X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=9397cebbeaae42116937602076ff815fb8e382d4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6c968a259c8042c1d73253037bf3fa8e40292eba;hpb=a8458ff4b33d8deb7e09a39b8ce5576880f6a862;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 6c968a2..9397ceb 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,382 +1,483 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 = 30; - int boxX = -1; - int boxY = -1; - int boxWidth = -1; - int boxHeight = -1; - boolean resizing = false; - - /** - * Creates a new OverviewPanel object. - * - * @param ap DOCUMENT ME! - */ - public OverviewPanel(AlignmentPanel ap) - { - this.av = ap.av; - this.ap = ap; - setLayout(null); - - // scale the initial size of overviewpanel to shape of alignment - float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight(); - - if (av.alignment.getWidth() > av.alignment.getHeight()) - { - // wider - width = 400; - sequencesHeight = (int) (400f / initialScale); - } - 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) - { - doMouseDragged(evt); - } - }); - - addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - doMousePressed(evt); - } - - public void mouseReleased(MouseEvent evt) - { - doMouseReleased(evt); - } - }); - - updateOverviewImage(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMousePressed(MouseEvent evt) - { - boxX = evt.getX(); - boxY = evt.getY(); - - checkValid(); - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseReleased(MouseEvent evt) - { - boxX = evt.getX(); - boxY = evt.getY(); - checkValid(); - - if (!resizing) - { - ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()), - (int) (boxY / scaleh / av.getCharHeight())); - } - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseDragged(MouseEvent evt) - { - boxX = evt.getX(); - boxY = evt.getY(); - checkValid(); - - if (!resizing) - { - ap.setScrollValues((int) (boxX / scalew / av.getCharWidth()), - (int) (boxY / scaleh / av.getCharHeight())); - } - } - - /** - * 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)) - { - boxX = width - boxWidth; - } - } - - /** - * DOCUMENT ME! - */ - public void updateOverviewImage() - { - if (resizing) - { - resizeAgain = true; - return; - } - - resizing = true; - - 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; - - int alwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight(); - - if ((getWidth() > 0) && (getHeight() > 0)) - { - width = getWidth(); - sequencesHeight = getHeight() - graphHeight; - } - - 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(); - BufferedImage consensus = new BufferedImage(fullsizeWidth, 60, - BufferedImage.TYPE_3BYTE_BGR); - Graphics g = consensus.getGraphics(); - ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60); - mg.drawImage(consensus, 0, sequencesHeight, width, - sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this); - - boolean oldRenderGaps = av.renderGaps; - - try - { - // We'll have to draw the full size alignment in chunks, as an image of the - // whole alignment requires too much memory - // Max size depends on the font size, the following is a - // guess at a size which works - int maxSize = 2000 / av.getFont().getSize(); - BufferedImage block; - int blockx = 0; - int blocky = 0; - int blockw = 0; - int blockh = 0; - int eRes = 0; - int eSeq = 0; - - av.setRenderGaps(false); - - for (int sRes = 0, chunkx = 0; sRes < alwidth; - sRes += maxSize, chunkx++) - { - if(resizeAgain) - break; - - eSeq = 0; - eRes += maxSize; - - if (eRes > alwidth) - { - eRes = alwidth; - } - - for (int sSeq = 0, chunky = 0; sSeq < alheight; - sSeq += maxSize, chunky++) - { - eSeq += maxSize; - - if (eSeq > alheight) - { - eSeq = alheight; - } - - blocky = 0; - blockx = (int) ((float) sRes / (float) alwidth * width); - - block = new BufferedImage((eRes - sRes) * av.charWidth, - (eSeq - sSeq) * av.charHeight, - BufferedImage.TYPE_3BYTE_BGR); - g = block.getGraphics(); - - ap.seqPanel.seqCanvas.drawPanel(g, sRes, eRes, sSeq, eSeq, - sRes, sSeq, 0); - - blockh = (int) ((float) (eSeq - sSeq) / (float) alheight * sequencesHeight) + - 1; - blockw = (int) ((float) (eRes - sRes) / (float) alwidth * width) + - 1; - - blocky += (int) ((float) sSeq / (float) alheight * sequencesHeight); - - mg.drawImage(block, blockx, blocky, blockx + blockw, - blocky + blockh, 0, 0, block.getWidth(), - block.getHeight(), null); - - block = null; - } - } - } - catch (OutOfMemoryError error) - { - System.err.println( - "Out of memory when trying to calculate the overview window image!"); - } - - System.gc(); - - av.setRenderGaps(oldRenderGaps); - resizing = false; - - setBoxPosition(); - - if(resizeAgain) - { - resizeAgain = false; - updateOverviewImage(); - } - } - - /** - * DOCUMENT ME! - */ - public void setBoxPosition() - { - boxX = (int) (av.getStartRes() * av.getCharWidth() * scalew); - boxY = (int) (av.getStartSeq() * av.getCharHeight() * scaleh); - boxWidth = (int) ((av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth() * scalew); - boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - - boxY; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void paintComponent(Graphics g) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - g.setColor(Color.black); - - if (resizing) - { - g.setFont(new Font("Verdana", Font.BOLD, 15)); - g.drawString("Recalculating", 5, sequencesHeight / 2); - g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20); - } - 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); - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.renderer.AnnotationRenderer; + +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; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class OverviewPanel extends JPanel implements Runnable +{ + BufferedImage miniMe; + + AlignViewport av; + + AlignmentPanel ap; + + final AnnotationRenderer renderer = new AnnotationRenderer(); + + 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; + + jalview.renderer.seqfeatures.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.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; + } + } + + addComponentListener(new ComponentAdapter() + { + @Override + public void componentResized(ComponentEvent evt) + { + if ((getWidth() != width) + || (getHeight() != (sequencesHeight + graphHeight))) + { + updateOverviewImage(); + } + } + }); + + addMouseMotionListener(new MouseMotionAdapter() + { + @Override + public void mouseDragged(MouseEvent evt) + { + if (!av.getWrapAlignment()) + { + // TODO: feature: jv2.5 detect shift drag and update selection from + // it. + boxX = evt.getX(); + boxY = evt.getY(); + checkValid(); + } + } + }); + + addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent evt) + { + if (!av.getWrapAlignment()) + { + 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.getAlignment().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! + */ + @Override + public void run() + { + miniMe = null; + + if (av.isShowSequenceFeatures()) + { + fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + } + + int alwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight() + + av.getAlignment().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; + final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av + .hasHiddenColumns(); + 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 (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 ((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.isShowSequenceFeatures()) + { + color = fr.findFeatureColour(color, seq, lastcol); + } + } + else + { + color = -1; // White + } + + if (hiddenRow + || (hasHiddenCols && !av.getColumnSelection().isVisible( + lastcol))) + { + color = new Color(color).darker().darker().getRGB(); + } + + miniMe.setRGB(col, row, color); + + } + } + + if (av.getAlignmentConservationAnnotation() != null) + { + renderer.updateFromAlignViewport(av); + for (col = 0; col < width; col++) + { + lastcol = (int) (col * sampleCol); + { + mg.translate(col, sequencesHeight); + renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(), + av.getAlignmentConservationAnnotation().annotations, + (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.getAlignment().getWidth() * av.getCharWidth(); + int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment() + .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.getAlignment().getHiddenSequences() + .adjustForHiddenSeqs(startSeq); + + endSeq = av.getAlignment().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! + */ + @Override + 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); + + } +}