X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=43fef152578c8659c36f4bdb8ba741992445e5eb;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=b67b88fae9638f76b31e3ee5284fe3370e26f8af;hpb=b08edfd88ccaa692f47beae5a63f7b867b7f19db;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index b67b88f..43fef15 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -20,52 +20,48 @@ */ 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.ResidueColourFinder; +import jalview.renderer.seqfeatures.FeatureColourFinder; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ +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'; - AlignViewport av; + AlignViewportI av; FontMetrics fm; boolean renderGaps = true; - SequenceGroup currentSequenceGroup = null; - SequenceGroup[] allGroups = null; - Color resBoxColour; + // Color resBoxColour; Graphics graphics; boolean monospacedFont; - boolean forOverview = false; + ResidueColourFinder resColourFinder; /** - * 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; + resColourFinder = new ResidueColourFinder(); } /** @@ -82,32 +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; } - @Override - public Color getResidueBoxColour(SequenceI seq, int i) - { - allGroups = av.getAlignment().findAllGroups(seq); - - if (inCurrentSequenceGroup(i)) - { - if (currentSequenceGroup.getDisplayBoxes()) - { - getBoxColour(currentSequenceGroup.cs, seq, i); - } - } - else if (av.getShowBoxes()) - { - getBoxColour(av.getGlobalColourScheme(), 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 @@ -115,49 +91,16 @@ 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) - { - // TODO replace 8 or so code duplications with calls to this method - // (refactored as needed) - Color col = getResidueBoxColour(seq, position); - - if (fr != null) - { - col = fr.findFeatureColour(col, seq, position); - } - return col; - } - - /** - * DOCUMENT ME! - * - * @param cs - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param i - * DOCUMENT ME! - */ - void getBoxColour(ColourSchemeI cs, SequenceI seq, int i) + FeatureColourFinder finder) { - if (cs != null) - { - resBoxColour = cs.findColour(seq.getCharAt(i), i, seq); - } - else if (forOverview - && !jalview.util.Comparison.isGap(seq.getCharAt(i))) - { - resBoxColour = Color.lightGray; - } - else - { - resBoxColour = Color.white; - } + allGroups = av.getAlignment().findAllGroups(seq); + return resColourFinder.getResidueColour(av.getShowBoxes(), + av.getResidueShading(), allGroups, seq, position, finder); } /** @@ -189,7 +132,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer drawBoxes(seq, start, end, y1); - if (av.validCharWidth) + if (av.isValidCharWidth()) { drawText(seq, start, end, y1); } @@ -216,6 +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 @@ -224,8 +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; @@ -235,18 +180,21 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (i < length) { - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); + if (currentSequenceGroup != null) { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.cs, seq, i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } - } if (resBoxColour != tempColour) @@ -305,8 +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()) { @@ -315,8 +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 @@ -324,9 +285,8 @@ 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; - char sr_c; + Color resBoxColour = Color.white; + for (int i = start; i <= end; i++) { @@ -339,7 +299,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer continue; } - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); + if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) { @@ -350,7 +312,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer || currentSequenceGroup.getColourText()) { getboxColour = true; - getBoxColour(currentSequenceGroup.cs, seq, i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); if (currentSequenceGroup.getColourText()) { @@ -360,7 +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); } @@ -370,6 +334,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { graphics.setColor(currentSequenceGroup.textColour); } + boolean isgrep = currentSequenceGroup != null + ? currentSequenceGroup.getSeqrep() == seq + : false; if (!isarep && !isgrep && currentSequenceGroup.getShowNonconserved()) // todo // optimize @@ -390,7 +357,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.getGlobalColourScheme(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { @@ -406,7 +374,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (!getboxColour) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -449,21 +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; } @@ -473,35 +446,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer /** * DOCUMENT ME! * - * @param res - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - boolean inCurrentSequenceGroup(int res) - { - if (allGroups == null) - { - return false; - } - - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - currentSequenceGroup = allGroups[i]; - - return true; - } - } - - return false; - } - - /** - * DOCUMENT ME! - * * @param seq * DOCUMENT ME! * @param start @@ -517,8 +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; @@ -547,21 +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); }