X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=518c17924b7fea6fba291c2cefbc052e544c44c7;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=33596788d2bfe4c5e491372f21d02d74712ce8d2;hpb=fddf3084802b37e5cee17829e32692a4aac3e60d;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 3359678..518c179 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -22,13 +22,19 @@ 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; @@ -43,88 +49,18 @@ import java.awt.image.ImageObserver; import java.util.BitSet; import java.util.Hashtable; -import com.stevesoft.pat.Regex; - public class AnnotationRenderer { - /** - * flag indicating if timing and redraw parameter info should be output - */ - private final boolean debugRedraw; + private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32 - public AnnotationRenderer() - { - this(false); - } + private static final int CHAR_A = 'A'; // 65 + + private static final int CHAR_Z = 'Z'; // 90 /** - * Create a new annotation Renderer - * - * @param debugRedraw - * flag indicating if timing and redraw parameter info should be - * output + * flag indicating if timing and redraw parameter info should be output */ - public AnnotationRenderer(boolean debugRedraw) - { - this.debugRedraw = debugRedraw; - } - - public void drawStemAnnot(Graphics g, Annotation[] row_annotations, - int lastSSX, int x, int y, int iconOffset, int startRes, - int column, boolean validRes, boolean validEnd) - { - g.setColor(STEM_COLOUR); - int sCol = (lastSSX / charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * charWidth); - Regex closeparen = new Regex("(\\))"); - - 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; - // 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 && ResidueProperties.isCloseParenRNA(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); - } + private final boolean debugRedraw; private int charWidth, endRes, charHeight; @@ -132,16 +68,18 @@ public class AnnotationRenderer private FontMetrics fm; - private final boolean MAC = jalview.util.Platform.isAMac(); + private final boolean MAC = Platform.isAMac(); boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile = false; - ColourSchemeI profcolour = null; + ResidueShaderI profcolour = null; private ColumnSelection columnSelection; + + private HiddenColumns hiddenColumns; - private Hashtable[] hconsensus; + private ProfilesI hconsensus; private Hashtable[] complementConsensus; @@ -190,7 +128,96 @@ public class AnnotationRenderer */ private boolean canClip = false; - public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, + public AnnotationRenderer() + { + this(false); + } + + /** + * Create a new annotation Renderer + * + * @param debugRedraw + * flag indicating if timing and redraw parameter info should be + * output + */ + public AnnotationRenderer(boolean debugRedraw) + { + this.debugRedraw = debugRedraw; + } + + /** + * Remove any references and resources when this object is no longer required + */ + public void dispose() + { + 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 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) @@ -201,7 +228,6 @@ public class AnnotationRenderer int sCol = (lastSSX / charWidth) + startRes; int x1 = lastSSX; int x2 = (x * charWidth); - Regex closeparen = new Regex("}|]|<|[a-z]"); String dc = (column == 0 || row_annotations[column - 1] == null) ? "" : row_annotations[column - 1].displayCharacter; @@ -213,17 +239,16 @@ public class AnnotationRenderer || !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 (column > 0 && Rna.isClosingParenthesis(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); + g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX }, + new int[] { y + iconOffset, y + 14 + iconOffset, + y + 8 + iconOffset }, 3); x1 += 5; } if (diffdownstream) @@ -237,9 +262,8 @@ public class AnnotationRenderer // 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) @@ -286,22 +310,27 @@ public class AnnotationRenderer 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) + 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(); + hiddenColumns = av.getAlignment().getHiddenColumns(); hconsensus = av.getSequenceConsensusHash(); complementConsensus = av.getComplementConsensusHash(); hStrucConsensus = av.getRnaStructureConsensusHash(); @@ -317,7 +346,7 @@ public class AnnotationRenderer * @param column * @return */ - public int[] getProfileFor(AlignmentAnnotation aa, int column) + int[] getProfileFor(AlignmentAnnotation aa, int column) { // TODO : consider refactoring the global alignment calculation // properties/rendering attributes as a global 'alignment group' which holds @@ -333,7 +362,7 @@ public class AnnotationRenderer { // TODO? group consensus for cDNA complement return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], + aa.groupRef.consensusData.get(column), aa.groupRef.getIgnoreGapsConsensus()); } // TODO extend annotation row to enable dynamic and static profile data to @@ -347,7 +376,8 @@ public class AnnotationRenderer } else { - return