X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=72654893e7efe75edce5d3967a32daa468fff902;hb=8ea2930d1b4a23415ec924674d043999d3d6f2ce;hp=3cd229d884800b37b5cb1f0b8034bd9e67b1dee6;hpb=1c37c329efcec099e7af2eb3db81fc7182e5a51d;p=jalview.git diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index 3cd229d..7265489 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -23,20 +23,26 @@ import java.awt.*; import java.awt.event.*; public class OverviewPanel - extends Panel implements Runnable + extends Panel implements Runnable, MouseMotionListener, MouseListener { Image miniMe; + Image offscreen; AlignViewport av; AlignmentPanel ap; float scalew = 1f; float scaleh = 1f; public int width, sequencesHeight; - int graphHeight = 30; + int graphHeight = 20; int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1; boolean resizing = false; + // Can set different properties in this seqCanvas than + // main visible SeqCanvas + SequenceRenderer sr; + FeatureRenderer fr; + Frame nullFrame; public OverviewPanel(AlignmentPanel ap) @@ -47,14 +53,31 @@ public class OverviewPanel nullFrame = new Frame(); nullFrame.addNotify(); + sr = new SequenceRenderer(av); + sr.graphics = nullFrame.getGraphics(); + sr.renderGaps = false; + sr.forOverview = true; + fr = new FeatureRenderer(av); + fr.overview = true; + // scale the initial size of overviewpanel to shape of alignment float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight(); + + if (av.hconsensus == null) + { + graphHeight = 0; + } + if (av.alignment.getWidth() > av.alignment.getHeight()) { // wider width = 400; sequencesHeight = (int) (400f / initialScale); + if (sequencesHeight < 40) + { + sequencesHeight = 40; + } } else { @@ -81,59 +104,45 @@ public class OverviewPanel } }); - addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseDragged(MouseEvent evt) - { - doMouseDragged(evt); - } - }); + addMouseMotionListener(this); - addMouseListener(new MouseAdapter() - { - public void mousePressed(MouseEvent evt) - { - doMousePressed(evt); - } - - public void mouseReleased(MouseEvent evt) - { - doMouseReleased(evt); - } - }); + addMouseListener(this); updateOverviewImage(); } - public void doMousePressed(MouseEvent evt) + public void mouseEntered(MouseEvent evt) + {} + + public void mouseExited(MouseEvent evt) + {} + + public void mouseClicked(MouseEvent evt) + {} + + public void mouseMoved(MouseEvent evt) + {} + + public void mousePressed(MouseEvent evt) { boxX = evt.getX(); boxY = evt.getY(); - checkValid(); - repaint(); } - public void doMouseReleased(MouseEvent evt) + public void mouseReleased(MouseEvent evt) { boxX = evt.getX(); boxY = evt.getY(); checkValid(); - ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()), - (int) (boxY / scaleh / av.getCharHeight())); } - public void doMouseDragged(MouseEvent evt) + public void mouseDragged(MouseEvent evt) { boxX = evt.getX(); boxY = evt.getY(); checkValid(); - ap.setScrollValues( (int) (boxX / scalew / av.getCharWidth()), - (int) (boxY / scaleh / av.getCharHeight())); - - repaint(); - ap.repaint(); } void checkValid() @@ -143,7 +152,7 @@ public class OverviewPanel boxY = 0; } - if (boxY > sequencesHeight - boxHeight) + if (boxY > (sequencesHeight - boxHeight)) { boxY = sequencesHeight - boxHeight + 1; } @@ -153,10 +162,37 @@ public class OverviewPanel boxX = 0; } - if (boxX > width - boxWidth) + 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); + ap.paintAlignment(false); } /** @@ -166,8 +202,16 @@ public class OverviewPanel { if (resizing) { - resizeAgain = true; - return; + resizeAgain = true; + return; + } + + if (av.showSequenceFeatures) + { + fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer(). + featureGroups; + fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer(). + featureColours; } resizing = true; @@ -178,16 +222,15 @@ public class OverviewPanel sequencesHeight = getSize().height - graphHeight; } setSize(new Dimension(width, sequencesHeight + graphHeight)); - setBoxPosition(); Thread thread = new Thread(this); thread.start(); - repaint(); + repaint(); } // This is set true if the user resizes whilst // the overview is being calculated - boolean resizeAgain = false; + boolean resizeAgain = false; public void run() { @@ -195,6 +238,11 @@ public class OverviewPanel int alwidth = av.alignment.getWidth(); int alheight = av.alignment.getHeight(); + if (av.showSequenceFeatures) + { + fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); + } + if (getSize().width > 0 && getSize().height > 0) { width = getSize().width; @@ -210,90 +258,121 @@ public class OverviewPanel scaleh = (float) sequencesHeight / (float) fullsizeHeight; miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight); + offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight); Graphics mg = miniMe.getGraphics(); - Image consensus = nullFrame.createImage(fullsizeWidth, 60); - 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 + 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; + boolean hiddenRow = false; + for (row = 0; row <= sequencesHeight; row++) { - // We'll have to draw the full size alignment in chunks, as an image of the - // whole alignment requires too much memory + if ( (int) (row * sampleRow) == lastrow) + { + sameRow++; + continue; + } - // Max size depends on the font size, the following is a - // guess at a size which works - int maxSize = 2000 / av.getFont().getSize(); - Image block; - int blockx = 0, blocky = 0, blockw = 0, blockh = 0, eRes = 0, eSeq = 0; + hiddenRow = false; + if (av.hasHiddenRows) + { + seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow); + if (seq == null) + { + int index = + av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs( + lastrow); - av.setRenderGaps(false); - for (int sRes = 0, chunkx = 0; sRes < alwidth; sRes += maxSize, chunkx++) + seq = av.alignment.getSequenceAt(index); + } + else + { + hiddenRow = true; + } + } + else { - eSeq = 0; - eRes += maxSize; - if (eRes > alwidth) + seq = av.alignment.getSequenceAt(lastrow); + } + + for (col = 0; col < width; col++) + { + if ( (int) (col * sampleCol) == lastcol && + (int) (row * sampleRow) == lastrow) { - eRes = alwidth; + sameCol++; + continue; } - for (int sSeq = 0, chunky = 0; sSeq < alheight; sSeq += maxSize, chunky++) + lastcol = (int) (col * sampleCol); + + if (seq.getLength() > lastcol) { - if(resizeAgain) - break; + color = sr.getResidueBoxColour( + seq, lastcol); - eSeq += maxSize; - if (eSeq > alheight) + if (av.showSequenceFeatures) { - eSeq = alheight; + color = fr.findFeatureColour(color, seq, lastcol); } + } + else + { + color = Color.white; //White + } - blocky = 0; - blockx = (int) ( (float) sRes / (float) alwidth * width); - - block = nullFrame.createImage( (eRes - sRes) * av.charWidth, - (eSeq - sSeq) * av.charHeight); - 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(null), block.getHeight(null), this); + if (hiddenRow || + (av.hasHiddenColumns && !av.getColumnSelection().isVisible(lastcol))) + { + color = color.darker().darker(); + } - block = null; + 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; } - catch (OutOfMemoryError error) + + if (av.conservation != null) { - System.err.println( - "Out of memory when trying to calculate the overview window image!"); + 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(); - av.setRenderGaps(oldRenderGaps); resizing = false; setBoxPosition(); - if(resizeAgain) + if (resizeAgain) { resizeAgain = false; updateOverviewImage(); @@ -303,16 +382,49 @@ public class OverviewPanel public void setBoxPosition() { int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth(); - int fullsizeHeight = av.alignment.getHeight() * av.getCharHeight(); + 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) (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; + 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(); } @@ -323,23 +435,15 @@ public class OverviewPanel public void paint(Graphics g) { + Graphics og = offscreen.getGraphics(); if (miniMe != null) { - g.drawImage(miniMe, 0, 0, this); - } - else - { - g.setColor(Color.white); - g.fillRect(0, 0, getSize().width, getSize().height); - g.setColor(Color.black); - g.setFont(new Font("Verdana", Font.BOLD, 15)); - g.drawString("Recalculating", 5, sequencesHeight / 2); - g.drawString("Overview.....", 5, (sequencesHeight / 2) + 20); + og.drawImage(miniMe, 0, 0, this); + og.setColor(Color.red); + og.drawRect(boxX, boxY, boxWidth, boxHeight); + og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2); + g.drawImage(offscreen, 0, 0, this); } - - g.setColor(Color.red); - g.drawRect(boxX, boxY, boxWidth, boxHeight); - g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2); } }