+++ /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.appletgui;
-
-import jalview.datamodel.SequenceI;
-import jalview.viewmodel.OverviewDimensions;
-import jalview.datamodel.AlignmentI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Image;
-import java.awt.Panel;
-import java.awt.event.ComponentAdapter;
-import java.awt.event.ComponentEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-
-public class OverviewPanel extends Panel implements Runnable,
- MouseMotionListener, MouseListener
-{
- private OverviewDimensions od;
-
- private Image miniMe;
-
- private Image offscreen;
-
- 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 FeatureRenderer fr;
-
- private Frame nullFrame;
-
- public OverviewPanel(AlignmentPanel alPanel)
- {
- this.av = alPanel.av;
- this.ap = alPanel;
- setLayout(null);
- nullFrame = new Frame();
- nullFrame.addNotify();
-
- sr = new SequenceRenderer(av);
- sr.graphics = nullFrame.getGraphics();
- sr.renderGaps = false;
- sr.forOverview = true;
- fr = new FeatureRenderer(av);
-
- od = new OverviewDimensions(av.getRanges(), av.isShowAnnotation());
-
- setSize(new Dimension(od.getWidth(), od.getHeight()));
- addComponentListener(new ComponentAdapter()
- {
-
- @Override
- public void componentResized(ComponentEvent evt)
- {
- if ((getWidth() != od.getWidth())
- || (getHeight() != (od.getHeight())))
- {
- updateOverviewImage();
- }
- }
- });
-
- addMouseMotionListener(this);
-
- addMouseListener(this);
-
- updateOverviewImage();
-
- }
-
- @Override
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- @Override
- public void mouseExited(MouseEvent evt)
- {
- }
-
- @Override
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- @Override
- public void mouseMoved(MouseEvent evt)
- {
- }
-
- @Override
- public void mousePressed(MouseEvent evt)
- {
- mouseAction(evt);
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- mouseAction(evt);
- }
-
- @Override
- public void mouseDragged(MouseEvent evt)
- {
- mouseAction(evt);
- }
-
- private void mouseAction(MouseEvent evt)
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
- .getHiddenSequences(), av.getColumnSelection(), av
- .getRanges());
- ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
- ap.paintAlignment(false);
- }
-
- /**
- * Updates the overview image when the related alignment panel is updated
- */
- public void updateOverviewImage()
- {
- if (resizing)
- {
- resizeAgain = true;
- return;
- }
-
- if (av.isShowSequenceFeatures())
- {
- fr.transferSettings(ap.seqPanel.seqCanvas.fr);
- }
-
- resizing = true;
-
- if ((getSize().width > 0) && (getSize().height > 0))
- {
- od.setWidth(getSize().width);
- od.setHeight(getSize().height);
- }
- setSize(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.seqPanel.seqCanvas.getFeatureRenderer());
- }
-
- if (getSize().width > 0 && getSize().height > 0)
- {
- od.setWidth(getSize().width);
- od.setHeight(getSize().height);
- }
-
- setSize(new Dimension(od.getWidth(), od.getHeight()));
-
- miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
- offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
-
- Graphics mg = miniMe.getGraphics();
-<<<<<<< HEAD
-
- int alwidth = av.getAlignment().getWidth();
- int alheight = av.getAlignment().getAbsoluteHeight();
- float sampleCol = alwidth / (float) od.getWidth();
- float sampleRow = alheight / (float) od.getSequencesHeight();
-=======
- float sampleCol = (float) alwidth / (float) width;
- float sampleRow = (float) alheight / (float) sequencesHeight;
-
- int lastcol = 0, lastrow = 0;
- int xstart = 0, ystart = 0;
- Color color = Color.yellow;
- int row, col, sameRow = 0, sameCol = 0;
- jalview.datamodel.SequenceI seq;
- final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
- .hasHiddenColumns();
- boolean hiddenRow = false;
- AlignmentI alignment = av.getAlignment();
-
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- for (row = 0; row <= sequencesHeight; row++)
- {
- if (resizeAgain)
- {
- break;
- }
- if ((int) (row * sampleRow) == lastrow)
- {
- sameRow++;
- continue;
- }
-
- hiddenRow = false;
- if (hasHiddenRows)
- {
- seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
- if (seq == null)
- {
- int index = alignment.getHiddenSequences()
- .findIndexWithoutHiddenSeqs(lastrow);
-
- seq = alignment.getSequenceAt(index);
- }
- else
- {
- hiddenRow = true;
- }
- }
- else
- {
- seq = alignment.getSequenceAt(lastrow);
- }
-
- for (col = 0; col < width; col++)
- {
- if ((int) (col * sampleCol) == lastcol
- && (int) (row * sampleRow) == lastrow)
- {
- sameCol++;
- 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();
- }
-
- mg.setColor(color);
- if (sameCol == 1 && sameRow == 1)
- {
- mg.drawLine(xstart, ystart, xstart, ystart);
- }
- else
- {
- mg.fillRect(xstart, ystart, sameCol, sameRow);
- }
->>>>>>> bug/JAL-2436featureRendererThreading
-
- buildImage(sampleRow, sampleCol, mg);
-
- if (av.isShowAnnotation())
- {
- for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
- {
- mg.translate(col, od.getSequencesHeight());
- ap.annotationPanel.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;
-
- setBoxPosition();
-
- if (resizeAgain)
- {
- resizeAgain = false;
- updateOverviewImage();
- }
- }
-
- /*
- * Build the overview panel image
- */
- private void buildImage(float sampleRow, float sampleCol, Graphics mg)
- {
- int lastcol = 0;
- int lastrow = 0;
- int xstart = 0;
- int ystart = 0;
- Color color = Color.yellow;
- int sameRow = 0;
- int sameCol = 0;
-
- SequenceI seq = null;
-
- final boolean hasHiddenCols = av.hasHiddenColumns();
- boolean hiddenRow = false;
-
- for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
- {
- 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);
-
- 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;
- }
- }
- }
-
- /*
- * Find the colour of a sequence at a specified column position
- */
- private Color getColumnColourFromSequence(
- jalview.datamodel.SequenceI seq, boolean hiddenRow,
- boolean hasHiddenCols, int lastcol)
- {
- Color color;
- if (seq.getLength() > lastcol)
- {
- color = sr.getResidueBoxColour(seq, lastcol);
-
- if (av.isShowSequenceFeatures())
- {
- color = fr.findFeatureColour(color, seq, lastcol);
- }
- }
- else
- {
- color = Color.white;
- }
-
- if (hiddenRow
- || (hasHiddenCols && !av.getColumnSelection()
- .isVisible(lastcol)))
- {
- color = color.darker().darker();
- }
- 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 update(Graphics g)
- {
- paint(g);
- }
-
- @Override
- public void paint(Graphics g)
- {
- Graphics og = offscreen.getGraphics();
- if (miniMe != null)
- {
- og.drawImage(miniMe, 0, 0, this);
- og.setColor(Color.red);
- od.drawBox(og);
- g.drawImage(offscreen, 0, 0, this);
- }
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff