+++ /dev/null
-/*
- * 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.gui;
-
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseMotionAdapter;
-import java.awt.image.BufferedImage;
-
-import javax.swing.JPanel;
-
-/**
- * Panel displaying an overview of the full alignment, with an interactive box
- * representing the viewport onto the alignment.
- *
- * @author $author$
- * @version $Revision$
- */
-public class OverviewPanel extends JPanel implements Runnable
-{
- private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
-
- private final AnnotationRenderer renderer = new AnnotationRenderer();
-
- private OverviewDimensions od;
-
- private BufferedImage miniMe;
-
- private BufferedImage lastMiniMe = null;
-
- private AlignViewport av;
-
- private AlignmentPanel ap;
-
- //
- private boolean resizing = false;
-
- // This is set true if the user resizes whilst
- // the overview is being calculated
- private boolean resizeAgain = false;
-
- // Can set different properties in this seqCanvas than
- // main visible SeqCanvas
- private SequenceRenderer sr;
-
- private jalview.renderer.seqfeatures.FeatureRenderer fr;
-
- /**
- * Creates a new OverviewPanel object.
- *
- * @param alPanel
- * The alignment panel which is shown in the overview panel
- */
- public OverviewPanel(AlignmentPanel alPanel)
- {
- this.av = alPanel.av;
- this.ap = alPanel;
- setLayout(null);
-
- sr = new SequenceRenderer(av);
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(alPanel);
-
- od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
-
- addComponentListener(new ComponentAdapter()
- {
- @Override
- public void componentResized(ComponentEvent evt)
- {
- if ((getWidth() != od.getWidth())
- || (getHeight() != (od.getHeight())))
- {
- updateOverviewImage();
- }
- }
- });
-
- addMouseMotionListener(new MouseMotionAdapter()
- {
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- if (!av.getWrapAlignment())
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av
- .getColumnSelection(), av.getRanges());
- ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
- }
- }
- });
-
- addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (!av.getWrapAlignment())
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av
- .getAlignment().getHiddenSequences(), av
- .getColumnSelection(), av.getRanges());
- ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
- }
- }
- });
-
- updateOverviewImage();
- }
-
- /**
- * Updates the overview image when the related alignment panel is updated
- */
- public void updateOverviewImage()
- {
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- resizing = true;
-
- if ((getWidth() > 0) && (getHeight() > 0))
- {
- od.setWidth(getWidth());
- od.setHeight(getHeight());
- }
-
- setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
- Thread thread = new Thread(this);
- thread.start();
- repaint();
- }
-
- @Override
- public void run()
- {
- 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());
-
-<<<<<<< HEAD
- // 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);
-=======
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = -1, lastrow = -1;
- Color color = Color.white;
- int row, col;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), 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
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
-
- for (row = 0; row < sequencesHeight; row++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- // No need to recalculate the colours,
- // Just copy from the row above
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
- }
- continue;
- }
-
- lastrow = (int) (row * sampleRow);
-
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = av.getAlignment().getHiddenSequences()
- .getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = av.getAlignment().getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = av.getAlignment().getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = av.getAlignment().getSequenceAt(lastrow);
- }
-
- if (seq == null)
- {
- System.out.println(lastrow + " null");
- continue;
- }
-
- for (col = 0; col < width; col++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- miniMe.setRGB(col, row, color.getRGB());
- continue;
- }
-
- lastcol = (int) (col * sampleCol);
-
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueColour(seq, lastcol, finder);
- }
- else
- {
- color = Color.WHITE;
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection().isVisible(
- lastcol)))
- {
- color = color.darker().darker();
- }
-
- miniMe.setRGB(col, row, color.getRGB());
->>>>>>> bug/JAL-2436featureRendererThreading
-
- if (av.isShowAnnotation())
- {
- 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;
- }
-
- setBoxPosition();
- }
-
- /*
- * Build the overview panel image
- */
- private void buildImage(float sampleRow, float sampleCol)
- {
- int lastcol = -1;
- int lastrow = -1;
- int color = Color.white.getRGB();
-
- SequenceI seq = null;
-
- 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++)
- {
- 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() && !resizeAgain; col++)
- {
- if (doCopy)
- {
- color = 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);
- }
- // else we just use the color we already have , so don't need to set it
-
- miniMe.setRGB(col, row, color);
- }
- }
- }
-
- /*
- * Find the colour of a sequence at a specified column position
- */
- private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
- boolean hiddenRow, boolean hasHiddenCols, int lastcol)
- {
- int color;
-
- if (seq == null)
- {
- 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();
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = new Color(color).darker().darker().getRGB();
- }
-
- return color;
- }
-
- /**
- * 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();
- }
-
-
- @Override
- public void paintComponent(Graphics g)
- {
- if (resizing || resizeAgain)
- {
- 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);
- }
-}
git://source.jalview.org / jalview.git / blobdiff