X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=518c17924b7fea6fba291c2cefbc052e544c44c7;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=9610a7925863d4fada42638cf727ffa21174fa2e;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 9610a79..518c179 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -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; @@ -43,8 +49,6 @@ 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 @@ -58,6 +62,72 @@ public class AnnotationRenderer */ 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() { this(false); @@ -75,15 +145,26 @@ public class AnnotationRenderer 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) + /** + * 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); - Regex closeparen = new Regex("(\\))"); char dc = (column == 0 || row_annotations[column - 1] == null) ? ' ' : row_annotations[column - 1].secondaryStructure; @@ -93,15 +174,17 @@ public class AnnotationRenderer 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 (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); @@ -114,10 +197,13 @@ public class AnnotationRenderer } 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; @@ -131,71 +217,7 @@ public class AnnotationRenderer g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7); } - private int charWidth, endRes, charHeight; - - private boolean validCharWidth, hasHiddenColumns; - - private FontMetrics fm; - - private final boolean MAC = 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[] 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 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor, + 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) @@ -206,7 +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; @@ -218,8 +239,7 @@ 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) @@ -290,22 +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(); @@ -321,7 +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 @@ -337,7 +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 @@ -351,7 +376,8 @@ public class AnnotationRenderer } else { - return AAFrequency.extractProfile(hconsensus[column], + return AAFrequency.extractProfile( +hconsensus.get(column), av_ignoreGapsConsensus); } } @@ -567,7 +593,7 @@ public class AnnotationRenderer { if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(startRes + x); + column = hiddenColumns.adjustForHiddenColumns(startRes + x); if (column > row_annotations.length - 1) { break; @@ -598,14 +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); } } } @@ -755,7 +776,7 @@ public class AnnotationRenderer validEnd); break; } - + // no break if isRNA - falls through to drawNotCanonicalAnnot! case 'E': if (!isRNA) { @@ -764,6 +785,7 @@ public class AnnotationRenderer validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case '{': case '}': @@ -871,7 +893,6 @@ public class AnnotationRenderer { validRes = true; } - // x ++; if (row.hasIcons) @@ -886,6 +907,7 @@ public class AnnotationRenderer startRes, column, validRes, validEnd); break; } + // no break if isRNA - fall through to drawNotCanonicalAnnot! case 'E': if (!isRNA) @@ -894,6 +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 @@ -1074,15 +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) @@ -1106,8 +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); @@ -1166,7 +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) { @@ -1212,7 +1235,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.adjustForHiddenColumns(column); } if (column > aaMax) @@ -1259,7 +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) @@ -1291,7 +1314,7 @@ public class AnnotationRenderer column = sRes + x; if (hasHiddenColumns) { - column = columnSelection.adjustForHiddenColumns(column); + column = hiddenColumns.adjustForHiddenColumns(column); } if (column > aaMax) @@ -1390,8 +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