/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.renderer;
import jalview.analysis.AAFrequency;
+import jalview.analysis.CodingUtils;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
import java.awt.BasicStroke;
import java.awt.Color;
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
- String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
- : row_annotations[column - 1].displayCharacter;
+ char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
+ : row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ || dc != row_annotations[sCol - 1].secondaryStructure;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
- || !dc.equals(row_annotations[column].displayCharacter);
+ || dc != row_annotations[column].secondaryStructure;
// System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
// If a closing base pair half of the stem, display a backward arrow
- if (column > 0 && closeparen.search(dc))
+ if (column > 0 && ResidueProperties.isCloseParenRNA(dc))
{
if (diffupstream)
private FontMetrics fm;
- private final boolean MAC = new jalview.util.Platform().isAMac();
+ private final boolean MAC = jalview.util.Platform.isAMac();
boolean av_renderHistogram = true, av_renderProfile = true,
av_normaliseProfile = false;
private Hashtable[] hconsensus;
+ private Hashtable[] complementConsensus;
+
private Hashtable[] hStrucConsensus;
private boolean av_ignoreGapsConsensus;
: new jalview.schemes.ZappoColourScheme();
}
columnSelection = av.getColumnSelection();
- hconsensus = av.getSequenceConsensusHash();// hconsensus;
- hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
- av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
+ hconsensus = av.getSequenceConsensusHash();
+ complementConsensus = av.getComplementConsensusHash();
+ hStrucConsensus = av.getRnaStructureConsensusHash();
+ av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
}
+ /**
+ * Returns profile data; the first element is the profile type, the second is
+ * the number of distinct values, the third the total count, and the remainder
+ * depend on the profile type.
+ *
+ * @param aa
+ * @param column
+ * @return
+ */
public int[] getProfileFor(AlignmentAnnotation aa, int column)
{
// TODO : consider refactoring the global alignment calculation
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated && aa.label.startsWith("Consensus"))
+ if (aa.autoCalculated
+ && (aa.label.startsWith("Consensus") || aa.label
+ .startsWith("cDNA Consensus")))
{
+ boolean forComplement = aa.label.startsWith("cDNA Consensus");
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
+ // TODO? group consensus for cDNA complement
return AAFrequency.extractProfile(
aa.groupRef.consensusData[column],
aa.groupRef.getIgnoreGapsConsensus());
// be stored
if (aa.groupRef == null && aa.sequenceRef == null)
{
- return AAFrequency.extractProfile(hconsensus[column],
- av_ignoreGapsConsensus);
+ if (forComplement)
+ {
+ return AAFrequency.extractCdnaProfile(
+ complementConsensus[column], av_ignoreGapsConsensus);
+ }
+ else
+ {
+ return AAFrequency.extractProfile(hconsensus[column],
+ av_ignoreGapsConsensus);
+ }
}
}
else
return null;
}
+ boolean rna = false;
+
/**
* Render the annotation rows associated with an alignment.
*
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
- boolean centreColLabels, centreColLabelsDef = av
- .getCentreColumnLabels();
+ boolean centreColLabels;
+ boolean centreColLabelsDef = av.isCentreColumnLabels();
boolean scaleColLabel = false;
- AlignmentAnnotation consensusAnnot = av
- .getAlignmentConsensusAnnotation(), structConsensusAnnot = av
+ final AlignmentAnnotation consensusAnnot = av
+ .getAlignmentConsensusAnnotation();
+ final AlignmentAnnotation structConsensusAnnot = av
.getAlignmentStrucConsensusAnnotation();
- boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
+ final AlignmentAnnotation complementConsensusAnnot = av
+ .getComplementConsensusAnnotation();
+ boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
+ isRNA = row.isRNA();
{
// check if this is a consensus annotation row and set the display
// settings appropriately
renderProfile = row.groupRef.isShowSequenceLogo();
normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
}
- else if (row == consensusAnnot || row == structConsensusAnnot)
+ else if (row == consensusAnnot || row == structConsensusAnnot
+ || row == complementConsensusAnnot)
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
{
validRes = true;
}
+ final String displayChar = validRes ? row_annotations[column].displayCharacter
+ : null;
if (x > -1)
{
if (activeRow == i)
}
}
}
- if (!row.isValidStruc())
+ if (row.getInvalidStrucPos() > x)
{
g.setColor(Color.orange);
- g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
- charWidth, charHeight);
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
- if (validCharWidth
- && validRes
- && row_annotations[column].displayCharacter != null
- && (row_annotations[column].displayCharacter.length() > 0))
+ else if (row.getInvalidStrucPos() == x)
+ {
+ g.setColor(Color.orange.darker());
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
+ if (validCharWidth && validRes && displayChar != null
+ && (displayChar.length() > 0))
{
- if (centreColLabels || scaleColLabel)
+ fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ displayChar.length());
+ if (/* centreColLabels || */scaleColLabel)
{
- fmWidth = fm.charsWidth(
- row_annotations[column].displayCharacter
- .toCharArray(), 0,
- row_annotations[column].displayCharacter.length());
-
- if (scaleColLabel)
- {
+ // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
+ // displayChar.length());
+ //
+ // if (scaleColLabel)
+ // {
// justify the label and scale to fit in column
if (fmWidth > charWidth)
{
// and update the label's width to reflect the scaling.
