X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=2c779427635f7dcb63595b9cdf97cfeddba36e88;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=aa3c9aef445b29154b1d29f5e4080ddb0c1cf6af;hpb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index aa3c9ae..2c77942 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,442 +1,365 @@ -/* - * 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(av); - - // 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 (miniMe != null && !resizing) - { - 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 ($$Version-Rel$$) + * 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 . + * 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 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.getPosProps(), 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.getPosProps()); + 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.getPosProps()); + 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()); + + // 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); + + 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 + // 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() && !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.getPosProps()); + 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); + } +}