From: kiramt Date: Wed, 22 Mar 2017 14:47:23 +0000 (+0000) Subject: Merge remote-tracking branch 'origin/develop' into X-Git-Tag: Release_2_10_2~3^2~92^2~25 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=299d350019dc2701cd2d9812e8ce1285146bc045;p=jalview.git Merge remote-tracking branch 'origin/develop' into features/JAL-2388OverviewWindow Conflicts: src/jalview/gui/OverviewPanel.java --- 299d350019dc2701cd2d9812e8ce1285146bc045 diff --cc src/jalview/gui/OverviewCanvas.java index 7d42e5e,0000000..6a7e56c mode 100644,000000..100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@@ -1,243 -1,0 +1,233 @@@ +package jalview.gui; + +import jalview.api.AlignViewportI; +import jalview.datamodel.SequenceI; +import jalview.renderer.AnnotationRenderer; ++import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.viewmodel.OverviewDimensions; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Graphics; +import java.awt.image.BufferedImage; + +import javax.swing.JComponent; + +public class OverviewCanvas extends JComponent +{ + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); + + private BufferedImage miniMe; + + private BufferedImage lastMiniMe = null; + + public boolean updating = false; + + // This is set true if the user resizes whilst + // the overview is being calculated + public volatile boolean updateAgain = false; + + // Can set different properties in this seqCanvas than + // main visible SeqCanvas + private SequenceRenderer sr; + + private jalview.renderer.seqfeatures.FeatureRenderer fr; + + private final AnnotationRenderer renderer = new AnnotationRenderer(); + + OverviewDimensions od; + + OverviewPanel op; + + AlignViewport av; + + AlignmentPanel ap; + + public OverviewCanvas(OverviewDimensions overviewDims, + AlignViewportI alignvp, AlignmentPanel alignp, OverviewPanel overp) + { + od = overviewDims; + av = alignp.av; + ap = alignp; + op = overp; + + sr = new SequenceRenderer(av); + sr.renderGaps = false; + sr.forOverview = true; + fr = new FeatureRenderer(ap); + } + + public void draw(boolean showSequenceFeatures, boolean showAnnotation) + { + miniMe = null; + + if (showSequenceFeatures) + { + fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + } + + // why do we need to set preferred size again? was set in + // updateOverviewImage + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + + miniMe = new BufferedImage(od.getWidth(), od.getHeight(), + BufferedImage.TYPE_INT_RGB); + + Graphics mg = miniMe.getGraphics(); + mg.setColor(Color.orange); + mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight()); + + // calculate sampleCol and sampleRow + // alignment width is max number of residues/bases + // alignment height is number of sequences + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getAbsoluteHeight(); + + // sampleCol or sampleRow is the width/height allocated to each residue + // in particular, sometimes we may need more than one row/col of the + // BufferedImage allocated + // sampleCol is how much of a residue to assign to each pixel + // sampleRow is how many sequences to assign to each pixel + float sampleCol = alwidth / (float) od.getWidth(); + float sampleRow = alheight / (float) od.getSequencesHeight(); + + buildImage(sampleRow, sampleCol); + + if (showAnnotation) + { + renderer.updateFromAlignViewport(av); + for (int col = 0; col < od.getWidth() && !updateAgain; col++) + { + mg.translate(col, od.getSequencesHeight()); + renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, + (int) (sampleCol) + 1, od.getGraphHeight(), + (int) (col * sampleCol), (int) (col * sampleCol) + 1); + mg.translate(-col, -od.getSequencesHeight()); + + } + } + System.gc(); + + updating = false; + + if (updateAgain) + { + updateAgain = false; + op.updateOverviewImage(); + } + else + { + lastMiniMe = miniMe; + } + } + + @Override + public void paintComponent(Graphics g) + { + if (updating || updateAgain) + { + if (lastMiniMe == null) + { + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); + } + else + { + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + } + g.setColor(TRANS_GREY); + g.fillRect(0, 0, getWidth(), getHeight()); + } + else if (lastMiniMe != null) + { + g.drawImage(lastMiniMe, 0, 0, this); + if (lastMiniMe != miniMe) + { + g.setColor(TRANS_GREY); + g.fillRect(0, 0, getWidth(), getHeight()); + } + } + + g.setColor(Color.red); + od.drawBox(g); + } + + /* + * Build the overview panel image + */ + private void buildImage(float sampleRow, float sampleCol) + { + int lastcol = -1; + int lastrow = -1; - int color = Color.white.getRGB(); ++ int rgbcolor = Color.white.getRGB(); + + SequenceI seq = null; ++ FeatureColourFinder finder = new FeatureColourFinder(fr); + + final boolean hasHiddenCols = av.hasHiddenColumns(); + boolean hiddenRow = false; + // get hidden row and hidden column map once at beginning. + // clone featureRenderer settings to avoid race conditions... if state is + // updated just need to