+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.renderer.seqfeatures;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+import jalview.util.Platform;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.AlphaComposite;
import java.awt.Color;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
+import java.util.ArrayList;
+import java.util.List;
-public class FeatureRenderer extends
- jalview.viewmodel.seqfeatures.FeatureRendererModel
+public class FeatureRenderer extends FeatureRendererModel
{
+ private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
+ .getInstance(AlphaComposite.SRC_OVER, 1.0f);
- FontMetrics fm;
-
- int charOffset;
-
- boolean offscreenRender = false;
+ /**
+ * Constructor given a viewport
+ *
+ * @param viewport
+ */
+ public FeatureRenderer(AlignViewportI viewport)
+ {
+ this.av = viewport;
+ }
/**
- * DOCUMENT ME!
+ * Renders the sequence using the given feature colour between the given start
+ * and end columns. Returns true if at least one column is drawn, else false
+ * (the feature range does not overlap the start and end positions).
*
* @param g
- * DOCUMENT ME!
* @param seq
- * DOCUMENT ME!
- * @param sg
- * DOCUMENT ME!
+ * @param featureStart
+ * @param featureEnd
+ * @param featureColour
* @param start
- * DOCUMENT ME!
* @param end
- * DOCUMENT ME!
- * @param x1
- * DOCUMENT ME!
* @param y1
- * DOCUMENT ME!
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
+ * @param colourOnly
+ * @return
*/
- protected SequenceI lastSeq;
-
- char s;
-
- int i;
-
- int av_charHeight, av_charWidth;
-
- boolean av_validCharWidth, av_isShowSeqFeatureHeight;
-
- protected void updateAvConfig()
+ boolean renderFeature(Graphics g, SequenceI seq, int featureStart,
+ int featureEnd, Color featureColour, int start, int end, int y1,
+ boolean colourOnly)
{
- av_charHeight = av.getCharHeight();
- av_charWidth = av.getCharWidth();
- av_validCharWidth = av.isValidCharWidth();
- av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight();
- }
+ int charHeight = av.getCharHeight();
+ int charWidth = av.getCharWidth();
+ boolean validCharWidth = av.isValidCharWidth();
- void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
- Color featureColour, int start, int end, int y1)
- {
- updateAvConfig();
- if (((fstart <= end) && (fend >= start)))
+ if (featureStart > end || featureEnd < start)
{
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
-
- if (fend >= end)
- {
- fend = end;
- }
- int pady = (y1 + av_charHeight) - av_charHeight / 5;
- for (i = fstart; i <= fend; i++)
- {
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
-
- g.fillRect((i - start) * av_charWidth, y1, av_charWidth,
- av_charHeight);
-
- if (offscreenRender || !av_validCharWidth)
- {
- continue;
- }
-
- g.setColor(Color.white);
- charOffset = (av_charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av_charWidth * (i - start)), pady);
+ return false;
+ }
- }
+ if (featureStart < start)
+ {
+ featureStart = start;
}
- }
+ if (featureEnd >= end)
+ {
+ featureEnd = end;
+ }
+ int pady = (y1 + charHeight) - charHeight / 5;
- void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
- Color featureColour, int start, int end, int y1, byte[] bs)
- {
- updateAvConfig();
- if (((fstart <= end) && (fend >= start)))
+ FontMetrics fm = g.getFontMetrics();
+ char s = '\0';
+ for (int i = featureStart; i <= featureEnd; i++)
{
- if (fstart < start)
- { // fix for if the feature we have starts before the sequence start,
- fstart = start; // but the feature end is still valid!!
- }
- if (fend >= end)
- {
- fend = end;
- }
- int pady = (y1 + av_charHeight) - av_charHeight / 5;
- int ystrt = 0, yend = av_charHeight;
- if (bs[0] != 0)
- {
- // signed - zero is always middle of residue line.