fmWidth = charWidth;
}
- }
- }
- else
- {
- fmWidth = fm
- .charWidth(row_annotations[column].displayCharacter
- .charAt(0));
+ // }
}
+ // TODO is it ok to use width of / show all characters here?
+ // else
+ // {
+ // fmWidth = fm.charWidth(displayChar.charAt(0));
+ // }
charOffset = (int) ((charWidth - fmWidth) / 2f);
if (row_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(row_annotations[column].colour);
+ }
if (column == 0 || row.graph > 0)
{
- g.drawString(row_annotations[column].displayCharacter,
- (x * charWidth) + charOffset, y + iconOffset);
+ g.drawString(displayChar, (x * charWidth) + charOffset, y
+ + iconOffset);
}
else if (row_annotations[column - 1] == null
|| (labelAllCols
- || !row_annotations[column].displayCharacter
- .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
+ || !displayChar
+ .equals(row_annotations[column - 1].displayCharacter) || (displayChar
.length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row_annotations[column].displayCharacter, x
- * charWidth + charOffset, y + iconOffset);
+ g.drawString(displayChar, x * charWidth + charOffset, y
+ + iconOffset);
}
g.setFont(ofont);
}
if (ss == '(')
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ if (displayChar.indexOf(')') > -1)
{
ss = ')';
}
if (ss == '[')
{
- if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
+ if ((displayChar.indexOf(']') > -1))
{
ss = ']';
if (ss == '{')
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ if (displayChar.indexOf('}') > -1)
{
ss = '}';
if (ss == '<')
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ if (displayChar.indexOf('<') > -1)
{
ss = '>';
if (ss >= 65)
{
// distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1)
+ if (displayChar.indexOf(ss + 32) > -1)
{
ss = (char) (ss + 32);
// System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
switch (lastSS)
{
-
- case '$':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
- case '�':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
case '(': // Stem case for RNA secondary structure
case ')': // and opposite direction
drawStemAnnot(g, row_annotations, lastSSX, x, y,
iconOffset, startRes, column, validRes, validEnd);
temp = x;
break;
+
+ case 'H':
+ if (!isRNA)
+ {
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+
case '{':
case '}':
case '[':
case 'c':
case 'D':
case 'd':
- case 'E':
case 'e':
case 'F':
case 'f':
case 'G':
case 'g':
- case 'H':
case 'h':
case 'I':
case 'i':
{
switch (lastSS)
{
- case '$':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
- case '�':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
- case 's':
- case 'S': // Stem case for RNA secondary structure
+ case 'H':
+ if (!isRNA)
+ {
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
+
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
+
+ case '(':
+ case ')': // Stem case for RNA secondary structure
drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
startRes, column, validRes, validEnd);
case 'c':
case 'D':
case 'd':
- case 'E':
case 'e':
case 'F':
case 'f':
case 'G':
case 'g':
- case 'H':
case 'h':
case 'I':
case 'i':
return !usedFaded;
}
- private final Color GLYPHLINE_COLOR = Color.gray;
+ public static final Color GLYPHLINE_COLOR = Color.gray;
- private final Color SHEET_COLOUR = Color.green;
+ public static final Color SHEET_COLOUR = Color.green;
- private final Color HELIX_COLOUR = Color.red;
+ public static final Color HELIX_COLOUR = Color.red;
- private final Color STEM_COLOUR = Color.blue;
+ public static final Color STEM_COLOUR = Color.blue;
private Color sdNOTCANONICAL_COLOUR;
}
if (aa_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[column].colour);
+ }
y1 = y
- (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
continue;
}
if (aa_annotations[column].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[column].colour);
+ }
y1 = y
- (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
if (renderProfile)
{
+ /*
+ * {profile type, #values, total count, char1, pct1, char2, pct2...}
