X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=b699543883ad291e3692317495304c0dc943763d;hb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;hp=476d7f7d0e7ef062a5194b5ad6ce7f3e4e5637a9;hpb=ee1c37b3e5d47128cb71ec2aa51c6e4a69dddbbe;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 476d7f7..b699543 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1,9 +1,11 @@ + package jalview.renderer; import jalview.analysis.AAFrequency; import jalview.analysis.StructureFrequency; import jalview.api.AlignViewportI; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; import jalview.schemes.ColourSchemeI; @@ -29,29 +31,33 @@ 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, 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; 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); + || row_annotations[column] == null + || !dc.equals(row_annotations[column].displayCharacter); // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); // If a closing base pair half of the stem, display a backward arrow if (column > 0 && closeparen.search(dc)) { + if (diffupstream) - // if (validRes && column>1 && row.annotations[column-2]!=null && - // dc.equals(row.annotations[column-2].displayCharacter)) + // if (validRes && column>1 && row_annotations[column-2]!=null && + // dc.equals(row_annotations[column-2].displayCharacter)) { g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, new int[] @@ -65,6 +71,7 @@ public class AnnotationRenderer } else { + // display a forward arrow if (diffdownstream) { @@ -81,42 +88,118 @@ 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 final 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; + private int imgWidth; + - // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI av) - public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, AlignViewportI av) + 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(nonCanColor); + int sCol = (lastSSX / charWidth) + startRes; + int x1 = lastSSX; + int x2 = (x * charWidth); + Regex closeparen = new Regex("}|]|<|a|b|c|d|e|f|g|h|i|j|k|l|m|n|o|p|q|r|s|t|u|v|w|x|y|z"); + + 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); + // If a closing base pair half of the stem, display a backward arrow + if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc)) ) + { + + if (diffupstream) + // 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); + x1 += 5; + } + if (diffdownstream) + { + x2 -= 1; + } + } + 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); + x2 -= 5; + } + if (diffupstream) + { + x1 += 1; + } + } + // draw arrow body + g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); + } + // 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(); @@ -126,37 +209,42 @@ 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 @@ -164,20 +252,19 @@ 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) + && av_renderProfile && hStrucConsensus != null + && hStrucConsensus.length > column) { return StructureFrequency.extractProfile(hStrucConsensus[column], av_ignoreGapsConsensus); @@ -186,26 +273,34 @@ public class AnnotationRenderer } return null; } - + /** - * DOCUMENT ME! - * - * @param annotationPanel TODO + * Render the annotation rows associated with an alignment. + * @param annotPanel + * container frame + * @param av + * data and view settings to render * @param g - * DOCUMENT ME! + * destination for graphics + * @param activeRow + * row where a mouse event occured (or -1) * @param startRes - * DOCUMENT ME! + * first column that will be drawn * @param endRes - * DOCUMENT ME! + * last column that will be drawn + * @return true if the fadedImage was used for any alignment annotation rows currently being calculated */ - public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, 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; // NOTES: - // AnnotationPanel needs to implement: ImageObserver, access to AlignViewport + // AnnotationPanel needs to implement: ImageObserver, access to + // AlignViewport updateFromAwtRenderPanel(annotPanel, av); - fm = g.getFontMetrics(); + fm = g.getFontMetrics(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - + int x = 0, y = 0; int column = 0; char lastSS; @@ -226,7 +321,7 @@ public class AnnotationRenderer for (int i = 0; i < aa.length; i++) { AlignmentAnnotation row = aa[i]; - + Annotation[] row_annotations=row.annotations; if (!row.visible) { continue; @@ -242,10 +337,10 @@ 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(); @@ -255,50 +350,46 @@ public class AnnotationRenderer else if (row.hasText) { iconOffset = charHeight - fm.getDescent(); - + } else { iconOffset = 0; } - - if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i])) + + if (row.autoCalculated && av.isCalculationInProgress(row)) { y += charHeight; - + usedFaded=true; g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y - row.height, imgWidth, y, annotationPanel); g.setColor(Color.black); // 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; @@ -306,9 +397,8 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns( - startRes + x); - if (column > row.annotations.length - 1) + column = columnSelection.adjustForHiddenColumns(startRes + x); + if (column > row_annotations.length - 1) { break; } @@ -317,9 +407,9 @@ public class AnnotationRenderer { column = startRes + x; } - - if ((row.annotations == null) || (row.annotations.length <= column) - || (row.annotations[column] == null)) + + if ((row_annotations == null) || (row_annotations.length <= column) + || (row_annotations[column] == null)) { validRes = false; } @@ -332,17 +422,16 @@ 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); } } } @@ -350,21 +439,22 @@ public class AnnotationRenderer if (!row.isValidStruc()) { g.setColor(Color.orange); - g.fillRect((int)row.getInvalidStrucPos()*charWidth, y, charWidth, charHeight); + g.fillRect((int) row.getInvalidStrucPos() * charWidth, y, + charWidth, charHeight); } if (validCharWidth && validRes - && row.annotations[column].displayCharacter != null - && (row.annotations[column].displayCharacter.length() > 0)) + && row_annotations[column].displayCharacter != null + && (row_annotations[column].displayCharacter.length() > 0)) { - + if (centreColLabels || scaleColLabel) { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter + fmWidth = fm.charsWidth( + row_annotations[column].displayCharacter .toCharArray(), 0, - row.annotations[column].displayCharacter.length()); - + row_annotations[column].displayCharacter.length()); + if (scaleColLabel) { // justify the label and scale to fit in column @@ -382,29 +472,30 @@ public class AnnotationRenderer } else { - fmWidth = (float) fm - .charWidth(row.annotations[column].displayCharacter + fmWidth = fm + .charWidth(row_annotations[column].displayCharacter .charAt(0)); } charOffset = (int) ((charWidth - fmWidth) / 2f); - - if (row.annotations[column].colour == null) + + if (row_annotations[column].colour == null) g.setColor(Color.black); else - g.setColor(row.annotations[column].colour); - + g.setColor(row_annotations[column].colour); + if (column == 0 || row.graph > 0) { - g.drawString(row.annotations[column].displayCharacter, + g.drawString(row_annotations[column].displayCharacter, (x * charWidth) + charOffset, y + iconOffset); } - else if (row.annotations[column - 1] == null + else if (row_annotations[column - 1] == null || (labelAllCols - || !row.annotations[column].displayCharacter - .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter - .length() < 2 && row.annotations[column].secondaryStructure == ' '))) + || !row_annotations[column].displayCharacter + .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter + .length() < 2 && row_annotations[column].secondaryStructure == ' '))) { - g.drawString(row.annotations[column].displayCharacter, x + g.drawString(row_annotations[column].displayCharacter + , x * charWidth + charOffset, y + iconOffset); } g.setFont(ofont); @@ -412,16 +503,285 @@ public class AnnotationRenderer } if (row.hasIcons) { - char ss = validRes ? row.annotations[column].secondaryStructure - : ' '; - if (ss == 'S') + char ss = validRes ? row_annotations[column].secondaryStructure + : '-'; + + if (ss == '(') { // distinguish between forward/backward base-pairing - if (row.annotations[column].displayCharacter.indexOf(')') > -1) + if (row_annotations[column].displayCharacter.indexOf(')') > -1) + { + + ss = ')'; + + } + } + if (ss == '[') + { + if ((row_annotations[column].displayCharacter.indexOf(']') > -1)) { - ss = 's'; + 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 == 'A') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('a') > -1) + { + ss = 'a'; + + + } + } + + if (ss == 'B') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('b') > -1) + { + ss = 'b'; + + } + } + + if (ss == 'C') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('c') > -1) + { + ss = 'c'; + + } + } + if (ss == 'D') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('d') > -1) + { + ss = 'd'; + + } + } + if (ss == '1') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('e') > -1) + { + ss = 'e'; + + } + } + if (ss == 'F') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('f') > -1) + { + ss = 'f'; + + } + } + if (ss == 'G') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('g') > -1) + { + ss = 'g'; + + } + } + if (ss == '2') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('h') > -1) + { + ss = 'h'; + + } + } + if (ss == 'I') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('i') > -1) + { + ss = 'i'; + + } + } + if (ss == 'J') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('j') > -1) + { + ss = 'j'; + + } + } + if (ss == 'K') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('k') > -1) + { + ss = 'k'; + + } + } + if (ss == 'L') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('l') > -1) + { + ss = 'l'; + + } + } + if (ss == 'M') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('m') > -1) + { + ss = 'm'; + + } + } + if (ss == 'N') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('n') > -1) + { + ss = 'n'; + + } + } + if (ss == 'O') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('o') > -1) + { + ss = 'o'; + + } + } + if (ss == 'P') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('p') > -1) + { + ss = 'p'; + + } + } + if (ss == 'Q') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('q') > -1) + { + ss = 'q'; + + } + } + if (ss == 'R') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('r') > -1) + { + ss = 'r'; + + } + } + if (ss == 'S') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('s') > -1) + { + ss = 's'; + + } + } + if (ss == 'T') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('t') > -1) + { + ss = 't'; + + } + } + if (ss == 'U') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('u') > -1) + { + ss = 'u'; + + } + } + if (ss == 'V') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('v') > -1) + { + ss = 'v'; + + } + } + if (ss == 'W') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('w') > -1) + { + ss = 'w'; + + } + } + if (ss == 'X') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('x') > -1) + { + ss = 'x'; + + } + } + if (ss == 'Y') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('y') > -1) + { + ss = 'y'; + + } + } + if (ss == 'Z') + { + // distinguish between forward/backward base-pairing + if (row_annotations[column].displayCharacter.indexOf('z') > -1) + { + ss = 'z'; + + } + } if (!validRes || (ss != lastSS)) { if (x > -1) @@ -429,26 +789,88 @@ public class AnnotationRenderer switch (lastSS) { case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; - + case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; - - case 'S': // Stem case for RNA secondary structure - case 's': // and opposite direction - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + + case '(': // Stem case for RNA secondary structure + case ')': // and opposite direction + 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 '1': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case '2': + 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': + //System.out.println(lastSS); + Color nonCanColor= getNotCanonicalColor(lastSS); + drawNotCanonicalAnnot(g, nonCanColor, row_annotations, 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; } } @@ -469,17 +891,17 @@ public class AnnotationRenderer column++; x++; } - if (column >= row.annotations.length) + if (column >= row_annotations.length) { - column = row.annotations.length - 1; + column = row_annotations.length - 1; validEnd = false; } else { validEnd = true; } - if ((row.annotations == null) || (row.annotations.length <= column) - || (row.annotations[column] == null)) + if ((row_annotations == null) || (row_annotations.length <= column) + || (row_annotations[column] == null)) { validRes = false; } @@ -487,34 +909,95 @@ public class AnnotationRenderer { validRes = true; } - + // x ++; - + if (row.hasIcons) { switch (lastSS) { case 'H': - drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; - + case 'E': - drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; case 's': case 'S': // Stem case for RNA secondary structure - drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes, + drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; + case '{': + case '}': + case '[': + case ']': + case '>': + case '<': + case 'A': + case 'a': + case 'B': + case 'b': + case 'C': + case 'c': + case 'D': + case 'd': + case '1': + case 'e': + case 'F': + case 'f': + case 'G': + case 'g': + case '2': + 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, lastSSX, x, y, iconOffset, startRes, + drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes, column, validRes, validEnd); break; } } - + if (row.graph > 0 && row.graphHeight > 0) { if (row.graph == AlignmentAnnotation.LINE_GRAPH) @@ -528,12 +1011,12 @@ public class AnnotationRenderer { continue; } - + if (aa[gg] != row) { aa[gg].visible = false; } - + if (aa[gg].graphMax > groupmax) { groupmax = aa[gg].graphMax; @@ -543,97 +1026,106 @@ public class AnnotationRenderer groupmin = aa[gg].graphMin; } } - + for (int gg = 0; gg < aa.length; gg++) { if (aa[gg].graphGroup == row.graphGroup) { - drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, + drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin, groupmax, row.graphHeight); } } - + graphGroupDrawn[row.graphGroup] = true; } else { - drawLineGraph( g, row, startRes, endRes, y, row.graphMin, + drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin, row.graphMax, row.graphHeight); } } else if (row.graph == AlignmentAnnotation.BAR_GRAPH) { - drawBarGraph(g, row, startRes, endRes, row.graphMin, + drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin, row.graphMax, y); } } - + if (row.graph > 0 && row.hasText) { y += charHeight; } - + if (row.graph == 0) { y += aa[i].height; } } + 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; - + private final Color GLYPHLINE_COLOR = Color.gray; + + private final Color SHEET_COLOUR = Color.green; + + private final Color HELIX_COLOUR = Color.red; + + private final 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 sdNOTCANONICAL_COLOUR; + + public 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) + public void drawSheetAnnot(Graphics g, Annotation[] row, + + int lastSSX, int x, int y, int iconOffset, int startRes, + int column, boolean validRes, boolean validEnd) { g.setColor(SHEET_COLOUR); - - if (!validEnd || !validRes || row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'E') + + if (!validEnd || !validRes || row==null || row[column] == null + || row[column].secondaryStructure != 'E') { - g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - - 4, 7); - 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, 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 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 @@ -642,79 +1134,80 @@ 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); - + } - + 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) + public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, + int eRes, int y, float min, float max, int graphHeight) { - if (sRes > aa.annotations.length) + if (sRes > aa_annotations.length) { return; } - + 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; @@ -722,87 +1215,88 @@ public class AnnotationRenderer { column = columnSelection.adjustForHiddenColumns(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); - + g.setColor(aa_annotations[column].colour); + y1 = y - - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight); + - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight); y2 = y - - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - + - (int) (((aa_annotations[column].value - min) / range) * graphHeight); + g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth + charWidth / 2, y2); x++; } - - if (aa.threshold != null) + + if (_aa.threshold != null) { - g.setColor(aa.threshold.colour); + g.setColor(_aa.threshold.colour); Graphics2D g2 = (Graphics2D) g; g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); - - y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight); + + y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight); g.drawLine(0, y2, (eRes - sRes) * charWidth, y2); g2.setStroke(new BasicStroke()); } } - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, 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) { - 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")) + int aaMax = aa_annotations.length - 1; + boolean renderHistogram = true, renderProfile = true, normaliseProfile = false; + // if (aa.autoCalculated && aa.label.startsWith("Consensus")) { // TODO: generalise this to have render styles for consensus/profile data - if (aa.groupRef != null) + if (_aa.groupRef != null) { - renderHistogram = aa.groupRef.isShowConsensusHistogram(); - renderProfile = aa.groupRef.isShowSequenceLogo(); - normaliseProfile= aa.groupRef.isNormaliseSequenceLogo(); + renderHistogram = _aa.groupRef.isShowConsensusHistogram(); + renderProfile = _aa.groupRef.isShowSequenceLogo(); + normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo(); } else { renderHistogram = av_renderHistogram; renderProfile = av_renderProfile; - normaliseProfile= av_normaliseProfile; + normaliseProfile = av_normaliseProfile; } } while (x < eRes - sRes) @@ -812,25 +1306,25 @@ public class