/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program 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 2 * of the License, or (at your option) any later version. * * This program 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 this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA */ package jalview.gui; import java.awt.*; import java.awt.event.*; import java.awt.image.*; import javax.swing.*; /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ public class OverviewPanel extends JPanel implements Runnable { BufferedImage miniMe; AlignViewport av; AlignmentPanel ap; float scalew = 1f; float scaleh = 1f; int width; int sequencesHeight; int graphHeight = 20; int boxX = -1; int boxY = -1; int boxWidth = -1; int boxHeight = -1; boolean resizing = false; // Can set different properties in this seqCanvas than // main visible SeqCanvas SequenceRenderer sr; FeatureRenderer fr; /** * Creates a new OverviewPanel object. * * @param ap DOCUMENT ME! */ public OverviewPanel(AlignmentPanel ap) { this.av = ap.av; this.ap = ap; setLayout(null); sr = new SequenceRenderer(av); sr.renderGaps = false; sr.forOverview = true; fr = new FeatureRenderer(ap); // scale the initial size of overviewpanel to shape of alignment float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight(); if (av.conservation == null) { graphHeight = 0; } if (av.alignment.getWidth() > av.alignment.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; } } addComponentListener(new ComponentAdapter() { public void componentResized(ComponentEvent evt) { if ( (getWidth() != width) || (getHeight() != (sequencesHeight + graphHeight))) { updateOverviewImage(); } } }); addMouseMotionListener(new MouseMotionAdapter() { public void mouseDragged(MouseEvent evt) { if (!av.wrapAlignment) { boxX = evt.getX(); boxY = evt.getY(); checkValid(); } } }); addMouseListener(new MouseAdapter() { public void mousePressed(MouseEvent evt) { if (!av.wrapAlignment) { boxX = evt.getX(); boxY = evt.getY(); checkValid(); } } }); updateOverviewImage(); } /** * DOCUMENT ME! */ void checkValid() { if (boxY < 0) { boxY = 0; } if (boxY > (sequencesHeight - boxHeight)) { boxY = sequencesHeight - boxHeight + 1; } if (boxX < 0) { boxX = 0; } if (boxX > (width - boxWidth)) { if (av.hasHiddenColumns) { //Try smallest possible box boxWidth = (int) ( (av.endRes - av.startRes + 1) * av.getCharWidth() * scalew); } boxX = width - boxWidth; } int col = (int) (boxX / scalew / av.getCharWidth()); int row = (int) (boxY / scaleh / av.getCharHeight()); if (av.hasHiddenColumns) { if (!av.getColumnSelection().isVisible(col)) { return; } col = av.getColumnSelection().findColumnPosition(col); } if (av.hasHiddenRows) { row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(row); } ap.setScrollValues(col, row); } /** * DOCUMENT ME! */ public void updateOverviewImage() { if (resizing) { resizeAgain = true; return; } resizing = true; if ( (getWidth() > 0) && (getHeight() > 0)) { width = getWidth(); sequencesHeight = getHeight() - graphHeight; } setPreferredSize(new Dimension(width, sequencesHeight + graphHeight)); Thread thread = new Thread(this); thread.start(); repaint(); } // This is set true if the user resizes whilst // the overview is being calculated boolean resizeAgain = false; /** * DOCUMENT ME! */ public void run() { miniMe = null; if (av.showSequenceFeatures) { fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); } int alwidth = av.alignment.getWidth(); int alheight = av.alignment.getHeight() + av.alignment.getHiddenSequences().getSize(); setPreferredSize(new Dimension(width, sequencesHeight + graphHeight)); int fullsizeWidth = alwidth * av.getCharWidth(); int fullsizeHeight = alheight * av.getCharHeight(); scalew = (float) width / (float) fullsizeWidth; scaleh = (float) sequencesHeight / (float) fullsizeHeight; miniMe = new BufferedImage(width, sequencesHeight + graphHeight, BufferedImage.TYPE_INT_RGB); Graphics mg = miniMe.getGraphics(); mg.setColor(Color.orange); mg.fillRect(0, 0, width, miniMe.getHeight()); float sampleCol = (float) alwidth / (float) width; float sampleRow = (float) alheight / (float) sequencesHeight; int lastcol = -1, lastrow = -1; int color = Color.white.getRGB(); int row, col; jalview.datamodel.SequenceI seq; boolean hiddenRow = false; for (row = 0; row < sequencesHeight; row++) { if ( (int) (row * sampleRow) == lastrow) { //No need to recalculate the colours, //Just copy from the row above for (col = 0; col < width; col++) { miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1)); } continue; } lastrow = (int) (row * sampleRow); hiddenRow = false; if (av.hasHiddenRows) { seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow); if (seq == null) { int index = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs( lastrow); seq = av.alignment.getSequenceAt(index); } else { hiddenRow = true; } } else { seq = av.alignment.getSequenceAt(lastrow); } if (seq == null) { System.out.println(lastrow + " null"); continue; } for (col = 0; col < width; col++) { if ( (int) (col * sampleCol) == lastcol && (int) (row * sampleRow) == lastrow) { miniMe.setRGB(col, row, color); continue; } lastcol = (int) (col * sampleCol); if (seq.getLength() > lastcol) { color = sr.getResidueBoxColour( seq, lastcol).getRGB(); if (av.showSequenceFeatures) { color = fr.findFeatureColour(color, seq, lastcol); } } else { color = -1; //White } if (hiddenRow || (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol))) { color = new Color(color).darker().darker().getRGB(); } miniMe.setRGB(col, row, color); } } if (av.conservation != null) { for (col = 0; col < width; col++) { lastcol = (int) (col * sampleCol); { mg.translate(col, sequencesHeight); ap.annotationPanel.drawGraph(mg, av.conservation, (int) (sampleCol) + 1, graphHeight, (int) (col * sampleCol), (int) (col * sampleCol) + 1); mg.translate( -col, -sequencesHeight); } } } System.gc(); resizing = false; setBoxPosition(); if (resizeAgain) { resizeAgain = false; updateOverviewImage(); } } /** * DOCUMENT ME! */ public void setBoxPosition() { int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth(); int fullsizeHeight = (av.alignment.getHeight() + av.alignment.getHiddenSequences().getSize()) * av.getCharHeight(); int startRes = av.getStartRes(); int endRes = av.getEndRes(); if (av.hasHiddenColumns) { startRes = av.getColumnSelection().adjustForHiddenColumns(startRes); endRes = av.getColumnSelection().adjustForHiddenColumns(endRes); } int startSeq = av.startSeq; int endSeq = av.endSeq; if (av.hasHiddenRows) { startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(startSeq); endSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(endSeq); } 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) { boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew); } else { boxWidth = (int) ( (endRes - startRes + 1) * av.getCharWidth() * scalew); } boxHeight = (int) ( (endSeq - startSeq) * av.getCharHeight() * scaleh); repaint(); } /** * DOCUMENT ME! * * @param g DOCUMENT ME! */ public void paintComponent(Graphics g) { if(resizing) { g.setColor(Color.white); g.fillRect(0,0,getWidth(),getHeight()); } else if (miniMe != null) { g.drawImage(miniMe, 0, 0, this); } g.setColor(Color.red); g.drawRect(boxX, boxY, boxWidth, boxHeight); g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2); } }