+ */
int profl[] = getProfileFor(_aa, column);
+
// just try to draw the logo if profl is not null
- if (profl != null && profl[1] != 0)
+ if (profl != null && profl[2] != 0)
{
+ boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
+ boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
float ht = normaliseProfile ? y - _aa.graphHeight : y1;
double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
double hght;
char[] dc;
/**
- * profl.length == 74 indicates that the profile of a secondary
- * structure conservation row was accesed. Therefore dc gets length 2,
- * to have space for a basepair instead of just a single nucleotide
+ * Render a single base for a sequence profile, a base pair for
+ * structure profile, and a triplet for a cdna profile
*/
- if (profl.length == 74)
- {
- dc = new char[2];
- }
- else
- {
- dc = new char[1];
- }
+ dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
+
LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
- double scale = 1f / (normaliseProfile ? profl[1] : 100f);
+ double scale = 1f / (normaliseProfile ? profl[2] : 100f);
float ofontHeight = 1f / lm.getAscent();// magnify to fill box
double scl = 0.0;
- for (int c = 2; c < profl[0];)
- {
- dc[0] = (char) profl[c++];
- if (_aa.label.startsWith("StrucConsensus"))
+ /*
+ * Traverse the character(s)/percentage data in the array
+ */
+ int c = 3;
+ int valuesProcessed = 0;
+ // profl[1] is the number of values in the profile
+ while (valuesProcessed < profl[1])
+ {
+ if (isStructureProfile)
{
+ // todo can we encode a structure pair as an int, like codons?
+ dc[0] = (char) profl[c++];
dc[1] = (char) profl[c++];
}
+ else if (isCdnaProfile)
+ {
+ dc = CodingUtils.decodeCodon(profl[c++]);
+ }
+ else
+ {
+ dc[0] = (char) profl[c++];
+ }
wdth = charWidth;
wdth /= fm.charsWidth(dc, 0, dc.length);
ht += scl;
+ // next profl[] position is profile % for the character(s)
+ scl = htn * scale * profl[c++];
+ lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
+ .getFontRenderContext());
+ g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+ wdth, scl / lm.getAscent())));
+ lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+
+ // Debug - render boxes around characters
+ // g.setColor(Color.red);
+ // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
+ // (int)(scl));
+ // g.setColor(profcolour.findColour(dc[0]).darker());
+
+ /*
+ * Set character colour as per alignment colour scheme; use the
+ * codon translation if a cDNA profile
+ */
+ Color colour = null;
+ if (isCdnaProfile)
+ {
+ final String codonTranslation = ResidueProperties
+ .codonTranslate(new String(dc));
+ colour = profcolour.findColour(codonTranslation.charAt(0),
+ column, null);
+ }
+ else
{
- scl = htn * scale * profl[c++];
- lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
- .getFontRenderContext());
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
- wdth, scl / lm.getAscent())));
- lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-
- // Debug - render boxes around characters
- // g.setColor(Color.red);
- // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
- // (int)(scl));
- // g.setColor(profcolour.findColour(dc[0]).darker());
- g.setColor(profcolour.findColour(dc[0], column, null));
-
- hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
- .getBaselineIndex()]));
-
- g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
+ colour = profcolour.findColour(dc[0], column, null);
}
+ g.setColor(colour == Color.white ? Color.lightGray : colour);
+
+ hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
+ .getBaselineIndex()]));
+
+ g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
+ valuesProcessed++;
}
g.setFont(ofont);
}
if (aa_annotations[j] != null)
{
if (aa_annotations[j].colour == null)
+ {
g.setColor(Color.black);
+ }
else
+ {
g.setColor(aa_annotations[j].colour);
+ }
height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
if (height > y)
git://source.jalview.org / jalview.git / blobdiff