+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.GAlignmentPanel;\r
+import jalview.analysis.*;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import jalview.jbgui.*;\r
+\r
+import jalview.schemes.*;\r
+\r
+import org.jibble.epsgraphics.*;\r
+\r
import java.awt.*;\r
-import java.awt.image.*;\r
import java.awt.event.*;\r
+import java.awt.image.*;\r
import java.awt.print.*;\r
+\r
+import java.io.*;\r
+\r
+import javax.imageio.*;\r
+\r
import javax.swing.*;\r
\r
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class AlignmentPanel extends GAlignmentPanel\r
+ implements AdjustmentListener, Printable\r
{\r
+ AlignViewport av;\r
+ OverviewPanel overviewPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
+ IdwidthAdjuster idwidthAdjuster;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public AlignFrame alignFrame;\r
+ ScalePanel scalePanel;\r
+ AnnotationPanel annotationPanel;\r
+ AnnotationLabels alabels;\r
+\r
+ // this value is set false when selection area being dragged\r
+ boolean fastPaint = true;\r
+ int hextent = 0;\r
+ int vextent = 0;\r
+\r
+ /**\r
+ * Creates a new AlignmentPanel object.\r
+ *\r
+ * @param af DOCUMENT ME!\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
+ {\r
+ alignFrame = af;\r
+ this.av = av;\r
+ seqPanel = new SeqPanel(av, this);\r
+ idPanel = new IdPanel(av, this);\r
+\r
+ scalePanel = new ScalePanel(av, this);\r
+\r
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);\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
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+\r
+ setScrollValues(0, 0);\r
+\r
+ hscroll.addAdjustmentListener(this);\r
+ vscroll.addAdjustmentListener(this);\r
+\r
+ setFocusable(true);\r
+ addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ av.setSelectionGroup(null);\r
+ repaint();\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_DOWN:\r
+ alignFrame.moveSelectedSequences(false);\r
+\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ alignFrame.moveSelectedSequences(true);\r
+\r
+ break;\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void fontChanged()\r
+ {\r
+ // set idCanvas bufferedImage to null\r
+ // to prevent drawing old image\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ scalePanelHolder.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
+\r
+ idPanel.idCanvas.gg = null;\r
+ annotationPanel.adjustPanelHeight();\r
+\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Dimension calculateIdWidth()\r
+ {\r
+ Graphics g = this.getGraphics();\r
+\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
+\r
+ while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
+ {\r
+ SequenceI s = al.getSequenceAt(i);\r
+\r
+ if (av.getShowFullId())\r
+ {\r
+ id = s.getDisplayId();\r
+ }\r
+ else\r
+ {\r
+ id = s.getName();\r
+ }\r
+\r
+ if (fm.stringWidth(id) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(id);\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ // Also check annotation label widths\r
+ i = 0;\r
+\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ fm = g.getFontMetrics(alabels.getFont());\r
+\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
+\r
+ if (fm.stringWidth(label) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(label);\r
+ }\r
+\r
+ i++;\r
+ }\r
+ }\r
+\r
+ return new Dimension(idWidth, 12);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(int[] results)\r
+ {\r
+ seqPanel.seqCanvas.highlightSearchResults(results);\r
+\r
+ // do we need to scroll the panel?\r
+ if (results != null)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+ int start = seq.findIndex(results[1]) - 1;\r
+ int end = seq.findIndex(results[2]) - 1;\r
+\r
+ if ((av.getStartRes() > start) || (av.getEndRes() < end) ||\r
+ ((av.getStartSeq() > results[0]) ||\r
+ (av.getEndSeq() < results[0])))\r
+ {\r
+ setScrollValues(start, results[0]);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+ return overviewPanel;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param op DOCUMENT ME!\r
+ */\r
+ public void setOverviewPanel(OverviewPanel op)\r
+ {\r
+ overviewPanel = op;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setAnnotationVisible(boolean b)\r
+ {\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationScroller.setVisible(b);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param wrap DOCUMENT ME!\r
+ */\r
+ public void setWrapAlignment(boolean wrap)\r
+ {\r
+ scalePanelHolder.setVisible(!wrap);\r
+ hscroll.setVisible(!wrap);\r
+ idwidthAdjuster.setVisible(!wrap);\r
+\r
+ av.setShowAnnotation(!wrap);\r
+ annotationScroller.setVisible(!wrap);\r
+ annotationSpaceFillerHolder.setVisible(!wrap);\r
+ idSpaceFillerPanel1.setVisible(!wrap);\r
+\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void setColourScheme()\r
+ {\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+\r
+ if (av.getConservationSelected())\r
+ {\r
+ Alignment al = (Alignment) av.getAlignment();\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth());\r
+\r
+ c.calculate();\r
+ c.verdict(false, av.ConsPercGaps);\r
+\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, cs);\r
+\r
+ av.setGlobalColourScheme(ccs);\r
+ }\r
+\r
+ repaint();\r
+ }\r
+\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
+ {\r
+ return false;\r
+ }\r
+\r
+ fastPaint = false;\r
+ vscroll.setValue(vscroll.getValue() - 1);\r
+ }\r
+ else\r
+ {\r
+ if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())\r
+ {\r
+ return false;\r
+ }\r
+\r
+ fastPaint = false;\r
+ vscroll.setValue(vscroll.getValue() + 1);\r
+ }\r
+\r
+ fastPaint = true;\r
+\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param right DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean scrollRight(boolean right)\r
+ {\r
+ if (right)\r
+ {\r
+ if (hscroll.getValue() < 1)\r
+ {\r
+ return false;\r
+ }\r
+\r
+ fastPaint = false;\r
+ hscroll.setValue(hscroll.getValue() - 1);\r
+ }\r
+ else\r
+ {\r
+ if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
+ {\r
+ return false;\r
+ }\r
+\r
+ fastPaint = false;\r
+ hscroll.setValue(hscroll.getValue() + 1);\r
+ }\r
+\r
+ fastPaint = true;\r
\r
- AlignViewport av;\r
- OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
- public AlignFrame alignFrame;\r
- ScalePanel scalePanel;\r
- ScorePanel scorePanel;\r
-\r
- public AlignmentPanel(AlignFrame af, AlignViewport av)\r
- {\r
- alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel (av, this);\r
- idPanel = new IdPanel (av, this);\r
- scalePanel = new ScalePanel(av);\r
- scorePanel = new ScorePanel(av);\r
-\r
- idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idPanel.addNotify();\r
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\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
- public void highlightSearchResults(int [] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults( results );\r
+ return true;\r
+ }\r
\r
- // do we need to scroll the panel?\r
- if(results!=null && (av.getStartSeq()>results[0]\r
- || av.getEndSeq()<results[0]\r
- || av.getStartRes()>results[1]\r
- || av.getEndRes()<results[2]))\r
- setScrollValues(results[1], results[0]);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param x DOCUMENT ME!\r
+ * @param y DOCUMENT ME!\r
+ */\r
+ public void setScrollValues(int x, int y)\r
+ {\r
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
+ 1);\r
\r
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
\r
- }\r
+ if (hextent > av.alignment.getWidth())\r
+ {\r
+ hextent = av.alignment.getWidth();\r
+ }\r
\r
+ if (vextent > av.alignment.getHeight())\r
+ {\r
+ vextent = av.alignment.getHeight();\r
+ }\r
\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ if ((hextent + x) > av.getAlignment().getWidth())\r
+ {\r
+ x = av.getAlignment().getWidth() - hextent;\r
+ }\r
\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
+ if ((vextent + y) > av.getAlignment().getHeight())\r
+ {\r
+ y = av.getAlignment().getHeight() - vextent;\r
+ }\r
\r
+ if (y < 0)\r
+ {\r
+ y = 0;\r
+ }\r
\r
- public void setGraphPanelVisible(boolean b)\r
- {\r
- scorePanelHolder.setVisible(b);\r
- idSpaceFillerPanel.setVisible(b);\r
- RefreshPanels();\r
- }\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
- public void setWrapAlignment(boolean wrap)\r
- {\r
- scalePanelHolder.setVisible(!wrap);\r
- scorePanelHolder.setVisible(!wrap);\r
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+ }\r
\r
- hscroll.setVisible(!wrap);\r
- idSpaceFillerPanel.setVisible(!wrap);\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
- }\r
+ public void this_mouseWheelMoved(MouseWheelEvent e)\r
+ {\r
+ if(e.getWheelRotation()>0)\r
+ scrollUp(false);\r
+ else\r
+ scrollUp(true);\r
+ }\r
\r
\r
- public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)\r
- {\r
- seqPanel.setColourScheme(cs, conservation);\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\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 x = hscroll.getValue();\r
+ av.setStartRes(x);\r
+ av.setEndRes((x +\r
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
+ }\r
\r
- public void RefreshPanels()\r
- {\r
- invalidate();\r
- seqPanel.seqCanvas.paintFlag = true;\r
- idPanel.idCanvas.paintFlag = true;\r
- idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- av.getConsensus(true);\r
- repaint();\r
- validate();\r
- if(overviewPanel!=null)\r
- overviewPanel.updateOverviewImage();\r
+ if (evt.getSource() == vscroll)\r
+ {\r
+ int offy = vscroll.getValue();\r
\r
- }\r
+ if (av.getWrapAlignment())\r
+ {\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
+ av.setStartSeq(offy);\r
+ av.setEndSeq(offy +\r
+ (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));\r
+ }\r
+ }\r
\r
- int hextent = 0;\r
- int vextent = 0;\r
+ if (overviewPanel != null)\r
+ {\r
+ overviewPanel.setBoxPosition();\r
+ }\r
\r
- public void setScrollValues(int x, int y)\r
- {\r
- hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());\r
- vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();\r
+ if (av.getWrapAlignment() || !fastPaint)\r
+ {\r
+ repaint();\r
+ }\r
+ else\r
+ {\r
+ idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);\r
+ seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,\r
+ av.getStartSeq() - oldY);\r
\r
- if(hextent+x > av.getAlignment().getWidth())\r
- x = av.getAlignment().getWidth()- hextent;\r
+ scalePanel.repaint();\r
\r
- if(vextent+y > av.getAlignment().getHeight())\r
- y = av.getAlignment().getHeight() - vextent;\r
+ if (av.getShowAnnotation())\r
+ {\r
+ annotationPanel.fastPaint(av.getStartRes() - oldX);\r
+ }\r
+ }\r
+ }\r
\r
- if(y<0)\r
- y = 0;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ invalidate();\r
\r
- if(x<0)\r
- x=0;\r
+ Dimension d = idPanel.idCanvas.getPreferredSize();\r
+ idPanelHolder.setPreferredSize(d);\r
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
+ validate();\r
\r
- hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
- vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
- repaint();\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
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
+ }\r
\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pf DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
+ {\r
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());\r
\r
+ int pwidth = (int) pf.getImageableWidth();\r
+ int pheight = (int) pf.getImageableHeight();\r
\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return printWrappedAlignment(pg, pwidth, pheight, pi);\r
+ }\r
+ else\r
+ {\r
+ return printUnwrapped(pg, pwidth, pheight, pi);\r
+ }\r
+ }\r
\r
- if (evt.getSource() == hscroll)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
+ throws PrinterException\r
{\r
- int x = hscroll.getValue();\r
- av.setStartRes(x);\r
- av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
+\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
+\r
+ int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -\r
+ 1;\r
+\r
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startRes;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endRes;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startSeq;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endSeq;\r
+ startRes = (pi % pagesWide) * totalRes;\r
+ endRes = (startRes + totalRes) - 1;\r
+\r
+ if (endRes > (av.getAlignment().getWidth() - 1))\r
+ {\r
+ endRes = av.getAlignment().getWidth() - 1;\r
+ }\r
+\r
+ startSeq = (pi / pagesWide) * totalSeq;\r
+ endSeq = startSeq + totalSeq;\r
+\r
+ if (endSeq > av.getAlignment().getHeight())\r
+ {\r
+ endSeq = av.getAlignment().getHeight();\r
+ }\r
+\r
+ int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
+\r
+ if (av.showAnnotation)\r
+ {\r
+ pagesHigh += annotationPanel.getHeight();\r
+ }\r
+\r
+ pagesHigh /= pheight;\r
+\r
+ if (pi >= (pagesWide * pagesHigh))\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
+\r
+ //draw Scale\r
+ pg.translate(idWidth, 0);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
+ pg.translate(-idWidth, scaleHeight);\r
+\r
+ ////////////////\r
+ // Draw the ids\r
+ Color currentColor = null;\r
+ Color currentTextColor = null;\r
+\r
+ for (int i = startSeq; i < endSeq; i++)\r
+ {\r
+ if ((av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
+ {\r
+ currentColor = Color.gray;\r
+ currentTextColor = Color.black;\r
+ }\r
+ else\r
+ {\r
+ currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
+ }\r
+\r
+ pg.setColor(currentColor);\r
+ pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,\r
+ av.getCharHeight());\r
+\r
+ pg.setColor(currentTextColor);\r
+\r
+ String string = av.getAlignment().getSequenceAt(i).getName();\r
+\r
+ if (av.getShowFullId())\r
+ {\r
+ string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
+ }\r
+\r
+ pg.drawString(string, 0,\r
