From: amwaterhouse Date: Mon, 25 Apr 2005 08:50:50 +0000 (+0000) Subject: Overviewpanel allows for large alignments X-Git-Tag: Release_2_0~374 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fdaf66178c7596335c3675ec3db0da8503dc61b2;p=jalview.git Overviewpanel allows for large alignments --- diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f165bd3..b217e9c 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -579,8 +579,10 @@ public class AlignFrame extends GAlignFrame JInternalFrame frame = new JInternalFrame(); FontChooser fc = new FontChooser( alignPanel, frame ); frame.setContentPane(fc); - Desktop.addInternalFrame(frame, "Change Font", 480,100); + Desktop.addInternalFrame(frame, "Change Font", 480,100, false); frame.setLayer(JLayeredPane.PALETTE_LAYER); + if(alignPanel.getOverviewPanel()!=null) + alignPanel.getOverviewPanel().updateOverviewImage(); } protected void fullSeqId_actionPerformed(ActionEvent e) @@ -674,27 +676,20 @@ public class AlignFrame extends GAlignFrame return; JInternalFrame frame = new JInternalFrame(); - OverviewPanel overview = alignPanel.getOverviewPanel(); - try{ - overview = new OverviewPanel(alignPanel, viewport); + OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); Desktop.addInternalFrame(frame, "Overview " + this.getTitle(), frame.getWidth(), frame.getHeight()); frame.pack(); + frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt) { alignPanel.setOverviewPanel(null); }; }); - alignPanel.setOverviewPanel( overview ); - }catch(java.lang.OutOfMemoryError ex) - { - JOptionPane.showInternalMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!" - +"\nTry reducing the font size.", - "Out of memory", JOptionPane.WARNING_MESSAGE); - } + alignPanel.setOverviewPanel( overview ); } @@ -870,8 +865,8 @@ public class AlignFrame extends GAlignFrame } } - - + if(alignPanel.getOverviewPanel()!=null) + alignPanel.getOverviewPanel().updateOverviewImage(); alignPanel.repaint(); } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 45edace..3257ce5 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -5,7 +5,7 @@ import java.awt.event.*; import java.awt.image.*; import java.awt.*; -public class OverviewPanel extends JPanel +public class OverviewPanel extends JPanel implements Runnable { BufferedImage miniMe; AlignViewport av; @@ -13,49 +13,47 @@ public class OverviewPanel extends JPanel float scalew = 1f; float scaleh = 1f; - int sequencesWidth, sequencesHeight; + int width, sequencesHeight; int graphHeight=30; int boxX=-1, boxY=-1, boxWidth=-1, boxHeight=-1; - public OverviewPanel(AlignmentPanel ap, AlignViewport av) + boolean resizing = false; + + public OverviewPanel(AlignmentPanel ap) { - this.av = av; + this.av = ap.av; this.ap = ap; + setLayout(null); // scale the initial size of overviewpanel to shape of alignment - - float initialScale = (float)av.getAlignment().getWidth()/(float)av.getAlignment().getHeight(); - if(av.getAlignment().getWidth() > av.getAlignment().getHeight()) + float initialScale = (float)av.alignment.getWidth()/(float)av.alignment.getHeight(); + if(av.alignment.getWidth() > av.alignment.getHeight()) { // wider - sequencesWidth = 400; + width = 400; sequencesHeight = (int)(400f/initialScale); } else { // taller - sequencesWidth = (int)(400f*initialScale); + width = (int)(400f*initialScale); sequencesHeight = 300; + if(width<120) + width = 120; } - - - setSize(sequencesWidth, sequencesHeight+graphHeight); - setLayout(null); - - updateOverviewImage(); - addComponentListener(new ComponentAdapter() { public void componentResized(ComponentEvent evt) { - if( getWidth()!=sequencesWidth || getHeight()!=sequencesHeight+graphHeight) + if( getWidth()!=width || getHeight()!