X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=fb967edde92f0503a01c399fb8e8ec8a8b93341a;hb=c679cc5e0b230c59517b89d50eb5b94dfe4a382a;hp=70acb7b89eeac12b9400924fd3f2ae7c9ba794e7;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 70acb7b..fb967ed 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 +91,18 @@ 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) - { - 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) - { - 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 +134,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer drawBoxes(seq, start, end, y1); - if (av.validCharWidth) + if (av.isValidCharWidth()) { drawText(seq, start, end, y1); } @@ -216,16 +161,18 @@ 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 } int i = start; 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 +182,23 @@ 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 +257,19 @@ 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()) { @@ -315,25 +278,34 @@ 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 { boolean srep = av.isDisplayReferenceSeq(); boolean getboxColour = false; + boolean isarep = av.getAlignment().getSeqrep() == seq; + Color resBoxColour = Color.white; + for (int i = start; i <= end; i++) { + graphics.setColor(av.getTextColour()); getboxColour = false; s = seq.getCharAt(i); + if (!renderGaps && jalview.util.Comparison.isGap(s)) { continue; } - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup( + allGroups, i); + if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) { @@ -344,7 +316,9 @@ 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()) { @@ -354,7 +328,8 @@ 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); } @@ -364,11 +339,14 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { graphics.setColor(currentSequenceGroup.textColour); } - if (currentSequenceGroup.getShowNonconserved()) // todo optimize + boolean isgrep = currentSequenceGroup != null + ? currentSequenceGroup.getSeqrep() == seq : false; + if (!isarep && !isgrep + && currentSequenceGroup.getShowNonconserved()) // todo + // optimize { // todo - use sequence group consensus - s = getDisplayChar(srep, i, s, - '.'); + s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); } @@ -383,7 +361,8 @@ 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()) { @@ -399,7 +378,8 @@ 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() @@ -408,10 +388,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer graphics.setColor(av.getTextColour2()); } } - if (av.getShowUnconserved()) + if (!isarep && av.getShowUnconserved()) { - s = getDisplayChar(srep, i, s, - '.'); + s = getDisplayChar(srep, i, s, '.', null); } @@ -419,8 +398,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), - charOffset + av.getCharWidth() - * (i - start), y1); + charOffset + av.getCharWidth() * (i - start), y1); } } @@ -438,14 +416,31 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer * @return */ private char getDisplayChar(final boolean usesrep, int position, - char sequenceChar, char conservedChar) + char sequenceChar, char conservedChar, SequenceGroup currentGroup) { // TODO - use currentSequenceGroup rather than alignment // currentSequenceGroup.getConsensus() - char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter - .charAt(0); - if (conschar != '-' - && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar)) + 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 = conservedChar; } @@ -455,35 +450,6 @@ 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 @@ -499,8 +465,8 @@ 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; @@ -529,21 +495,30 @@ 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); }