AnnotationRenderer { column = columnSelection.adjustForHiddenColumns(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); - + g.setColor(aa_annotations[column].colour); + y1 = y - - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - + - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight); + if (renderHistogram) { if (y1 - y2 > 0) @@ -843,25 +1337,24 @@ public class AnnotationRenderer } } // draw profile if available - if (renderProfile && aa.annotations[column].value != 0) + if (renderProfile) { - - int profl[] = getProfileFor(aa, column); + + int profl[] = getProfileFor(_aa, column); // just try to draw the logo if profl is not null - if (profl != null) + if (profl != null && profl[1] != 0) { - - float ht = normaliseProfile ? y-aa.graphHeight : y1; - double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight; + float ht = normaliseProfile ? y - _aa.graphHeight : y1; + double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight; + double hght; float wdth; double ht2 = 0; 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 == 74) { @@ -871,52 +1364,42 @@ 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")) + + if (_aa.label.startsWith("StrucConsensus")) { dc[1] = (char) profl[c++]; } - + wdth = charWidth; - wdth /= (float) fm.charsWidth(dc, 0, dc.length); - - ht += scl; + wdth /= fm.charsWidth(dc, 0, dc.length); + + 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 = htn * scale * 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); @@ -924,24 +1407,25 @@ public class AnnotationRenderer } x++; } - if (aa.threshold != null) + if (_aa.threshold != null) { - g.setColor(aa.threshold.colour); + g.setColor(_aa.threshold.colour); Graphics2D g2 = (Graphics2D) g; g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE, BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); - - y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight); + + y2 = (int) (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight); g.drawLine(0, y2, (eRes - sRes) * charWidth, y2); g2.setStroke(new BasicStroke()); } } + // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, + public void drawGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int width, int y, int sRes, int eRes) { - eRes = Math.min(eRes, aa.annotations.length); + eRes = Math.min(eRes, aa_annotations.length); g.setColor(Color.white); g.fillRect(0, 0, width, y); g.setColor(new Color(0, 0, 180)); @@ -950,14 +1434,14 @@ public class AnnotationRenderer for (int j = sRes; j < eRes; j++) { - if (aa.annotations[j] != null) + if (aa_annotations[j] != null) { - if (aa.annotations[j].colour == null) + if (aa_annotations[j].colour == null) g.setColor(Color.black); else - g.setColor(aa.annotations[j].colour); + g.setColor(aa_annotations[j].colour); - height = (int) ((aa.annotations[j].value / aa.graphMax) * y); + height = (int) ((aa_annotations[j].value / _aa.graphMax) * y); if (height > y) { height = y; @@ -968,4 +1452,135 @@ public class AnnotationRenderer x += charWidth; } } + + + Color getNotCanonicalColor(char lastss) + { + switch (lastss) + { + case '{': + case '}': + return Color.cyan; + + case '[': + case ']': + return Color.green; + + case '>': + case '<': + return Color.magenta; + + case 'A': + case 'a': + return Color.orange; + + case 'B': + case 'b': + return Color.pink; + + case 'C': + case 'c': + return Color.red; + + case 'D': + case 'd': + return Color.yellow; + + case '1': + case 'e': + return Color.black; + + case 'F': + case 'f': + return Color.darkGray; + + case 'G': + case 'g': + return Color.gray; + + case '2': + case 'h': + return Color.lightGray; + + case 'I': + case 'i': + return Color.white; + + case 'J': + case 'j': + return Color.cyan; + + case 'K': + case 'k': + return Color.magenta; + + case 'L': + case 'l': + return Color.orange; + + case 'M': + case 'm': + return Color.red; + + case 'N': + case 'n': + return Color.yellow; + + case 'O': + case 'o': + return Color.pink; + + case 'P': + case 'p': + return Color.black; + + case 'Q': + case 'q': + return Color.blue; + + case 'R': + case 'r': + return Color.cyan; + + case 'S': + case 's': + return Color.magenta; + + case 'T': + case 't': + return Color.darkGray; + + case 'U': + case 'u': + return Color.yellow; + + case 'V': + case 'v': + return Color.blue; + + case 'W': + case 'w': + return Color.orange; + + case 'X': + case 'x': + return Color.magenta; + + case 'Y': + case 'y': + return Color.blue; + + case 'Z': + case 'z': + return Color.blue; + + default : + System.out.println("This is not a interaction"); + return null; + + } + } } + + +