X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=5be7f55c0e2ce1752552a647413d21659d0736cc;hb=b7b29fb6c0b015ac4798ec4718ab0cfbdd79b20a;hp=2a2a0cfeafcd2acf730be6b8e2e16b920089c15f;hpb=3fca8f1a5cebad8b73747d121622d1f63a5f9178;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 2a2a0cf..5be7f55 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -23,9 +23,8 @@ 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 jalview.util.Comparison; import java.awt.Color; import java.awt.FontMetrics; @@ -41,17 +40,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer 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 @@ -61,6 +58,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public SequenceRenderer(AlignViewportI viewport) { this.av = viewport; + resColourFinder = new ResidueColourFinder(); } /** @@ -77,32 +75,12 @@ 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); - - if (inCurrentSequenceGroup(i)) - { - 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 @@ -117,40 +95,10 @@ 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 != null) - { - resBoxColour = shader.findColour(seq.getCharAt(i), - i, seq); - } - else if (forOverview && !Comparison.isGap(seq.getCharAt(i))) - { - resBoxColour = Color.lightGray; - } - else - { - resBoxColour = Color.white; - } + return resColourFinder.getResidueColour(av.getShowBoxes(), + av.getResidueShading(), + allGroups, seq, position, + finder); } /** @@ -209,6 +157,8 @@ 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 @@ -217,8 +167,8 @@ 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; @@ -228,17 +178,22 @@ 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.getGroupColourScheme(), seq, + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } } @@ -308,8 +263,9 @@ 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 @@ -317,9 +273,8 @@ 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++) { @@ -332,7 +287,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer continue; } - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup( + allGroups, i); + if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) { @@ -343,7 +301,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer || currentSequenceGroup.getColourText()) { getboxColour = true; - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); if (currentSequenceGroup.getColourText()) @@ -354,7 +313,8 @@ 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); } @@ -364,6 +324,8 @@ 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 @@ -384,7 +346,8 @@ 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()) { @@ -400,7 +363,8 @@ 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() @@ -443,21 +407,25 @@ 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; } @@ -467,35 +435,6 @@ 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 @@ -511,8 +450,8 @@ 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;