- if (bs[1] < 128)
- {
- yend = av_charHeight * (128 - bs[1]) / 512;
- ystrt = av_charHeight - yend / 2;
- }
- else
- {
- ystrt = av_charHeight / 2;
- yend = av_charHeight * (bs[1] - 128) / 512;
- }
- }
- else
- {
- yend = av_charHeight * bs[1] / 255;
- ystrt = av_charHeight - yend;
+ // colourOnly is just for Overview -- no need to check this again
- }
- for (i = fstart; i <= fend; i++)
+ if (!colourOnly && Comparison.isGap(s = seq.getCharAt(i)))
{
- s = seq.getCharAt(i);
-
- if (jalview.util.Comparison.isGap(s))
- {
- continue;
- }
-
- g.setColor(featureColour);
- int x = (i - start) * av_charWidth;
- g.drawRect(x, y1, av_charWidth, av_charHeight);
- g.fillRect(x, y1 + ystrt, av_charWidth, yend);
+ continue;
+ }
- if (offscreenRender || !av_validCharWidth)
- {
- continue;
- }
+ g.setColor(featureColour);
- g.setColor(Color.black);
- charOffset = (av_charWidth - fm.charWidth(s)) / 2;
- g.drawString(String.valueOf(s), charOffset
- + (av_charWidth * (i - start)), pady);
+ g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
+ if (colourOnly)
+ {
+ return true;
}
- }
- }
- BufferedImage offscreenImage;
+ if (!validCharWidth)
+ {
+ continue;
+ }
- public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
- {
- return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
+ g.setColor(Color.white);
+ int charOffset = (charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
+ }
+ return true;
}
/**
- * This is used by the Molecule Viewer and Overview to get the accurate
- * colourof the rendered sequence
+ *
+ * BH - this method is never called?
+ *
+ * Renders the sequence using the given SCORE feature colour between the given
+ * start and end columns. Returns true if at least one column is drawn, else
+ * false (the feature range does not overlap the start and end positions).
+ *
+ * @param g
+ * @param seq
+ * @param fstart
+ * @param fend
+ * @param featureColour
+ * @param start
+ * @param end
+ * @param y1
+ * @param bs
+ * @param colourOnly
+ * @return
*/
- public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
- int column)
+ boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,
+ int fend, Color featureColour, int start, int end, int y1,
+ byte[] bs, boolean colourOnly)
{
- if (!av.isShowSequenceFeatures())
+ if (fstart > end || fend < start)
{
- return initialCol;
+ return false;
+ }
+
+ if (fstart < start)
+ { // fix for if the feature we have starts before the sequence start,
+ fstart = start; // but the feature end is still valid!!
}
- final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq
- .getDatasetSequence() : seq;
- if (seq != lastSeq)
+ if (fend >= end)
{
- lastSeq = seq;
- sequenceFeatures = aseq.getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
+ fend = end;
}
- else
+ int charHeight = av.getCharHeight();
+ int pady = (y1 + charHeight) - charHeight / 5;
+ int ystrt = 0, yend = charHeight;
+ if (bs[0] != 0)
{
- if (sequenceFeatures != aseq.getSequenceFeatures())
+ // signed - zero is always middle of residue line.
+ if (bs[1] < 128)
{
- sequenceFeatures = aseq.getSequenceFeatures();
- if (sequenceFeatures != null)
- {
- sfSize = sequenceFeatures.length;
- }
+ yend = charHeight * (128 - bs[1]) / 512;
+ ystrt = charHeight - yend / 2;
+ }
+ else
+ {
+ ystrt = charHeight / 2;
+ yend = charHeight * (bs[1] - 128) / 512;
}
}
-
- if (sequenceFeatures == null || sfSize == 0)
- {
- return initialCol;
- }
-
- if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
+ else
{
- return Color.white.getRGB();
- }
+ yend = charHeight * bs[1] / 255;
+ ystrt = charHeight - yend;
- // Only bother making an offscreen image if transparency is applied
- if (transparency != 1.0f && offscreenImage == null)
- {
- offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
}
- currentColour = null;
- // TODO: non-threadsafe - each rendering thread needs its own instance of
- // the feature renderer - or this should be synchronized.
