import java.awt.*;\r
import java.awt.event.*;\r
import java.awt.print.*;\r
-\r
-import com.sun.image.codec.jpeg.*;\r
import java.io.*;\r
import java.awt.image.*;\r
+import org.jibble.epsgraphics.*;\r
+import javax.imageio.*;\r
+\r
\r
\r
public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
OverviewPanel overviewPanel;\r
SeqPanel seqPanel;\r
IdPanel idPanel;\r
- SecondaryStructurePanel ssPanel;\r
+ IdwidthAdjuster idwidthAdjuster;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
- ScorePanel scorePanel;\r
+ AnnotationPanel annotationPanel;\r
+ AnnotationLabels alabels;\r
+\r
+ // this value is set false when selection area being dragged\r
+ boolean fastPaint = true;\r
\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
this.av = av;\r
seqPanel = new SeqPanel (av, this);\r
idPanel = new IdPanel (av, this);\r
+\r
scalePanel = new ScalePanel(av, this);\r
- scorePanel = new ScorePanel(av);\r
- ssPanel = new SecondaryStructurePanel(av);\r
\r
- secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idPanel.addNotify();\r
+ idwidthAdjuster = new IdwidthAdjuster(this);\r
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
+\r
+ annotationPanel = new AnnotationPanel(this);\r
+ alabels = new AnnotationLabels(this);\r
+\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationScroller.setViewportView(annotationPanel);\r
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+\r
+ fontChanged();\r
+\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
- setScrollValues(0,0);\r
+\r
+ setScrollValues(0, 0);\r
\r
hscroll.addAdjustmentListener(this);\r
vscroll.addAdjustmentListener(this);\r
\r
- addComponentListener(new ComponentAdapter()\r
- {\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- RefreshPanels();\r
- }\r
- });\r
-\r
-\r
- hscroll.setFocusable(false);\r
- vscroll.setFocusable(false);\r
setFocusable(true);\r
-\r
addKeyListener(new KeyAdapter()\r
{\r
public void keyPressed(KeyEvent evt)\r
switch(evt.getKeyCode())\r
{\r
case 27: // escape key\r
- av.setRubberbandGroup(null);\r
- RefreshPanels();\r
+ av.setSelectionGroup(null);\r
+ repaint();\r
break;\r
case KeyEvent.VK_X:\r
+ if(evt.isControlDown())\r
alignFrame.cut_actionPerformed(null);\r
break;\r
case KeyEvent.VK_C:\r
+ if(evt.isControlDown())\r
alignFrame.copy_actionPerformed(null);\r
break;\r
case KeyEvent.VK_V:\r
+ if(evt.isControlDown())\r
alignFrame.paste(true);\r
break;\r
case KeyEvent.VK_A:\r
+ if(evt.isControlDown())\r
alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
break;\r
case KeyEvent.VK_DOWN:\r
alignFrame.moveSelectedSequences(true);\r
break;\r
case KeyEvent.VK_F:\r
+ if(evt.isControlDown())\r
alignFrame.findMenuItem_actionPerformed(null);\r
break;\r
}\r
});\r
}\r
\r
+ public void fontChanged()\r
+ {\r
+ // set idCanvas bufferedImage to null\r
+ // to prevent drawing old image\r
+ idPanel.idCanvas.gg = null;\r
+ annotationPanel.adjustPanelHeight();\r
+ Dimension d = calculateIdWidth();\r
+ d.setSize(d.width + 4, d.height);\r
+ idPanel.idCanvas.setPreferredSize(d);\r
+ hscrollFillerPanel.setPreferredSize(d);\r
+ repaint();\r
+ }\r
+\r
+\r
+ Dimension calculateIdWidth()\r
+ {\r
+ Graphics g = this.getGraphics();\r
+ if(g==null)\r
+ {\r
+ javax.swing.JFrame f = new javax.swing.JFrame();\r
+ f.addNotify();\r
+ g = f.getGraphics();\r
+ }\r
+\r
+ FontMetrics fm = g.getFontMetrics(av.font);\r
+ AlignmentI al = av.getAlignment();\r
+\r
+ int i = 0;\r
+ int idWidth = 0;\r
+ String id;\r
+ while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
+ {\r
+ SequenceI s = al.getSequenceAt(i);\r
+ if(av.getShowFullId())\r
+ id = s.getDisplayId();\r
+ else\r
+ id = s.getName();\r
+\r
+ if (fm.stringWidth(id) > idWidth)\r
+ idWidth = fm.stringWidth(id);\r
+ i++;\r
+ }\r
+\r
+ // Also check annotation label widths\r
+ i=0;\r
+ if(al.getAlignmentAnnotation()!=null)\r
+ {\r
+ fm = g.getFontMetrics(alabels.getFont());\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
+ if (fm.stringWidth(label) > idWidth)\r
+ idWidth = fm.stringWidth(label);\r
+ i++;\r
+ }\r
+ }\r
+\r
+ return new Dimension(idWidth, 12);\r
+ }\r
+\r
\r
public void highlightSearchResults(int [] results)\r
{\r
}\r
\r
\r
- public void setGraphPanelVisible(boolean b)\r
+ public void setAnnotationVisible(boolean b)\r
{\r
- idSpaceFillerPanel.setVisible(b);\r
- scorePanelHolder.setVisible(b);\r
-\r
- RefreshPanels();\r
- // bit annoying to call this twice, can you do better?\r
- RefreshPanels();\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationScroller.setVisible(b);\r
}\r
\r
- public void setSecondaryStructureVisible(boolean b)\r
- {\r
- secondaryPanelHolder.setVisible(b);\r
- RefreshPanels();\r
- }\r
\r
public void setWrapAlignment(boolean wrap)\r
{\r
- scorePanelHolder.setVisible(!wrap);\r
scalePanelHolder.setVisible(!wrap);\r
- secondaryPanelHolder.setVisible(!wrap);\r
