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package jalview.renderer; |
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import jalview.api.AlignmentColsCollectionI; |
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import jalview.api.AlignmentRowsCollectionI; |
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import jalview.api.RendererListenerI; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.Annotation; |
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import jalview.datamodel.SequenceGroup; |
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import jalview.datamodel.SequenceI; |
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import jalview.renderer.seqfeatures.FeatureColourFinder; |
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import jalview.renderer.seqfeatures.FeatureRenderer; |
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import jalview.viewmodel.OverviewDimensions; |
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import java.awt.AlphaComposite; |
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import java.awt.Color; |
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import java.awt.Graphics; |
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import java.awt.Graphics2D; |
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import java.awt.image.BufferedImage; |
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import java.beans.PropertyChangeSupport; |
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| 69.9% |
Uncovered Elements: 50 (166) |
Complexity: 32 |
Complexity Density: 0.28 |
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public class OverviewRenderer |
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{ |
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private final float TRANSPARENCY = 0.5f; |
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public static final String UPDATE = "OverviewUpdate"; |
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private static final int MAX_PROGRESS = 100; |
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private PropertyChangeSupport changeSupport = new PropertyChangeSupport( |
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this); |
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private FeatureColourFinder finder; |
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private BufferedImage miniMe; |
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private float pixelsPerCol; |
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private float pixelsPerSeq; |
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private int graphHeight; |
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private volatile boolean redraw = false; |
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private AlignmentI al; |
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private ResidueShaderI shader; |
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private OverviewResColourFinder resColFinder; |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
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public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,... |
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AlignmentI alignment, ResidueShaderI resshader, |
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OverviewResColourFinder colFinder) |
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{ |
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finder = new FeatureColourFinder(fr); |
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resColFinder = colFinder; |
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al = alignment; |
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shader = resshader; |
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pixelsPerCol = od.getPixelsPerCol(); |
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pixelsPerSeq = od.getPixelsPerSeq(); |
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graphHeight = od.getGraphHeight(); |
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miniMe = new BufferedImage(od.getWidth(), od.getHeight(), |
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BufferedImage.TYPE_INT_RGB); |
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} |
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@param |
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@param |
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@return |
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| 96.2% |
Uncovered Elements: 2 (52) |
Complexity: 8 |
Complexity Density: 0.21 |
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public BufferedImage draw(AlignmentRowsCollectionI rows,... |
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AlignmentColsCollectionI cols) |
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{ |
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int rgbcolor = Color.white.getRGB(); |
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int seqIndex = 0; |
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int pixelRow = 0; |
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int alignmentHeight = miniMe.getHeight() - graphHeight; |
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int totalPixels = miniMe.getWidth() * alignmentHeight; |
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int lastRowUpdate = 0; |
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int lastUpdate = 0; |
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changeSupport.firePropertyChange(UPDATE, -1, 0); |
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for (int alignmentRow : rows) |
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{ |
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if (redraw) |
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{ |
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break; |
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} |
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SequenceI seq = rows.getSequence(alignmentRow); |
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SequenceGroup[] allGroups = al.findAllGroups(seq); |
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int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1, |
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miniMe.getHeight() - 1); |
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int colIndex = 0; |
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int pixelCol = 0; |
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for (int alignmentCol : cols) |
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{ |
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if (redraw) |
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{ |
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break; |
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} |
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int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, |
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miniMe.getWidth() - 1); |
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if (pixelCol <= endCol) |
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{ |
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rgbcolor = getColumnColourFromSequence(allGroups, seq, |
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alignmentCol); |
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for (int row = pixelRow; row <= endRow; ++row) |
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{ |
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for (int col = pixelCol; col <= endCol; ++col) |
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{ |
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2300107 |
miniMe.setRGB(col, row, rgbcolor); |
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} |
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} |
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lastUpdate = sendProgressUpdate( |
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(pixelCol + 1) * (endRow - pixelRow), totalPixels, |
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lastRowUpdate, lastUpdate); |
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316280 |
pixelCol = endCol + 1; |
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} |
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colIndex++; |
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} |
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if (pixelRow != endRow + 1) |
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{ |
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lastRowUpdate = sendProgressUpdate(endRow + 1, alignmentHeight, 0, |
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lastUpdate); |
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lastUpdate = lastRowUpdate; |
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pixelRow = endRow + 1; |
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} |
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seqIndex++; |
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} |
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overlayHiddenRegions(rows, cols); |
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if (redraw) |
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{ |
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sendProgressUpdate(pixelRow - 1, alignmentHeight, 0, 0); |
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} |
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else |
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{ |
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sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0, 0); |
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} |
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return miniMe; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
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318686 |
private int sendProgressUpdate(int position, int maximum, int rowOffset,... |
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int lastUpdate) |
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{ |
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int newUpdate = rowOffset |
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+ Math.round(MAX_PROGRESS * ((float) position / maximum)); |
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if (newUpdate > lastUpdate) |
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{ |
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changeSupport.firePropertyChange(UPDATE, rowOffset, newUpdate); |
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return newUpdate; |
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} |
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return newUpdate; |
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} |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 3 |
Complexity Density: 0.75 |
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int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,... |
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int lastcol) |
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{ |