- offscreenRender = true;
-
- if (offscreenImage != null)
- {
- offscreenImage.setRGB(0, 0, initialCol);
- drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
+ FontMetrics fm = g.getFontMetrics();
+ int charWidth = av.getCharWidth();
- return offscreenImage.getRGB(0, 0);
- }
- else
+ for (int i = fstart; i <= fend; i++)
{
- drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
+ char s = seq.getCharAt(i);
- if (currentColour == null)
+ if (Comparison.isGap(s))
{
- return initialCol;
+ continue;
}
- else
+
+ g.setColor(featureColour);
+ int x = (i - start) * charWidth;
+ g.drawRect(x, y1, charWidth, charHeight);
+ g.fillRect(x, y1 + ystrt, charWidth, yend);
+
+ if (colourOnly || !av.isValidCharWidth())
{
- return ((Integer) currentColour).intValue();
+ continue;
}
- }
+ g.setColor(Color.black);
+ int charOffset = (charWidth - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s),
+ charOffset + (charWidth * (i - start)), pady);
+ }
+ return true;
}
- private volatile SequenceFeature[] sequenceFeatures;
-
- int sfSize;
-
- int sfindex;
-
- int spos;
-
- int epos;
-
- public synchronized void drawSequence(Graphics g, final SequenceI seq,
- int start, int end, int y1)
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Color findFeatureColour(SequenceI seq, int column, Graphics g)
{
- final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq
- .getDatasetSequence() : seq;
- if (aseq.getSequenceFeatures() == null
- || aseq.getSequenceFeatures().length == 0)
+ // BH 2019.08.01
+ // this is already checked in FeatureColorFinder
+ // if (!av.isShowSequenceFeatures())
+ // {
+ // return null;
+ // }
+
+ // column is 'base 1' but getCharAt is an array index (ie from 0)
+ if (Comparison.isGap(seq.getCharAt(column - 1)))
{
- return;
+ /*
+ * returning null allows the colour scheme to provide gap colour
+ * - normally white, but can be customised
+ */
+ return null;
}
- if (g != null)
+ Color renderedColour = null;
+ if (transparency == 1.0f)
{
- fm = g.getFontMetrics();
+ /*
+ * simple case - just find the topmost rendered visible feature colour
+ */
+ renderedColour = findFeatureColour(seq, column);
}
-
- updateFeatures();
-
- if (lastSeq == null || seq != lastSeq
- || aseq.getSequenceFeatures() != sequenceFeatures)
+ else
{
- lastSeq = seq;
- sequenceFeatures = aseq.getSequenceFeatures();
+ /*
+ * transparency case - draw all visible features in render order to
+ * build up a composite colour on the graphics context
+ */
+ renderedColour = drawSequence(g, seq, column, column, 0, true);
}
+ return renderedColour;
+ }
- if (transparency != 1 && g != null)
+ /**
+ * Draws the sequence features on the graphics context, or just determines the
+ * colour that would be drawn (if flag colourOnly is true). Returns the last
+ * colour drawn (which may not be the effective colour if transparency
+ * applies), or null if no feature is drawn in the range given.
+ *
+ * @param g
+ * the graphics context to draw on (may be null only if t == 1 from
+ * colourOnly==true)
+ * @param seq
+ * @param start
+ * start column
+ * @param end
+ * end column
+ * @param y1
+ * vertical offset at which to draw on the graphics
+ * @param colourOnly
+ * if true, only do enough to determine the colour for the position,
+ * do not draw the character
+ * @return
+ */
+ public synchronized Color drawSequence(final Graphics g,
+ final SequenceI seq, int start, int end, int y1,
+ boolean colourOnly)
+ {
+ // from SeqCanvas and OverviewRender
+ /*
+ * if columns are all gapped, or sequence has no features, nothing to do
+ */
+ ContiguousI visiblePositions;
+ if (!seq.getFeatures().hasFeatures() || (visiblePositions = seq
+ .findPositions(start + 1, end + 1)) == null)
{
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- transparency));
+ return null;
}
- if (!offscreenRender)
+ int vp0 = visiblePositions.getBegin();
+ int vp1 = visiblePositions.getEnd();
+
+ updateFeatures();
+
+ if (transparency != 1f) // g cannot be null here if trans == 1f - BH // && g
+ // != null)
{
- spos = lastSeq.findPosition(start);
- epos = lastSeq.findPosition(end);
+ ((Graphics2D) g).setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ transparency));
}
- sfSize = sequenceFeatures.length;
- String type;
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
- {
- type = renderOrder[renderIndex];
+ Color drawnColour = null;
- if (type == null || !showFeatureOfType(type))
+ /*
+ * iterate over features in ordering of their rendering (last is on top)
+ */
+ for (int renderIndex = 0, n = renderOrder.length; renderIndex < n; renderIndex++)
+ {
+ String type = renderOrder[renderIndex];
+ if (!seq.hasFeatures(type) || !showFeatureOfType(type))
{
continue;
}
- // loop through all features in sequence to find
- // current feature to render
- for (sfindex = 0; sfindex < sfSize; sfindex++)
+ FeatureColourI fc = getFeatureStyle(type);
+ List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(vp0,
+ vp1, type);
+
+ // colourOnly (i.e. Overview) can only be here if translucent, so
+ // there is no need to check for filtering
+ if (!colourOnly && fc.isSimpleColour())
+ {
+ filterFeaturesForDisplay(overlaps);
+ }
+
+ for (int i = overlaps.size(); --i >= 0;)
{
- if (!sequenceFeatures[sfindex].type.equals(type))
+ SequenceFeature sf = overlaps.get(i);
+ Color featureColour = getColor(sf, fc);
+ if (featureColour == null)
{
+ /*
+ * feature excluded by visibility settings, filters, or colour threshold
+ */
continue;
}
- if (featureGroups != null
- && sequenceFeatures[sfindex].featureGroup != null
- && sequenceFeatures[sfindex].featureGroup.length() != 0
- && featureGroups
- .containsKey(sequenceFeatures[sfindex].featureGroup)
- && !((Boolean) featureGroups
- .get(sequenceFeatures[sfindex].featureGroup))
- .booleanValue())
+ /*
+ * if feature starts/ends outside the visible range,
+ * restrict to visible positions (or if a contact feature,
+ * to a single position)
+ */
+ int sf0 = sf.getBegin();
+ int sf1 = sf.getEnd();
+ int visibleStart = sf0;
+ if (visibleStart < vp0)
{
- continue;
+ visibleStart = sf.isContactFeature() ? sf1 : vp0;
}
-
- if (!offscreenRender
- && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
- .getEnd() < spos))
+ int visibleEnd = sf1;
+ if (visibleEnd > vp1)
{
- continue;
+ visibleEnd = sf.isContactFeature() ? sf0 : vp1;
}
- if (offscreenRender && offscreenImage == null)
- {
- if (sequenceFeatures[sfindex].begin <= start
- && sequenceFeatures[sfindex].end >= start)
- {
- // this is passed out to the overview and other sequence renderers
- // (e.g. molecule viewer) to get displayed colour for rendered
- // sequence
- currentColour = new Integer(
- getColour(sequenceFeatures[sfindex]).getRGB());
- // used to be retreived from av.featuresDisplayed
- // currentColour = av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type);
+ int featureStartCol = seq.findIndex(visibleStart);
+ int featureEndCol = (sf.begin == sf.end ? featureStartCol
+ : seq.findIndex(visibleEnd));
- }
- }
- else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
- {