-\r
hscroll.setVisible(!wrap);\r
+ idwidthAdjuster.setVisible(!wrap);\r
\r
- idSpaceFillerPanel.setVisible(!wrap);\r
+ av.setShowAnnotation(!wrap);\r
+ annotationScroller.setVisible(!wrap);\r
+ annotationSpaceFillerHolder.setVisible(!wrap);\r
idSpaceFillerPanel1.setVisible(!wrap);\r
\r
- RefreshPanels();\r
+ repaint();\r
\r
}\r
\r
al.getWidth() );\r
\r
c.calculate();\r
- c.verdict(false, 100);\r
+ c.verdict(false, av.ConsPercGaps);\r
ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
\r
av.setGlobalColourScheme( ccs );\r
\r
}\r
\r
- RefreshPanels();\r
+ repaint();\r
}\r
\r
- public void RefreshPanels()\r
- {\r
- requestFocus();\r
- invalidate();\r
- idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
\r
- if(av.getWrapAlignment())\r
- {\r
- int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;\r
+ int hextent = 0;\r
+ int vextent = 0;\r
\r
- int h = (av.alignment.getHeight() + 2)*av.charHeight;\r
- vextent = seqPanel.seqCanvas.getHeight()/h;\r
- vscroll.setValues(0,vextent,0,max);\r
+ // return value is true if the scroll is valid\r
+ public boolean scrollUp(boolean up)\r
+ {\r
+ if(up)\r
+ {\r
+ if(vscroll.getValue()<1)\r
+ return false;\r
+ fastPaint = false;\r
+ vscroll.setValue(vscroll.getValue() - 1);\r
}\r
else\r
+ {\r
+ if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())\r
+ return false;\r
+ fastPaint = false;\r
+ vscroll.setValue(vscroll.getValue() + 1);\r
+ }\r
+ fastPaint = true;\r
+ return true;\r
+ }\r
\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- av.getConsensus(true);\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
-\r
- validate();\r
- repaint();\r
+ public boolean scrollRight(boolean right)\r
+ {\r
\r
+ if (right)\r
+ {\r
+ if (hscroll.getValue() < 1)\r
+ return false;\r
+ fastPaint = false;\r
+ hscroll.setValue(hscroll.getValue() - 1);\r
+ }\r
+ else\r
+ {\r
+ if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
+ return false;\r
+ fastPaint = false;\r
+ hscroll.setValue(hscroll.getValue() + 1);\r
+ }\r
+ fastPaint = true;\r
+ return true;\r
}\r
\r
- int hextent = 0;\r
- int vextent = 0;\r
\r
public void setScrollValues(int x, int y)\r
{\r
- hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();\r
- vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\r
+ av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);\r
+\r
+ hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;\r
+\r
+ if(hextent > av.alignment.getWidth())\r
+ hextent = av.alignment.getWidth();\r
+ if(vextent > av.alignment.getHeight())\r
+ vextent = av.alignment.getHeight();\r
\r
if(hextent+x > av.getAlignment().getWidth())\r
x = av.getAlignment().getWidth()- hextent;\r
vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
\r
\r
- repaint();\r
\r
}\r
\r
\r
public void adjustmentValueChanged(AdjustmentEvent evt)\r
{\r
+ int oldX = av.getStartRes();\r
+ int oldY = av.getStartSeq();\r
\r
if (evt.getSource() == hscroll)\r
{\r
int offy = vscroll.getValue();\r
if (av.getWrapAlignment())\r
{\r
- av.setStartRes( vscroll.getValue() * av.getChunkWidth());\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ av.setStartRes( vscroll.getValue() * rowSize );\r
+ av.setEndRes( (vscroll.getValue()+1) * rowSize );\r
}\r
else\r
{\r
}\r
}\r
\r
-\r
if(overviewPanel!=null)\r
overviewPanel.setBoxPosition();\r
\r
- repaint();\r
+ if(av.getWrapAlignment() || !fastPaint)\r
+ repaint();\r
+ else\r
+ {\r
+ idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
+ seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,\r
+ av.getStartSeq() - oldY);\r
+\r
+ scalePanel.repaint();\r
+ if (av.getShowAnnotation())\r
+ annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ }\r
+\r
+ }\r
+\r
+\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ invalidate();\r
+ Dimension d = idPanel.idCanvas.getPreferredSize();\r
+ idPanelHolder.setPreferredSize(d);\r
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
+ validate();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ vscroll.setMaximum(max);\r
+ vscroll.setUnitIncrement(1);\r
+ vscroll.setVisibleAmount(1);\r
+ }\r
+ else\r
+ {\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
+\r
+\r
+\r
}\r
\r
public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
{\r
\r
- int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
+ int idWidth = calculateIdWidth().width + 4;\r
\r
\r
pg.setColor(Color.white);\r
////////////////\r
//draw Scale\r
pg.translate(idWidth,0);\r
- scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
\r
pg.translate(-idWidth, 30);\r
////////////////\r
Color currentTextColor=null;\r
for(int i=startSeq; i<endSeq; i++)\r
{\r
- if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
+ if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))\r
{\r
currentColor = Color.gray;\r
currentTextColor = Color.black;\r
\r
pg.setColor(currentTextColor);\r
