X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=d87285c63079761b69151e3125d5724bbbf8f9fc;hb=fce4313f5daea7f5b5914bfaefd11e946664942c;hp=a0d8151172bb2848e3eef2c67e6ed5073f16972c;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index a0d8151..d87285c 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -1,260 +1,385 @@ -package jalview.gui; - -import javax.swing.*; -import java.awt.event.*; -import java.awt.image.*; -import java.awt.*; - -public class OverviewPanel extends JPanel implements Runnable -{ - BufferedImage miniMe; - AlignViewport av; - AlignmentPanel ap; - float scalew = 1f; - float scaleh = 1f; - - int width, sequencesHeight; - int graphHeight=30; - int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1; - - boolean resizing = false; - - 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(); - - } - - public void doMousePressed(MouseEvent evt) - { - boxX = evt.getX(); - boxY = evt.getY(); - - checkValid(); - repaint(); - } - - 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()) ); - } - - 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()) ); - } - - 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; - } - - public void updateOverviewImage() - { - if(resizing) - { - return; - } - - resizing = true; - Thread thread = new Thread(this); - thread.start(); - repaint(); - } - - 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, blocky=0, blockw=0, blockh=0, eRes=0, eSeq=0; - - av.setRenderGaps(false); - for(int sRes=0, chunkx=0; sResalwidth) - eRes = alwidth; - - for(int sSeq=0, chunky=0; sSeqalheight) - 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(), this); - - block = null; - } - - } - - }catch(OutOfMemoryError error) - { System.err.println("Out of memory when trying to calculate the overview window image!"); } - - - av.setRenderGaps(oldRenderGaps); - resizing = false; - - setBoxPosition(); - } - - 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(); - } - - - 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 ($$Version-Rel$$) + * 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.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); + + 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()) + { + // TODO: feature: jv2.5 detect shift drag and update selection from + // it. + od.setBoxPositionByMouse(evt.getX(), evt.getY()); + ap.setScrollValues(od.getScrollCol(), od.getScrollRow()); + } + } + }); + + addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent evt) + { + if (!av.getWrapAlignment()) + { + od.setBoxPositionByMouse(evt.getX(), evt.getY()); + 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()); // width = getWidth(); + od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight; + } + + 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 scale based on current alignment width and height + od.updateScales(); + + // 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().getHeight() + + av.getAlignment().getHiddenSequences().getSize(); + + // 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.getAlignmentConservationAnnotation() != null) + { + 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(); + } + + private void buildImage(float sampleRow, float sampleCol) + { + int lastcol = -1; + int lastrow = -1; + int color = Color.white.getRGB(); + + jalview.datamodel.SequenceI seq = null; + final boolean hasHiddenRows = av.hasHiddenRows(); + 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; + + hiddenRow = false; + // should be method(s) in Alignment + 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); + } + // end of Alignment method(s) + } + + if (seq == null) + { + System.out.println(lastrow + " null"); + continue; + } + + 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 if ((int) (col * sampleCol) == lastcol && (int) (row * + // sampleRow) == lastrow)) + // 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.getLength() > lastcol) + { + color = sr.getResidueBoxColour(seq, lastcol).getRGB(); + + if (av.isShowSequenceFeatures()) + { + color = fr.findFeatureColour(color, seq, lastcol); + } + } + else + { + color = Color.white.getRGB(); // White + } + + 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(); + 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()); + } + } + // TODO: render selected regions + g.setColor(Color.red); + od.drawBox(g); + } +}