X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=4498f881dd3689751d9132be8dcfaf36a5e6791c;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=8c4ead82acfd5011b37a51746463066c85e2e758;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 8c4ead8..4498f88 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.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. * @@ -20,26 +20,22 @@ */ package jalview.gui; -import jalview.api.FeatureRenderer; +import jalview.api.AlignViewportI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.schemes.ColourSchemeI; +import jalview.renderer.ResidueShaderI; +import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.util.Comparison; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ public class SequenceRenderer implements jalview.api.SequenceRenderer { final static int CHAR_TO_UPPER = 'A' - 'a'; - AlignViewport av; + AlignViewportI av; FontMetrics fm; @@ -58,14 +54,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer boolean forOverview = false; /** - * Creates a new SequenceRenderer object. + * Creates a new SequenceRenderer object * - * @param av - * DOCUMENT ME! + * @param viewport */ - public SequenceRenderer(AlignViewport av) + public SequenceRenderer(AlignViewportI viewport) { - this.av = av; + this.av = viewport; } /** @@ -82,27 +77,27 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer // If EPS graphics, stringWidth will be a double, not an int double dwidth = fm.getStringBounds("M", g).getWidth(); - monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && av - .getCharWidth() == dwidth); + monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() + && av.getCharWidth() == dwidth); this.renderGaps = renderGaps; } - @Override - public Color getResidueBoxColour(SequenceI seq, int i) + protected Color getResidueBoxColour(SequenceI seq, int i) { + // rate limiting step when rendering overview for lots of groups allGroups = av.getAlignment().findAllGroups(seq); if (inCurrentSequenceGroup(i)) { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.cs, seq, i); + getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } return resBoxColour; @@ -115,20 +110,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer * * @param seq * @param position - * @param fr + * @param finder * @return */ @Override public Color getResidueColour(final SequenceI seq, int position, - FeatureRenderer fr) + FeatureColourFinder finder) { - // TODO replace 8 or so code duplications with calls to this method - // (refactored as needed) Color col = getResidueBoxColour(seq, position); - if (fr != null) + if (finder != null) { - col = fr.findFeatureColour(col, seq, position); + col = finder.findFeatureColour(col, seq, position); } return col; } @@ -136,21 +129,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer /** * DOCUMENT ME! * - * @param cs + * @param shader * DOCUMENT ME! * @param seq * DOCUMENT ME! * @param i * DOCUMENT ME! */ - void getBoxColour(ColourSchemeI cs, SequenceI seq, int i) + void getBoxColour(ResidueShaderI shader, SequenceI seq, int i) { - if (cs != null) + if (shader.getColourScheme() != null) { - resBoxColour = cs.findColour(seq.getCharAt(i), i, seq); + resBoxColour = shader.findColour(seq.getCharAt(i), i, seq); } - else if (forOverview - && !jalview.util.Comparison.isGap(seq.getCharAt(i))) + else if (forOverview && !Comparison.isGap(seq.getCharAt(i))) { resBoxColour = Color.lightGray; } @@ -189,7 +181,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer drawBoxes(seq, start, end, y1); - if (av.validCharWidth) + if (av.isValidCharWidth()) { drawText(seq, start, end, y1); } @@ -224,8 +216,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer int length = seq.getLength(); int curStart = -1; - int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), avHeight = av - .getCharHeight(); + int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(), + avHeight = av.getCharHeight(); Color tempColour = null; @@ -239,14 +231,14 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.cs, seq, i); + getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, + i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } - } if (resBoxColour != tempColour) @@ -315,8 +307,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer else { char gap = av.getGapCharacter(); - graphics.drawString(seq.getSequenceAsString(start, end + 1) - .replace(gap, ' '), 0, y1); + graphics.drawString( + seq.getSequenceAsString(start, end + 1).replace(gap, ' '), + 0, y1); } } else @@ -324,8 +317,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer boolean srep = av.isDisplayReferenceSeq(); boolean getboxColour = false; boolean isarep = av.getAlignment().getSeqrep() == seq; - boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup - .getSeqrep() == seq : false; + boolean isgrep = currentSequenceGroup != null + ? currentSequenceGroup.getSeqrep() == seq + : false; char sr_c; for (int i = start; i <= end; i++) { @@ -350,7 +344,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer || currentSequenceGroup.getColourText()) { getboxColour = true; - getBoxColour(currentSequenceGroup.cs, seq, i); + getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, + i); if (currentSequenceGroup.getColourText()) { @@ -360,7 +355,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (currentSequenceGroup.thresholdTextColour > 0) { if (resBoxColour.getRed() + resBoxColour.getBlue() - + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour) + + resBoxColour + .getGreen() < currentSequenceGroup.thresholdTextColour) { graphics.setColor(currentSequenceGroup.textColour2); } @@ -390,7 +386,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.getGlobalColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { @@ -406,7 +402,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (!getboxColour) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -417,7 +413,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } if (!isarep && av.getShowUnconserved()) { - s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); + s = getDisplayChar(srep, i, s, '.', null); } @@ -447,18 +443,27 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { // TODO - use currentSequenceGroup rather than alignment // currentSequenceGroup.getConsensus() - char conschar = (usesrep) ? (currentGroup == null ? av.getAlignment() - .getSeqrep().getCharAt(position) - : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep() - .getCharAt(position) : av.getAlignment().getSeqrep() - .getCharAt(position))) - : (currentGroup != null && currentGroup.getConsensus() != null) ? currentGroup - .getConsensus().annotations[position].displayCharacter - .charAt(0) - : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter - .charAt(0); + char conschar = (usesrep) ? (currentGroup == null + || position < currentGroup.getStartRes() + || position > currentGroup.getEndRes() + ? av.getAlignment().getSeqrep().getCharAt(position) + : (currentGroup.getSeqrep() != null + ? currentGroup.getSeqrep().getCharAt(position) + : av.getAlignment().getSeqrep() + .getCharAt(position))) + : (currentGroup != null && currentGroup.getConsensus() != null + && position >= currentGroup.getStartRes() + && position <= currentGroup.getEndRes() + && currentGroup + .getConsensus().annotations.length > position) + ? currentGroup + .getConsensus().annotations[position].displayCharacter + .charAt(0) + : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter + .charAt(0); if (!jalview.util.Comparison.isGap(conschar) - && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar)) + && (sequenceChar == conschar + || sequenceChar + CHAR_TO_UPPER == conschar)) { sequenceChar = conservedChar; } @@ -512,8 +517,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer * @param height * DOCUMENT ME! */ - public void drawHighlightedText(SequenceI seq, int start, int end, - int x1, int y1) + public void drawHighlightedText(SequenceI seq, int start, int end, int x1, + int y1) { int pady = av.getCharHeight() / 5; int charOffset = 0;