=sequencesHeight+graphHeight) + { updateOverviewImage(); + } } }); - addMouseMotionListener(new MouseMotionAdapter() { public void mouseDragged(MouseEvent evt) @@ -70,112 +68,169 @@ public class OverviewPanel extends JPanel { doMouseReleased(evt);} }); + updateOverviewImage(); + } public void doMousePressed(MouseEvent evt) { - checkValid(evt.getX(), evt.getY()); + boxX = evt.getX(); + boxY = evt.getY(); + + checkValid(); repaint(); } public void doMouseReleased(MouseEvent evt) { - int x = evt.getX(); - int y = evt.getY(); - checkValid(x, y); - ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) ); + 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) { - int x = evt.getX(); - int y = evt.getY(); - checkValid(x, y); - ap.setScrollValues( (int)(x/scalew/av.getCharWidth()), (int)(y/scaleh/av.getCharHeight()) ); - repaint(); + boxX = evt.getX(); + boxY = evt.getY(); + checkValid(); + if(!resizing) + ap.setScrollValues( (int)(boxX/scalew/av.getCharWidth()), + (int)(boxY/scaleh/av.getCharHeight()) ); } - void checkValid(int x, int y) + void checkValid() { + if (boxY < 0) + boxY = 0; - if (y < 0) - y = 0; - if (y > sequencesHeight - boxHeight) - y = sequencesHeight- boxHeight; + if (boxY > sequencesHeight - boxHeight) + boxY = sequencesHeight - boxHeight+1; + if (boxX < 0) + boxX = 0; - if (x < 0) - x = 0; + if (boxX > width - boxWidth) + boxX = width - boxWidth; + } - if (x > sequencesWidth - boxWidth) - x = sequencesWidth - boxWidth; + public void updateOverviewImage() + { + if(resizing) + { + return; + } - boxX = x; - boxY = y; + resizing = true; + Thread thread = new Thread(this); + thread.start(); + repaint(); } - public void updateOverviewImage() + public void run() { + miniMe = null; + int alwidth = av.alignment.getWidth(); + int alheight = av.alignment.getHeight(); - boolean oldRenderGaps = av.renderGaps; - av.setRenderGaps(false); - miniMe = null; - setPreferredSize (new Dimension(sequencesWidth, sequencesHeight+graphHeight)); - sequencesWidth=getWidth(); - sequencesHeight=this.getHeight()-graphHeight; + if(getWidth()>0 && getHeight()>0) + { + width = getWidth(); + sequencesHeight = getHeight() - graphHeight; + } + setPreferredSize (new Dimension(width, sequencesHeight+graphHeight)); - int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth(); - int fullsizeHeight = av.getAlignment().getHeight()* av.getCharHeight(); + int fullsizeWidth = alwidth * av.getCharWidth(); + int fullsizeHeight = alheight * av.getCharHeight(); + scalew = (float) width / (float) fullsizeWidth; + scaleh = (float) sequencesHeight / (float) fullsizeHeight; - BufferedImage fullSize = new BufferedImage(fullsizeWidth, - fullsizeHeight, - BufferedImage.TYPE_INT_RGB); + miniMe = new BufferedImage(width, sequencesHeight + graphHeight, + BufferedImage.TYPE_INT_RGB); + Graphics mg = miniMe.getGraphics(); BufferedImage consensus = new BufferedImage(fullsizeWidth, - 60, - BufferedImage.TYPE_INT_RGB); + 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); - Graphics g = fullSize.getGraphics(); - ap.seqPanel.seqCanvas.drawPanel(g,0,av.getAlignment().getWidth(),0,av.getAlignment().getHeight(),0,0,0); + 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 - g = consensus.getGraphics(); + // 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; - ap.annotationPanel.drawGraph(g, av.conservation, fullsizeWidth, 60); + 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.out.println("out of memory"); } - try{ - miniMe = new BufferedImage(sequencesWidth, sequencesHeight + graphHeight, - BufferedImage.TYPE_INT_RGB); - Graphics mg = miniMe.getGraphics(); - - mg.drawImage(fullSize, 0, 0, sequencesWidth, sequencesHeight, 0, 0, - fullsizeWidth, fullsizeHeight, this); - mg.drawImage(consensus, 0, sequencesHeight, sequencesWidth, - sequencesHeight + graphHeight, 0, 0, fullsizeWidth, 60, this); - - scalew = (float) sequencesWidth / (float) fullsizeWidth; - scaleh = (float) sequencesHeight / (float) fullsizeHeight; - - setBoxPosition(); - }catch(Exception ex) - {// most likely the frame size is zero - miniMe = null; - } 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.getCharWidth() * scalew) - boxX; + boxWidth = (int) ((av.getEndRes()-av.getStartRes()+1)* av.getCharWidth() * scalew) ; boxHeight = (int) (av.getEndSeq() * av.getCharHeight() * scaleh) - boxY; repaint(); - } @@ -183,13 +238,23 @@ public class OverviewPanel extends JPanel { g.setColor(Color.white); g.fillRect(0,0,getWidth(),getHeight()); - if(miniMe!=null) - g.drawImage(miniMe, 0,0,this); + g.setColor(Color.black); - g.setColor(Color.red); + 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.drawRect(boxX, boxY, boxWidth, boxHeight); - g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2); + g.setColor(Color.red); + g.drawRect(boxX, boxY, boxWidth, boxHeight); + g.drawRect(boxX+1, boxY+1, boxWidth-2, boxHeight-2); + } } }