X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=a382c604a4937f0d54a03395780236d15c6cb6d0;hb=refs%2Fheads%2Ffeature%2FJAL-2611;hp=feb2705ab03b2e711cd192a4a258d8697377ac31;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index feb2705..a382c60 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -20,10 +20,10 @@ */ package jalview.appletgui; -import jalview.api.FeatureRenderer; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.schemes.ColourSchemeI; +import jalview.renderer.ResidueShaderI; +import jalview.renderer.seqfeatures.FeatureColourFinder; import java.awt.Color; import java.awt.Font; @@ -32,6 +32,8 @@ import java.awt.Graphics; public class SequenceRenderer implements jalview.api.SequenceRenderer { + final static int CHAR_TO_UPPER = 'A' - 'a'; + AlignViewport av; FontMetrics fm; @@ -67,7 +69,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer this.renderGaps = renderGaps; } - public Color getResidueBoxColour(SequenceI seq, int i) + protected Color getResidueBoxColour(SequenceI seq, int i) { allGroups = av.getAlignment().findAllGroups(seq); @@ -75,12 +77,12 @@ 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); } return resBoxColour; @@ -93,29 +95,29 @@ 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; } - 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))) @@ -160,8 +162,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer int length = seq.getLength(); int curStart = -1; - int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av - .getCharHeight(); + int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), + avCharHeight = av.getCharHeight(); Color tempColour = null; while (i <= end) @@ -173,12 +175,13 @@ 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); } } @@ -251,13 +254,12 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (currentSequenceGroup.getColourText()) { - getBoxColour(currentSequenceGroup.cs, seq, i); + getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i); graphics.setColor(resBoxColour.darker()); } if (currentSequenceGroup.getShowNonconserved()) { - s = getDisplayChar(srep, i, s, - '.'); + s = getDisplayChar(srep, i, s, '.', currentSequenceGroup); } } else @@ -269,7 +271,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { - getBoxColour(av.getGlobalColourScheme(), seq, i); + getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { graphics.setColor(resBoxColour.darker()); @@ -281,8 +283,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } if (av.getShowUnconserved()) { - s = getDisplayChar(srep, i, s, - '.'); + s = getDisplayChar(srep, i, s, '.', null); } } @@ -308,24 +309,53 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } charOffset = (avCharWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + avCharWidth - * (i - start), y1); + graphics.drawString(String.valueOf(s), + charOffset + avCharWidth * (i - start), y1); } } + /** + * Returns 'conservedChar' to represent the given position if the sequence + * character at that position is equal to the consensus (ignoring case), else + * returns the sequence character + * + * @param usesrep + * @param position + * @param sequenceChar + * @param conservedChar + * @return + */ private char getDisplayChar(final boolean usesrep, int position, - char s, char c) + char sequenceChar, char conservedChar, SequenceGroup currentGroup) { - // TODO - use currentSequenceGroup rather than alignemnt + // 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 != '-' && s == 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)) { - s = c; + sequenceChar = conservedChar; } - return s; + return sequenceChar; } boolean inCurrentSequenceGroup(int res) @@ -348,14 +378,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer return false; } - 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 avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); int pady = avCharHeight / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight); + graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), + avCharHeight); graphics.setColor(Color.white); char s = '~'; @@ -370,8 +401,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer } charOffset = (avCharWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1 - + avCharWidth * (i - start), y1 + avCharHeight - pady); + graphics.drawString(String.valueOf(s), + charOffset + x1 + avCharWidth * (i - start), + y1 + avCharHeight - pady); } } }