+ // Color featureColour = getColour(sequenceFeature);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- getColour(sequenceFeatures[sfindex])
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex])
- // new Color(((Integer) av.featuresDisplayed
- // .get(sequenceFeatures[sfindex].type)).intValue())
- , start, end, y1);
+ boolean isContactFeature = sf.isContactFeature();
+ if (isContactFeature)
+ {
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureStartCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ drawn |= renderFeature(g, seq, featureEndCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
}
- else if (showFeature(sequenceFeatures[sfindex]))
+ else
{
- if (av_isShowSeqFeatureHeight
- && sequenceFeatures[sfindex].score != Float.NaN)
+ /*
+ * showing feature score by height of colour
+ * is not implemented as a selectable option
+ *
+ if (av.isShowSequenceFeaturesHeight()
+ && !Float.isNaN(sequenceFeature.score))
{
- renderScoreFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1,
- normaliseScore(sequenceFeatures[sfindex]));
+ boolean drawn = renderScoreFeature(g, seq,
+ seq.findIndex(sequenceFeature.begin) - 1,
+ seq.findIndex(sequenceFeature.end) - 1, featureColour,
+ start, end, y1, normaliseScore(sequenceFeature),
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
}
else
{
- renderFeature(g, seq,
- seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
- seq.findIndex(sequenceFeatures[sfindex].end) - 1,
- getColour(sequenceFeatures[sfindex]), start, end, y1);
+ */
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
}
+ /*}*/
}
-
}
-
}
- if (transparency != 1.0f && g != null && transparencyAvailable)
+ if (transparency != 1.0f)
{
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
- 1.0f));
+ /*
+ * reset transparency
+ */
+ ((Graphics2D) g).setComposite(NO_TRANSPARENCY);
}
- }
-
- boolean transparencyAvailable = true;
-
- protected void setTransparencyAvailable(boolean isTransparencyAvailable)
- {
- transparencyAvailable = isTransparencyAvailable;
- }
- @Override
- public boolean isTransparencyAvailable()
- {
- return transparencyAvailable;
+ return drawnColour;
}
/**
* discover and display.
*
*/
+ @Override
public void featuresAdded()
{
- lastSeq = null;
findAllFeatures();
}
+
+ private List<SequenceFeature> overlaps = (Platform.isJS()
+ ? new ArrayList<>()
+ : null);
+
+ /**
+ * Returns the sequence feature colour rendered at the given column position,
+ * or null if none found. The feature of highest render order (i.e. on top) is
+ * found, subject to both feature type and feature group being visible, and
+ * its colour returned. This method is suitable when no feature transparency
+ * applied (only the topmost visible feature colour is rendered).
+ * <p>
+ * Note this method does not check for a gap in the column so would return the
+ * colour for features enclosing a gapped column. Check for gap before calling
+ * if different behaviour is wanted.
+ *
+ * BH 2019.07.30
+ *
+ * Adds a result ArrayList to parameters in order to avoid an unnecessary
+ * construction of that for every pixel checked.
+ *
+ *
+ * @param seq
+ * @param column
+ * (1..)
+ * @return
+ */
+ private Color findFeatureColour(SequenceI seq, int column)
+ {
+ /*
+ * check for new feature added while processing
+ */
+ updateFeatures();
+
+ /*
+ * inspect features in reverse renderOrder (the last in the array is
+ * displayed on top) until we find one that is rendered at the position
+ */
+ for (int renderIndex = renderOrder.length; --renderIndex >= 0;)
+ {
+ String type = renderOrder[renderIndex];
+ if (!seq.hasFeatures(type) || !showFeatureOfType(type))
+ {
+ continue;
+ }
+
+ if (overlaps != null)
+ {
+ overlaps.clear();
+ }
+ List<SequenceFeature> list = seq.findFeatures(column, type, overlaps);
+ if (list.size() > 0)
+ {
+ for (int i = 0, n = list.size(); i < n; i++)
+ {
+ SequenceFeature sf = list.get(i);
+ if (featureGroupNotShown(sf))
+ {
+ continue;
+ }
+ Color col = getColour(sf);
+ if (col != null)
+ {
+ return col;
+ }
+ }
+ }
+ }
+
+ /*
+ * no displayed feature found at position
+ */
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff