X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=43fef152578c8659c36f4bdb8ba741992445e5eb;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=9874fd2529abba3d311b7ab5de0a380d874966fc;hpb=060557f7086fd2aab4fea43ecbf21e2ef4191dd1;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 9874fd2..43fef15 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -23,13 +23,16 @@ package jalview.gui; import jalview.api.AlignViewportI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.renderer.ResidueShaderI; +import jalview.renderer.ResidueColourFinder; import jalview.renderer.seqfeatures.FeatureColourFinder; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; +import org.jfree.graphics2d.svg.SVGGraphics2D; +import org.jibble.epsgraphics.EpsGraphics2D; + public class SequenceRenderer implements jalview.api.SequenceRenderer { final static int CHAR_TO_UPPER = 'A' - 'a'; @@ -42,12 +45,14 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer SequenceGroup[] allGroups = null; - Color resBoxColour; + // Color resBoxColour; Graphics graphics; boolean monospacedFont; + ResidueColourFinder resColourFinder; + /** * Creates a new SequenceRenderer object * @@ -56,6 +61,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public SequenceRenderer(AlignViewportI viewport) { this.av = viewport; + resColourFinder = new ResidueColourFinder(); } /** @@ -72,33 +78,12 @@ 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; } - protected Color getResidueBoxColour(SequenceI seq, int i) - { - // rate limiting step when rendering overview for lots of groups - allGroups = av.getAlignment().findAllGroups(seq); - - SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i); - if (currentSequenceGroup != null) - { - if (currentSequenceGroup.getDisplayBoxes()) - { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i); - } - } - else if (av.getShowBoxes()) - { - getBoxColour(av.getResidueShading(), seq, i); - } - - return resBoxColour; - } - /** * Get the residue colour at the given sequence position - as determined by * the sequence group colour (if any), else the colour scheme, possibly @@ -113,35 +98,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public Color getResidueColour(final SequenceI seq, int position, FeatureColourFinder finder) { - Color col = getResidueBoxColour(seq, position); - - if (finder != null) - { - col = finder.findFeatureColour(col, seq, position); - } - return col; - } - - /** - * DOCUMENT ME! - * - * @param shader - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param i - * DOCUMENT ME! - */ - void getBoxColour(ResidueShaderI shader, SequenceI seq, int i) - { - if (shader.getColourScheme() != null) - { - resBoxColour = shader.findColour(seq.getCharAt(i), i, seq); - } - else - { - resBoxColour = Color.white; - } + allGroups = av.getAlignment().findAllGroups(seq); + return resColourFinder.getResidueColour(av.getShowBoxes(), + av.getResidueShading(), allGroups, seq, position, finder); } /** @@ -200,6 +159,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1) { + Color resBoxColour = Color.white; + if (seq == null) { return; // fix for racecondition @@ -208,8 +169,8 @@ 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; @@ -219,18 +180,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (i < length) { - SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i); + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); if (currentSequenceGroup != null) { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, - i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } } @@ -290,8 +253,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } graphics.setColor(av.getTextColour()); - if (monospacedFont && av.getShowText() && allGroups.length == 0 - && !av.getColourText() && av.getThresholdTextColour() == 0) + boolean drawAllText = monospacedFont && av.getShowText() + && allGroups.length == 0 && !av.getColourText() + && av.getThresholdTextColour() == 0; + + /* + * EPS or SVG misaligns monospaced strings (JAL-3239) + * so always draw these one character at a time + */ + if (graphics instanceof EpsGraphics2D + || graphics instanceof SVGGraphics2D) + { + drawAllText = false; + } + if (drawAllText) { if (av.isRenderGaps()) { @@ -300,8 +275,9 @@ 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 @@ -309,6 +285,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer boolean srep = av.isDisplayReferenceSeq(); boolean getboxColour = false; boolean isarep = av.getAlignment().getSeqrep() == seq; + Color resBoxColour = Color.white; for (int i = start; i <= end; i++) { @@ -322,7 +299,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer continue; } - SequenceGroup currentSequenceGroup = inCurrentSequenceGroup(i); + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) @@ -334,8 +312,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer || currentSequenceGroup.getColourText()) { getboxColour = true; - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, - i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); if (currentSequenceGroup.getColourText()) { @@ -345,7 +323,8 @@ 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); } @@ -356,7 +335,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer graphics.setColor(currentSequenceGroup.textColour); } boolean isgrep = currentSequenceGroup != null - ? currentSequenceGroup.getSeqrep() == seq : false; + ? currentSequenceGroup.getSeqrep() == seq + : false; if (!isarep && !isgrep && currentSequenceGroup.getShowNonconserved()) // todo // optimize @@ -377,7 +357,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { @@ -393,7 +374,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (!getboxColour) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -436,21 +418,25 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer // currentSequenceGroup.getConsensus() 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))) + || 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); + && 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; } @@ -460,33 +446,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer /** * DOCUMENT ME! * - * @param res - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - SequenceGroup inCurrentSequenceGroup(int res) - { - if (allGroups == null) - { - return null; - } - - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - return (allGroups[i]); - } - } - - return null; - } - - /** - * DOCUMENT ME! - * * @param seq * DOCUMENT ME! * @param start @@ -502,8 +461,8 @@ 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; @@ -532,21 +491,30 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } } - public void drawCursor(SequenceI seq, int res, int x1, int y1) + /** + * Draw a sequence canvas cursor + * + * @param g + * graphics context to draw on + * @param s + * character to draw at cursor + * @param x1 + * x position of cursor in graphics context + * @param y1 + * y position of cursor in graphics context + */ + public void drawCursor(Graphics g, char s, int x1, int y1) { int pady = av.getCharHeight() / 5; int charOffset = 0; - graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); + g.setColor(Color.black); + g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); if (av.isValidCharWidth()) { - graphics.setColor(Color.white); - - char s = seq.getCharAt(res); - + g.setColor(Color.white); charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1, + g.drawString(String.valueOf(s), charOffset + x1, (y1 + av.getCharHeight()) - pady); }