+ (((i-startSeq) * av.charHeight) + av.getCharHeight()) -\r
+ (av.getCharHeight() / 5));\r
+ }\r
+\r
+ // draw main sequence panel\r
+ pg.translate(idWidth, 0);\r
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
+ startRes, startSeq, 0);\r
+\r
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\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 +\r
+ 1);\r
+ }\r
+\r
+ return Printable.PAGE_EXISTS;\r
}\r
\r
- if (evt.getSource() == vscroll)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
+ int pi) throws PrinterException\r
{\r
- int offy = vscroll.getValue();\r
- av.setStartSeq(offy);\r
- av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());\r
+ int idWidth = calculateIdWidth().width + 4;\r
+\r
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
+ idWidth);\r
+ int totalHeight = totalHeight = (av.alignment.getHeight() + 2) * ((av.alignment.getWidth() / resWidth) +\r
+ 1) * av.charHeight;\r
+\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
+\r
+ ////////////////\r
+ // Draw the ids\r
+ pg.setColor(Color.black);\r
+\r
+ pg.translate(0, -pi * pheight);\r
+\r
+ pg.setClip(0, pi * pheight, pwidth, pheight);\r
+\r
+ int ypos = 2 * av.charHeight;\r
+\r
+ do\r
+ {\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ String string = s.getName();\r
+\r
+ if (av.getShowFullId())\r
+ {\r
+ string = s.getDisplayId();\r
+ }\r
+\r
+ pg.drawString(string, 0,\r
+ ((i * av.charHeight) + ypos + av.charHeight) -\r
+ (av.charHeight / 5));\r
+ }\r
+\r
+ ypos += ((av.alignment.getHeight() + 2) * av.charHeight);\r
+ }\r
+ while (ypos < totalHeight);\r
+\r
+ pg.translate(idWidth, 0);\r
+\r
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
+\r
+ if ((pi * pheight) < totalHeight)\r
+ {\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+ else\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makeEPS(File epsFile)\r
+ {\r
+ if(epsFile == null)\r
+ {\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.\r
+ JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Create EPS file from alignment");\r
+ chooser.setToolTipText("Save");\r
\r
- if(overviewPanel!=null)\r
- overviewPanel.setBoxPosition();\r
+ int value = chooser.showSaveDialog(this);\r
\r
- seqPanel.seqCanvas.paintFlag=true;\r
- repaint();\r
- }\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ return;\r
+ }\r
\r
+ epsFile = chooser.getSelectedFile();\r
\r
- public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
- {\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+ }\r
\r
- pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());\r
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
\r
- int pwidth = (int)pf.getImageableWidth();\r
- int pheight = (int)pf.getImageableHeight();\r
- int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
+ av.chunkHeight;\r
+ width = seqPanel.getWidth() + idPanel.getWidth();\r
\r
- //BufferedImage printImage = new BufferedImage(pwidth,pheight,BufferedImage.TYPE_INT_RGB);\r
- // Graphics pg = printImage.getGraphics();\r
- pg.setColor(Color.white);\r
- pg.fillRect(0,0,pwidth, pheight);\r
- pg.setFont( av.getFont() );\r
+ }\r
\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- int totalRes = (int)((pwidth - idWidth)/av.getCharWidth());\r
- int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;\r
- int pagesWide = av.getAlignment().getWidth() / totalRes +1;\r
- int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;\r
\r
- if (pi >= pagesWide*pagesHigh)\r
- return Printable.NO_SUCH_PAGE;\r
+ if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
+ }\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int startRes, endRes, startSeq, endSeq;\r
- startRes = (pi % pagesWide) * totalRes;\r
- endRes = startRes + totalRes-1;\r
- if(endRes>av.getAlignment().getWidth())\r
- endRes = av.getAlignment().getWidth();\r
+ try\r
+ {\r
+ FileOutputStream out = new FileOutputStream(epsFile);\r
+ EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,\r
+ height);\r
\r
- startSeq = (pi / pagesWide) * totalSeq;\r
- endSeq = startSeq + totalSeq;\r
- if(endSeq > av.getAlignment().getHeight())\r
- endSeq = av.getAlignment().getHeight();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ printWrappedAlignment(pg, width, height, 0);\r
+ }\r
+ else\r
+ {\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
- ////////////////\r
- //draw Scale\r
- pg.translate(idWidth,0);\r
- scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);\r
\r
- pg.translate(-idWidth, 30);\r
- ////////////////\r
- // Draw the ids\r
- Color currentColor=null;\r