AAFrequency.extractProfile(hconsensus[column], + return AAFrequency.extractProfile( +hconsensus.get(column), av_ignoreGapsConsensus); } } @@ -563,7 +593,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.adjustForHiddenColumns(startRes + x); if (column > row_annotations.length - 1) { break; @@ -594,14 +624,9 @@ public class AnnotationRenderer if (columnSelection != null) { - for (int n = 0; n < columnSelection.size(); n++) + if (columnSelection.contains(column)) { - int v = columnSelection.columnAt(n); - - if (v == column) - { - g.fillRect(x * charWidth, y, charWidth, charHeight); - } + g.fillRect(x * charWidth, y, charWidth, charHeight); } } } @@ -628,17 +653,17 @@ public class AnnotationRenderer // // if (scaleColLabel) // { - // justify the label and scale to fit in column - if (fmWidth > charWidth) - { - // scale only if the current font isn't already small enough - fmScaling = charWidth; - fmScaling /= fmWidth; - g.setFont(ofont.deriveFont(AffineTransform - .getScaleInstance(fmScaling, 1.0))); - // and update the label's width to reflect the scaling. - fmWidth = charWidth; - } + // justify the label and scale to fit in column + if (fmWidth > charWidth) + { + // scale only if the current font isn't already small enough + fmScaling = charWidth; + fmScaling /= fmWidth; + g.setFont(ofont.deriveFont(AffineTransform + .getScaleInstance(fmScaling, 1.0))); + // and update the label's width to reflect the scaling. + fmWidth = charWidth; + } // } } // TODO is it ok to use width of / show all characters here? @@ -715,14 +740,14 @@ public class AnnotationRenderer } } - if (ss >= 65) + if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z)) { // distinguish between forward/backward base-pairing - if (displayChar.indexOf(ss + 32) > -1) + int ssLowerCase = ss + UPPER_TO_LOWER; + // TODO would .equals() be safer here? or charAt(0)? + if (displayChar.indexOf(ssLowerCase) > -1) { - - ss = (char) (ss + 32); - + ss = (char) ssLowerCase; } } @@ -751,7 +776,7 @@ public class AnnotationRenderer validEnd); break; } - + // no break if isRNA - falls through to drawNotCanonicalAnnot! case 'E': if (!isRNA) { @@ -760,6 +785,7 @@ public class AnnotationRenderer validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '{': case '}': @@ -867,7 +893,6 @@ public class AnnotationRenderer { validRes = true; } - // x ++; if (row.hasIcons) @@ -882,6 +907,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case 'E': if (!isRNA) @@ -890,6 +916,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '(': case ')': // Stem case for RNA secondary structure @@ -1070,15 +1097,15 @@ public class AnnotationRenderer private Color sdNOTCANONICAL_COLOUR; - public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, - int x, int y, int iconOffset, int startRes, int column, + 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); } - public void drawSheetAnnot(Graphics g, Annotation[] row, + void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd) @@ -1090,11 +1117,9 @@ public class AnnotationRenderer { 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[] - { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, - 3); + g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4, + (x * charWidth) }, new int[] { y + iconOffset, + y + 14 + iconOffset, y + 7 + iconOffset }, 3); } else { @@ -1104,8 +1129,8 @@ public class AnnotationRenderer } - public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, - int x, int y, int iconOffset, int startRes, int column, + 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); @@ -1164,7 +1189,7 @@ public class AnnotationRenderer g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } - public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, + void drawLineGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes, int eRes, int y, float min, float max, int graphHeight) { @@ -1210,7 +1235,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.adjustForHiddenColumns(column); } if (column > aaMax) @@ -1249,8 +1274,7 @@ public class AnnotationRenderer 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)); + BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight); g.drawLine(0, y2, (eRes - sRes) * charWidth, y2); @@ -1258,7 +1282,7 @@ public class AnnotationRenderer } } - public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, + 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) @@ -1290,7 +1314,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.adjustForHiddenColumns(column); } if (column > aaMax) @@ -1389,8 +1413,9 @@ public class AnnotationRenderer scl = htn * scale * profl[c++]; lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics() .getFontRenderContext()); - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, scl / lm.getAscent()))); + 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 @@ -1433,8 +1458,7 @@ public class AnnotationRenderer 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)); + BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f)); y2 = (int) (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight);