/*
- * 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.gui;
-import jalview.datamodel.AlignmentAnnotation;
+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
{
- AlignViewport av;
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
+ 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();
}
/**
// If EPS graphics, stringWidth will be a double, not an int
double dwidth = fm.getStringBounds("M", g).getWidth();
- monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
+ monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth()
+ && av.getCharWidth() == dwidth);
this.renderGaps = renderGaps;
}
- 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;
- }
-
/**
- * DOCUMENT ME!
+ * Get the residue colour at the given sequence position - as determined by
+ * the sequence group colour (if any), else the colour scheme, possibly
+ * overridden by a feature colour.
*
- * @param cs
- * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
- * @param i
- * DOCUMENT ME!
+ * @param position
+ * @param finder
+ * @return
*/
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ @Override
+ public Color getResidueColour(final SequenceI seq, int position,
+ 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);
}
/**
drawBoxes(seq, start, end, y1);
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
drawText(seq, start, end, y1);
}
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.charWidth;
+ int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(),
+ avHeight = av.getCharHeight();
Color tempColour = null;
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)
{
if (tempColour != null)
{
- graphics.fillRect(av.charWidth * (curStart - start), y1,
- curWidth, av.charHeight);
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth,
+ avHeight);
}
graphics.setColor(resBoxColour);
curStart = i;
- curWidth = av.charWidth;
+ curWidth = avWidth;
tempColour = resBoxColour;
}
else
{
- curWidth += av.charWidth;
+ curWidth += avWidth;
}
i++;
}
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
- av.charHeight);
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
}
*/
public void drawText(SequenceI seq, int start, int end, int y1)
{
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ y1 += av.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
int charOffset = 0;
char s;
{
end = seq.getLength() - 1;
}
- graphics.setColor(av.textColour);
-
- if (monospacedFont && av.showText && allGroups.length == 0
- && !av.getColourText() && av.thresholdTextColour == 0)
+ graphics.setColor(av.getTextColour());
+
+ 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.renderGaps)
+ if (av.isRenderGaps())
{
graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
}
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.textColour);
+
+ 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())
{
|| currentSequenceGroup.getColourText())
{
getboxColour = true;
- getBoxColour(currentSequenceGroup.cs, seq, i);
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
if (currentSequenceGroup.getColourText())
{
if (currentSequenceGroup.thresholdTextColour > 0)
{
if (resBoxColour.getRed() + resBoxColour.getBlue()
- + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
+ + resBoxColour
+ .getGreen() < currentSequenceGroup.thresholdTextColour)
{
graphics.setColor(currentSequenceGroup.textColour2);
}
{
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(av.getAlignmentConsensusAnnotation(), i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
}
if (av.getColourText())
{
getboxColour = true;
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
if (av.getShowBoxes())
{
}
}
- if (av.thresholdTextColour > 0)
+ if (av.getThresholdTextColour() > 0)
{
if (!getboxColour)
{
- getBoxColour(av.getGlobalColourScheme(), seq, i);
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
}
if (resBoxColour.getRed() + resBoxColour.getBlue()
- + resBoxColour.getGreen() < av.thresholdTextColour)
+ + resBoxColour.getGreen() < av.getThresholdTextColour())
{
- graphics.setColor(av.textColour2);
+ graphics.setColor(av.getTextColour2());
}
}
- if (av.getShowUnconserved())
+ if (!isarep && av.getShowUnconserved())
{
- s = getDisplayChar(av.getAlignmentConsensusAnnotation(), i, s,
- '.');
+ s = getDisplayChar(srep, i, s, '.', null);
}
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + av.charWidth
- * (i - start), y1);
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + av.getCharWidth() * (i - start), y1);
}
}
}
- private char getDisplayChar(AlignmentAnnotation consensus, int position,
- char s, char c)
- {
- char conschar = consensus.annotations[position].displayCharacter
- .charAt(0);
- if (conschar != '-' && s == conschar)
- {
- s = c;
- }
- return s;
- }
-
/**
- * DOCUMENT ME!
- *
- * @param res
- * DOCUMENT ME!
+ * 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
*
- * @return DOCUMENT ME!
+ * @param usesrep
+ * @param position
+ * @param sequenceChar
+ * @param conservedChar
+ * @return
*/
- boolean inCurrentSequenceGroup(int res)
+ private char getDisplayChar(final boolean usesrep, int position,
+ char sequenceChar, char conservedChar, SequenceGroup currentGroup)
{
- if (allGroups == null)
+ // TODO - use currentSequenceGroup rather than alignment
+ // 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)))
+ : (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))
{
- return false;
+ sequenceChar = conservedChar;
}
-
- for (int i = 0; i < allGroups.length; i++)
- {
- if ((allGroups[i].getStartRes() <= res)
- && (allGroups[i].getEndRes() >= res))
- {
- currentSequenceGroup = allGroups[i];
-
- return true;
- }
- }
-
- return false;
+ return sequenceChar;
}
/**
* @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.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
graphics.setColor(Color.BLACK);
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
- av.charHeight);
+ graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1),
+ av.getCharHeight());
graphics.setColor(Color.white);
char s = '~';
// Need to find the sequence position here.
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
for (int i = start; i <= end; i++)
{
s = seq.getCharAt(i);
}
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1
- + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + (av.getCharWidth() * (i - start)),
+ (y1 + av.getCharHeight()) - pady);
}
}
}
- 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.charHeight / 5;
+ int pady = av.getCharHeight() / 5;
int charOffset = 0;
- graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+ g.setColor(Color.black);
+ g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
- if (av.validCharWidth)
+ if (av.isValidCharWidth())
{
- graphics.setColor(Color.white);
-
- char s = seq.getCharAt(res);
-
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.charHeight) - pady);
+ g.setColor(Color.white);
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.getCharHeight()) - pady);
}
}
git://source.jalview.org / jalview.git / blobdiff