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316456 |
Color color = resColFinder.gapColour; |
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if ((seq != null) && (seq.getLength() > lastcol)) |
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{ |
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314582 |
color = resColFinder.getResidueColour(true, shader, allGroups, seq, |
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lastcol, finder); |
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} |
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return color.getRGB(); |
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} |
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@param |
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@param |
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| 28.6% |
Uncovered Elements: 5 (7) |
Complexity: 3 |
Complexity Density: 0.6 |
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private void overlayHiddenRegions(AlignmentRowsCollectionI rows,... |
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AlignmentColsCollectionI cols) |
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{ |
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if (cols.hasHidden() || rows.hasHidden()) |
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{ |
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BufferedImage mask = buildHiddenImage(rows, cols, miniMe.getWidth(), |
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miniMe.getHeight()); |
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Graphics2D g = (Graphics2D) miniMe.getGraphics(); |
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g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, |
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TRANSPARENCY)); |
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g.drawImage(mask, 0, 0, miniMe.getWidth(), miniMe.getHeight(), null); |
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} |
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} |
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@param |
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@param |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 38 (38) |
Complexity: 6 |
Complexity Density: 0.21 |
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private BufferedImage buildHiddenImage(AlignmentRowsCollectionI rows,... |
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AlignmentColsCollectionI cols, int width, int height) |
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{ |
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BufferedImage hiddenImage = new BufferedImage(width, height, |
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BufferedImage.TYPE_INT_ARGB); |
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int colIndex = 0; |
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int pixelCol = 0; |
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Color hidden = resColFinder.getHiddenColour(); |
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Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics(); |
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g2d.setComposite(AlphaComposite.Src); |
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for (int alignmentCol : cols) |
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{ |
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if (redraw) |
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{ |
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break; |
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} |
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int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, |
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hiddenImage.getWidth() - 1); |
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if (pixelCol <= endCol) |
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{ |
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if (cols.isHidden(alignmentCol)) |
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{ |
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g2d.setColor(hidden); |
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g2d.fillRect(pixelCol, 0, endCol - pixelCol + 1, height); |
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} |
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pixelCol = endCol + 1; |
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} |
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colIndex++; |
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} |
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int seqIndex = 0; |
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int pixelRow = 0; |
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for (int alignmentRow : rows) |
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{ |
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if (redraw) |
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{ |
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break; |
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} |
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0 |
int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1, |
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miniMe.getHeight() - 1); |
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if (rows.isHidden(alignmentRow)) |
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{ |
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g2d.setColor(hidden); |
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g2d.fillRect(0, pixelRow, width, endRow - pixelRow + 1); |
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} |
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pixelRow = endRow + 1; |
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seqIndex++; |
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} |
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return hiddenImage; |
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} |
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@param |
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@param |
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@param |
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@param |
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| 88.2% |
Uncovered Elements: 4 (34) |
Complexity: 6 |
Complexity Density: 0.25 |
|
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public void drawGraph(Graphics g, AlignmentAnnotation anno, int y,... |
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AlignmentColsCollectionI cols) |
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{ |
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Annotation[] annotations = anno.annotations; |
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g.setColor(Color.white); |
366 |
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g.fillRect(0, 0, miniMe.getWidth(), y); |
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int height; |
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int colIndex = 0; |
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int pixelCol = 0; |
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for (int alignmentCol : cols) |
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{ |
373 |
19079 |
if (redraw) |
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{ |
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110 |
changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, 0); |
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break; |
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} |
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18969 |
if (alignmentCol >= annotations.length) |
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{ |
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break; |
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} |
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else |
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{ |
385 |
18967 |
int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, |
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miniMe.getWidth() - 1); |
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18967 |
if (annotations[alignmentCol] != null) |
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{ |
390 |
18965 |
if (annotations[alignmentCol].colour == null) |
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{ |
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g.setColor(Color.black); |
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} |
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else |
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{ |
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18965 |
g.setColor(annotations[alignmentCol].colour); |
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} |
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18965 |
height = (int) ((annotations[alignmentCol].value / anno.graphMax) |
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* y); |
401 |
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if (height > y) |
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{ |
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height = y; |
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} |
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18965 |
g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height); |
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} |
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18967 |
pixelCol = endCol + 1; |
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18967 |
colIndex++; |
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} |
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} |
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245 |
changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, |
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MAX_PROGRESS); |
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} |
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@param |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
424 |
151 |
public void setRedraw(boolean b)... |
425 |
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{ |
426 |
151 |
synchronized (this) |
427 |
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{ |
428 |
151 |
redraw = b; |
429 |
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} |
430 |
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} |
431 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
432 |
249 |
public void addPropertyChangeListener(RendererListenerI listener)... |
433 |
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{ |
434 |
249 |
changeSupport.addPropertyChangeListener(listener); |
435 |
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} |
436 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
437 |
244 |
public void removePropertyChangeListener(RendererListenerI listener)... |
438 |
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{ |
439 |
244 |
changeSupport.removePropertyChangeListener(listener); |
440 |
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} |
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} |