - 1; - validEnd = false; - } - else - { - 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) - { - case 'H': - 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': - case 'S': // Stem case for RNA secondary structure - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - default: - drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, - column, validRes, validEnd); - break; - } - } - - if (row.graph > 0 && row.graphHeight > 0) - { - if (row.graph == AlignmentAnnotation.LINE_GRAPH) + + if (row.graph > 0 && row.graphHeight > 0) { - if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) + if (row.graph == AlignmentAnnotation.LINE_GRAPH) { - float groupmax = -999999, groupmin = 9999999; - for (int gg = 0; gg < aa.length; gg++) + if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup)) { - if (aa[gg].graphGroup != row.graphGroup) - { - continue; - } - - if (aa[gg] != row) + // 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++) { - aa[gg].visible = false; - } - - if (aa[gg].graphMax > groupmax) - { - groupmax = aa[gg].graphMax; + if (aa[gg].graphGroup != row.graphGroup) + { + continue; + } + + if (aa[gg] != row) + { + aa[gg].visible = false; + } + if (aa[gg].graphMax > groupmax) + { + groupmax = aa[gg].graphMax; + } + if (aa[gg].graphMin < groupmin) + { + groupmin = aa[gg].graphMin; + } } - if (aa[gg].graphMin < groupmin) + + for (int gg = 0; gg < aa.length; gg++) { - groupmin = aa[gg].graphMin; + if (aa[gg].graphGroup == row.graphGroup) + { + drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, + endRes, y, groupmin, groupmax, row.graphHeight); + } } + + graphGroupDrawn.set(row.graphGroup); } - - for (int gg = 0; gg < aa.length; gg++) + else { - if (aa[gg].graphGroup == row.graphGroup) - { - drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, - groupmax, row.graphHeight); - } + drawLineGraph(g, row, row_annotations, startRes, endRes, y, + row.graphMin, row.graphMax, row.graphHeight); } - - graphGroupDrawn[row.graphGroup] = true; } - else + else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { - drawLineGraph( g, row, startRes, endRes, y, row.graphMin, - row.graphMax, row.graphHeight); + drawBarGraph(g, row, row_annotations, startRes, endRes, + row.graphMin, row.graphMax, y, renderHistogram, + renderProfile, normaliseProfile); } } - else if (row.graph == AlignmentAnnotation.BAR_GRAPH) + } + else + { + if (clipst && !clipend) { - drawBarGraph(g, row, startRes, endRes, row.graphMin, - row.graphMax, y); + clipend = true; } - } - + } // end if_in_visible_region if (row.graph > 0 && row.hasText) { y += charHeight; } - + if (row.graph == 0) { 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; } - 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) + public static final Color GLYPHLINE_COLOR = Color.gray; + + public static final Color SHEET_COLOUR = Color.green; + + public static final Color HELIX_COLOUR = Color.red; + + public static final Color STEM_COLOUR = Color.blue; + + private Color sdNOTCANONICAL_COLOUR; + + void drawGlyphLine(Graphics g, Annotation[] 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) + 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); + 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) + 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); - - int sCol = (lastSSX / charWidth) + startRes; + + int sCol = (lastSSX / charWidth) + + hiddenColumns.visibleToAbsoluteColumn(startRes); int x1 = lastSSX; int x2 = (x * charWidth); - + if (MAC) { int ofs = charWidth / 2; // 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 @@ -641,195 +1171,191 @@ 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') { - + } else { // g.setColor(Color.magenta); - g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs - + 1, 8, 0, 0); - + 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') + + 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); + 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) + 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; } - + int x = 0; - + // Adjustment for fastpaint to left if (eRes < endRes) { eRes++; } - - eRes = Math.min(eRes, aa.annotations.length); - + + 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); - + + 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) { column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } - + if (column > aaMax) { 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); - - 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); + { + 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) + + 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, int eRes, float min, float max, int y) + 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) + 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; - + float range = max - min; - + if (min < 0) { - y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); + 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")) - { - // 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; - } - } + int aaMax = aa_annotations.length - 1; while (x < eRes - sRes) { column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.visibleToAbsoluteColumn(column); } - + if (column > aaMax) { 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); - - y1 = y - - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - + { + g.setColor(aa_annotations[column].colour); + } + + y1 = y - (int) (((aa_annotations[column].value - min) / (range)) + * _aa.graphHeight); + if (renderHistogram) { if (y1 - y2 > 0) @@ -842,105 +1368,128 @@ public class AnnotationRenderer } } // draw profile if available - if (renderProfile && aa.annotations[column].value != 0) + if (renderProfile) { - - int profl[] = getProfileFor(aa, column); + + /* + * {profile type, #values, total count, char1, pct1, char2, pct2...} + */ + int profl[] = getProfileFor(_aa, column); + // just try to draw the logo if profl is not null - if (profl != null) + if (profl != null && profl[2] != 0) { - - float ht = normaliseProfile ? y-aa.graphHeight : y1; - double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight; + boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE; + boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE; + 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 + * Render a single base for a sequence profile, a base pair for + * structure profile, and a triplet for a cdna profile */ - if (profl.length == 52) - { - dc = new char[2]; - } - else - { - 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];) + dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)]; + + LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g); + double scale = 1f / (normaliseProfile ? profl[2] : 100f); + float ofontHeight = 1f / lm.getAscent();// magnify to fill box + double scl = 0.0; + + /* + * Traverse the character(s)/percentage data in the array + */ + int c = 3; + int valuesProcessed = 0; + // profl[1] is the number of values in the profile + while (valuesProcessed < profl[1]) { - dc[0] = (char) profl[c++]; - - if (aa.label.startsWith("StrucConsensus")) + if (isStructureProfile) { + // todo can we encode a structure pair as an int, like codons? + dc[0] = (char) profl[c++]; dc[1] = (char) profl[c++]; } - + else if (isCdnaProfile) + { + dc = CodingUtils.decodeCodon(profl[c++]); + } + else + { + dc[0] = (char) profl[c++]; + } + wdth = charWidth; - wdth /= (float) fm.charsWidth(dc, 0, dc.length); - - ht += scl; + wdth /= fm.charsWidth(dc, 0, dc.length); + + ht += scl; + // next profl[] position is profile % for the character(s) + scl = htn * scale * profl[c++]; + lm = ofont.getLineMetrics(dc, 0, 1, + g.getFontMetrics().getFontRenderContext()); + 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 + // g.setColor(Color.red); + // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, + // (int)(scl)); + // g.setColor(profcolour.findColour(dc[0]).darker()); + + /* + * Set character colour as per alignment colour scheme; use the + * codon translation if a cDNA profile + */ + Color colour = null; + if (isCdnaProfile) { - // 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()); - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - 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.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(); + final String codonTranslation = ResidueProperties + .codonTranslate(new String(dc)); + colour = profcolour.findColour(codonTranslation.charAt(0), + column, null); + } + else + { + colour = profcolour.findColour(dc[0], column, null); } + g.setColor(colour == Color.white ? Color.lightGray : colour); + + hght = (ht + (scl - lm.getDescent() + - lm.getBaselineOffsets()[lm.getBaselineIndex()])); + + g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght); + valuesProcessed++; } g.setFont(ofont); } } 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, - 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); + eRes = Math.min(eRes, aa_annotations.length); g.setColor(Color.white); g.fillRect(0, 0, width, y); g.setColor(new Color(0, 0, 180)); @@ -949,14 +1498,18 @@ 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; @@ -967,4 +1520,131 @@ 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; + + } + } }