refresh again + for (int row = 0; row < od.getSequencesHeight() && !updateAgain; row++) + { + boolean doCopy = true; + int currentrow = (int) (row * sampleRow); + if (currentrow != lastrow) + { + doCopy = false; + + lastrow = currentrow; + + // get the sequence which would be at alignment index 'lastrow' if no + // rows were hidden, and determine whether it is hidden or not + hiddenRow = av.getAlignment().isHidden(lastrow); + seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow); + } + + for (int col = 0; col < od.getWidth() && !updateAgain; col++) + { + if (doCopy) + { - color = miniMe.getRGB(col, row - 1); ++ rgbcolor = miniMe.getRGB(col, row - 1); + } + else if ((int) (col * sampleCol) != lastcol + || (int) (row * sampleRow) != lastrow) + { + lastcol = (int) (col * sampleCol); - color = getColumnColourFromSequence(seq, hiddenRow, - hasHiddenCols, lastcol); ++ rgbcolor = getColumnColourFromSequence(seq, hiddenRow, ++ hasHiddenCols, lastcol, finder); + } + // else we just use the color we already have , so don't need to set it + - miniMe.setRGB(col, row, color); ++ miniMe.setRGB(col, row, rgbcolor); + } + } + } + + /* + * Find the colour of a sequence at a specified column position + */ + private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol) ++ boolean hiddenRow, boolean hasHiddenCols, int lastcol, ++ FeatureColourFinder finder) + { - int color; ++ Color color = Color.white; + - if (seq == null) ++ if ((seq != null) && (seq.getLength() > lastcol)) + { - color = Color.white.getRGB(); - } - else if (seq.getLength() > lastcol) - { - color = sr.getResidueBoxColour(seq, lastcol).getRGB(); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = Color.white.getRGB(); ++ color = sr.getResidueColour(seq, lastcol, finder); + } + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) + { - color = new Color(color).darker().darker().getRGB(); ++ color = color.darker().darker(); + } + - return color; ++ return color.getRGB(); + } + +} diff --cc src/jalview/gui/OverviewPanel.java index f9f3e4c,c530fdc..f58a2a5 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@@ -59,13 -83,17 +59,15 @@@ public class OverviewPanel extends JPan { this.av = alPanel.av; this.ap = alPanel; - setLayout(null); - - sr = new SequenceRenderer(av); - sr.renderGaps = false; - sr.forOverview = true; - fr = new FeatureRenderer(ap); - od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation()); + od = new OverviewDimensions(av.getRanges(), + (av.isShowAnnotation() && av + .getAlignmentConservationAnnotation() != null)); + oviewCanvas = new OverviewCanvas(od, av, ap, this); + setLayout(new BorderLayout()); + add(oviewCanvas, BorderLayout.CENTER); + addComponentListener(new ComponentAdapter() { @Override @@@ -141,7 -169,70 +143,9 @@@ @Override public void run() { - oviewCanvas.draw(av.isShowSequenceFeatures(), av.isShowAnnotation()); - miniMe = null; - - if (av.isShowSequenceFeatures()) - { - fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); - } - - // why do we need to set preferred size again? was set in - // updateOverviewImage - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - - miniMe = new BufferedImage(od.getWidth(), od.getHeight(), - BufferedImage.TYPE_INT_RGB); - - Graphics mg = miniMe.getGraphics(); - mg.setColor(Color.orange); - mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight()); - - // calculate sampleCol and sampleRow - // alignment width is max number of residues/bases - // alignment height is number of sequences - int alwidth = av.getAlignment().getWidth(); - int alheight = av.getAlignment().getAbsoluteHeight(); - - // sampleCol or sampleRow is the width/height allocated to each residue - // in particular, sometimes we may need more than one row/col of the - // BufferedImage allocated - // sampleCol is how much of a residue to assign to each pixel - // sampleRow is how many sequences to assign to each pixel - float sampleCol = alwidth / (float) od.getWidth(); - float sampleRow = alheight / (float) od.getSequencesHeight(); - - buildImage(sampleRow, sampleCol); - - // check for conservation annotation to make sure overview works for DNA too - if (av.isShowAnnotation() - && (av.getAlignmentConservationAnnotation() != null)) - { - renderer.updateFromAlignViewport(av); - for (int col = 0; col < od.getWidth() && !resizeAgain; col++) - { - mg.translate(col, od.getSequencesHeight()); - renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), - av.getAlignmentConservationAnnotation().annotations, - (int) (sampleCol) + 1, od.getGraphHeight(), - (int) (col * sampleCol), (int) (col * sampleCol) + 1); - mg.translate(-col, -od.getSequencesHeight()); - - } - } - System.gc(); - - resizing = false; - - if (resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - else - { - lastMiniMe = miniMe; - } - ++ oviewCanvas.draw(av.isShowSequenceFeatures(), ++ (av.isShowAnnotation() && av ++ .getAlignmentConservationAnnotation() != null)); setBoxPosition(); }