- Color currentTextColor=null;\r
- for(int i=startSeq; i<endSeq; i++)\r
+ public void makePNGImageMap(File imgMapFile, String imageName)\r
{\r
- if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))\r
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
+ //////////////////////////////////////////////\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+ // Gen image map\r
+ //////////////////////////////////\r
+ if(imgMapFile!=null)\r
+ {\r
+ try\r
+ {\r
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
+ out.println("<img src=\"" + imageName +\r
+ "\" border=\"0\" usemap=\"#Map\" >"\r
+ +"<map name=\"Map\">");\r
+\r
+ for (int s = 0; s < av.alignment.getHeight(); s++)\r
+ {\r
+ SequenceI seq = av.alignment.getSequenceAt(s);\r
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
+ for (int i = 0; i < groups.length; i++)\r
+ {\r
+ int sy = s * av.charHeight + scaleHeight;\r
+ for (int res = groups[i].getStartRes();\r
+ res < groups[i].getEndRes() + 1; res++)\r
+ {\r
+ int alIndex = seq.findPosition(res);\r
+ Object obj = ResidueProperties.aa2Triplet.get(\r
+ seq.getCharAt(res) + "");\r
+ if (obj == null)\r
+ continue;\r
+\r
+ String triplet = obj.toString();\r
+\r
+ out.println(\r
+ "<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet +\r
+ "<br><em>" + groups[i].getName() +\r
+ "</em>')\"; onMouseOut=\"toolTip()\"; "\r
+ + " href=\"#\">");\r
+ }\r
+ }\r
+ }\r
+\r
+ out.println("</map></body></html>");\r
+ out.close();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }///////////END OF IMAGE MAP\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makePNG(File pngFile)\r
+ {\r
+ if(pngFile==null)\r
{\r
- currentColor = Color.gray;\r
- currentTextColor = Color.black;\r
+ jalview.io.JalviewFileChooser chooser = new jalview.io.\r
+ JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
+ "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
+\r
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ return;\r
+ }\r
+\r
+ pngFile = chooser.getSelectedFile();\r
+\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
}\r
- else\r
+\r
+\r
+\r
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
+\r
+ if (av.getWrapAlignment())\r
{\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
+ height = ( (av.alignment.getWidth() / av.getChunkWidth()) + 1) *\r
+ av.chunkHeight;\r
+ width = seqPanel.getWidth() + idPanel.getWidth();\r
+\r
}\r
\r
- pg.setColor(currentColor);\r
- pg.fillRect(0, jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),\r
- getWidth(),\r
- av.getCharHeight());\r
\r
- pg.setColor(currentTextColor);\r
+ if (av.getShowAnnotation())\r
+ {\r
+ height += annotationPanel.getPreferredSize().height;\r
+ }\r
+\r
+ try\r
+ {\r
+\r
+ FileOutputStream out = new FileOutputStream(pngFile);\r
\r
- String string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
- pg.drawString(string, 0, jalview.analysis.AlignmentUtil.getPixelHeight\r
- (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));\r
+ BufferedImage bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics2D png = (Graphics2D) bi.getGraphics();\r
+\r
+ png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ printWrappedAlignment(png, width, height, 0);\r
+ }\r
+ else\r
+ {\r
+ printUnwrapped(png, width, height, 0);\r
+ }\r
+\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
+ }\r
+ catch(OutOfMemoryError err)\r
+ {\r
+ System.out.println("########################\n"\r
+ +"OUT OF MEMORY "+pngFile+"\n"\r
+ +"########################");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
+}\r
\r
- // draw main sequence panel\r
- pg.translate(idWidth,0);\r
- seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);\r
\r
- return Printable.PAGE_EXISTS;\r
- }\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+class Preview extends JFrame\r
+{\r
+ /**\r
+ * Creates a new Preview object.\r
+ *\r
+ * @param image DOCUMENT ME!\r
+ */\r
+ public Preview(Image image)\r
+ {\r
+ setResizable(true);\r
+ setSize(image.getWidth(this), image.getHeight(this));\r
+ setVisible(true);\r
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
+ validate();\r
+ repaint();\r
+ }\r
}\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+class PreviewPanel extends JPanel\r
+{\r
+ Image image;\r
+\r
+ /**\r
+ * Creates a new PreviewPanel object.\r
+ *\r
+ * @param image DOCUMENT ME!\r
+ */\r
+ public PreviewPanel(Image image)\r
+ {\r
+ this.image = image;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
+ else\r
+ {\r
+ System.out.println("DEBUG:image is null");\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff