From: kiramt Date: Wed, 22 Mar 2017 12:36:24 +0000 (+0000) Subject: Merge remote-tracking branch 'origin/develop' into X-Git-Tag: Release_2_10_2~3^2~150 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6e5286721b2711415a80d34364ae24b7a81fe2f9;p=jalview.git Merge remote-tracking branch 'origin/develop' into bug/JAL-2436featureRendererThreading Conflicts: src/jalview/appletgui/OverviewPanel.java src/jalview/gui/OverviewPanel.java --- 6e5286721b2711415a80d34364ae24b7a81fe2f9 diff --cc src/jalview/appletgui/OverviewPanel.java index 251e1c8,e2d986e..2fc5716 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@@ -20,8 -20,8 +20,9 @@@ */ package jalview.appletgui; - import jalview.datamodel.AlignmentI; + import jalview.datamodel.SequenceI; +import jalview.renderer.seqfeatures.FeatureColourFinder; + import jalview.viewmodel.OverviewDimensions; import java.awt.Color; import java.awt.Dimension; @@@ -417,52 -234,112 +235,104 @@@ public class OverviewPanel extends Pane } } - public void setBoxPosition() + /* + * Build the overview panel image + */ + private void buildImage(float sampleRow, float sampleCol, Graphics mg) { - int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth(); - int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment() - .getHiddenSequences().getSize()) - * av.getCharHeight(); - - int startRes = av.getStartRes(); - int endRes = av.getEndRes(); + int lastcol = 0; + int lastrow = 0; + int xstart = 0; + int ystart = 0; + Color color = Color.yellow; + int sameRow = 0; + int sameCol = 0; - if (av.hasHiddenColumns()) - { - startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); - endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); - } + SequenceI seq = null; ++ FeatureColourFinder finder = new FeatureColourFinder(fr); - int startSeq = av.startSeq; - int endSeq = av.endSeq; + final boolean hasHiddenCols = av.hasHiddenColumns(); + boolean hiddenRow = false; - if (av.hasHiddenRows()) + for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++) { - startSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(startSeq); - - endSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(endSeq); + if ((int) (row * sampleRow) == lastrow) + { + sameRow++; + } + else + { + // get the sequence which would be at alignment index 'lastrow' if no + // columns 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(); col++) + { + if ((int) (col * sampleCol) == lastcol + && (int) (row * sampleRow) == lastrow) + { + sameCol++; + } + else + { + lastcol = (int) (col * sampleCol); + + color = getColumnColourFromSequence(seq, hiddenRow, - hasHiddenCols, lastcol); ++ hasHiddenCols, lastcol, finder); + + mg.setColor(color); + if (sameCol == 1 && sameRow == 1) + { + mg.drawLine(xstart, ystart, xstart, ystart); + } + else + { + mg.fillRect(xstart, ystart, sameCol, sameRow); + } + + xstart = col; + sameCol = 1; + } + } + lastrow = (int) (row * sampleRow); + ystart = row; + sameRow = 1; + } } + } - scalew = (float) width / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; - - boxX = (int) (startRes * av.getCharWidth() * scalew); - boxY = (int) (startSeq * av.getCharHeight() * scaleh); - - if (av.hasHiddenColumns()) + /* + * Find the colour of a sequence at a specified column position + */ + private Color getColumnColourFromSequence( + jalview.datamodel.SequenceI seq, boolean hiddenRow, - boolean hasHiddenCols, int lastcol) ++ boolean hasHiddenCols, int lastcol, FeatureColourFinder finder) + { - Color color; ++ Color color = Color.white; + if (seq.getLength() > lastcol) { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); - color = sr.getResidueBoxColour(seq, lastcol); - - if (av.isShowSequenceFeatures()) - { - color = fr.findFeatureColour(color, seq, lastcol); - } - } - else - { - color = Color.white; ++ color = sr.getResidueColour(seq, lastcol, finder); } - else + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); + color = color.darker().darker(); } + return color; + } - boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh); - + /** + * Update the overview panel box when the associated alignment panel is + * changed + * + */ + public void setBoxPosition() + { + od.setBoxPosition(av.getAlignment() + .getHiddenSequences(), av.getColumnSelection(), av.getRanges()); repaint(); } diff --cc src/jalview/gui/OverviewPanel.java index 4097c40,67cdbc2..ac2138f --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@@ -20,8 -20,9 +20,10 @@@ */ package jalview.gui; + 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; @@@ -73,9 -68,9 +69,9 @@@ public class OverviewPanel extends JPan // Can set different properties in this seqCanvas than // main visible SeqCanvas - SequenceRenderer sr; + private SequenceRenderer sr; - private jalview.renderer.seqfeatures.FeatureRenderer fr; + jalview.renderer.seqfeatures.FeatureRenderer fr; /** * Creates a new OverviewPanel object. @@@ -92,38 -87,9 +88,9 @@@ sr = new SequenceRenderer(av); sr.renderGaps = false; sr.forOverview = true; - fr = new FeatureRenderer(alPanel); + fr = new FeatureRenderer(ap); - // scale the initial size of overviewpanel to shape of alignment - float initialScale = (float) av.getAlignment().getWidth() - / (float) av.getAlignment().getHeight(); - - if (av.getAlignmentConservationAnnotation() == null) - { - graphHeight = 0; - } - - if (av.getAlignment().getWidth() > av.getAlignment().getHeight()) - { - // wider - width = 400; - sequencesHeight = (int) (400f / initialScale); - if (sequencesHeight < 40) - { - sequencesHeight = 40; - } - } - else - { - // taller - width = (int) (400f * initialScale); - sequencesHeight = 300; - - if (width < 120) - { - width = 120; - } - } + od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation()); addComponentListener(new ComponentAdapter() { @@@ -426,66 -231,107 +232,97 @@@ setBoxPosition(); } - /** - * DOCUMENT ME! + /* + * Build the overview panel image */ - public void setBoxPosition() + private void buildImage(float sampleRow, float sampleCol) { - int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth(); - int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment() - .getHiddenSequences().getSize()) - * av.getCharHeight(); + int lastcol = -1; + int lastrow = -1; - int color = Color.white.getRGB(); ++ int rgbColour = Color.white.getRGB(); - int startRes = av.getStartRes(); - int endRes = av.getEndRes(); + SequenceI seq = null; ++ FeatureColourFinder finder = new FeatureColourFinder(fr); - if (av.hasHiddenColumns()) + 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() && !resizeAgain; row++) { - startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); - endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); - } + boolean doCopy = true; + int currentrow = (int) (row * sampleRow); + if (currentrow != lastrow) + { + doCopy = false; - int startSeq = av.startSeq; - int endSeq = av.endSeq; + lastrow = currentrow; - if (av.hasHiddenRows()) - { - startSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(startSeq); + // 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); + } - endSeq = av.getAlignment().getHiddenSequences() - .adjustForHiddenSeqs(endSeq); + for (int col = 0; col < od.getWidth() && !resizeAgain; col++) + { + if (doCopy) + { - color = miniMe.getRGB(col, row - 1); ++ rgbColour = 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); ++ rgbColour = 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, rgbColour); + } } + } - scalew = (float) width / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; - - boxX = (int) (startRes * av.getCharWidth() * scalew); - boxY = (int) (startSeq * av.getCharHeight() * scaleh); + /* + * Find the colour of a sequence at a specified column position + */ - private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq, - boolean hiddenRow, boolean hasHiddenCols, int lastcol) ++ private int getColumnColourFromSequence( ++ jalview.datamodel.SequenceI seq, ++ boolean hiddenRow, boolean hasHiddenCols, int lastcol, ++ FeatureColourFinder finder) + { - int color; ++ Color color = Color.white; - if (av.hasHiddenColumns()) - if (seq == null) ++ if ((seq != null) && (seq.getLength() > lastcol)) { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); - 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); } - else + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection() + .isVisible(lastcol))) { - boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew); - color = new Color(color).darker().darker().getRGB(); ++ color = color.darker().darker(); } - boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh); - - repaint(); - return color; ++ return color.getRGB(); } - private BufferedImage lastMiniMe = null; - /** - * DOCUMENT ME! + * Update the overview panel box when the associated alignment panel is + * changed * - * @param g - * DOCUMENT ME! */ + public void setBoxPosition() + { + od.setBoxPosition(av.getAlignment() + .getHiddenSequences(), av.getColumnSelection(), av.getRanges()); + repaint(); + } + + @Override public void paintComponent(Graphics g) {