\r
- String string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
+ String string = av.getAlignment().getSequenceAt(i).getName();\r
+ if(av.getShowFullId())\r
+ string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
+\r
pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
(startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));\r
}\r
\r
// draw main sequence panel\r
pg.translate(idWidth,0);\r
- pg.setClip(0,0,pwidth-idWidth, pheight);\r
seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\r
\r
+\r
+ if(av.getShowAnnotation())\r
+ {\r
+ pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);\r
+ alabels.drawComponent((Graphics2D)pg);\r
+ pg.translate(idWidth,0);\r
+ annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);\r
+ }\r
+\r
return Printable.PAGE_EXISTS;\r
}\r
\r
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException\r
{\r
\r
- int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
+ int idWidth = calculateIdWidth().width+4;\r
\r
if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)\r
pwidth = seqPanel.seqCanvas.getWidth() + idWidth;\r
\r
////////////////\r
// Draw the ids\r
- pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);\r
+// pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);\r
\r
- int row = pi*noChunksOnPage;\r
pg.setColor(Color.black);\r
- for(int ypos=2*av.charHeight;\r
- ypos <= pheight && row*chunkWidth<da.getWidth();\r
- ypos += chunkHeight, row++ )\r
+\r
+ int rowSize = av.getEndRes() - av.getStartRes();\r
+ for(int ypos=2*av.charHeight, row=av.getEndRes()-rowSize;\r
+ ypos <= pheight && row<av.alignment.getWidth();\r
+ ypos += av.chunkHeight, row+=rowSize )\r
{\r
for (int i = 0; i < endy; i++)\r
{\r
SequenceI s = da.getSequenceAt(i);\r
- pg.drawString(s.getDisplayId(), 0,\r
+ String string = s.getName();\r
+ if (av.getShowFullId())\r
+ string = s.getDisplayId();\r
+\r
+ pg.drawString(string, 0,\r
AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +\r
av.charHeight - (av.charHeight / 5));\r
}\r
\r
}\r
\r
- public void makeJPG(int width, int height)\r
+\r
+ public void makeEPS()\r
{\r
+ int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
+ int width = seqPanel.getWidth() + idPanel.getWidth();\r
+\r
+ if (!av.getWrapAlignment())\r
+ {\r
+ height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
+ width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
+ }\r
+ if(av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
+ }\r
+\r
try\r
{\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create EPS file from alignment");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ return;\r
\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics pg = bi.getGraphics();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
+ EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);\r
\r
- try\r
- {\r
if (av.getWrapAlignment())\r
printWrappedAlignment(pg, width, height, 0);\r
else\r
printUnwrapped(pg, width, height, 0);\r
+\r
+\r
+ pg.flush();\r
+ pg.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ public void makePNG()\r
+ {\r
+ int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;\r
+ int width = seqPanel.getWidth() + idPanel.getWidth();\r
+\r
+ if (!av.getWrapAlignment())\r
+ {\r
+ height = (av.alignment.getHeight()+1) * av.charHeight + 30;\r
+ width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;\r
}\r
- catch (Exception ex)\r
- {}\r
\r
- javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"));\r
- chooser.setDialogTitle("Create JPG image from alignment");\r
+ if(av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
+ }\r
+\r
+\r
+\r
+ try\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create EPS file from alignment");\r
chooser.setToolTipText("Save");\r
\r
int value = chooser.showSaveDialog(this);\r
- if (value == javax.swing.JFileChooser.APPROVE_OPTION)\r
- {\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ return;\r
\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);\r
- JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);\r
- param.setQuality(1.0f, true);\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());\r
+ FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
\r
- jie.encode(bi, param);\r
- out.close();\r
- }\r
+ BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);\r
+ Graphics2D png = (Graphics2D)bi.getGraphics();\r
+\r
+ png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+ if (av.getWrapAlignment())\r
+ printWrappedAlignment(png, width, height, 0);\r
+ else\r
+ printUnwrapped(png, width, height, 0);\r
\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
}\r
- catch (IOException ex)\r
+ catch (Exception ex)\r
{\r
- System.out.println("ex Writing image ");\r
+ ex.printStackTrace();\r
}\r
}\r
\r
\r
\r
\r
+\r
git://source.jalview.org / jalview.git / blobdiff